Biology subjects

Nijenhuis, W.

Publications and source records attributed to Nijenhuis, W..

17 recordsLinked to original sources

bioRxiv2026

Rapid removal of nuclear aggregates via proteasome- and VCP-dependent disaggregation

Cells use multiple protein quality control (PQC) mechanisms to counteract the toxic effects of protein aggregation caused by cellular stress, ageing or disease. While it is known that PQC mechanisms differ between cellular compartments, studying such differences has remained challenging. Previously, we developed an assay to study cytosolic PQC using aggregates formed through chemically-induced dimerization (termed PIMs, particles induced by multimerization). Here, we introduce nuclear PIMs as a tool to study nuclear quality control. Using high-resolution and high-throughput imaging, we show that nuclear aggregate removal depends on the proteasome and the unfoldase VCP, but not on Hsp70. Strikingly, following dissolution many PIM subunits were exported to the cytosol via exportin-1-dependent shuttling, indicating that disaggregation and resolubilization dominated over degradation. Proteasomal disaggregation was confirmed using live-cell turnover experiments. Together, these findings reveal a mechanism in which the proteasome and VCP disaggregate, rather than degrade, nuclear protein aggregates, with the resulting subunits subsequently cleared via cytosolic aggrephagy.

cell biology↗

bioRxiv2026

Engineered microRNA feedback circuits enable tunable and autonomous control of synthetic receptor activity

Synthetic receptors are powerful tools for cellular engineering, yet their utility is often constrained by constitutive activity and the absence of natural feedback mechanisms that maintain cellular homeostasis. To address this, we engineered an autonomous regulatory circuit for synthetic Notch (synNotch) receptor activation using an orthogonal microRNA (miRNA)-mediated negative feedback mechanism in mammalian cells. Specifically, synNotch activation induces the expression of a synthetic miRNA that targets complementary sites engineered into the synNotch transcript, resulting in a self-limiting feedback loop. We demonstrate that synNotch repression positively correlates with the number of miRNA target sites integrated into the receptor transcript, enabling tunable control of receptor expression. Furthermore, flow cytometry and live-cell imaging analyses revealed effective suppression of synNotch expression following activation. Downstream target gene expression peaked at approximately 48 hours post-activation before gradually declining as the feedback circuit engaged. This approach achieves autonomous synthetic receptor regulation--eliminating the need for external intervention--and enables tunable response dynamics through rational circuit design. Our miRNA feedback strategy provides a generalizable platform for engineering self-regulating synthetic receptor systems with improved control and predictability for cellular engineering applications.

synthetic biology↗

bioRxiv2026

Spatial control of light-responsive proteins and optogenetics within hydrogels via volumetric bioprinting

Spatiotemporal control over cell fate and behaviour within bioprinted constructs remains a key challenge in tissue engineering. Optogenetics offers versatile potential for non-invasive regulation of biological processes. Yet, its integration within large-scale, cell-laden bioprinted materials is still limited, especially considering spatial constraints of existing light delivery methods. In this study, we introduce a novel approach that repurposes tomographic volumetric bioprinting to enable post-printing stimulation of photosensitive protein-switches and optogenetic circuits in cells deep within hydrogel constructs. By converging different bioprinting approaches, computer vision, context-aware model generation, and synthetic biology and cell engineering, we demonstrated selective activation of a fluorescent, light-responsive protein probe within multi-material centimeter-scale constructs. Moreover, leveraging a multi-wavelength volumetric bioprinter, we further demonstrate this concept by selectively stimulating cells expressing a near-infrared optogenetic system that triggers gene expression and the induction of pancreas-specific transcription factors. The described methods provide platforms for remote, repeatable, and localized control of biological events in volumetric constructs, opening new possibilities for advanced tissue models, and dynamic tuning of cell-mediated protein production in engineered living systems.

bioengineering↗

bioRxiv2025

Rab27-dependent egress of SARS-CoV-2 via secretory amphisomes

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of COVID-19, hijacks host cellular machinery to replicate and spread. Understanding how SARS-CoV-2 reorganizes host cell architecture to accommodate this is essential for elucidating its pathogenesis and identifying therapeutic targets. While the molecular mechanisms of SARS-CoV-2 entry are well characterized, the pathways governing viral egress remain incompletely understood. Conventional approaches such as transcriptomics and electron microscopy have provided valuable insights but lack the combined spatial and molecular resolution needed to map these processes within intact cells. Here, we apply Ten-fold Robust Expansion Microscopy (TREx) to visualize SARS-CoV-2-induced remodeling of the endolysosomal system in multiciliated cells of primary human airway epithelial tissue. This approach reveals Golgi fragmentation and the formation of enlarged virus-containing organelles. Analysis of endolysosomal markers in Vero E6 cells shows that these structures are positive for CD63, Rab7, and LC3, consistent with amphisome identity. Moreover, pharmacological inhibition of Rab27-dependent amphisome-plasma membrane fusion with Nexinhib20 reduces viral infection, implicating secretory autophagy as a pathway for SARS-CoV-2 egress. These findings establish expansion microscopy as a powerful tool for spatial virology and uncover a Rab27-mediated amphisome fusion mechanism as a druggable route for SARS-CoV-2 release.

cell biology↗

bioRxiv2025

Immortalization of human nasal and bronchial airway epithelial cells for genome editing applications

In vitro air-liquid interface culture of airway epithelial cells is used as a model system to study respiratory diseases. This culture system not only overcomes the need for animal models or continuous biopsies from individuals but also enables studies of pathophysiology associated with the disease in a patient background. Human airway basal cells serve as progenitor cells for a functional pseudostratified airway epithelium composed mainly of multiciliated and secretory cells. However, due to the limited ability of basal cells to proliferate and differentiate, the long-term use of primary material in culture is restricted. This challenges research that requires genome editing. Here, we describe airway stem cells from nasal and bronchial origin immortalized by hTERT overexpression followed by polyclonal expansion. We demonstrate that this diverse panel of cell lines shows differentiation patterns similar to primary stem cells and can be used for lentiviral and CRISPR/Cas9 genome editing. These cell lines and optimized protocols facilitate airway biology research and disease phenotyping.

cell biology↗

bioRxiv2024

Outcome-Driven Microscopy: Closed-Loop Optogenetic Control of Cell Biology

Smart microscopy is transforming biological imaging by integrating real-time analysis with adaptive acquisition to enhance imaging efficiency. Whereas many emerging implementations are event-driven and focus on on-demand data acquisition to reduce phototoxicity, we here present outcome-driven microscopy, which combines smart microscopy with optogenetics to achieve subcellular spatiotemporal control of biology to predefined outcomes. We validate this approach using light-based control of cell migration and nucleocytoplasmic transport, and demonstrate unprecedented spatiotemporal control over cellular behaviour.

cell biology↗

bioRxiv2024

Spherical harmonics texture extraction for versatile analysis of biological objects

The characterization of phenotypes in cells or organisms from microscopy data largely depends on differences in the spatial distribution of image intensity. Multiple methods exist for quantifying the intensity distribution - or image texture - across objects in natural images. However, many of these texture extraction methods do not directly adapt to 3D microscopy data. Here, we present Spherical Texture extraction, which measures the variance in intensity per angular wavelength by calculating the Spherical Harmonics or Fourier power spectrum of a spherical or circular projection of the angular mean intensity of the object. This method provides a 20-value characterization that quantifies the scale of features in the spherical projection of the intensity distribution, giving a different signal if the intensity is, for example, clustered in parts of the volume or spread across the entire volume. We apply this method to different systems and demonstrate its ability to describe various biological problems through feature extraction. The Spherical Texture extraction characterizes biologically defined gene expression patterns in Drosophila melanogaster embryos, giving a quantitative read-out for pattern formation. Our method can also quantify morphological differences in Caenorhabditis elegans germline nuclei, which lack a predefined pattern. We show that the classification of germline nuclei using their Spherical Texture outperforms a convolutional neural net when training data is limited. Additionally, we use a similar pipeline on 2D cell migration data to extract polarization direction, quantifying the alignment of fluorescent markers to the migration direction. We implemented the Spherical Texture method as a plugin in ilastik, making it easy to install and apply to any segmented 3D or 2D dataset. Additionally, this technique can also easily be applied through a Python package to provide extra feature extraction for any object classification pipeline or downstream analysis. Author summaryWe introduce a novel method to extract quantitative data from microscopy images by precisely measuring the distribution of intensities within objects in both 3D or 2D. This method is easily accessible through the object classification workflow of ilastik, provided the original image is segmented into separate objects. The method is specifically designed to analyze mostly convex objects, focusing on the variation in fluorescence intensity caused by differences in their shapes or patterns. We demonstrate the versatility of our method by applying it to very different biological samples. Specifically, we showcase its effectiveness in quantifying the patterning in D. melanogaster embryos, in classifying the nuclei in C. elegans germlines, and in extracting polarization information from individual migratory cells. Through these examples, we illustrate that our technique can be employed across different biological scales. Furthermore, we highlight the multiple ways in which the data generated by our method can be used, including quantifying the strength of a specific pattern, employing machine learning to classify diverse morphologies, or extracting directionality or polarization from fluorescence intensity.

bioinformatics↗

bioRxiv2024

Aurora B controls microtubule stability to regulate abscission dynamics in stem cells

Abscission is the last step of cell division leading to the complete separation of the two sister cells and consists of the cutting of a cytoplasmic bridge. Abscission is mediated by the ESCRT membrane remodeling machinery which also triggers the severing of a thick bundle of microtubules that needs to be cleared prior to abscission. Here, we show that rather than being passive actors in abscission, microtubules control abscission speed. Using mouse embryonic stem cells, which transition from slow to fast abscission during exit from naive pluripotency, we investigate the molecular mechanism for the regulation of abscission dynamics and identify a feedback loop between the activity of Aurora B and microtubule stability. We demonstrate that naive stem cells maintain high Aurora B activity after cytokinesis. This high Aurora B activity leads to transient microtubule stabilization that delays abscission. In turn, stable microtubules promote the activity of Aurora B. When cells exit naive pluripotency, a decrease in Wnt signaling leads to a decrease in the activity of Aurora B, less stable microtubules, and a faster abscission. Overall, our data demonstrate that Aurora B-dependent microtubule stability controls abscission dynamics.

cell biology↗

bioRxiv2022

The SARS-CoV-2 accessory factor ORF7a downregulates MHC class I surface expression

The pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has resulted in over 500 million infections and more than six million deaths worldwide. Although the viral genomes of SARS-CoV-1 and SARS-CoV-2 share high sequence homology, the clinical and pathological features of COVID-19 differ profoundly from those of SARS. It is apparent that changes in viral genes contribute to the increased transmissibility of SARS-CoV-2 and pathology of COVID-19. Cytotoxic T lymphocytes play a key role in the elimination of virus-infected cells, mediated by recognition of virus-derived peptides that are presented on MHC class I molecules. Here, we show that SARS-CoV-2 can interfere with antigen presentation thereby evading immune surveillance. SARS-CoV-2 infection of monkey and human cell lines resulted in reduced cell-surface expression of MHC class I molecules. We identified a single viral gene product, the accessory factor open reading frame 7a (ORF7a), that mediates this effect. ORF7a interacts with HLA class I molecules in the ER, resulting in ER retention or impaired HLA heavy chain (HC) trafficking to the Golgi. Ultimately, these actions result in reduced HLA class I surface expression on infected cells. Whereas ORF7a from SARS-CoV-2 reduces surface HLA class I levels, the homologous ORF7a from the 2002 pandemic SARS-CoV-1 did not, suggesting that SARS-CoV-2 ORF7a acquired the ability to downregulate HLA-I during evolution of the virus. We identified a single amino acid in the SARS-CoV-1 ORF7a luminal domain that, upon mutating to the corresponding SARS-CoV-2 ORF7a sequence, induced a gain-of-function in HLA surface downregulation. By abrogating HLA class I antigen presentation via ORF7a, SARS-CoV-2 may evade host immune responses by inhibiting anti-viral cytotoxic T cell activity, thereby contributing to the pathology of COVID-19.

microbiology↗

bioRxiv2022

A motor-based approach to induce chromosome-specific mis-segregations in human cells

Various cancer types exhibit highly characteristic and recurrent aneuploidy patterns. The origin of these cancer type-specific karyotypes, and the extent to which they contribute to cancer progression, remains to be elucidated, partly because introducing or eliminating specific chromosomes in human cells still poses a challenge. Here, we describe a novel strategy to mis-segregate specific chromosomes at will in different human cell types. We employed Tet repressor (TetR) or nuclease dead Cas9 (dCas9) to link a plant-derived microtubule minus-end-directed kinesin (Physcomitrella patens Kinesin14VIb) to integrated Tet operon repeats and chromosome-specific endogenous repeats, respectively. By live- and fixed-cell imaging, we observed poleward movement of the targeted loci during (pro)metaphase. Kinesin14VIb-mediated pulling forces on the targeted chromosome were often counteracted by forces from kinetochore-attached microtubules. This tug of war resulted in chromosome-specific segregation errors during anaphase, and revealed that spindle forces can heavily stretch chromosomal arms. Using chromosome-specific FISH and single-cell whole genome sequencing, we established that motor-induced mis-segregations result in specific arm-level, and to a lesser extent, whole chromosome aneuploidies, after a single cell division. Our kinesin-based strategy to manipulate individual mitotic chromosomes opens up the possibility to investigate the immediate cellular responses to specific (arm level) aneuploidies in different cell types; an important step towards understanding how recurrent aneuploidy patterns arise in different cancer types.

cell biology↗

bioRxiv2021

Opto-Katanin: An Optogenetic Tool for Localized Microtubule Disassembly

Microtubules are major cytoskeletal filaments that drive chromosome separation during cell division, serve as rails for intracellular transport and as a scaffold for organelle positioning. Experimental manipulation of microtubules is widely used in cell and developmental biology, but tools for precise subcellular spatiotemporal control of microtubule integrity are currently lacking. Here, we exploit the dependence of the mammalian microtubule-severing protein katanin on microtubule-targeting co-factors to generate a light-activated system for localized microtubule disassembly that we named opto-katanin. Targeted illumination with blue light induces rapid and localized opto-katanin recruitment and local microtubule depolymerization, which is quickly reversible after stopping light-induced activation. Opto-katanin can be employed to locally perturb microtubule-based transport and organelle morphology in dividing cells and differentiated neurons with high spatiotemporal precision. We show that different microtubule-associated proteins can be used to recruit opto-katanin to microtubules and induce severing, paving the way for spatiotemporally precise manipulation of specific microtubule subpopulations.

cell biology↗

bioRxiv2021

Centriole-independent centrosome assembly in interphase mammalian cells

AbstractThe major microtubule-organizing center (MTOC) in animal cells, the centrosome, comprises a pair of centrioles surrounded by pericentriolar material (PCM), which nucleates and anchors microtubules. Centrosome assembly depends on PCM binding to centrioles, PCM self-association and dynein{-}mediated PCM transport, but the self-assembly properties of PCM in interphase cells are poorly understood. Here, we used experiments and modeling to study centriole-independent features of interphase PCM assembly. We showed that when centrioles are lost due to PLK4 depletion or inhibition, dynein-based PCM transport and PCM self-clustering are sufficient to form a single compact MTOC, which generates a dense radial microtubule array. Interphase PCM self-assembly depends on {gamma}-tubulin, pericentrin, CDK5RAP2 and ninein, but not NEDD1, CEP152 or CEP192. Formation of a compact acentriolar MTOC is inhibited by AKAP450-dependent PCM recruitment to the Golgi or by randomly organized CAMSAP2-stabilized microtubules, which keep PCM mobile and prevent its coalescence. Linking of CAMSAP2 to a minus-end-directed motor leads to the formation of an MTOC, but MTOC compaction requires cooperation with pericentrin-containing self-clustering PCM. Our data reveal that interphase PCM contains a set of components that can self-assemble into a compact structure and organize microtubules, but PCM self-organization is sensitive to motor-and microtubule-based rearrangement.

cell biology↗

bioRxiv2021

Optical nanoscopy reveals SARS-CoV-2-induced remodeling of human airway cells

A better understanding of host cell remodeling by the coronavirus SARS-CoV-2 is urgently needed to understand viral pathogenesis and guide drug development. Expression profiling and electron microscopy have frequently been used to study virus-host interactions, but these techniques do not readily enable spatial, sub-cellular and molecular analysis of specific cellular compartments. Here, we use diffraction-unlimited fluorescence microscopy to analyze how SARS-CoV-2 infection exploits and repurposes the subcellular architecture of primary human airway cells. Using STED nanoscopy, we detect viral entry factors along the motile cilia of ciliated cells and visualize key aspects of the viral life cycle. Using Tenfold Robust Expansion (TREx) microscopy, we analyze the extensively remodeled three-dimensional ultrastructure of SARS-CoV-2-infected ciliated cells and uncover Golgi fragmentation, emergence of large and atypical multivesicular bodies enclosing viral proteins, ciliary clustering, and remodeling of the apical surface. These results demonstrate a broadly applicable strategy to study how viruses reorganize host cells with spatial and molecular specificity and provide new insights into SARS-CoV-2 infection in primary human cell models.

cell biology↗

bioRxiv2021

CFTR modulator response measurements in subjects with cystic fibrosis using 2D differentiated nasal epithelia converted into spheroids

Cystic Fibrosis (CF) is caused by genetic defects that impair the cystic fibrosis transmembrane conductance regulator (CFTR) channel in airway epithelial cells. These defects may be overcome by specific CFTR modulating drugs, for which the efficacy can be predicted in a personalized manner using 3D nasal-brushing-derived airway organoids in a forskolin-induced swelling assay. Despite of this, previously described application of 3D airway organoids in CFTR function assays have not been fully optimal. In this report we therefore describe an alternative method of culturing nasal brushing-derived airway organoids, which are created from an equally differentiated airway epithelial monolayer of a 2D air-liquid interface culture. In addition, we have defined organoid culture conditions, with the growth factor/cytokine combination neuregulin-1{beta} and interleukine-1{beta}, which enabled consistent detection of CFTR modulator responses in nasal airway organoids cultures from subjects with CF.

cell biology↗

bioRxiv2021

Direct observation of aggregate-triggered selective autophagy

Degradation of aggregates by selective autophagy is important as damaged proteins may impose a threat to cellular homeostasis. Although the core components of the autophagy machinery are well-characterized, the spatiotemporal regulation of many selective autophagy processes, including aggrephagy, remains largely unexplored. Furthermore, because most live-cell imaging studies have so far focused on starvation-induced autophagy, little is known about the dynamics of aggrephagy. Here, we describe the development and application of the mKeima-PIM assay, which enables live-cell observation of autophagic turnover and degradation of inducible protein aggregates in conjunction with key autophagy players. This allowed us to quantify the relative timing and duration of different steps of aggrephagy and revealed the short-lived nature of the autophagosome. The assay furthermore showed the spatial distribution of omegasome formation, highlighting that autophagy initiation is directly instructed by the cargo. Moreover, we found that nascent autophagosomes mostly remain immobile until acidification occurs. Thus, our assay provides new insights into the spatiotemporal regulation and dynamics of aggrephagy.

cell biology↗

bioRxiv2020

Co-translational targeting of transcripts to endosomes

Asymmetric localization and translation of mRNAs is used by single cells to sense their environment and integrate extrinsic cues with the appropriate cellular response. Here we investigate the extent to which endosomes impact subcellular patterning of transcripts and provide a platform for localized translation. Using image-based transcriptomics, indirect immunofluorescence, and RNAseq of isolated organelles, we discover mRNAs that associate with early endosomes in a translation-dependent and -independent manner. We explore this in more detail for the mRNA of a major endosomal tethering factor and fusogen, Early Endosomal Antigen 1, EEA1, which localizes to early endosomes in a puromycin-sensitive manner. By reconstituting EEA1 knock-out cells with either the coding sequence or 3UTR of EEA1, we show that the coding region is sufficient for endosomal localization of mRNA. Finally, we use quantitative proteomics to discover proteins associated with EEA1 mRNA and identify CSRP1 as a factor that controls EEA1 translational efficiency. Our findings reveal that multiple transcripts associate with early endosomes in a translation-dependent manner and identify mRNA-binding proteins that may participate in controlling endosome-localized translation.

cell biology↗

bioRxiv2020

The structure and global distribution of the endoplasmic reticulum network is actively regulated by lysosomes

The endoplasmic reticulum (ER) comprises morphologically and functionally distinct domains, sheets and interconnected tubules. These domains undergo dynamic reshaping, in response to changes in the cellular environment. However, the mechanisms behind this rapid remodeling within minutes are largely unknown. Here, we report that ER remodeling is actively driven by lysosomes, following lysosome repositioning in response to changes in nutritional status. The anchorage of lysosomes to ER growth tips is critical for ER tubule elongation and connection. We validate this causal link via the chemo- and optogenetically driven re-positioning of lysosomes, which leads to both a redistribution of the ER tubules and its global morphology. Lysosomes sense metabolic change in the cell and regulate ER tubule distribution accordingly. Dysfunction in this mechanism during axonal extension may lead to axonal growth defects. Our results demonstrate a critical role of lysosome-regulated ER dynamics and reshaping in nutrient responses and neuronal development.

cell biology↗