Biology subjects

Sohn, M.

Publications and source records attributed to Sohn, M..

11 recordsLinked to original sources

bioRxiv2025

Phosphatidylserine and RhoB connect phosphatidylinositol 4-phosphate and phosphatidic acid metabolism at the plasma membrane

Cells tightly control the homeostatic levels and subcellular localizations of membrane phospholipids through the regulation of the activities of numerous lipid-metabolizing enzymes and lipid transfer proteins. Yet, the mechanisms by which lipid imbalances are sensed and corrected to establish and maintain homeostasis are, in most cases, unknown. Here we present an expanded view of plasma membrane (PM) phosphoinositide metabolism by revealing an unexpected metabolic connection between two key anionic lipids in this membrane, phosphatidylinositol 4-phosphate (PI4P) and phosphatidic acid (PA). PM pools of PI4P are generated by PI 4-kinase Type III (PI4KIII/PI4KA), an essential enzyme whose partial dysfunction leads to numerous hereditary human diseases. We find that depletion of PI4P by pharmacological inhibition of PI4KA increases the activity of phospholipase Ds (PLDs) and the levels of their lipid product, PA, in the PM. Guided by RNA-seq analysis and proximity labeling proteomics, we elucidate how cells connect this PI4P decrease to a compensatory increase in PA levels. Loss of PM PI4P induces a concomitant decrease of phosphatidylserine (PS) levels, and this metabolic rewiring activates a reciprocal relationship between PS synthesis and PLD-mediated PA generation. These metabolic changes also lead to transcriptional and translational upregulation of the small GTPase RhoB, which enhances PLD-mediated PA synthesis and subsequent actin cytoskeletal remodeling. Our study reveals how disease-relevant perturbation of phosphoinositide synthesis induces an integrated response that ultimately boosts levels of PA, a key anionic lipid and metabolic intermediate in phosphoinositide resynthesis.

cell biology↗

bioRxiv2025

Potentiating CAR-T bystander killing by enhanced Fas/FasL signaling mitigates antigen escape in heterogeneous tumors

Antigen (Ag) escape is a frequent mechanism of relapse after CAR-T therapy, even though only [~]1% of leukemic and [~]0.1% of lymphoma cells are Ag- at baseline. In this study, we modeled extreme Ag heterogeneity (>20%) to define how Fas/FasL-dependent bystander killing contributes to tumor clearance. Across patient cohorts, Fas expression predicted survival after CD19 CAR-T therapy, particularly in CD19-low disease. In both murine and human systems, Fas-dependent bystander killing required Ag stimulation and cell contact, operated within a defined therapeutic window, and could eradicate large fractions of Ag- tumors in vivo. Pharmacologic potentiation with inhibitor of apoptosis protein antagonists or genetic stabilization of CAR-T membrane-bound FasL enhanced bystander killing but simultaneously induced CD4 T cell fratricide, which was rescued by CAR-T Fas knockout. Importantly, Fas sensitization also enabled bispecific antibody-redirected T cells to mediate bystander killing in resistant tumors. Finally, targeting tumor-associated macrophages triggered Fas-dependent clearance of neighboring tumor cells. These findings establish Fas-mediated bystander killing as a generalizable and therapeutically actionable axis to prevent Ag escape and broaden the scope of targeted T cell therapies. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=177 SRC="FIGDIR/small/677496v1_ufig1.gif" ALT="Figure 1"> View larger version (66K): org.highwire.dtl.DTLVardef@11bedorg.highwire.dtl.DTLVardef@d09d07org.highwire.dtl.DTLVardef@1f53c1dorg.highwire.dtl.DTLVardef@13d96f9_HPS_FORMAT_FIGEXP M_FIG C_FIG Fas-mediated bystander killing can be potentiated by IAP inhibition and FasL stabilization, and further improved by decoupling CD4 T cell fratricide via Fas knockout. Schematic representation of CAR-T bystander killing across three mechanistic states. Left (Baseline): Antigen-positive (CD19) tumor cells activate CAR-T cells, leading to FasL-mediated cytotoxicity of neighboring antigen-negative (CD19-) tumor cells via membrane-bound FasL. Limited FasL expression and ADAM10-mediated shedding constrain bystander killing, and CD4 T cells are largely spared. Middle (Potentiated): Enhancing Fas signaling through IAP inhibition (IAPi), increasing FasL expression, and reducing FasL shedding result in improved bystander killing but also increased CD4 T cell fratricide. Right (Potentiated & Decoupled): Combining IAPi with FasL stabilization and CAR-T Fas knockout (FasKO) augments bystander killing while eliminating CD4 T cell fratricide.

immunology↗

bioRxiv2025

Reducing methylation of histone 3.3 lysine 4 in the medial ganglionic eminence and hypothalamus recapitulates neurodevelopmental disorder phenotypes

Methylation of lysine 4 on histone H3 (H3K4) is enriched on active promoters and enhancers and correlates with gene activation. Disruption of H3K4 methylation is associated with numerous neurodevelopmental diseases (NDDs) that display intellectual disability and abnormal body growth. Here, we perturb H3K4 methylation in the medial ganglionic eminence (MGE) and the hypothalamus, two brain regions associated with these disease phenotypes. These mutant mice have fewer forebrain interneurons, deficient network rhythmogenesis, and increased spontaneous seizures and seizure susceptibility. Mutant mice are significantly smaller than control littermates, but they eventually became obese due to striking changes in the genetic and cellular hypothalamus environment in these mice. Perturbation of H3K4 methylation in these cells produces deficits in numerous NDD-associated behaviors, with a bias for more severe phenotypes in female mice. Single cell sequencing reveals transcriptional changes in the embryonic and adult brain that underlie many of these phenotypes. In sum, our findings highlight the critical role of H3K4 methylation in regulating survival and cell-specific gene regulatory mechanisms in forebrain GABAergic and hypothalamic cells during neurodevelopment to control network excitability and body size homoeostasis.

neuroscience↗

bioRxiv2025

SANS ambages: phylogenomics with abundance-filter, multi-threading, and bootstrapping on amino-acid or genomic sequences

BackgroundThe increasing amount of available genome sequence data enables large-scale comparative studies. A common task is the inference of phylogenies -- a challenging task if close reference sequences are not available, genome sequences are incompletely assembled, or the high number of genomes precludes multiple sequence alignment in reasonable time. SANS is an alignment-free, whole-genome based approach for phylogeny estimation. ResultsHere we present a new implementation SANS ambages with a significantly increased application spectrum. It offers additional types of input data, parallelized processing, and bootstrapping. The source code (C++), documentation, and example data are freely available for download at: https://github.com/gi-bielefeld/sans. SANS can also be launched via the webinterface of the CloWM platform--free of charge, with a standard Life Science account: https://clowm.bi.denbi.de. ConclusionsThe new version not only shortens processing time on large datasets immensely by parallelization. Being able to also process amino acid sequences and offering a filter for low-abundant DNA read segments also enables new application cases. Bootstrapping and integrated visualization ease and enrich the interpretation of the resulting phylogenies.

bioinformatics↗

bioRxiv2024

Bispecific antibody targeting of lipid nanoparticles

Lipid nanoparticles (LNP) are the most clinically advanced non-viral gene delivery system. While progress has been made for enhancing delivery, cell specific targeting remains a challenge. Targeting moieties such as antibodies can be chemically-conjugated to LNPs however, this approach is complex and has challenges for scaling up. Here, we developed an approach to generate antibody-conjugated LNPs that utilizes a bispecific antibody (bsAb) as the targeting bridge. As a docking site for the bsAb, we generated LNPs with a short epitope, derived from hemagglutinin antigen (HA), embedded in the PEG component of the particle (LNPHA). We generated bsAb in which one domain binds HA and the other binds different cell surface proteins, including PD-L1, CD4, CD5, and SunTag. Non-chemical conjugation of the bsAb and LNP resulted in a major increase in the efficiency and specificity of transfecting cells expressing the cognate target. LNP/bsAb mediated a 4-fold increase in in vivo transfection of PD-L1 expressing cancer cells, and a 26-fold increase in ex vivo transfection of quiescent primary human T cells. Additionally, we created a universal bsAb recognizing HA and anti-rat IgG2, enabling LNP tethering to off-the-shelf antibodies such as CD4, CD8, CD20, CD45, and CD3. By utilizing a molecular dock and bsAb technology, these studies demonstrate a simple and effective strategy to generate antibody-conjugated LNPs, enabling precise and efficient mRNA delivery.

bioengineering↗

bioRxiv2024

A whole-animal phenotypic drug screen identifies suppressors of atherogenic lipoproteins.

Lipoproteins are essential for lipid transport in all bilaterians. A single Apolipoprotein B (ApoB) molecule is the inseparable structural scaffold of each ApoB-containing lipoprotein (B-lps), which are responsible for transporting lipids to peripheral tissues. The cellular mechanisms that regulate ApoB and B-lp production, secretion, transport, and degradation remain to be fully defined. In humans, elevated levels of vascular B-lps play a causative role in cardiovascular disease. Previously, we have detailed that human B-lp biology is remarkably conserved in the zebrafish using an in vivo chemiluminescent reporter of ApoB (LipoGlo) that does not disrupt ApoB function. Thus, the LipoGlo model is an ideal system for identifying novel mechanisms of ApoB modulation and, due to the ability of zebrafish to generate many progeny, is particularly amenable to large-scale phenotypic drug screening. Here, we report a screen of roughly 3000 compounds that identified 49 unique ApoB-lowering hits. Nineteen hits passed orthogonal screening criteria and seven were subjected to extensive phenotyping. A licorice root component, enoxolone, significantly lowered B-lps only in animals that express a functional allele of the nuclear hormone receptor Hepatocyte Nuclear Factor 4 (HNF4). Consistent with this result, inhibitors of HNF4 also reduce B-lp levels. These data demonstrate that mechanism(s) of action can be rapidly determined from a whole animal zebrafish phenotypic screen. Given the well documented role of HNF4 in human B-lp biology, these data validate the LipoGlo screening platform for identifying small molecule modulators of B-lps that play a critical role in a leading cause of worldwide mortality.

physiology↗

bioRxiv2023

Loss of Ezh2 in the medial ganglionic eminence alters interneuron fate, cell morphology and gene expression profiles

Enhancer of zeste homolog 2 (Ezh2) is responsible for trimethylation of histone 3 at lysine 27 (H3K27me3), resulting in gene repression. Here, we explore the role of Ezh2 in forebrain GABAergic interneuron development. Loss of Ezh2 increases somatostatin-expressing (SST+) and decreases parvalbumin-expressing (PV+) interneurons in multiple brain regions. We also observe fewer MGE-derived interneurons in the first postnatal week, indicating reduced interneuron production. Intrinsic electrophysiological properties in SST+ and PV+ interneurons are normal, but PV+ interneurons display increased axonal complexity in Ezh2 mutant mice. Single cell multiome analysis revealed differential gene expression patterns in the embryonic MGE that are predictive of these cell fate changes. Lastly, CUT&Tag analysis revealed differential H3K27me3 levels at specific genomic loci, with some genes displaying a relative increase in H3K27me3 indicating they may be resistant to epigenetic modifications. Thus, loss of Ezh2 in the MGE alters interneuron fate, morphology, and gene expression and regulation.

neuroscience↗

bioRxiv2022

Non-productive exposure of PBMCs to SARS-CoV-2 induces cell-intrinsic innate immunity responses

Cell-intrinsic responses mounted in vivo in PBMCs during mild and severe COVID-19 differ quantitatively and qualitatively. Whether they are triggered by signals emitted by productively infected cells of the respiratory tract or are, at least partially, resulting from physical interaction with virus particles, remains unclear. Here, we analyzed susceptibility and expression profiles of PBMCs from healthy donors upon ex vivo exposure to SARS-CoV and SARS-CoV-2. In line with the absence of detectable ACE2 receptor expression, human PBMCs were refractory to productive infection. Bulk and single cell RNA-sequencing revealed JAK/STAT-dependent induction of interferon-stimulated genes, but not pro-inflammatory cytokines. This SARS-CoV-2-specific response was most pronounced in monocytes. SARS-CoV-2-RNA-positive monocytes displayed a lower ISG signature as compared to bystander cells of the identical culture. This suggests a preferential invasion of cells with a low ISG base-line profile or delivery of a SARS-CoV-2-specific sensing antagonist upon efficient particle internalization. Together, non-productive physical interaction of PBMCs with SARS-CoV-2-but not SARS-CoV particles stimulates JAK/STAT-dependent, monocyte-accentuated innate immune responses that resemble those detected in vivo in patients with mild COVID-19.

immunology↗

bioRxiv2021

Transkingdom Analysis of the Female Reproductive Tract Reveals Bacteriophages Form Communities

The female reproductive tract (FRT) microbiome plays an important role in maintaining vaginal health. Viruses play a key role in regulating other microbial ecosystems, but little is known about how the FRT viruses (virome), particularly bacteriophages, impacts FRT health and dysbiosis. We hypothesize that bacterial vaginosis is associated with alterations in the FRT virome, and these changes correlate with bacteriome shifts. We conducted a retrospective, longitudinal analysis of vaginal swabs collected from 54 bacterial vaginosis (BV)-positive and 46 BV-negative South African women. Bacteriome analysis revealed samples clustered into five distinct bacterial community groups (CG). Bacterial alpha diversity was significantly associated with BV. Virome analysis on a subset of baseline samples showed FRT bacteriophages clustering into novel viral state types (VSTs), a viral community clustering system based on virome composition and abundance. Distinct BV bacteriophage signatures included increased alpha diversity along with Bacillus, Burkholderia and Escherichia bacteriophages. Discriminate bacteriophage-bacteria transkingdom associations were also identified between Bacillus and Burkholderia viruses and BV-associated bacteria, providing key insight for future studies elucidating transkingdom interactions driving BV-associated microbiome perturbations. In this cohort, bacteriophage-bacterial associations suggest complex interactions which may play a role in the establishment and maintenance of BV.

microbiology↗

bioRxiv2020

Single Cell RNA-Sequencing-based Analysis of CD4+ T-Cell Subset-Specific Susceptibility to Transcriptional Modulation by HIV-1 Latency-Reversing Agents

Shock-and-kill is one of the most advanced, yet unrealized, concepts towards establishment of HIV-1 cure. Treatment with latency-reversing agents (LRAs), including histone deacetylase inhibitors (HDACis) exerting chromatin remodelling and gene expression reprogramming, combined with anti-retroviral therapy reactivates HIV-1 transcription in vitro, ex vivo and in vivo. However, HDACi treatment fails to significantly reduce the size of the viral reservoir in people living with HIV-1 (PLHIV). Here, by combining scRNA-seq and functional approaches, we characterised the HDACi treatment-imposed remodulation of CD4+ T-cells state and its consequences for HIV-1 latency reversal and the apparent resistance of HIV-1-reactivating cells to immune-mediated elimination. Exposure of CD4+ T-cells from three aviremic PLHIV with clinically applicable concentrations of Panobinostat markedly reduced the expression of genes mediating T-cell activation and IFN-driven antiviral immunity in a largely CD4+ T-cell subset-nonspecific manner, with exception of an PLHIV-specific exhausted CD4+ T-cell subpopulation. Altered transcriptomic profiles were accompanied by large refractoriness to peptide and IL-2/PHA stimulation, and to exogenous type I interferon, that would otherwise induce T-cell activation and expression of a plethora of antiviral genes, respectively. Type I interferon, when added to Panobinostat during HIV-1 reactivation, was unable to counteract HDACi-mediated inhibition of IFN signalling and failed to interfere with HIV-1 reactivation per se. However, it imposed a pre-budding block and boosted surface levels of HIV-1 Env on reactivating cells. Co-treatment with type I IFNs, most prominently IFN-{beta} and -14, sensitised HIV-1-reactivating cells for killing by NK cells through antibody-dependent cytotoxicity. Together, our study provides proof-of-concept of the benefit of combining a potent LRA with immunostimulatory molecules, such as type I IFNs, to reduce the resistance of HIV-1-reactivating T-cells to immune-mediated elimination to improve current shock-and-kill strategies.

microbiology↗

bioRxiv2019

Combined use of design of experiments and metabolic engineering for optimization of nogalamycin production

Nogalamycin is an anthracycline antibiotic produced from Streptomyces nogalater that exerts its mechanism of action via inhibition of topoisomerase I. Nogalamycin has a unique tetracyclic structure composed of a 7-O-glycosidically linked L-nogalose sugar and a C2-C5\"-linked L-nogalamine residue that forms an epoxyoxacin ring. Nogalamycin was originally developed as an anticancer agent in the 1970s, however, it exhibited dose-limiting cardiotoxicity. Shortly after the discovery of nogalamycin, the semi-synthetic analogue 7-O-methylnogarol, or menogaril, was synthesized and exhibited a mild improvement in cardiotoxicity and anticancer efficacy. Menogaril lacks the 7-O-L-nogalose moiety and functions as a topoisomerase II inhibitor, like most anthracyclines, however this agent still proved too toxic for clinical use. Our laboratory is developing a production platform for microbial synthesis of novel nogalamycin analogs useful for treatment of human cancers or as antibiotics. Our initial hypothesis is that overexpression of structural genes responsible for synthesis of TDP-deoxysugar and polyketide precursor substrates, respectively, will increase carbon flux towards nogalamycin production. In this study, we have employed metabolic engineering to enhance nogalamycin production in Streptomyces nogalater. In this work, we used an optimized soytone glucose production medium to produce nogalamycin. We also overexpressed copies of structural biosynthetic genes to bolster substrate precursor building blocks for nogalamycin production. First, overexpression of the TDP-glucose synthase and TDP-D-glucose-4,6-dehydratase enzymes (mtmDE) resulted in a 50% increase in nogalamycin production (160 mg/L) as compared to wildtype S. nogalater (100 mg/L). Secondly, overexpression of the minimal polyketide synthase genes (snoa123) resulted in a fourfold production increase in nogalamycin (400 mg/L). This production platform will serve as the fundament for production of nogalamycin analogues for future drug development efforts.

microbiology↗