Biology subjects

Gomes, E. R.

Publications and source records attributed to Gomes, E. R..

11 recordsLinked to original sources

bioRxiv2026

Myofibers drive postnatal myonuclear accretion through Arp2/3-dependent membrane protrusions

Skeletal muscle postnatal growth depends on myoblast fusion with pre-existing myofibers, but whether myofibers actively regulate this process remains unclear. The Arp2/3 complex, which nucleates branched actin networks, is required for myoblast fusion during embryogenesis, but its role in postnatal myofibers is unknown. Here, we investigated the role of the Arp2/3 complex in myofibers using an inducible skeletal muscle-specific Arpc4 knockout model. We find that loss of Arp2/3 in myofibers impairs myonuclear accretion, resulting in smaller myofibers and reduced muscle strength. Satellite cells are still activated and able to differentiate but accumulate around Arpc4-deficient myofibers rather than fusing, pointing to a myofiber-intrinsic defect. In co-culture, myofibers form long-lived membrane protrusions enriched in Arp2/3 at myoblast contact sites, and optogenetic activation of protrusion in myofibers induced myoblast fusion. Genetic depletion of Arpc4 in myofibers markedly reduces membrane protrusions both in vitro and in vivo. These findings unveil a fundamental role for the Arp2/3 complex in postnatal muscle growth, and reveal a mechanism by which myofibers actively extend membrane protrusions to drive myoblast fusion. This repositions myofibers as active fusogenic partners and cell-autonomous drivers of their own nuclear accretion.

cell biology↗

bioRxiv2026

A 3D Tumor-on-a-chip Platform to Identify Drugs that Block Breast Cancer Cell Intravasation

Metastasis is the leading cause of death in breast cancer patients, yet there are no drugs specifically designed to block cancer cell intravasation, an early step of the metastatic cascade that originates circulating tumour cells (CTCs). A major challenge in developing anti-intravasation drugs is the scarcity of relevant in vitro platforms suitable for predictable drug discovery. Intravasation is a fundamental step of metastasis and involves the crossing of cancer cells through an endothelial barrier to enter the blood circulation. Here we developed an intravasation-on-a-chip model with controlled extracellular matrix composition, fluid flow and shear stress, which mimics the dynamic tumour-endothelium interface. The systems allows real-time imaging of intravasation and the isolation and quantification of intravasated cancer cells. As a proof-of-concept for drug testing, we show that perfusion with the PI3K/mTOR inhibitor Dactolisib, significantly reduced intravasation without compromising endothelial cell viability. The system also provides the capability to evaluate inhibitor on-target activity via imaging analysis. This intravasation-on-a-chip model offers a powerful, scalable, and imaging-compatible platform for discovering and evaluating anti-intravasation compounds.

cancer biology↗

bioRxiv2024

Microtubules coordinate mitochondria transport with myofibril morphogenesis during muscle development

Muscle morphogenesis creates highly specialised muscle cells containing contractile myofibrils and energy producing mitochondria. Myofibrils are chains of sarcomeres, whose myosin motors slide over actin filaments at the expense of ATP. Thus, myofibrils and mitochondria are in intimate contact in mature muscles. However, how mitochondria morphogenesis is coordinated with myofibrillogenesis during development remains largely unknown. Here, we used in vivo imaging to investigate myofibril and mitochondria network dynamics in developing Drosophila flight muscles. We found that mitochondria rapidly intercalate from the surface of actin bundles to their interior; concomitantly, actin filaments condense to individual myofibrils. This ensures that mitochondria are in intimate proximity to each myofibril. Interestingly, antiparallel microtubules bundle in concert with the assembling myofibrils, suggesting a key role in myofibril orientation. Indeed, light-induced microtubule severing directly affects myofibril orientation, whereas knock-down of kinesin heavy chain specifically blocks mitochondria intercalation and long-range transport. Importantly, mitochondria-myofibril intercalation and microtubule-based transport of mitochondria is conserved in developing mammalian muscle. Together, these data identify a key role for microtubules in coordinating mitochondria and myofibril morphogenesis to build functional muscles.

developmental biology↗

bioRxiv2024

Arp2/3 iso-complexes limit t-tubule overgrowth to ensure myofiber formation and synchronous contraction

Muscle cells form a network of plasma membrane invaginations called t-tubules that control calcium release from the endoplasmic reticulum at the triads during muscle contraction. Although the importance of t-tubules for muscle physiology is well established, and abnormalities are found in multiple disorders, the mechanisms that mediate t-tubule growth are unknown. We show that the actomyosin cortex beneath the plasma membrane, regulated by Arp2/3 complexes containing Arpc5, acts as a gatekeeper for the membrane availability required for t-tubule growth. Enlarged t-tubules are formed upon disruption of Arpc5, impairing the synchronisation between plasma membrane depolarization and calcium release. Additionally, ablation of Arpc5 postnatally in myofibers results in muscle fatigue and t-tubule abnormalities, as observed in muscle disorders. We propose that the actomyosin cortex impacts muscle function, offering a potential pathophysiological mechanism for muscle disorders.

cell biology↗

bioRxiv2022

Generating fast-twitch myotubes in vitro using an optogenetic-based, quantitative contractility assay

The composition of fiber types within skeletal muscle impacts the tissues physiological characteristics and susceptibility to disease and ageing. In vitro systems should therefore account for fiber type composition when modelling muscle conditions. To induce fiber specification in vitro, we designed a quantitative contractility assay based on optogenetics and particle image velocimetry. We submitted cultured myotubes to long-term intermittent light stimulation patterns and characterized their structural and functional adaptations. After several days of in vitro exercise, myotubes contract faster and are more resistant to fatigue. The enhanced contractile functionality was accompanied by advanced maturation such as increased width and upregulation of neuron receptor genes. We observed an upregulation in the expression of distinct myosin heavy chain isoforms (namely, neonatal-Myh8 and fast-Myh), which induced a shift towards a fast fiber phenotype. This long-term in vitro exercise strategy can be used to study fiber specification and refine muscle disease modelling.

cell biology↗

bioRxiv2021

An in vitro - agent based modelling approach to optimisation of culture medium for generating muscle cells

Methodologies for culturing muscle tissue are currently lacking in terms of quality and quantity of mature cells produced. We analyse images from in vitro experiments to quantify the effects of culture media composition on mouse-derived myoblast behaviour and myotube quality. Computational modelling was used to predict an optimum media composition for culturing. Metrics of early indicators of cell quality were defined. Images of muscle cell differentiation reveal that altering culture media significantly affects quality indicators and myoblast migratory behaviours. To predict cell quality from early-stage myoblast behaviours, metrics drawn from experimental images or inferred by Approximate Bayesian Computation were applied as inputs to an agent-based model (ABM) of differentiation with quality indicator metrics as outputs. We describe cell behaviours as a set of functions of media composition to predict cell quality using the ABM. Our results suggest that culturing muscle cells in neural cell differentiation medium reduces cell-cell fusion but does not diminish cell quality and that increasing serum concentration increases myoblast fusion implying a trade-off between the quantity and quality of cells produced when choosing a culture medium. Our model provided a good prediction of experimental results for media with 5% serum provided the myoblast proliferation rate was known. Author summaryFunctional skeletal muscle tissue can be grown in the lab but is most useful if the constituent muscle cells behave as they would in vivo. Optimising the conditions to promote precursor muscle cell fusion and growth is therefore vital. With many different factors influencing cell growth finding optimal conditions through rounds of experimentation alone is difficult especially as we strive to complexify our cultures with multiple cell types. We created metrics quantifying mature muscle cell quality at an early stage of development and applied them to experiments with a variety of culture media compositions. Changing the concentration of serum and proportion of neuron differentiation medium produced differences in the behaviour of fusing cells and in the quality and quantity of mature cells. From these results we created phenomenological models describing the behaviour of fusing cells for any combination of serum and neuron medium concentration. We integrated these models into a multiscale agent-based computational model of cell fusion to predict cell quality and quantity through virtual experiments in an emergent fashion. Our model suggests that choosing culture media composition will involve fundamental compromises between cell quantity and quality and that cells which initially fuse quickly may produce less final yield.

bioengineering↗

bioRxiv2021

B cells adapt their nuclear morphology to organize the immune synapse and help antigen extraction

Upon interaction with immobilized antigens B cells form an immune synapse, where actin remodeling and re-positioning of the microtubule-organizing center (MTOC) together with lysosomes can facilitate antigen extraction. B cells have restricted cytoplasmic space, mainly occupied by a large nucleus, yet the role of nuclear morphology in the formation of the immune synapse has not been addressed. Here we show that, upon activation, B cells re-orientate and adapt the size of their nuclear groove facing the immune synapse, where the MTOC sits and lysosomes accumulate. Silencing nuclear envelope proteins, Nesprin-1 and Sun-1, impairs nuclear reorientation towards the synapse and leads to defects in actin organization at this level. Consequently, B cells are unable to internalize the BCR after antigen activation. Nesprin-1 and Sun-1-silenced B cells also fail to accumulate the tethering factor Exo70 at the center of the synaptic membrane and display defective lysosome positioning, impairing efficient antigen extraction at the immune synapse. Thus, changes in nuclear morphology and positioning emerge as critical regulatory steps to coordinate B cell activation.

cell biology↗

bioRxiv2021

Motor neuron boutons remodel through membrane blebbing

Wired neurons form new presynaptic boutons in response to increased synaptic activity, but the mechanism by which this occurs remains uncertain. The neuromuscular junction (NMJ) is a synapse formed between motor neurons (MNs) and skeletal muscle fibers and is critical for control of muscle contraction. Because Drosophila MNs have clearly discernible boutons that display robust structural plasticity, it is the ideal system in which to study bouton genesis. Here we show using ex-vivo and by live imaging that in response to depolarization, MNs form new boutons by membrane blebbing, a pressure-driven mechanism used in 3-D migration, but never described as a neuronal remodeling strategy. In accordance, F-actin is decreased during bouton growth (a hallmark of blebs) and we show that non-muscle myosin-II (a master regulator of blebbing) is recruited to newly formed boutons. Furthermore, we discovered that muscle contraction plays a mechanical role in activity-dependent plasticity, promoting bouton addition by increasing MNs confinement. Overall, we provide a novel mechanism by which established circuits create new boutons allowing their structural expansion and plasticity, using trans-synaptic physical forces as the main driving force. Understanding MN-muscle interplay during activity-dependent plasticity can help clarify the mechanisms leading to MN degeneracy observed in neuromuscular diseases.

cell biology↗

bioRxiv2020

Ctdnep1 and Eps8L2 regulate dorsal actin cables for nuclear positioning during cell migration

Cells actively position their nuclei within the cytoplasm for multiple cellular and physiological functions. Different cell types position their nuclei away from the leading edge to migrate properly. In migrating fibroblasts, nuclear positioning is driven by dorsal actin cables connected to the nuclear envelope by the LINC complex on Transmembrane Actin-associated Nuclear (TAN) lines. How dorsal actin cables are organized to form TAN lines is unknown. Here, we report a role for Ctdnep1/Dullard, a nuclear envelope phosphatase, and the actin regulator Eps8L2, on nuclear positioning. We demonstrate that Ctdnep1 and Eps8L2 directly interact to regulate the formation and thickness of dorsal actin cables required for TAN lines engagement for nuclear positioning. Our work establishes a novel mechanism to locally regulate actin at the nuclear envelope for nuclear positioning.

cell biology↗

bioRxiv2019

LINC complexes are mechanotransducers that discriminate Epithelial-Mesenchymal Transition programs

LINC complexes are transmembrane protein assemblies that physically connect the nucleo- and cytoskeletons through the nuclear envelope. Dysfunctions of LINC complexes are associated with pathologies such as cancer and muscular disorders. The mechanical roles of LINC complexes in these contexts are poorly understood. To address this, we used genetically encoded FRET biosensors of molecular tension in LINC complex proteins of fibroblastic and epithelial cells in culture. We exposed cells to mechanical, genetic and pharmacological perturbations, mimicking a range of physiological and pathological situations. We show that LINC complex proteins experience tension generated by the cytoskeleton and act as mechanical sensors of cell packing. Moreover, the LINC complex discriminates between inductions of partial and complete epithelial-mesenchymal transitions (EMT). We identify the implicated mechanisms, which associate nesprin tension sensing with -catenin capture at the nuclear envelope, thereby regulating {beta}-catenin transcription. Our data thus implicate that LINC complexes are mechanotransducers that fine-tune {beta}-catenin signaling in a manner dependent on the Epithelial-Mesenchymal Transition program.

cell biology↗

bioRxiv2019

DypFISH: Dynamic Patterned FISH to Interrogate RNA and Protein Spatial and Temporal Subcellular Distribution

Advances in single cell RNA sequencing have allowed for the identification and characterization of cellular subtypes based on quantification of the number of transcripts in each cell. However, cells may differ not only in the number of mRNA transcripts that they exhibit, but also in their spatial and temporal distribution, intrinsic to the definition of their cellular state. Here we describe DypFISH, an approach to quantitatively investigate the spatial and temporal subcellular localization of RNA and protein, by combining micropatterning of cells with fluorescence microscopy at high resolution. We introduce a range of analytical techniques for quantitatively interrogating single molecule RNA FISH data in combination with protein immunolabeling over time. Strikingly, our results show that constraining cellular architecture reduces variation in subcellular mRNA and protein distributions, allowing the characterization of their localization and dynamics with high reproducibility. Many tissues contain cells that exist in similar constrained architectures. Thus DypFISH reveals reproducible patterns of clustering, strong correlative influences of mRNA-protein localization on MTOC orientation when they are present and interdependent dynamics globally and at specific subcellular locations which can be extended to physiological systems.

systems biology↗