Biology subjects

Beckwith, K. S.

Publications and source records attributed to Beckwith, K. S..

7 recordsLinked to original sources

bioRxiv2025

NINJ1 is activated by Mycobacterium tuberculosis ESX-1 secreted effector EsxA and mediates necrosis of infected human macrophages

Lytic cell death contributes to tissue damage and dissemination during Mycobacterium tuberculosis (Mtb) infection, yet the mechanisms governing plasma membrane rupture (PMR) remain incompletely defined. Here, we identify Ninjurin-1 (NINJ1), a mediator of PMR, as a central effector of macrophage lysis during Mtb infection. Mtb infection induced NINJ1 oligomerization, and genetic deletion or pharmacological inhibition of NINJ1 markedly reduced lactate dehydrogenase (LDH) release. Cytokine secretion was largely preserved in NINJ1-deficient macrophages, with the exception of CXCL10. Unexpectedly, inhibition of pyroptosis, apoptosis, necroptosis, and ferroptosis - individually or in combination - did not prevent NINJ1 activation or PMR, indicating that Mtb-induced membrane rupture proceeds independently of canonical regulated cell death pathways. However, NINJ1 oligomerization and PMR required the Mtb ESX-1 secretion system, identifying a bacterial virulence determinant as a critical upstream trigger. Although osmoprotective PEG partially reduced LDH release, neither calcium signaling nor cell swelling accounted for NINJ1-dependent PMR in Mtb-infected macrophages. Together, these findings establish NINJ1 as a key executioner of Mtb-induced lytic cell death and reveal an ESX-1-dependent pathway of PMR that is uncoupled from canonical host cell death programs. TeaserNINJ1 mediates plasma membrane rupture of macrophages infected with Mycobacterium tuberculosis

microbiology↗

bioRxiv2024

Nanoscale 3D DNA tracing reveals the mechanism of self-organization of mitotic chromosomes

How genomic DNA is folded during cell division to form the characteristic rod-shaped mitotic chromosomes essential for faithful genome inheritance is a long-standing open question in biology. Here, we use nanoscale DNA-tracing in single dividing cells to directly visualize how the 3D fold of genomic DNA changes during mitosis, at scales from single loops to entire chromosomes. Our structural analysis reveals a characteristic genome scaling minimum at 6-8 Mbp in mitosis. Combined with data-driven modeling and molecular perturbations, we can show that very large and strongly overlapping loops formed by Condensins are the fundamental structuring principle of mitotic chromosomes. These loops compact chromosomes locally and globally to the limit set by chromatin self-repulsion. The characteristic length, density and increasingly overlapping structure of mitotic loops we observe in 3D, fully explain how the rod-shaped mitotic chromosome structure emerges by self-organization during cell division.

cell biology↗

bioRxiv2024

Quantitative imaging of loop extruders rebuilding interphase genome architecture after mitosis

How cells establish the interphase genome organization after mitosis is incompletely understood. Using quantitative and super-resolution microscopy, we show that the transition from a Condensin to a Cohesin-based genome organization occurs dynamically over two hours. While a significant fraction of Condensins remains chromatin-bound until early Gl, Cohesin-STAGl and its boundary factor CTCF are rapidly imported into daughter nuclei in telophase, immediately bind chromosomes as individual complexes and are sufficient to build the first interphase TAD structures. By contrast, the more abundant Cohesin-STAG2 accumulates on chromosomes only gradually later in Gl, is responsible for compaction inside TAD structures and forms paired complexes upon completed nuclear import. 0ur quantitative time-resolved mapping of mitotic and interphase loop extruders in single cells reveals that the nested loop architecture formed by sequential action of two Condensins in mitosis is seamlessly replaced by a less compact, but conceptually similar hierarchically nested loop architecture driven by sequential action of two Cohesins.

cell biology↗

bioRxiv2021

Visualization of loop extrusion by DNA nanoscale tracing in single cells

The spatial organization of the genome is essential for its functions, including gene expression, DNA replication and repair, as well as chromosome segregation. Biomolecular condensates and loop extrusion have been proposed as the principal driving forces that underlie the formation of chromatin compartments and topologically associating domains, respectively. However, whether the actual 3D-fold of DNA in single cells is consistent with these mechanisms has been difficult to address in situ. Here, we present LoopTrace, a workflow for nanoscale 3D imaging of the genome sequence in structurally well-preserved nuclei in single human cells. Tracing the in situ structure of DNA in thousands of individual cells reveals that genomic DNA folds as a flexible random coil in the absence of loop extruding enzymes such as Cohesin. In the presence of Cohesin and its boundary factor CTCF, reproducibly positioned loop structures dominate the folds, while Cohesin alone leads to randomly positioned loops. The 3D structure and size variability of DNA loops we observe in a large number of single cells allow us to formulate a data-constrained computational model of genomic DNA folding that explains how sparse and dynamic loops in single cells lead to the emergence of compact topological domains in averages of cell populations.

cell biology↗

bioRxiv2019

Electron beam lithography fabrication of SU-8 polymer structures for cell studies

Flat surfaces decorated with micro- and nanostructures are important tools in biomedical research used to control cellular shape, in studies of mechanotransduction, membrane mechanics, cell migration and cellular interactions with nanostructured surfaces. Existing methods to fabricate surface-bound nanostructures are typically limited either by resolution, aspect ratio or throughput. In this work, we explore electron beam lithography based structuring of the epoxy resist SU-8 on glass substrate. We focus on a systematic investigation of the process parameters and determine limits of the fabrication process, both in terms of spatial resolution, structure aspect ration and fabrication throughput. The described approach is capable of producing high-aspect ratio, surface bound nanostructures with height ranging from 100 nm to 4000 nm and with in-plane resolution below 100 nm directly on a transparent substrate. Fabricated nanostructured surfaces can be integrated with common techniques for biomedical research, such as high numerical aperture optical microscopy. Further more, we show how the described approach can be used to make nanostructures with multiple heights on the same surface, something which is not readily achievable using alternative fabrication approaches. Our research paves an alternative way of manufacturing nanostructured surfaces with applications in life science research.

biophysics↗

bioRxiv2019

Plasma membrane damage causes NLRP3 activation and pyroptosis during Mycobacterium tuberculosis infection

Mycobacterium tuberculosis (Mtb) is a major global health problem and causes extensive cytotoxicity in patient cells and tissues. Here we define an NLRP3, caspase-1 and gasdermin D-mediated pathway to pyroptosis in human monocytes following exposure to Mtb. We demonstrate an ESX-1 mediated, contact-induced plasma membrane (PM) damage response that occurs during phagocytosis or from the cytosolic side of the PM after phagosomal rupture in Mtb infected cells. This PM injury in turn causes K+ efflux and activation of NLRP3 dependent IL-1{beta} release and pyroptosis, facilitating the spread of Mtb to neighbouring cells. Further we reveal a dynamic interplay of pyroptosis with ESCRT-mediated PM repair. Collectively, these findings reveal a novel mechanism for pyroptosis and spread of infection acting through dual PM disturbances both during and after phagocytosis. We also highlight dual PM damage as a common mechanism utilized by other NLRP3 activators that have previously been shown to act through lysosomal damage.\n\nGraphical abstract\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=115 SRC=\"FIGDIR/small/747014v1_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (28K):\norg.highwire.dtl.DTLVardef@1911356org.highwire.dtl.DTLVardef@18c99dcorg.highwire.dtl.DTLVardef@1c94bb9org.highwire.dtl.DTLVardef@8a69db_HPS_FORMAT_FIGEXP M_FIG C_FIG

immunology↗

bioRxiv2019

Influence of nanopillar arrays on fibroblast motility, adhesion and migration mechanisms

Surfaces decorated with high aspect ratio nanostructures are a promising tool to study cellular processes and design novel devices to control cellular behaviour, perform intracellular sensing or deliver effector molecules to cells in culture. However, little is known about the dynamics of cellular phenomenon such as adhesion, spreading and migration on such surfaces. In particular, how these are influenced by the surface properties. In this work, we investigate fibroblast behaviour on regular arrays of 1 micrometer high, polymer nanopillars with varying pillar to pillar distance (array pitch). NIH-3T3 fibroblasts spread on all arrays, and on contact with the substrate engulf nanopillars independently of the array pitch. As the cells start to spread, different behaviour is observed. On dense arrays which have the pitch equal or below 1 micrometer, cells are suspended on top of the nanopillars, making only sporadic contact with the glass support. Cells stay attached to the glass support and fully engulf nanopillars during spreading and migration on the sparse arrays which are characterized by a pitch of 2 micrometers and above. These alternate states have a profound effect on cell migration rates, which are strongly reduced on nanopillar sparse arrays. Dynamic actin puncta colocalize with nanopillars during cell spreading and migration. Strong membrane association with engulfed nanopillars might explain the reduced migration rates on sparse arrays. This work reveals several interesting phenomenon of dynamical cell behaviour on nanopillar arrays, and provides important perspectives on design and applications of high aspect ratio nanostructures.

biophysics↗