Biology subjects

Hawkins, R.

Publications and source records attributed to Hawkins, R..

11 recordsLinked to original sources

bioRxiv2025

The Endo-GeneScreen Platform Identifies Drug-Like Probes that Regulate Endogenous Protein Levels within Physiological Contexts

Traditional phenotypic drug discovery platforms have suffered from poor scalability and a lack of mechanistic understanding of newly discovered phenotypic probes. To address this, we created Endo-GeneScreen (EGS), a high-throughput enabled screening platform that identifies bioactive small molecules capable of regulating endogenous protein expression encoded by any preselected target gene within a biologically appropriate context. As a proof-of-concept, EGS successfully identified drug candidates that up-regulate endogenous expression of neuronal Syngap1, a gene that causes a neurodevelopmental disorder when haploinsufficient. For example, SR-1815, a previously unknown and undescribed kinase inhibitor, alleviated major cellular consequences of Syngap1 loss-of-function by restoring normal SynGAP protein levels and dampening neuronal hyperactivity within haploinsufficient neurons. Moreover, we demonstrate that EGS assays accelerate preclinical development of identified drug candidates and facilitate mode-of-action deconvolution studies. Thus, EGS identifies first-in-class bioactive small molecule probes that promote biological discovery and precision therapeutic development.

neuroscience↗

bioRxiv2025

The mechanism how Pretubulysin-induced microtubule disassembly improves T cell search efficiency

To clean tissue from tumorigenic and infected cells, cytotoxic T lymphocytes (CTLs) must navigate confined environments in vivo, locate the infected cells and eliminate them. Impaired CTL migration towards the tumor can limit the efficacy of immunotherapy. Microtubules (MTs) have emerged as promising targets, because destabilizing MTs enhances T-cell migration and subsequent killing, yet the underlying mechanisms are poorly understood. Here, we use pretubulysin, a potent MT depolymerizer, to uncover how MT dynamics regulate CTL motility. Complete MT disassembly markedly increased CTL infiltration and migration in 3D matrices. To investigate how altered migration affects target elimination, we employed a persistent random-walk model parameterized solely with experimental motility data. The model shows that the increase in speed and persistence induced by pretubulysin explains enhanced search efficiency increasing the encounter rate of CTLs with target cells. The simulations also predict how these gains in search efficiency scale with tissue thickness and CTL density. Mechanistically, MT depolymerization in activated CTLs triggers localized actomyosin accumulation at the uropod. This enhances rear contraction forces and promotes faster, more persistent migration and efficient search. Our findings clarify how MT dynamics influence CTL ability to eliminate targets in 3D environments and highlights the potential of MT-targeting agents such as pretubulysin to optimize T cell-based immunotherapies.

cell biology↗

bioRxiv2024

ReSCU-Nets: recurrent U-Nets for segmentation of multidimensional microscopy data

Segmenting multi-dimensional microscopy data requires high accuracy across many images (e.g. timepoints or Z slices) and is thus a labour-intensive part of biological image processing pipelines. We present ReSCU-Nets, recurrent convolutional neural networks that use the segmentation results from the previous frame as a prompt to segment the current frame. We demonstrate that ReSCU-Nets outperform state-of-the-art image segmentation models in different segmentation tasks on time-lapse microscopy sequences.

bioinformatics↗

bioRxiv2023

Integrin-based adhesions promote cell-cell junction remodelling and cytoskeletal rearrangements to drive embryonic wound healing

Embryos have a remarkable ability to repair wounds rapidly, with no inflammation or scarring. Embryonic wound healing is driven by the collective movement of the surrounding cells to seal the lesion. During embryonic wound closure, the cells adjacent to the wound polarize the cytoskeletal protein actin and the molecular motor non-muscle myosin II, which accumulate at the wound edge forming a supracellular cable around the wound. Adherens junction proteins including E-cadherin are internalized from the interface with the lesion and localize to former tricellular junctions at the wound margin, in a process necessary for cytoskeletal polarity. Using quantitative live microscopy, we found that the cells adjacent to wounds in the Drosophila epidermis also polarized Talin, a core component of cell-extracellular matrix (ECM) adhesions that links integrins to the actin cytoskeleton. Integrin knock-down and inhibition of integrin binding delayed wound closure and were associated with a reduction in actin levels around the wound. Additionally, disrupting integrins caused a defect in E-cadherin reinforcement at tricellular junctions along the wound edge, suggesting crosstalk between integrin-based and cadherin-based adhesions. Together, our results show that cell-ECM adhesion contributes to embryonic wound repair and reveal an interplay between cell-cell and cell-ECM adhesion in the collective cell movements that drive rapid wound healing.

cell biology↗

bioRxiv2022

Engineered retrovirus-like Arc extracellular vesicles for the in vivo targeted delivery of mRNA into the brain

Systemic delivery of mRNAs into disease neurons is first limited by the blood-brain-barrier (BBB). Leukocyte-derived extracellular vesicles (EVs) can cross the BBB at inflammatory sites, emerging as promising carriers to target the disease brain. However, efficient mRNA loading into EVs and their uptake by neurons remain challenges. Here we incorporated inside EVs the endogenous retrovirus-like Arc protein capsids, stabilized by Arc 5UTR RNA elements, to effectively load and deliver mRNAs. Produced from self-derived leukocytes, engineered retrotransposon Arc EVs (eraEVs) are immunologically inert with minimal clearance. Equipped with endothelial adhesion molecules from donor leukocytes, circulating eraEVs enter the brain enriching at neuro-inflammatory sites. During self-assembly, Arc recruits enveloping proteins onto eraEVs further promoting neuronal uptake. Possessing high effectiveness like viral vectors and biocompatibility as natural vesicles, eraEV-nanocarriers can be produced from virtually all donor cell types, potentially leading to the development of future clinical therapies for a range of diseases. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=125 SRC="FIGDIR/small/518870v2_ufig1.gif" ALT="Figure 1"> View larger version (35K): org.highwire.dtl.DTLVardef@260a4aorg.highwire.dtl.DTLVardef@16da754org.highwire.dtl.DTLVardef@4a79dorg.highwire.dtl.DTLVardef@1983da8_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioengineering↗

bioRxiv2021

The role of actin and myosin II in the cell cortex of adhered and suspended cells

Adhesion induces dramatic morphological and mechanical changes to cells, which are reflected by changes to the actin cortex. Among the many different proteins involved in this sub-membranous layer, motor proteins (e.g., nonmuscle myosin II [NMII]) and actin nucleators (e.g., Arp2/3, formins) are known to have significant influences on its dynamics and structure. The different roles of NMII, Arp2/3, and formins in the dynamics, structure, and mechanics of the actin cortex depend on the adhesion state of the cell. In this study, we unravel the interplay between the dynamics, structure, and mechanics of the actin cortex in adhered cells and in cells in suspension. We show that treatments with extrinsic cellular perturbants lead to alterations of all three properties that are correlated. However, intrinsic actin cortex variations between different cell adhesion states lead to unexpected correlations. Surprisingly, we find that NMII minifilaments have a minor influence on the actin cortex. Using new microscopy techniques, we show that NMII minifilaments are not localized within the actin cortex, as previously thought, but concentrated in a layer beneath it. Our treatments affecting Arp2/3 and formin reveal correlations between the actin cortex characteristics. Our data build towards a comprehensive understanding of the actin cortex. This understanding allows the prediction and control of cortical changes, which is essential for the study of general cellular processes, such as cell migration, metastasis, and differentiation.

biophysics↗

bioRxiv2021

Chemical Editing of Proteoglycan Architecture

Proteoglycans are heterogeneous macromolecular glycoconjugates that orchestrate many important cellular processes. While much attention has focused on the poly-sulfated glycosaminoglycan chains that decorate proteoglycans, other important elements of proteoglycan architecture, such as their core proteins and cell surface localization, have garnered less emphasis. Hence, comprehensive structure-function relationships that consider the replete proteoglycan architecture as glycoconjugates are limited. Here, we present a comprehensive approach to study proteoglycan structure and biology by fabricating defined semi-synthetic modular proteoglycans that can be tailored for cell surface display. To do so, we integrate amber codon reassignment in the expression of sequence-fined proteoglycan core proteins, metabolic oligosaccharide engineering to produce functionalizable glycosaminoglycans, and bioorthogonal click chemistry to covalently tether the two components. These materials permit the methodical dissection of the parameters required for optimal binding and function of various proteoglycan-binding proteins, and they can be modularly displayed on the surface of any living cell. We demonstrate that these sophisticated materials can recapitulate the functions of native proteoglycans in mouse embryonic stem cell differentiation and cancer cell spreading, while permitting the identification of the most important contributing elements of proteoglycan architecture toward function. This technology platform will confer structural resolution toward the investigation of proteoglycan structure-function relationships in cell biology.

biochemistry↗

bioRxiv2020

Mapping glycan-mediated galectin-3 interactions by live cell proximity labeling

Galectin-3 is a glycan-binding protein (GBP) that binds {beta}-galactoside glycan structures to orchestrate a variety of important biological events, including the activation of hepatic stellate cells to cause hepatic fibrosis. While the requisite glycan epitopes needed to bind galectin-3 have long been elucidated, the cellular glycoproteins that bear these glycan signatures remain unknown. Given the importance of the three-dimensional arrangement of glycans in dictating GBP interactions, strategies that allow the identification of GBP receptors in live cells, where the native glycan presentation and glycoprotein expression are preserved, possess significant advantages over static and artificial systems. Here, we describe the integration of a proximity labeling method and quantitative mass spectrometry to map the glycan and glycoprotein interactors for galectin-3 in live hepatic stellate cells. Understanding the identity of the glycoproteins and defining the structures of the glycans required for galectin-3 mediated hepatic stellate cell activation will empower efforts to design and develop selective therapeutics to mitigate hepatic fibrosis. SignificanceBecause of the weak interactions between individual glycan-binding proteins (GBP), such as galectin-3, and glycans, strategies that allow the direct interrogation of these interactions in living cells remain limited. Thus, the glycan and glycoprotein ligands that are physiologically relevant for galectin-3 binding are insufficiently described. Here, we used a proximity labeling approach that catalytically tags interactors for galectin-3 and identified its pertinent glycan and glycoprotein counter-receptors in live hepatic stellate cells. This study demonstrates that proximity labeling is a powerful tool for mapping GBP complexes in living cells, and when coupled with chemical inhibitors, it can discriminate between protein-protein and protein-glycan interactions. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=57 SRC="FIGDIR/small/058586v1_ufig1.gif" ALT="Figure 1"> View larger version (19K): org.highwire.dtl.DTLVardef@163b731org.highwire.dtl.DTLVardef@19021ddorg.highwire.dtl.DTLVardef@19f53beorg.highwire.dtl.DTLVardef@133009a_HPS_FORMAT_FIGEXP M_FIG C_FIG

biochemistry↗

bioRxiv2020

Mechanical Heterogeneity in the Bone Microenvironment as Characterised by Atomic Force Microscopy

Bones are structurally heterogeneous organs with diverse functions that undergo mechanical stimuli across multiple length scales. Mechanical characterisation of the bone microenvironment is important for understanding how bones function in health and disease. Here we describe the mechanical architecture of cortical bone, the growth plate, metaphysis and marrow in fresh murine bones, probed using atomic force microscopy in physiological buffer. Both elastic and viscoelastic properties are found to be highly heterogeneous with moduli ranging over 3 to 5 orders of magnitude, both within and across regions. All regions include extremely soft areas, with moduli of a few Pascal and viscosities as low as tens Pa*s. Aging impacts the viscoelasticity of the bone marrow strongly but has limited effect on the other regions studied. Our approach provides the opportunity to explore the mechanical properties of complex tissues at the length scale relevant to cellular processes and how these impact on aging and disease. SIGNIFICANCEThe mechanical properties of biological materials at cellular scale are involved in guiding cell fate. However, there is a critical gap in our knowledge of such properties in complex tissues. The physiochemical environment surrounding the cells in in-vitro studies differs significantly from that found in vivo. Existing mechanical characterisation of real tissues are largely limited to properties at larger scales, structurally simple (e.g. epithelial monolayers) or non-intact (e.g. through fixation) tissues. In this paper, we address this critical gap and present the micro-mechanical properties of the relatively intact bone microenvironment. The measured Youngs moduli and viscosity provide a sound guidance in bioengineering designs. The striking heterogeneity at supracellular scale reveals the potential contribution of the mechanical properties in guiding cell behaviour.

biophysics↗

bioRxiv2019

Designing viscoelastic mucin-based hydrogels

We report the design of a mucin hydrogel created using a thiol-based cross-linking strategy. By using a cross-linking reagent capable of forming disulfide linkages between mucins, the mucin-based hydrogels possess viscoelastic properties comparable to native mucus as measured by bulk rheology. We confirmed disulfide cross-links mediate gel formation in our system using chemical treatments to block and reduce cysteines where we found mucin hydrogel network formation was inhibited and disrupted, respectively. Particle tracking microrheology was used to investigate the kinetics and evolution of microstructure and viscoelasticity within the hydrogel as it formed. We found that the rate of gel formation could be tuned by varying the mucin to crosslinker ratio, producing network pore sizes in the range measured previously in human mucus. The results of this work provide a new, simple method for creating mucin hydrogels with physiologically relevant properties using readily available reagents.

bioengineering↗

bioRxiv2017

Epigenomic and 3D genome architecture in naïve and primed human embryonic stem cell states

During mammalian embryogenesis changes in morphology and gene expression are concurrent with epigenomic reprogramming. Using human embryonic stem cells representing the pre-implantation blastocyst (naive) and post-implantation epiblast (primed), our data demonstrate that a substantial portion of known human enhancers are pre-marked by H3K4me1 in naive cells, providing an enhanced open chromatin state in naive pluripotency. The naive enhancer repertoire occupies nine percent of the genome, three times that of primed cells, and can exist in broad chromatin domains over fifty kilobases. Enhancer chromatin states are largely poised. Seventy-seven percent of naive enhancers are decommissioned in a stepwise manner as cells become primed. While primed topological associated domains are unaltered upon differentiation, naive domains expand across primed boundaries, impacting three dimensional genome architecture. Differential topological associated domain edges coincide with naive H3K4me1 enrichment. Our results suggest that naive-derived cells have a chromatin landscape reflective of early embryogenesis.

developmental biology↗