Biology subjects

Scarpa, E.

Publications and source records attributed to Scarpa, E..

15 recordsLinked to original sources

bioRxiv2026

A dynein-driven nucleokinesis program enables neural crest migration through confined tissues in vivo

Cell migration through confined tissue environments requires precise coordination between the nucleus and the cytoskeleton. Translocation of the nucleus through small pores is a limiting step in confined cell migration. Work in immune and cancer cells has illuminated a key role for actin polymerization and Myosin-II contractility in facilitating nucleus translocation through confinement. However, the microtubule cytoskeleton can also adaptively stabilise under confinement. Microtubule-dependent nucleokinesis constitutes an evolutionarily conserved cellular program ensuring directional nucleus translocation by deployment of cytoplasmic dynein motors. However, whether microtubule-driven nucleokinesis can operate during cell migration through confinement remained so far unexplored. The zebrafish neural crest (NC) provides a unique in vivo system to address this question. NC cells are a highly migratory, multipotent precursors of the vertebrate peripheral nervous system, which traverse diverse environments along the anterior-posterior axis of the embryo. In the head, cranial neural crest (cNC) cells migrate through loosely organised tissues, whereas trunk neural crest (tNC) cells navigate narrowly confined tissue spaces. Here, we show that tNC cells engage a microtubule motor-driven program of nuclear deformation and translocation during confined migration in vivo. Under confinement, tNC cells reorganize their microtubules from a perinuclear meshwork into a polarized, centrosome-associated bundle positioned ahead of the nucleus. Laser ablation reveals that this microtubule array actively pulls and deforms the nucleus. Using pharmacological and genetic approaches, we discover that dynein-dependent pulling forces enable nucleus translocation through confinement. Strikingly, this process occurs independently of Rho/ROCK/myosin II-mediated contractility, revealing a novel neuronal-like mode of nucleokinesis operating in confined tissue environments. Together, our findings uncover a conserved nuclear translocation program deployed during neural crest migration and suggest that microtubule-based nucleokinesis represents a fundamental strategy for navigating tissue confinement in vivo during both central and peripheral nervous system development.

cell biology↗

bioRxiv2025

A vesicle-based platform for high-efficiency, high-viability CRISPR/Cas9 knockout in primary human myeloid cells

Myeloid cells, including monocytes, macrophages, and dendritic cells, are central to host defence, inflammation, and antigen presentation. However, functional genetics studies in corresponding primary cells remain limited due to inefficient delivery methods. Here we report a vesicle-based CRISPR/Cas9 platform for effective genome editing in primary human myeloid cells using engineered virus-like particles (VLPs) and extracellular vesicles (EVs) to deliver Cas9-gRNA ribonucleoproteins (RNPs). Targeting primary CD14+ monocytes enables rapid generation of robust polyclonal knockouts while preserving cell viability and subsequent differentiation into macrophages and dendritic cells. Because our workflow relies on standard cell-culture handling rather than electroporation instrumentation, it is inexpensive, highly scalable and readily transferable across laboratories. Edited cells remain compatible with diverse downstream assays and functional readouts, enabling scalable loss-of-function studies and mechanistic dissection of primary human myeloid cell biology in health and disease. Vesicle-mediated RNP delivery thus provides a broadly applicable route to genetic perturbation in primary human myeloid lineages. SummaryFiori and colleagues describe a vesicle-based platform for efficient CRISPR/Cas9 knockout in primary human myeloid cells. This approach preserves cell viability, enables near-complete gene disruption, and supports functional studies of innate immunity, antigen presentation, and HIV-1 infection.

immunology↗

bioRxiv2025

Mechanical Cues Regulate Cargo Sorting and Export at the Golgi

The secretory pathway is a sophisticated endomembrane machinery designed to transport and deliver proteins and lipids to intracellular organelles and the extracellular space. While the molecular components of the secretory pathway are well understood, less is known about their regulation, especially by mechanical cues. Here, we report that substrate stiffness stimulates conventional secretion. We have unravelled a molecular pathway that links a mechanical cue through Src and FAK kinases to promote the trafficking of secretory proteins out of the Golgi apparatus and prevent their post-Golgi lysosomal degradation. Phosphoproteomic analysis revealed the Golgi-specific Brefeldin A resistance factor 1 (GBF1) as a key downstream mechano-responsive regulator, whose phosphorylation state orchestrates post-Golgi cargo sorting, directing proteins either toward secretion or to lysosomes. Finally, we identified AMPK as a stiffness-dependent upstream regulator of GBF1 phosphorylation. Together, our data reveal a molecular regulatory loop in which matrix stiffness positively regulates cellular secretion via the Src-FAK-AMPK-GBF1 axis, which can have relevant medical implications in conditions like cancer and fibrosis and their treatment.

cell biology↗

bioRxiv2025

In vivo nuclear envelope adaptation during cell migration across confining embryonic tissue environments

In physiology and in disease, cells often migrate through narrow spaces, such as leukocytes undergoing diapedesis or cancer cells during dissemination. Cultured cells under physical confinement have been shown to experience mechanical stress due to deformation of the nucleus. Nuclear deformation can lead to loss of nuclear integrity and DNA damage, and it has been proposed to underlie cancer initiation and progression. In vivo, the consequences of physical confinement on physiological, developmental cell migration remain so far unexplored. Here, we use the zebrafish neural crest as an in vivo model to address how multipotent embryonic cells respond to physical confinement during developmental migration. By measuring the extracellular space from head to tail along the embryonic body axis, we found that the level of tissue scale confinement increases along the antero-posterior axis. We found that neural crest experience dramatic nuclear deformation during their migrating between adjacent tissues, which quantitatively scales with tissue confinement. By using complementary genetic and mechanical strategies to ablate the surrounding tissue, we observe a rescue of nuclear deformation in vivo. Surprisingly, we found that while deformation of the NC nucleus causes stretching of the nuclear envelope, it does not cause DNA damage even upon extreme deformations. Instead, cells adapt, by decreasing both their DNA damage and LaminB2 levels upon entering confined spaces. In summary, we establish the neural crest as a physiological framework uncovering a dynamic adaptation to tissue confinement in vivo.

developmental biology↗

bioRxiv2024

Chronic mycobacteria infection triggers macrophage senescence

Chronic infections with intracellular pathogens such as Mycobacterium abscessus (Mab) pose significant health challenges due to their capacity to persist within host cells and evade immune responses. This study investigates the cellular responses to chronic Mab infection in macrophages, particularly focusing on cellular senescence. Using an in vitro model of chronic infection in murine alveolar-like macrophages, we found that Mab induces a senescent phenotype characterised by decreased proliferation, altered morphology, DNA damage signalling activation, and upregulation of senescence markers such as p21 and SA-{beta}-galactosidase. Intriguingly, senescent macrophages secreted pro-inflammatory cytokines, consistent with a senescence-associated secretory phenotype (SASP), which promoted secondary senescence in neighbouring uninfected cells. This paracrine transmission of senescence underscores a potentially deleterious effect of Mab-induced SASP on tissue microenvironments, fostering a pro-inflammatory niche that may contribute to pathogen persistence. These findings highlight Mab-induced senescence as a key factor in chronic infection pathology, suggesting that targeting senescent cells and SASP-related pathways could enhance treatment outcomes in chronic bacterial infections.

microbiology↗

bioRxiv2024

Autosomal Dominant-Hyper-IgE Syndrome patients contain pre-Th17-cells that are activated by opportunistic pathogens to produce IL-10

BackgroundAutosomal Dominant-Hyper-IgE Syndrome (AD-HIES) is caused by dominant-negative (DN) STAT3 mutations and characterized by high IgE levels, a lack of Th17-cells and recurrent infections with extracellular pathogens. We previously identified an enigmatic population of IL-10 producing CCR6+B-helper T-cells and investigated here their relationship to Th17-cells and STAT3 signalling requirements. MethodsHuman blood lymphocytes were analysed by multiparametric flow cytometry in healthy donors and AD-HIES patients. Analysis was performed by conventional gating or with bioinformatic tools. FACS-purified T-cell subsets were activated in vitro and Th17 differentiation assessed. T-cell antigen specificities were assessed by activation with heat-killed pathogens or antigenic peptide pools. B helper capacities were determined according to antibody secretion in B-T co-cultures by ELISA. ResultsCCR6+Th-cells that lacked subset-defining differentiation markers were mostly non-polarised central memory T-cells (TCM) that produced IL-10 and expressed ROR{gamma}t. They were pre-committed to a Th17 fate, since TCR stimulation in the absence of polarising cytokines induced efficient Th17 differentiation. The latter was promoted by an autocrine loop of STAT3-activating cytokines. CCR6+Th-cells were reduced in patients with DN-STAT3 mutations but contained activated CCR6+TCM that produced IL-10 and responded vigorously to AD-HIES-associated pathogens. These residual CCR6+Th-cells provided B-cell help for IgG and IgE production. ConclusionsTh17 differentiation in AD-HIES patients was not completely impaired but arrested at an intermediate stage of IL-10 producing "pre-Th17"-cells. Surprisingly, DN-STAT3 mutations did not inhibit IL-10 production by CD4+T-cells. Pre-Th17-cells were activated by AD-HIES-associated pathogens and possessed B-helper functions, suggesting that they are not protective but promote aberrant IgE production.

immunology↗

bioRxiv2023

Endolysin B: A new archetype in M. tuberculosis treatment

So far it is thanks to antibiotics that illnesses, such as Tuberculosis (TB), are treatable. However, antimicrobial misuse combined with Mycobacterium tuberculosis phenotypic plasticity are nullifying the effects of the existing therapies. As a result, increasingly people are dying (one person dies of TB every 20 seconds), especially due to the rise of multi-and extensively drug-resistant strains. There is indeed a urgent need for new and more effective therapies, which should match the requirement of avoiding the rise in drug resistance. Among them, the use of bacteriophage - bacteria-restricted viruses - or simply phage lytic enzyme (i.e., endolysin) represents one of the most promising alternatives. All phages encode for the endolysin A (LysA), which degrades the bacteria cell wall, finally leading to the release of the newly synthesized virions. Nevertheless, mycobacteriophages (bacterial viruses selectively infecting mycobacteria), evolved the additional endolysin B (LysB) to selectively damage the complex mycobacteria cell wall, and to evade from their host. LysB, owing a lipolytic enzyme, can degrade the thick mycolic acid layer, and hence disrupt the integrity of the mycobacterial membrane. Despite its key role in mediating mycobacteria lysis, the molecular mechanism regulating LysB binding to its target remains poorly characterized. Herein, we selected Ms6LysB and created a fluorescent engineered version as a proxy to analyze LysB binding qualitatively and quantitatively to both the fast-growing non-pathogenic Mycobacterium smegmatis and the slow-growing pathogenic M. tuberculosis. Additionally, we shed light on LysB antimicrobial activity upon M. tuberculosis infection, by using alveolar-like mouse macrophages (mAMs) as a cellular model that closely recapitulates the natural niche of M. tuberculosis infection. Our study provides the proof-of-principle that Ms6 LysB binding to the outer mycobacterial membrane can impair M. tuberculosis growth homeostasis and that LysB retain its lytic properties even when internalized by mAMs. This lays the groundwork for the use of LysB as a new therapeutic strategy to undermine M. tuberculosis infection.

microbiology↗

bioRxiv2023

Mechanical stress combines with planar polarised patterning during metaphase to orient embryonic epithelial cell divisions

The orientation of cell division (OCD) in the plane of epithelia drives tissue morphogenesis and relaxes stresses, with errors leading to pathologies. Stress anisotropy, cell elongation and planar polarisation can all contribute to the OCD, but it is unclear how these interact in vivo. In the planar polarised Drosophila embryonic ectoderm during axis elongation, planar OCD is highly variable. We show that both a temporary reversal of tissue stress anisotropy and local compression from neighbouring dividing cells re-orient mitotic spindles during metaphase, independently of interphase cell elongation. Isotropic cells align their OCD to the anterior-posterior (AP) embryonic axis, mediated by tissue-wide planar polarised Myosin II, while the spindle of elongated cells is sterically constrained to cell long axes. Thus AP-patterning ensures that cell division combines with cell rearrangement to extend the body axis, except when strong local stress anisotropy is dissipated by cells dividing according to their elongation.

biophysics↗

bioRxiv2022

A Multiscale study of phosphorylcholine driven cellular phenotypic targeting

Phenotypic targeting requires the ability of the drug delivery system to discriminate over cell populations expressing a particular receptor combination. Such selectivity control can be achieved using multiplexed-multivalent carriers often decorated with multiple ligands. Here, we demonstrate that the promiscuity of a single ligand can be leveraged to create multiplexed-multivalent carriers achieving phenotypic targeting. We show how the cellular uptake of poly(2-methacryloyloxyethyl phosphorylcholine)-poly(2- (diisopropylamino)ethyl methacrylate) (PMPC-PDPA) polymersomes varies depending on the receptor expression among different cells. We investigate the PMPC-PDPA polymersome insertion at the single chain/receptor level using all-atom molecular modelling. We propose a theoretical statistical mechanics-based model for polymersome-cell association that explicitly considers the interaction of the polymersome with the cell glycocalyx shedding light on its effect on the polymersome binding. We validate our model experimentally and show that the binding energy is a non-linear function, allowing us to tune interaction by varying the radius and degrees of polymerisation. Finally, we show that PMPC-PDPA polymersomes can be used to target monocytes in vivo due to their promiscuous interaction with SRB1, CD36 and CD81.

biochemistry↗

bioRxiv2021

Targeting activated macrophages intracellular milieu to augment anti-inflammatory drug potency

We present pH-responsive phosphorylcholine polymersomes ability to target activated macrophages via scavenger receptors, enter them via endocytosis, and escape from early endosomes enabling the intra-cellular drug delivery. Using an arthritis experimental model and the gold standard disease modifying anti-rheumatic drug, methotrexate, we prove that polymersomes augments therapeutic efficacy, while minimizing the off-target effect. First, we demonstrate the selective accumulation of polymersomes within the inflamed synovial tissues and cells, including macrophages. Second, we show the beneficial therapeutic effect of methotrexate loaded polymersomes in preventing both joint inflammation and further damage. Hence, we prove the therapeutic potential of polymersomes in enhancing the complete prevention of arthritis progression, which makes it a promising nanotherapy for arthritis treatment as well as other inflammatory disorders. TeaserWe show that the effective targeting and delivery of drugs to the main inflammation actors, the macrophages, enhances arthritis therapy.

immunology↗

bioRxiv2020

Combinatorial Intracellular Delivery Screening (CIDS) of Anticancer Drugs

Conventional drug solubilisation strategies limit the understanding of the full potential of poorly water-soluble drugs during drug screening. Here, we propose a screening approach in which poorly water-soluble drugs are entrapped in poly (2-(methacryloyloxyethyl phosphorylcholine)-poly(2-(diisopropylaminoethyl methacryate) (PMPC-PDPA) polymersomes (POs) to enhance drug solubility and facilitate intracellular delivery. By using a human paediatric glioma cell model, we demonstrated that PMPC-PDPA POs mediated intracellular delivery of cytotoxic and epigenetic drugs by receptor-mediated endocytosis. Additionally, when delivered in combination, drug-loaded PMPC-PDPA POs triggered both an enhanced drug efficacy and synergy compared to that of a conventional combinatorial screening. Hence, our comprehensive synergy analysis illustrates that our screening methodology, in which PMPC-PDPA POs are used for intracellular co-delivery of drugs, allows us to identify potent synergistic profiles of anticancer drugs.

bioengineering↗

bioRxiv2020

On the shuttling across the blood-brain barrier via tubules formation: mechanism and cargo avidity bias

The blood-brain barrier is made of polarised brain endothelial cells (BECs) phenotypically conditioned by the central nervous system (CNS). Transport across BECs is of paramount importance for nutrient uptake as well as to rid the brain of waste products. Nevertheless, currently we do not understand how large macromolecular cargo shuttles across and how BECs discriminate between the brain-bound and own nutrients. Here, we study the low-density lipoprotein receptor-related protein 1 (LRP1) an essential regulator of BEC transport, and show that it is associated with endocytic effectors, endo-lysosomal compartments as well as syndapin-2, a member of the Bin/Amphiphysin/Rvs (BAR) domain superfamily known to stabilise tubular carriers. We employed synthetic self-assembled vesicles, polymersomes, as a multivalent system with tunable avidity as a tool to investigate the mechanism of transport across BECs. We used a combination of conventional and super-resolution microscopy, both in vivo and in vitro, accompanied with biophysical modelling of transport kinetics and membrane-bound interactions. Our results demonstrate that the avidity of the ligand-receptor interaction (the overall cargo binding energy) determines the mechanism of sorting during the early stages of endocytosis and consequent trafficking. We show that high avidity cargo biases the LRP1 towards internalisation and fast degradation in BECs, while mid avidity augments the formation of syndapin-2 stabilised tubular carriers and promotes fast shuttling across BECs. Thus, we map out a very detailed mechanism where clathrin, actin, syndapin-2, dynamin and SNARE act synergistically to enable fast shuttling across BECs.

neuroscience↗

bioRxiv2019

Joint Motion Estimation and Source Identification using Convective Regularisation with an Application to the Analysis of Laser Nanoablations

We propose a variational method for joint motion estimation and source identification in one-dimensional image sequences. The problem is motivated by fluorescence microscopy data of laser nanoablations of cell membranes in live Drosophila embryos, which can be conveniently--and without loss of significant information--represented in space-time plots, so called kymographs. Based on mechanical models of tissue formation, we propose a variational formulation that is based on the nonhomogenous continuity equation and investigate the solution of this ill-posed inverse problem using convective regularisation. We show existence of a minimiser of the minimisation problem, derive the associated Euler-Lagrange equations, and numerically solve them using a finite element discretisation together with Newtons method. Based on synthetic data, we demonstrate that source estimation can be crucial whenever signal variations can not be explained by advection alone. Furthermore, we perform an extensive evaluation and comparison of various models, including standard optical flow, based on manually annotated kymographs that measure velocities of visible features. Finally, we present results for data generated by a mechanical model of tissue formation and demonstrate that our approach reliably estimates both a velocity and a source.

biophysics↗

bioRxiv2018

Actomyosin-driven tension at compartmental boundaries orients cell division independently of cell geometry in vivo

During animal development, planar polarization of the actomyosin cytoskeleton underlies key morphogenetic events such as axis extension and boundary formation. Actomyosin is enriched along compartment boundaries during segmentation of the Drosophila embryo, forming supracellular contractile cables that keep cells segregated at boundaries. Here, we show that these contractile actomyosin cables bias the orientation of division in cells in contact with compartment boundaries. By decreasing actomyosin cable tension locally using laser ablation or, conversely ectopically increasing tension using laser wounding, we demonstrate that localised subcellular force is necessary and sufficient to orient mitoses in vivo. Moreover this bias is independent of cell geometry and involves capture of the spindle pole by the actomyosin cortex.

developmental biology↗

bioRxiv2017

Par3/Baz levels control epithelial folding at actomyosin-enriched compartmental boundaries

Epithelial folding is crucial to shape embryos and tissues during development. Here we investigate the coupling between epithelial folding and actomyosin-rich boundaries. The mechanistic relationship between the two is unclear, since actomyosin-rich boundaries can be either associated with folds or not, while epithelial folding has been found to be either dependent or independent of actomyosin contractility. Here we investigate the shallow folds that form at compartmental parasegment boundaries (PSBs) in the early Drosophila embryo. First, we demonstrate that formation of these folds is dependent on the contractility of supracellular actomyosin cables. When the Myosin II phosphatase Flawing is depleted at the PSBs, actomyosin contractility increases, resulting in deeper folds. Conversely, in wingless mutants, actomyosin enrichment and increased contractility at PSBs are lost and this correlates with an absence of folding. Furthermore, when we make ectopic PSBs by expressing Wingless ubiquitously, the ectopic boundaries become enriched in actomyosin and epithelial folds form. Ectopic PSB folds, however, are much deeper than endogenous ones, indicating that epithelial folding is normally under inhibitory control. We present evidence that depletion of Bazooka/Par-3 levels at PSB cell-cell contacts, which is under Wingless signaling control, is responsible for this inhibition. Bazooka is found depleted at endogenous but not ectopic PSBs. In embryos overexpressing Bazooka, endogenous PSB folds form earlier and are much deeper. To ask how local signaling at the boundaries control Bazooka levels at cell-cell contacts, we examined embryos that ectopically expressed Wingless in an hedgehog mutant background. In these embryos, inhibition of folding is rescued, with ectopic PSBs now forming shallow folds as endogenous PSBs. Bazooka is depleted at these ectopic PSBs in absence of Hedgehog, suggesting an opposite effect of Wingless and Hedgehog signaling on Bazooka levels at PSB cell-cell contacts. This uncovers a new role of Bazooka in controlling fold formation at actomyosin-rich compartmental boundaries.

cell biology↗