Biology subjects

Fackler, O. T.

Publications and source records attributed to Fackler, O. T..

8 recordsLinked to original sources

bioRxiv2025

A genetically encoded marker for imaging membranes of Plasmodium

Fluorescence microscopy is a powerful tool to analyze subcellular architecture, and long-term live-cell imaging permits the analysis of the dynamics of intracellular structures. Applying this approach to the membranes of Plasmodium spp., the causative agent of malaria, yielded important insight. Fluorescent labelling of Plasmodiums plasma membrane via membrane-resident proteins has been described, but proteins, which broadly mark internal membranes are currently elusive. Alternatively, general membrane dyes can be employed to study membrane dynamics, however, we find that the membrane dye BODIPY TR Ceramide has adverse effects on cell viability during live-cell imaging. To overcome this limitation, we present FLUMMI (Fixed-and-Live-cell Universal Membrane Marker for Imaging), a 32-amino acid long peptide derived from P. falciparum PCNA1, which targets (fluorescent) protein tags to internal membranes for detection in live or fixed samples. Importantly, FLUMMI enables non-invasive, long-term live-cell imaging of internal membranes without affecting P. falciparum viability and is functional in blood stages of both, the human malaria parasite P. falciparum and the rodent-infecting parasite P. berghei, as well as in P. berghei mosquito stages. FLUMMI is also compatible with advanced techniques such as expansion microscopy. Together, our results establish FLUMMI as a versatile and non-toxic tool for membrane imaging in Plasmodium.

microbiology↗

bioRxiv2023

An Environmental Restriction impairs HIV-1 virion fusion and triggers innate immune recognition

In vivo, HIV-1 replicates within tissue, but how three-dimensional (3D) tissue-like environments influence viral spread and pathogenesis remains largely unknown. We previously identified an Environmental Restriction to cell-free Virus Infectivity (ERVI), imposed by collagen-rich 3D extracellular matrix (ECM), which diminishes HIV-1 particle infectivity. Here we report that ERVI is broadly implemented by various adhesive ECM components assembled into tissue-like 3D scaffolds. This restriction rapidly reduces infectivity within minutes, is saturable, and affects diverse primary HIV-1 strains and virions with distinct viral glycoproteins by impairing their ability to fuse with target cells. Importantly, particles subjected to ERVI also trigger pronounced pro-inflammatory cytokine secretion by monocyte-derived macrophages. Mechanistic analyses reveal that transient contact with collagen fibers induces conformational changes in the viral envelope glycoprotein (Env) and enhance its recognition by toll-like receptor (TLR) 2. This recognition promotes routing of viral particles into TLR8-positive endosomes, amplifying innate immune sensing of viral RNA genomes. ERVI thus acts via a dual mechanism: directly limiting the fusogenicity of cell-free virions and sensitizing them for innate immune detection. These findings highlight the biophysical properties of the ECM as a previously unrecognized, tissue-intrinsic barrier that restricts HIV-1 spread and promotes local inflammation representing a novel, broadly acting arm of antiviral innate immunity.

immunology↗

bioRxiv2023

A General Method to Accurately Count Molecular Complexes and Determine the Degree of Labelling in Cells Using Protein Tags

Determining the label to target ratio, also known as degree of labelling (DOL), is crucial for quantitative fluorescence microscopy and a high DOL with minimal unspecific labelling is beneficial for fluorescence microscopy in general. Yet, robust, versatile, and easy-to-use tools for measuring cell-specific labelling efficiencies are not available. This study presents a novel DOL determination technique named Protein-tag DOL (ProDOL), which enables fast DOL measurements and optimisation of protein-tag labelling. With ProDOL various factors affecting labelling efficiency, including substrate type, incubation time, and concentration, as well as sample fixation and cell type can be easily assessed. We applied ProDOL to investigate how HIV-1 pathogenesis factor Nef modulates CD4 T cell activation measuring total and activated copy numbers of the adaptor protein SLP-76 in signalling microclusters. ProDOL proved to be a versatile and robust tool for labelling calibration, enabling determination of labelling efficiencies, optimisation of strategies, and quantification of protein stoichiometry.

cell biology↗

bioRxiv2023

ediTONSIL: Activation-Neutral Gene Editing of CD4 T cells in Human ex Vivo Tonsil Cultures

MotivationCD4 T cells are central players of adaptive immunity that rapidly change activation states in response to exogenous T cell receptor (TCR) stimulation. While molecular processes in activated human CD4 T cells from peripheral blood are well studied, resting CD4 T cells are refractory to gene-editing transduction and transfection methods without prior activation. Knowledge on the molecular biology of truly resting CD4 T cells is therefore lacking. We present here the culture and editing workflow ediTONSIL that allows for gene editing of tissue-resident CD4 T cells without compromising their activation state or immunological function. This will enable molecular mechanistic analyses of this cell type in their native/physiological tissue context. SummaryThe molecular and immunological properties of resting CD4 T cell biology are understudied due to the lack of suitable gene editing methods. Here we describe the ex vivo culture and gene editing methodology ediTONSIL for tissue-resident CD4 T cells from human tonsil tissue. CRISPR/Cas9 RNP nucleofection under optimized culture conditions and cytokine concentrations results in knock out efficacies of over 90%, which are e.g. sufficient to prevent HIV-1 infection when targeting the viral entry co-receptor CXCR4. EdiTONSIL does not impair tonsil CD4 T cell viability, activation state or immunocompetence and does not require exogenous activation. Editing can be performed on multiple cell types in bulk cultures or of CD4 T cells previously isolated from tonsils that can be added back to the non-CD4 T cell fraction post gene editing to reassemble into immunocompetent organotypic lymphoid aggregate structures. This highly efficient and versatile workflow for gene editing of tonsillar CD4 T cells enables the dissection of molecular mechanisms in ex vivo cultures of human lymphoid tissue and can be adapted to other tonsil-resident cell types. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=170 SRC="FIGDIR/small/554089v1_ufig1.gif" ALT="Figure 1"> View larger version (32K): org.highwire.dtl.DTLVardef@1ece503org.highwire.dtl.DTLVardef@1af2d0corg.highwire.dtl.DTLVardef@1b67f14org.highwire.dtl.DTLVardef@510d63_HPS_FORMAT_FIGEXP M_FIG C_FIG

immunology↗

bioRxiv2022

The Ebola virus VP40 matrix undergoes endosomal disassembly essential for membrane fusion

Ebola viruses (EBOVs) are filamentous particles, whose shape and stability are determined by the VP40 matrix. Virus entry into host cells occurs via membrane fusion in late endosomes; however, the mechanism of how the remarkably long virions undergo uncoating including virion disassembly and nucleocapsid release into the cytosol, remains unknown. Here, we investigate the structural architecture of EBOVs entering host cells and discover that the VP40 matrix disassembles prior to membrane fusion. We reveal that VP40 disassembly is caused by the weakening of VP40-lipid interactions driven by low endosomal pH that equilibrates passively across the viral envelope without a dedicated ion channel. We further show that viral membrane fusion depends on VP40 matrix integrity, and its disassembly reduces the energy barrier for fusion stalk formation. Thus, pH-driven structural remodeling of the VP40 matrix acts as a molecular switch coupling viral matrix uncoating to membrane fusion during EBOV entry.

microbiology↗

bioRxiv2022

Inferring cell motility in complex environments with incomplete tracking data

Cell motility has important influence on cell interactions and functionality for various biological aspects. Deciphering these dynamics often relies on live-cell microscopy measurements, which partly have to deal with limitations that could impair a reliable quantification of their motility. Especially given complex environments and tissue structures, limited observation periods, cells moving in and out of focus and impaired calibration of observation axes often lead to loss of cell tracks and insufficient tracking of motility within several dimensions. However, a reliable quantification of cell motility dynamics is essential when aiming at extrapolating the observed dynamics in order to understand cell population dynamics at larger temporal and spatial scales using appropriate simulation environments. To analyze how incomplete observations affect interpretation and parameterization of cell motility, we combined experimental observations with computational models. Studying individual cell dynamics within 3D collagen environments, we found that the gradual loss of cell tracks leads to an underestimation of several motility parameters with the effect dependent on the collagen density. By extending the automated fitting strategy FitMultiCell to account for cell track loss, we show that we are able to retrieve the actual cell dynamics and, thus, to reliably parameterize cell motility from such incomplete data. Applying our approach to the analysis of CD4+ T cells within 3D collagen environments that were infected with HIV-1, we could show that despite a considerable loss of cell tracks, the data still contained sufficient information to compare individual cell motilities by inferring and simulating their dynamics. Thereby, the analysis allowed us to disentangle the effect of HIV-1 infection and collagen density on individual cell motility. Our extended FitMultiCell-approach presented here provides a solution for the elimination of artifacts from cell track data analysis to robustly infer cell motility dynamics.

systems biology↗

bioRxiv2022

Temporal control of the integrated stress response by a stochastic molecular switch

Stress granules (SGs) are formed in the cytosol as an acute response to environmental cues and activation of the integrated stress response (ISR), a central signaling pathway controlling protein synthesis. Using chronic virus infection as stress model, we previously uncovered a unique temporal control of the ISR resulting in recurrent phases of SG assembly and disassembly. Here, we elucidate the molecular network generating this fluctuating stress response, by integrating quantitative experiments with mathematical modeling, and find that the ISR operates as a stochastic switch. Key elements controlling this switch are the cooperative activation of the stress-sensing kinase PKR, the ultrasensitive response of SG formation to the phosphorylation of the translation initiation factor eIF2, and negative feedback via GADD34, a stress-induced subunit of protein phosphatase 1. We identify GADD34 mRNA levels as the molecular memory of the ISR that plays a central role in cell adaptation to acute and chronic stress.

cell biology↗

bioRxiv2021

The FDA-approved drug cobicistat synergizes with remdesivir to inhibit SARS-CoV-2 replication

Combinations of direct-acting antivirals are needed to minimize drug-resistance mutations and stably suppress replication of RNA viruses. Currently, there are limited therapeutic options against the Severe Acute Respiratory Syndrome Corona Virus 2 (SARS-CoV-2) and testing of a number of drug regimens has led to conflicting results. Here we show that cobicistat, which is an-FDA approved drug-booster that blocks the activity of the drug metabolizing proteins Cytochrome P450-3As (CYP3As) and P-glycoprotein (P-gp), inhibits SARS-CoV-2 replication. Cell-to-cell membrane fusion assays indicated that the antiviral effect of cobicistat is exerted through inhibition of spike protein-mediated membrane fusion. In line with this, incubation with low micromolar concentrations of cobicistat decreased viral replication in three different cell lines including cells of lung and gut origin. When cobicistat was used in combination with the putative CYP3A target and nucleoside analog remdesivir, a synergistic effect on the inhibition of viral replication was observed in cell lines and in a primary human colon organoid. The cobicistat/remdesivir combination was able to potently abate viral replication to levels comparable to mock-infected cells leading to an almost complete rescue of infected cell viability. These data highlight cobicistat as a therapeutic candidate for treating SARS-CoV-2 infection and as a potential building block of combination therapies for COVID-19.

microbiology↗