Biology subjects

De Sutter, D.

Publications and source records attributed to De Sutter, D..

11 recordsLinked to original sources

bioRxiv2025

Proximity map for p53 unveils a strong link with PML Nuclear Bodies in HEK293 cells

The tumor suppressor p53 is among the most studied proteins in cancer, with mutations in nearly half of all tumors. Even when TP53 is intact, its regulatory pathways are often disrupted, underscoring its central role in tumorigenesis. To explore how cellular context shapes the subcellular environment of p53, we used BioID proximity labeling in HEK293 cells. These experiments revealed a striking enrichment of proteins involved in SUMOylation and proteins that reside in PML nuclear bodies. A strong enrichment of the adenoviral E1B protein, originally used for transformation of this cell line, may explain this striking observation, and can shed light on the remarkable difference with the proximity map of p53 in the HCT116 colon carcinoma cell line. Strong enrichment of the mediator complex in HCT116, related to active p53-dependent transcription, is missing in 293 cells and can explain the lack of p53 transcriptional activity in these cells. This study emphasizes how cellular transformation can affect the proximal proteome of a key protein in cell cycle control, DNA repair, apoptosis, senescence and metabolism, and confirms previously reported inhibition of p53-dependent transcription by sequestering the protein in PML nuclear bodies.

systems biology↗

bioRxiv2025

TurboID proximity interactome mapping reveals NR2E3 association with AP-1 and retinal developmental complexes

The photoreceptor-specific nuclear receptor NR2E3 is a key transcription factor in the retinal transcriptional network, essential in photoreceptor cell fate and maintenance. Various biallelic loss-of-function variants lead to autosomal recessive inherited retinal disease (IRD), while a single missense variant G56R has been identified to cause autosomal dominant retinitis pigmentosa (adRP). However, a comprehensive understanding of the interactome of NR2E3 remains elusive. Here, we aimed to map the interactome of this nuclear receptor and the G56R pathogenic variant through proximity labelling followed by mass spectrometry. We used the TurboID "T2A split/link design" to identify the proximity interactome of wild-type NR2E3 and mutant G56R-NR2E3 in ARPE-19 cells. Several protein complexes involved in retinal development, including the AP-1 complex, were enriched. The results suggest similar interactomes for NR2E3 and G56R-NR2E3 in ARPE-19. However, BCOR was exclusively enriched in the G56R-NR2E3 network, strengthening the connection with the IRD phenotype. In conclusion, our approach has mapped the proximity interactome of NR2E3 and G56R-NR2E3, revealing interaction with protein complexes involved in (retinal) development.

systems biology↗

bioRxiv2025

Rapid assay optimization by plug-and-play MAPPIT

Studying protein-protein interactions, which are crucial for all cellular processes in both health and disease, offers valuable insights into underlying mechanisms and reveals promising therapeutic targets. While efforts have been made to vastly increase the scale of MAPPIT assays, covering the full protein interactome remains challenging, in particular when considering the availability of different assay configurations. In this study, we expanded our Golden Gate modular cloning platform to enable rapid, customizable construct assembly for MAPPIT assays. We demonstrate the strength of this expanded toolbox for multiple distinct protein-protein interactions, including a MAPPIT assay for six different intracellular VHH targeting the anti-viral effector protein MXA.

synthetic biology↗

bioRxiv2025

Virotrap Reveals Salmonella SopB as A Ubiquitinated Cargo for Host ESCRT-0

The pathogenic bacterium Salmonella survives and replicates in host cells within a Salmonella-containing vacuole (SCV), a membranous niche it actively remodels via secreted effectors. The phosphoinositide phosphatase SopB is a key effector implicated in SCV biogenesis, yet its host protein interactome has remained incompletely defined. Using the mass spectrometry-based interactomics technology Virotrap, we identify a novel set of SopB-associated host proteins, including the ESCRT-0 subunit HGS and other membrane remodeling proteins. We demonstrate that SopB directly interacts with HGS via its ubiquitin-binding domains, and show that SopB promotes ESCRT-0 recruitment to the SCV, yet ultimately counteracts its anti-replicative effect. As the ESCRT machinery plays a central role in cargo sorting and membrane remodeling, we propose a new SopB-dependent strategy by which Salmonella hijacks host endosomal trafficking to build its intracellular niche.

microbiology↗

bioRxiv2023

Leveraging a self-cleaving peptide for tailored control in proximity labeling proteomics

Protein-protein interactions play an important biological role in every aspect of cellular homeostasis and functioning. Proximity labeling mass spectrometry-based proteomics overcomes challenges typically associated with other methods, and has quickly become the current state-of-the-art in the field. Nevertheless, tight control of proximity labeling enzymatic activity and expression levels is crucial to accurately identify protein interactors. Here, we leverage a T2A self-cleaving peptide and a non-cleaving mutant to accommodate the protein-of-interest in the experimental and control TurboID setup. To allow easy and streamlined plasmid assembly, we built a Golden Gate modular cloning system to generate plasmids for transient expression and stable integration. To highlight our T2A Split-link design, we applied it to identify protein interactions of the glucocorticoid receptor and SARS-CoV-2 nucleocapsid and NSP7 proteins by TurboID proximity labeling. Our results demonstrate that our T2A split-link provides an opportune control that builds upon previously established control requirements in the field. MotivationIn proximity labeling proteomics protein-protein interactions are identified by in vivo biotinylation. However, the current lack of a universally applicable negative control for differential analysis affects accurate mapping of the interactome. To bridge this gap, we conceptualized a system based on the T2A self-cleaving peptide to match expression levels between control and bait protein setups while using the same bait protein. In addition, we implemented a versatile modular cloning system to build mammalian expression vectors for, but not limited to, proximity labeling assays.

biochemistry↗

bioRxiv2023

Activation of goblet cell stress sensor IRE1β is controlled by the mucin chaperone AGR2

As secretory cells specialized in the production of mucins, intestinal goblet cells are challenged by the need for efficient protein folding. Goblet cells express Inositol-Requiring Enzyme 1{beta} (IRE1{beta}), a unique unfolded protein response (UPR) sensor that is part of an adaptive mechanism that regulates the demands of mucin production and secretion. However, how IRE1{beta} activity is tuned to mucus folding load remains unknown. We identified the disulfide isomerase and mucin chaperone AGR2 as a goblet cell specific protein that crucially regulates IRE1{beta}-, but not IRE1-mediated signaling. AGR2 binding to IRE1{beta} disrupts IRE1{beta} dimerization, thereby blocking its downstream endonuclease activity. Depletion of endogenous AGR2 from goblet cells induces spontaneous IRE1{beta} activation, suggesting that alterations in AGR2 availability in the endoplasmic reticulum sets the threshold for IRE1{beta} activation. We found that AGR2 mutants lacking their catalytic cysteine or displaying the disease-associated mutation H117Y were no longer able to dampen IRE1{beta} activity. Collectively, these results demonstrate that AGR2 is a central chaperone regulating the goblet cell UPR by acting as a rheostat of IRE1{beta} endonuclease activity.

cell biology↗

bioRxiv2023

MX2 restricts HIV-1 and herpes simplex virus-1 by forming cytoplasmic biomolecular condensates that mimic nuclear pore complexes

Human myxovirus resistance 2 (MX2) can potently restrict HIV-1 and herpesviruses at a post-entry step by a process that requires MX2 interaction with the capsids of these viruses. The involvement of other host cell factors in this process, however, remains poorly understood. Here, we mapped the proximity interactome of MX2 revealing strong enrichment of phenylalanine-glycine (FG)-rich proteins related to the nuclear pore complex as well as proteins that are part of cytoplasmic ribonucleoprotein granules. MX2 interacted with these proteins to form multiprotein cytoplasmic biomolecular condensates that were essential for its anti-HIV-1 and -herpes simplex virus-1 (HSV-1) activity. MX2 condensate formation required the disordered N-terminal region of MX2 and its dimerization. Incoming HIV-1 and HSV-1 capsids associated with MX2 at these dynamic cytoplasmic biomolecular condensates. Our results demonstrate that MX2 forms cytoplasmic condensates that act as nuclear pore decoys, which trap capsids and induce premature viral genome release, and thereby interfere with nuclear targeting of HIV-1 and HSV-1.

microbiology↗

bioRxiv2022

Novel assays monitoring direct glucocorticoid receptor protein activity exhibit high predictive power for ligand activity on endogenous gene targets

Exogenous glucocorticoids are widely used in the clinic for the treatment of inflammatory disorders and auto-immune diseases. Unfortunately, their use is hampered by many side effects and therapy resistance. Efforts to find more selective glucocorticoid receptor (GR) agonists and modulators (called SEGRAMs) that are able to separate anti-inflammatory effects via gene repression from metabolic effects via gene activation, have been unsuccessful so far. In this study, we characterized a set of functionally diverse GR ligands in A549 cells, first using a panel of luciferase-based reporter gene assays evaluating GR-driven gene activation and gene repression. We expanded this minimal assay set with novel luciferase-based read-outs monitoring GR protein levels, GR dimerization and GR Serine 211 (Ser211) phosphorylation status and compared their outcomes with compound effects on the mRNA levels of known GR target genes in A549 cells and primary hepatocytes. We found that luciferase reporters evaluating GR-driven gene activation and gene repression were not always reliable predictors for effects on endogenous target genes. Remarkably, our novel assay monitoring GR Ser211 phosphorylation levels proved to be the most reliable predictor for compound effects on almost all tested endogenous GR targets, both driven by gene activation and repression. The integration of this novel assay in existing screening platforms running both in academia and industry may therefore boost chances to find novel GR ligands with an actual improved therapeutic benefit.

pharmacology and toxicology↗

bioRxiv2021

Ring Finger Protein 213 Assembles into a Sensor for ISGylated Proteins with Antimicrobial Activity

ISG15 is an interferon-stimulated, ubiquitin-like protein that can conjugate to substrate proteins (ISGylation) to counteract microbial infection, but the underlying mechanisms remain elusive. Here, we used a viral-like particle trapping technology to identify ISG15-binding proteins and discovered Ring Finger Protein 213 (RNF213) as an ISG15 interactor and cellular sensor of ISGylated proteins. RNF213 is a poorly-characterized, interferon-induced megaprotein that is frequently mutated in Moyamoya disease, a rare cerebrovascular disorder. We found that interferon induces ISGylation and oligomerization of RNF213 on lipid droplets, where it acts as a sensor for ISGylated proteins. We showed that RNF213 has broad antimicrobial activity in vitro and in vivo, counteracting infection with Listeria monocytogenes, herpes simplex virus 1 (HSV-1), human respiratory syncytial virus (RSV) and coxsackievirus B3 (CVB3), and we observed a striking co-localization of RNF213 with intracellular bacteria. Together, our findings provide novel molecular insights into the ISGylation pathway and reveal RNF213 as a key antimicrobial effector.

cell biology↗

bioRxiv2019

IRE1β negatively regulates IRE1α signaling in response to endoplasmic reticulum stress

IRE1{beta} is an ER stress sensor uniquely expressed in epithelial cells lining mucosal surfaces. Here, we show that intestinal epithelial cells expressing IRE1{beta} have an attenuated response to ER stress. IRE1{beta} assembles with and blocks activation of the closely related and most evolutionarily ancient stress-sensor IRE1 to suppress stress-induced xbp1 splicing, a key mediator of the unfolded protein response. In comparison, IRE1{beta} has weak xbp1 splicing activity, largely explained by a non-conserved amino acid in the kinase domain that impairs its phosphorylation and restricts oligomerization. This enables IRE1{beta} to act as a dominant negative suppressor of IRE1. The inhibitory effect is amplified in cells by disrupting an XBP1-dependent feedback loop regulating stress-induced expression of IRE1. Thus IRE1{beta} functions to negatively regulate IRE1 signaling, perhaps enabling intestinal epithelial cells to manage the response to chronic stress stimuli at the host-environment interface.

cell biology↗

bioRxiv2018

A well-controlled BioID design for endogenous bait proteins.

The CRISPR/Cas9 revolution is profoundly changing the way life sciences technologies are used. Many assays now rely on engineered clonal cell lines to eliminate overexpression of bait proteins. Control cell lines are typically non-engineered cells or engineered clones implying a considerable risk for artefacts because of clonal variation. Genome engineering can also transform BioID, a proximity labelling method that relies on fusing a bait protein to a promiscuous biotin ligase, BirA*, resulting in the tagging of vicinal proteins. We here propose an innovative design to enable BioID for endogenous proteins wherein we introduce a T2A-BirA* module at the C-terminus of endogenous p53 by genome engineering, leading to bi-cistronic expression of both p53 and BirA* under control of the endogenous promoter. By targeting a Cas9-cytidine deaminase base editor to the T2A auto-cleavage site, we can efficiently derive an isogenic population expressing a functional p53-BirA* fusion protein. Using quantitative proteomics we show significant benefits over classical ectopic expression of p53-BirA*, and we provide a first well-controlled view on the proximal proteins of endogenous p53 in colon carcinoma cells. This novel application for base editors expands the CRISPR/Cas9 toolbox and can be a valuable addition for synthetic biology.\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=142 SRC=\"FIGDIR/small/427807v2_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (20K):\norg.highwire.dtl.DTLVardef@404da1org.highwire.dtl.DTLVardef@1a8af36org.highwire.dtl.DTLVardef@18741a6org.highwire.dtl.DTLVardef@e73ab3_HPS_FORMAT_FIGEXP M_FIG C_FIG

biochemistry↗