Biology subjects

Schultz, C.

Publications and source records attributed to Schultz, C..

At least 19 recordsLinked to original sources

bioRxiv2026

Identifying Novel Estrogenic Mitochondrial Targets in Hypothalamic Proopiomelanocortin Neurons by Chemoproteomics

Loss of estrogens at menopause is linked to impaired brain metabolism and increased risk of Alzheimers disease (AD). However, estrogen replacement therapies are limited due to the deleterious effects of estrogen on peripheral organs and increased risk of vascular dementia. We have developed a non-steroidal estrogenic compound, STX, which does not bind to the classical estrogen receptors and {beta}, but mimics estrogenic signaling in the central nervous system (CNS) without the peripheral reproductive actions. STX is protective against neurodegeneration in stroke and AD models, but its molecular targets are unknown. Here, we identified and validated STX neural targets using chemoproteomic, molecular biological, electrophysiological and metabolic assays of hypothalamic proopiomelanocortin (POMC) neurons. Chemoproteomic profiling identified voltage dependent anion channels (VDAC1-3) as major intracellular binding partners in mHypo43 (POMC) cells. Based on quantitative single-cell PCR, Vdac2 was identified as the dominant isoform in female hypothalamic POMC neurons. Seahorse metabolic flux analyses showed that STX potently increased glycolysis, oxidative respiration and mitochondrial ATP production in mHypo43 cells. Nanomolar concentrations of STX enhanced VDAC2 voltage-dependent gating in reconstituted lipid membranes and shifted the low-conductance states toward anion selectivity, consistent with increased ATP flux. Together, these findings reveal a mechanism for the neuroprotective effects of STX through enhancing mitochondrial bioenergetics and modulating VDAC channel properties, potentially increasing cellular energy stores. Therefore, this work identifies previously unrecognized estrogenic mitochondrial targets and provides a mechanistic basis for the neuroprotective actions of STX relevant to menopause-associated brain vulnerability.

neuroscience↗

bioRxiv2026

Periweaning diet-induced activation of an IFNγ-mediated regulatory circuit promotes the homeostasis of cytotoxic CD8+ T Cells

Balancing pathogen defence with maintaining tolerance to environmental antigens, such as food or commensals, in neonates is essential for survival and the establishment of life-long immune homeostasis. Instructed by environmental signals type 1 conventional dendritic cells (cDC1) drive either T cell tolerance or immunity. Here, we uncover an interferon (IFN)-{gamma}-driven regulatory circuit in early life that relays dietary cues to spleen cDC1. Loss-of-function demonstrates that IFN{gamma}-mediated STAT1-signaling induces an immunogenic maturation program in spleen cDC1 that instructs cDC1 to expand effector memory CD8 T cells. This program emerges during weaning, when IFN{gamma} production from lymphocytes rises, it occurs in germ-free mice and remains responsive to dietary intervention in adult mice. During the transition from breastfeeding to solid food at weaning, this circuit relays dietary information to spleen cDC1 to shape the effector phenotype of food-antigen specific CD8+ T cells in a feed-forward manner, allowing cDC1 to recalibrate the T cell pool at the moment of nutritional independence.

immunology↗

bioRxiv2026

An Integrated Method for Profiling Lipid-Protein Interactions Using Multifunctional Lipid Probes

Cellular lipids shape health and disease through specific protein interactions, yet lipid-protein networks remain poorly defined. Despite rapid advances in functional lipid probes, the field still lacks a practical, dedicated protocol for conducting lipid-protein interaction studies. We describe detailed methods for determining lipid interactomes from cells using multifunctionalized lipid derivatives. We provide protocols that detail 1) how to treat cells with lipid derivatives and perform photochemistry to obtain lipid-protein conjugates; 2) how to perform click chemistry with a fluorophore and observe lipid-protein conjugates by in-gel fluorescence; 3) how to perform click chemistry with azide beads and prepare lipid-protein conjugates for proteomic analysis. We provide context on important parameters for each step and include guidelines for controls, as well as suggestions for troubleshooting based on common problems encountered during the preparation of this protocol. This protocol enables mapping lipid interactomes across diverse biological systems. The entire workflow from cell treatment to complete proteomic sample preparation requires [~]15 hours over four days, depending on the type of experimental readout (in-gel fluorescence or proteomics), and the usage of pause points. Practitioners are expected to be familiar with standard biochemical techniques, such as sterile sample handling and tissue culture and gel electrophoresis. Additional skills are needed for mass spectrometric analysis, and collaboration with a proteomics core facility is recommended. The described procedures uniquely enable the identification of the protein interactors (the interactome) of select lipid species, providing for a major shift in the characterization of the biological roles of lipids in cellular systems.

biochemistry↗

bioRxiv2025

A quantitative approach to discover nonlinear signaling linking combinatorial environments with cellular responses

Cells constantly integrate diverse inputs from the extracellular environment, yet our understanding of how cells effectively process information from multiple cues at the same time remains limited. We utilized an integrated imaging platform and RNAseq analysis to investigate the combined effects of growth factors on cellular signaling and gene expression. Paired stimuli by receptor ligands revealed diverse signaling signatures-- ranging from antagonism to synergy--driving global signaling programs and gene expression. Notably, correlation networks based on signaling signatures identified vulnerabilities in cancer cells when compared to synergistic drug combinations. Profiling kinase and phosphatase activities uncovered a crucial interplay, where cellular sensitivity and phospho-turnover dynamics are modulated by input history through coordinated basal kinase and phosphatase activities. Our novel methodology sheds light on cellular processing of multiple cues, elucidating intricate mechanisms underlying cellular adaptation to extracellular environmental variations. Based on previous preprint: doi: https://doi.org/10.1101/346957

cell biology↗

bioRxiv2025

Glucagon and GLP-1 Accelerate Pseudo-Islet Assembly and Unmask Sex-Specific Islet Fragmentation Dynamics

Pancreatic hormones are best known for their role in regulating blood sugar levels as well as islet cell function and proliferation. However, their impact on maintaining and inducing cell aggregation in culture remains under-explored. In this study, we investigated the effects of glucagon (GCG) and glucagon-like-peptide 1(GLP-1) on the formation and integrity of human islet clusters. Native human islets were dissociated and sorted into pure -, {beta}-, and {delta}-cell populations using antibody-based fluorescence-activated cell sorting (FACS). The sorted cells were then co-cultured with mouse endothelial MS1 cells in suspension to generate pseudo-islets of varying cell composition. Hormonal supplementation with GCG or GLP-1 versus blank was administered during the tissue culture phase. Hormone-treated pseudo-islets formed faster, dependent on the cellular composition and the sex of the donor. In parallel, we also exposed native islets, maintained in suspension without prior dissociation or sorting, to hormone supplementation. These islets exhibited accelerated fragmentation under hormone treatment compared to controls, again dependent on donor sex with islets from female donors fragmenting faster than from male donors. These findings suggest that GCG and GLP-1 enhance pseudo-islet formation and affect the structural integrity of native islets in a sex-specific manner, offering insights into islet biology and implications for diabetes research and therapy. Article HighlightsWe established a manipulatable, expandable human pseudo-islet platform to investigate islet morphogenesis, architecture, and intercellular signaling. We examined the contribution of individual -, {beta}-, and {delta}-cell populations and assessed how glucagon (GCG) and glucagon-like peptide-1 (GLP-1) modulate islet integrity in culture. In native islets, hormonal supplementation attenuated fragmentation in male donors but accelerated it in females. In pseudo-islets, cellular composition was the predominant determinant of maturation versus fragmentation, with donor sex exerting a secondary influence. We present methodological guidelines for generating and maintaining human pseudo-islets, thereby providing a framework to optimize donor selection, culture conditions, and experimental design in diabetes research.

biochemistry↗

bioRxiv2025

CCR2+ neutrophils exhibit a proinflammatory phenotype and promote plaque destabilization

BackgroundAtherosclerotic plaque destabilization is promoted by inflammatory cell recruitment, tissue cell death and mechanical weakening. Neutrophils are key instigators of vascular tissue injury and perpetuation of inflammation, and targeting their actions is a viable therapeutic opportunity. We here identify a distinct subset of activated neutrophils within atherosclerotic lesions that express the chemokine receptor CCR2, which directs their migration toward areas enriched with smooth muscle cells (SMCs) and contributes to plaque instability. MethodsFlow cytometry and single cell transcriptomic analysis of CCR2+ neutrophils within murine and human atherosclerotic plaques. Tracking of CCR2+ neutrophil in hypercholesterolemic Ldlr-/- mice and in mice reconstituted with Ccr2GFP/- bone marrow. In vivo reactive oxygen species (ROS) and neutrophil extracellular trap (NET) analysis in lipopolysaccharide-induced peritonitis. In vitro migration assays of neutrophils deficient for or treated with specific antagonist against chemokine receptors. In vivo neutrophil recruitment and atherosclerotic plaque destabilization analysis upon CCR2 and CCL2 blockade in a model of advanced atherosclerosis in Apoe-/- mice. ResultsCCR2+ neutrophils preferentially populate mouse and human atherosclerotic lesions and displayed a proinflammatory phenotype with enhanced capacity for ROS production and NET release. Genetic deletion or pharmacologic inhibition of CCR2 significantly reduces neutrophil migration and infiltration to the atherosclerotic lesion, reducing their presence in SMC-rich areas. Consistently, neutralization of the CCR2 ligand CCL2 decreased lesional neutrophil numbers and preserved fibrous cap integrity by increasing SMC content and decreasing overall plaque instability. ConclusionsOur data suggest that a subset of CCR2-expressing neutrophils senses SMC-derived CCR2 ligands to infiltrate and destabilize atherosclerotic lesions. These results support the existence of neutrophil functional heterogeneity within the atherosclerotic lesions contributing to alterations of lesion stability. Specific targeting thereof may improve plaque stability without impacting host defense.

immunology↗

bioRxiv2025

Multi-Omic Profiling Identifies Conserved Metabolic Pathways Critical for SARS-CoV-2 Variants Infection

AO_SCPLOWBSTRACTC_SCPLOWThe rapid evolution of SARS-CoV-2 has led to the emergence of numerous variants with enhanced transmissibility and immune evasion. Despite widespread vaccination, infections persist, and the mechanisms by which SARS-CoV-2 reprograms host metabolism remain incompletely understood. Here, we investigated whether virus-induced lipid remodeling is conserved across variants and whether changes in lipid abundance correlate with alterations in lipid biosynthetic enzymes. Using global untargeted lipidomics and quantitative proteomics, we analyzed A549-ACE2 cells infected with the Delta (B.1.617.2) or Omicron (B.1.1.529) variants and compared them to cells infected with the ancestral WA1 strain. In parallel, we conducted quantitative proteomics to assess virus-induced changes in the host proteome. Our results reveal that SARS-CoV-2 drives a remarkably consistent pattern of metabolic rewiring at both the lipidomic and proteomic levels across all three variants. We mapped changes in the expression of host metabolic enzymes and compared these to corresponding shifts in lipid abundance. This integrative analysis identified key host proteins involved in virus-mediated lipid remodeling, including fatty acid synthase (FASN), lysosomal acid lipase (LIPA), and ORM1-like protein 2 (ORMDL2). Together, these findings highlight conserved metabolic dependencies of SARS-CoV-2 variants and underscore host lipid metabolism as a potential target for broad-spectrum antiviral strategies.

systems biology↗

bioRxiv2024

A genetically encoded sensor for real-time monitoring of poly-ADP-ribosylation dynamics in-vitro and in cells

ADP-ribosylation, the transfer of ADP-ribose (ADPr) from nicotinamide adenine dinucleotide (NAD+) groups to proteins, is a conserved post-translational modification (PTM) that occurs most prominently in response to DNA damage. ADP-ribosylation is a dynamic PTM regulated by writers (PARPs), erasers (ADPr hydrolases), and readers (ADPR binders). PARP1 is the primary DNA damage-response writer responsible for adding a polymer of ADPR to proteins (PARylation). Real-time monitoring of PARP1-mediated PARylation, especially in live cells, is critical for understanding the spatial and temporal regulation of this unique PTM. Here, we describe a genetically encoded FRET probe (pARS) for semi-quantitative monitoring of PARylation dynamics. pARS feature a PAR-binding WWE domain flanked with turquoise and Venus. With a ratiometric readout and excellent signal-to-noise characteristics, we show that pARS can monitor PARP1-dependent PARylation temporally and spatially in real-time. pARS provided unique insights into PARP1-mediated PARylation kinetics in vitro and high-sensitivity detection of PARylation in live cells, even under mild DNA damage. We also show that pARS can be used to determine the potency of PARP inhibitors in vitro and, for the first time, in live cells in response to DNA damage. The robustness and ease of use of pARS make it an important tool for the PARP field.

biochemistry↗

bioRxiv2024

Trifunctional fatty acid derivatives demonstrate the impact of diazirine placement

Functionalized lipid probes are a critical new tool to interrogate the function of individual lipid species, but the structural parameters that constrain their utility have not been thoroughly described. Here, we synthesize three palmitic acid derivatives with a diazirine at different positions on the acyl chain and examine their metabolism, subcellular localization, and protein interactions. We demonstrate that while they produce very similar metabolites and subcellular distributions, probes with the diazirine at either end pulldown distinct subsets of proteins after photo-crosslinking. This highlights the importance of thoughtful diazirine placement when developing probes based on biological molecules.

biochemistry↗

bioRxiv2024

Trace Amines are Essential Metabolites for the Autocrine Regulation of β-Cell Signaling and Insulin Secretion

Secretion of insulin in response to extracellular stimuli, such as elevated glucose levels and small molecules that act on G-protein coupled receptors (GPCRs), is the hallmark of {beta}-cell physiology. Trace amines (TAs) are small aromatic metabolites that were identified as low-abundant ligands of the trace amine-associated receptor 1 (TAAR1) in the central nervous system (CNS), a GPCR that is also expressed by pancreatic {beta}-cells. In the present work, we identify TAs as essential autocrine signaling factors for {beta}-cell activity and insulin secretion. We find that {beta}-cells are producing TAs in significant amounts and that the modulation of endogenous TA levels by the selective inhibition of TA biosynthetic pathways directly translated into changes of oscillations of the intracellular Ca2+ concentration ([Ca2+]i oscillations) and insulin secretion. Selective TAAR1 agonists or inhibitors of monoamine oxidases increased [Ca2+]i oscillations and insulin secretion. Opposite effects were mediated by selective TAAR1 antagonists, by recombinant monoamine oxidase action and by the inhibition of amino acid decarboxylase. As the modulation of TA biochemical pathways immediately translated into changes of [Ca2+]i oscillations, we inferred high metabolic turnover rates of TAs and autocrine feedback. We found that psychotropic drugs modulate [Ca2+]i oscillations and insulin secretion, either directly acting on TAAR1 or by altering endogenous TA levels. Our combined data support the hypothesis of TAs as essential autocrine signaling factors for {beta}-cell activity and insulin secretion as well as TAAR1 as an important mediator of amine-modulated insulin secretion.

biochemistry↗

bioRxiv2024

Cannabinoid Receptor Signaling is Dependent on Sub-Cellular Location

G protein-coupled receptors (GPCRs) are membrane bound signaling molecules that regulate many aspects of human physiology. Recent advances have demonstrated that GPCR signaling can occur both at the cell surface and internal cellular membranes. Our findings suggest that cannabinoid receptor 1 (CB1) signaling is highly dependent on its subcellular location. We find that intracellular CB1 receptors predominantly couple to Gi while plasma membrane receptors couple to Gs. Here we show subcellular location of CB1, and its signaling, is contingent on the choice of promoters and receptor tags. Heterologous expression with a strong promoter or N-terminal tag resulted in CB1 predominantly localizing to the plasma membrane and signaling through Gs. Conversely, CB1 driven by low expressing promoters and lacking N-terminal genetic tags largely localized to internal membranes and signals via Gi. Lastly, we demonstrate that genetically encodable non-canonical amino acids (ncAA) offer a solution to the problem of non-native N-terminal tags disrupting CB1 signaling. We identified sites in CB1R and CB2R which can be tagged with fluorophores without disrupting CB signaling or trafficking using (trans-cyclooctene attached to lysine (TCO*A)) and copper-free click chemistry to attach fluorophores in live cells. Together, our data demonstrate the origin of location bias in cannabinoid signaling which can be experimentally controlled and tracked in living cells through promoters and novel CBR tagging strategies.

molecular biology↗

bioRxiv2024

Microenvironment Shapes Cell State, Plasticity, and Heterogeneity of Small Cell Lung Cancer

Small-cell lung cancer (SCLC) is the most fatal form of lung cancer. Intra-tumoral heterogeneity, marked by neuroendocrine (NE) and non-neuroendocrine (non-NE) cell states, defines SCLC, but the drivers of SCLC plasticity are poorly understood. To map the landscape of SCLC tumor microenvironment (TME), we apply spatially resolved transcriptomics and quantitative mass spectrometry-based proteomics to metastatic SCLC tumors obtained via rapid autopsy. The phenotype and overall composition of non-malignant cells in the tumor microenvironment (TME) exhibits substantial variability, closely mirroring the tumor phenotype, suggesting TME-driven reprogramming of NE cell states. We identify cancer-associated fibroblasts (CAF) as a crucial element of SCLC TME heterogeneity, contributing to immune exclusion, and predicting exceptionally poor prognosis. Together, our work provides a comprehensive map of SCLC tumor and TME ecosystems, emphasizing their pivotal role in SCLCs adaptable nature, opening possibilities for re-programming the intercellular communications that shape SCLC tumor states.

cancer biology↗

bioRxiv2023

Estimating butterfly population trends from sparse monitoring data using Generalized Additive Models

Concerns of declines in insects and population level responses to climate change have highlighted the importance of estimating trends in abundance and phenology from existing monitoring data. As the taxa with the most systematic monitoring data, butterflies are a frequent focus for understanding trends in insects. Even so, ecologists often have only sparse monitoring data for at-risk butterfly populations. As existing statistical techniques are typically poorly suited to such data, these at-risk populations are frequently excluded from analyses of butterfly trends. Here we present guidelines for estimating population trends from sparse butterfly monitoring data using generalized additive models (GAMs), based on extensive simulations and our experiences fitting hundreds of butterfly species. These recommendations include pre-processing steps, model structure choices, and post-hoc analysis decisions that reduce bias and prevent or mitigate biologically implausible model fits. We also present the ButterflyGamSim package for the programming language R, available at https://github.com/cbedwards/butterflyGamSims. This open source software provides tools for ecologists and applied statisticians to simulate realistic butterfly monitoring data and test the efficacy of different GAM model choices or monitoring schemes.

ecology↗

bioRxiv2023

Trifunctional sphinganine: a new tool to dissect sphingolipid function

Functions of the sphingolipids sphingosine and sphinganine in cells are not well established. While some signaling roles for sphingosine have been elucidated, the closely related sphinganine has been described only insofar as it does not elicit many of the same signaling responses. The underlying mechanisms behind the cell biological differences between these lipids are not well understood. Here, we prepared multifunctionalized derivatives of the two lipid species that only differ in a single double bond of the carbon backbone. Using these novel probes, we were able to define their spatiotemporal distribution within cells. Furthermore, we used these tools to systematically map the protein interactomes of both lipids. The lipid-protein conjugates, prepared through photo-crosslinking in live cells and extraction via click chemistry to azide beads, revealed significant differences in the captured proteins, highlighting their distinct roles in various cellular processes. This work elucidates mechanistic differences between these critical lipids and sets the foundation for further studies on the functions of sphingosine and sphinganine.

biochemistry↗

bioRxiv2023

Thermogenetic control of Ca2+ levels in cells and tissues

Virtually all major processes in cells and tissues are regulated by calcium ions (Ca2+). Understanding the influence of Ca2+ on cell function requires technologies that allow for non-invasive manipulation of intracellular calcium levels including the formation of calcium patterns, ideally in a way that is expandable to intact organisms. The currently existing tools for optical and optogenetic Ca2+ manipulation are limited with respect to response time, and tissue penetration depth. Here we present Genetically Encoded Calcium Controller (GECCO), a system for thermogenetic Ca2+ manipulation based on snake TRP channels optically controlled by infrared illumination. GECCO is functional in animal and plant cells and allows studying how cells decode different profiles of Ca2+ signals. GECCO enabled the shaping of insulin release from {beta}-cells, the identification of drugs that potentiate Ca2+-induced insulin release, and the generation of synthetic Ca2+ signatures in plants.

synthetic biology↗

bioRxiv2023

Live imaging of excitable axonal microdomains in ankyrin-G-GFP mice

The axon initial segment (AIS) constitutes not only the site of action potential initiation, but also a hub for activity-dependent modulation of output generation. Recent studies shedding light on AIS function used predominantly post-hoc approaches since no robust murine in vivo live reporters exist. Here, we introduce a reporter line in which the AIS is intrinsically labeled by an ankyrin-G-GFP fusion protein activated by Cre recombinase, tagging the native Ank3 gene. Using confocal, superresolution, and two-photon microscopy as well as whole-cell patch-clamp recordings in vitro, ex vivo, and in vivo, we confirm that the subcellular scaffold of the AIS and electrophysiological parameters of labeled cells remain unchanged. We further uncover rapid AIS remodeling following increased network activity in this model system, as well as highly reproducible in vivo labeling of AIS over weeks. This novel reporter line allows longitudinal studies of AIS modulation and plasticity in vivo in real-time and thus provides a unique approach to study subcellular plasticity in a broad range of applications.

neuroscience↗

bioRxiv2022

Recently evolved combination of unique sulfatase and amidase genes enables bacterial degradation of the wastewater micropollutant acesulfame worldwide

Xenobiotics often challenge the principle of microbial infallibility. One example is acesulfame introduced in the 1980s as zero-calorie sweetener, which was recalcitrant in wastewater treatment plants until the early 2010s. Then, efficient removal has been reported with increasing frequency. By studying acesulfame metabolism in alphaproteobacterial degraders of the genera Bosea and Chelatococcus, we experimentally confirmed the previously postulated route of two subsequent hydrolysis steps via acetoacetamide-N-sulfonate (ANSA) to acetoacetate and sulfamate. Genome comparison of wildtype Bosea sp. 100-5 and a spontaneous acesulfame degradation-defective mutant revealed the involvement of two plasmid-borne gene clusters. The acesulfame-hydrolyzing sulfatase is strictly manganese-dependent and belongs to the metallo beta-lactamase family. In all degraders analyzed, it is encoded on a highly conserved gene cluster embedded in a composite transposon. The ANSA hydrolase, on the other hand, is an amidase signature domain enzyme encoded in another gene cluster showing variable length among degrading strains. Transposition of the sulfatase gene cluster between chromosome and plasmid explains how the two catabolic gene clusters recently combined for the degradation of acesulfame. Searching available genomes and metagenomes for the two hydrolases and associated genes indicates that the acesulfame plasmid evolved and spread worldwide in short time. While the sulfatase is unprecedented and unique for acesulfame degraders, the amidase occurs in different genetic environments and might have evolved for the degradation of other substrates. Evolution of the acesulfame degradation pathway might have been supported by the presence of structurally related natural and anthropogenic compounds, such as aminoacyl sulfamate ribonucleotide or sulfonamide antibiotics.

microbiology↗

bioRxiv2022

Targeting ATP12A, a non-gastric proton pump alpha subunit, for idiopathic pulmonary fibrosis treatment

Idiopathic Pulmonary Fibrosis (IPF) is a pathological condition of unknown etiology which results from injury to the lung and an ensuing fibrotic response that leads to thickening of the alveolar walls and obliteration of the alveolar space. The pathogenesis is not clear and there are currently no effective therapies for IPF. Small airway disease and mucus accumulation are prominent features in IPF lungs, similar to Cystic Fibrosis (CF) lung disease. The ATP12A gene encodes the alpha-subunit of the non-gastric H+, K+-ATPase, which functions to acidify the airway surface fluid and impairs mucociliary transport function in cystic fibrosis patients. We hypothesize that the ATP12A protein may play a role in the pathogenesis of IPF. Our studies demonstrate that ATP12A protein is overexpressed in distal small airways from IPF patient lungs compared to normal human lungs. In addition, overexpression of the ATP12A protein in mouse lungs worsened the bleomycin (BLEO)-induced experimental pulmonary fibrosis. This was prevented by a potassium-competitive proton pump blocker, vonoprazan (VON). This data supports the concept that the ATP12A protein plays an important role in the pathogenesis of lung fibrosis. Inhibition of the ATP12A protein has the potential as a novel therapeutic strategy in IPF.

cell biology↗