Biology subjects

Schmitt, C.

Publications and source records attributed to Schmitt, C..

15 recordsLinked to original sources

bioRxiv2026

Morphine causes distinct changes in the lipidome throughout the brain and body after acute or chronic administration: implications for novel endogenous lipid signaling systems involved in opioid reward and withdrawal

A growing body of evidence demonstrates that signaling pathways of endogenous lipids (endolipids) modulate the reinforcing properties of opioids including reward and withdrawal. Many of these studies are focused on the endocannabinoid (eCB) system, and its primary eCB ligands, Anandamide (AEA) and 2-arachidonoylglycerol (2-AG). The central hypothesis is that modulation of the eCB system through eCB receptors and enzymes may improve therapeutic outcomes for opioid use disorder (OUD). However, outcomes in preclinical and clinical studies using the low efficacy, CB1/CB2 orthosteric agonist, THC, found limited to no effectiveness, suggesting that targeting this aspect of CB1/CB2 is not a useful therapeutic tool for OUD. Previous studies finding that genetic deletion or pharmacological inhibition of endolipid-regulating enzymes (including eCBs) can alter behavioral sensitivity to opioids provide insight into an alternative approach. If opioid use dysregulates a wide range of endolipid biosynthesis and metabolism, then a clearer understanding of these changes, especially in signaling ligands, will provide a novel avenue to both understand the underlying physiological changes with opioid use as well as providing novel targets for therapeutic interventions. In this study, we tested the hypothesis that if morphine dysregulates multiple endolipid signaling systems in the brain and body, and this dysregulation evolves over time, then these differential effects will be measurable by changes in endolipid levels. Using an Acute (30 minutes post injection 20mg/kg) and a Chronic paradigm (5 days, twice daily, 20mg to 100mg/kg escalating dose) we measured 100 targeted endolipids in 8 brain regions, plasma, liver, and feces in male mice. In the Acute condition, we found that the most screened endolipids were changed in the striatum (42%), while the fewest were changed in the thalamus (19%) and 38% in the plasma. In the Chronic condition, 79% of plasma endolipids were changed. The highest level of change in the CNS was in the cortex (39%). Levels of AEA and 2-AG were largely unchanged; however, levels of the N-acyl GABAs, N-acyl valines, N-acyl taurines, and specific bile acids (e.g. DCA, TCA) showed the most dynamic changes by treatment group. These results provide information on novel endolipid signaling pathways that may contribute to the unwanted side effects of opioids, such as dependence and withdrawal, and provide novel avenues for the development of therapeutic strategies.

neuroscience↗

bioRxiv2026

Environment-dependent landscapes of coding variant impacts on coproporphyrinogen oxidase

Hereditary coproporphyria (HCP) -- caused by variants in coproporphyrinogen oxidase (CPOX) -- can be diagnosed via genome sequencing. However, 74% of clinically-reported CPOX missense variants are classified as variants of uncertain significance (VUS) due to lack of evidence. CPOX variant classification is further complicated by environment-dependence: For example, the CPOX variant p.Asn272His (c.814A>C) is classified as benign yet has been associated with HCP-like symptoms in the context of mercury exposure. Here we measured the functional impact of nearly all possible CPOX amino acid substitutions in both the presence and absence of mercury. The resulting CPOX variant effect maps reflect known protein structure and mutational tolerance patterns while also offering new sequence-structure-function insights. Scores from this atlas not only distinguish pathogenic from benign variants but also identify mercury-dependent variant impacts, thus informing our clinical, structural, and functional understanding of CPOX deficiency and illustrating the value of systematic context-dependent multiplexed assays of genetic variant effects.

molecular biology↗

bioRxiv2025

Repair of DNA double-strand breaks after low radiation doses in childhood cancer survivors and matched cancer-free individuals

DNA double-strand breaks (DSBs) which arise in G1- or G0-phase normal human cells are repaired by non-homologous end-joining (NHEJ), a pathway which is important for cell survival but can cause mutations at the break sites. DSB repair by NHEJ is very efficient at high damage levels of 1 or more DSBs per cell, much less efficient at lower damage levels and almost absent if only [~]0.05 DSBs per cell are induced. Repair at this low DSB level can be induced if cells are pre-treated prior to DSB induction with low concentrations of hydrogen peroxide, suggesting that the intracellular radical level modulates the efficiency of DSB repair at low damage levels. Here, we have investigated if the inefficiency of repair at low DSB levels contributes to the carcinogenic potential of DSBs or, counterintuitively, may serve as a mechanism to limit cancer development. We have analyzed the repair of high and low levels of radiation-induced DSBs in primary fibroblasts from 136 childhood cancer survivors, half of whom developed a second independent tumor later in life, and compared it to the response of primary fibroblasts from 68 individually matched cancer-free individuals. Although childhood cancer survivors and cancer-free individuals repaired DSBs at high damage levels equally efficiently, their response to low DSB levels differed drastically. While repair in cancer-free individuals was nearly absent at a level of [~]0.05 DSBs per cell, childhood cancer survivors repaired DSBs at this low damage level as efficiently as after high damage levels. These results suggest that most of the cancer survivors analyzed here carry a genetic predisposition that affects their response to low levels of DSBs. They also support the idea that the absence of repair observed in cancer-free individuals represents a mechanism limiting cancer formation.

cell biology↗

bioRxiv2025

Label-free in situ approach for characterizing the macromolecular composition and water content in biomolecular condensates

Biomolecular condensates are membraneless cellular organelles that form via liquid-liquid phase separation of proteins and nucleic acids. Their functional roles are tightly coupled to material properties like viscosity and hydrophobicity, which serve as key markers of cellular state. However, conventional determination of condensate composition and water content relies on invasive procedures that can damage samples. Here, we introduce Raman spectroscopy coupled with spectral phasor analysis as an in situ, label-free approach to resolve the chemical profiles and molecular concentrations within both the dense and dilute phases of biomolecular condensates. This method outperforms traditional regression and deconvolution approaches, yielding a precise readout of client molecule partitioning. By accounting for contributions of the protein backbone to the Raman spectra of condensates, we assess the signature of "solid-like" hydrogen-bonded water from protein hydration, revealing that most water molecules within condensates retain bulk, "liquid-like" properties. Finally, using environment-sensitive fluorescent probes, we demonstrate that macromolecular structure and water content--rather than hydrogen bonding alone--drive condensate hydrophobicity; notably, the dense phase remains predominantly water-rich even at low apparent dielectric constants.

biophysics↗

bioRxiv2025

Glucagon-induced PGC-1α4/PPARγ promotes hepatic lipid storage and macrosteatosis in fasting and MASLD

The liver plays a central role in regulating the transition between fasting and feeding states, coordinating glycogen breakdown, gluconeogenesis, fatty acid catabolism, and lipid storage. Disruptions in this balance contribute to metabolic disorders, including Metabolic dysfunction Associated Steatotic Liver Disease (MASLD). Here, we identify a novel biological pathway downstream of glucagon that promotes the hepatic lipid accumulation associated with fasting. Using gain- and loss-of-function in vivo and in vitro models, we found that glucagon induces sustained expression of PGC-14, promoting lipid uptake and storage in hepatocytes by increasing PPAR{gamma} activity. Increased PPAR{gamma}/PGC-14 promotes hepatic Fsp27/Cidec expression, leading to lipid droplet expansion and triglyceride trapping in liver. Activity of the PPARGC1A alternative promoter and PGC-14 expression were higher in livers of patients with MASLD, and PGC-14 expression correlated with macrosteatosis. Consistently, persistent expression of hepatic PGC-14 in mice fed a western diet promoted macrosteatosis, exacerbated oxidative stress and altered hepatic lipid composition to resemble worsening Metabolic dysfunction Associated Steatohepatitis (MASH) in humans. Our findings demonstrate that glucagon-induced hepatic PGC-14/PPAR{gamma} activity facilitates efficient uptake and storage of lipids during fasting, but over-activation of this coordinated metabolic pathway leads to lipid accumulation and worsening of steatosis in MASLD.

physiology↗

bioRxiv2025

Single-AAV CRISPR editing of skeletal muscle in non-human primates with NanoCas, an ultracompact nuclease

CRISPR gene editing is a transformative technology for addressing genetic diseases, but delivery constraints have largely limited its therapeutic applications to liver-targeted and ex vivo therapies. Here, we present the discovery and engineering of NanoCas, an ultracompact CRISPR nuclease capable of extending CRISPRs reach in vivo beyond liver targets. We experimentally screened 176 ultracompact CRISPR systems found in metagenomic data and applied protein engineering approaches to enhance the editing efficiency of NanoCas. The optimized NanoCas exhibits potent editing capabilities across various cell systems and tissues in vivo when administered via adeno-associated viral (AAV) vectors. This is accomplished despite NanoCas being approximately one-third the size of conventional CRISPR nucleases. In proof-of-concept experiments, we observed robust editing with our optimized NanoCas in mouse models targeting Pcsk9, a gene involved in cholesterol regulation, and targeting exon splice sites in dystrophin to address Duchenne muscular dystrophy (DMD) mutations. We further tested the efficacy of our NanoCas system in vivo in non-human primates (NHPs) resulting in editing levels above 30% in muscle tissues. The compact size of NanoCas, in combination with robust nuclease editing, opens the door for single-AAV editing of non-liver tissues in vivo, including the use of newer editing modalities such as reverse transcriptase (RT) editing, base editing, and epigenetic editing.

bioengineering↗

bioRxiv2023

Triplet-encoded prebiotic RNA aminoacylation

The encoding step of translation involves attachment of amino acids to cognate tRNAs by aminoacyl-tRNA synthetases, themselves the product of coded peptide synthesis. So, the question arises -- before these enzymes evolved, how were primordial tRNAs selectively aminoacylated? Here we demonstrate enzyme-free, sequence-dependent, chemoselective aminoacylation of RNA. We investigated two potentially prebiotic routes to aminoacyl-tRNA acceptor stem-overhang mimics and analyzed those oligonucleotides undergoing the most efficient aminoacylation. Overhang sequences do not influence the chemoselectivity of aminoacylation by either route. For aminoacyl-transfer from a mixed anhydride donor strand, the chemoselectivity and stereoselectivity of aminoacylation depends on the terminal three base pairs of the stem. The results support early suggestions of a second genetic code in the acceptor stem. One-Sentence SummarySelectivity of RNA stem-overhang aminoacylation is controlled by the terminal trinucleotide sequence of the stem.

molecular biology↗

bioRxiv2023

Logistics of Bone Mineralization in the Chick Embryo Studied by 3D Cryo FIB-SEM Imaging

During skeletal development, bone growth and mineralization require transport of substantial amounts of calcium, while maintaining very low concentration. How an organism overcomes this major logistical challenge remains mostly unexplained. To shed some light on the dynamics of this process, we use cryogenic Focused Ion Beam-Scanning Electron Microscopy (cryo-FIB/SEM) to image forming bone tissue at day 13 of a chick embryo femur. We visualize both cells and matrix in 3D and observe calcium-rich intracellular vesicular structures. Counting the number of these vesicles per unit volume and measuring their calcium content based on the electron back-scattering signal, we are able to estimate the intracellular velocity at which these vesicles need to travel to transport all the calcium required for the mineral deposited in one day within the collagenous tissue. We estimate this velocity at 0.27 m/s, which is too large for a diffusion process and rather suggests active transport through the cellular network. We conclude that calcium logistics is hierarchical and based on several transport mechanisms: first through the vasculature using calcium-binding proteins and the blood flow, then active transport over tens of micrometers through the network of osteoblasts and osteocytes and, finally, diffusive transport over the last one or two microns.

systems biology↗

bioRxiv2023

Systematically testing human HMBS missense variants to reveal mechanism and pathogenic variation

Defects in hydroxymethylbilane synthase (HMBS) can cause Acute Intermittent Porphyria (AIP), an acute neurological disease. Although sequencing-based diagnosis can be definitive, ~[1/3] of clinical HMBS variants are missense variants, and most clinically-reported HMBS missense variants are designated as "variants of uncertain significance" (VUS). Using saturation mutagenesis, en masse selection, and sequencing, we applied a multiplexed validated assay to both the erythroid-specific and ubiquitous isoforms of HMBS, obtaining confident functional impact scores for >84% of all possible amino-acid substitutions. The resulting variant effect maps generally agreed with biochemical expectation. However, the maps showed variants at the dimerization interface to be unexpectedly well tolerated, and suggested residue roles in active site dynamics that were supported by molecular dynamics simulations. Most importantly, these HMBS variant effect maps can help discriminate pathogenic from benign variants, proactively providing evidence even for yet-to-be-observed clinical missense variants.

molecular biology↗

bioRxiv2022

Genetically modified IL-2 bone marrow-derived myeloid cells reprogram the glioma immunosuppressive tumormicroenvironment

Gliomas are the most prevalent type of brain tumors and one of the leading causes of cancer-related death in the adolescent and young adult population (AYA). Two-thirds of glioma AYA patients are affected by low-grade gliomas (LGGs), but there are no specific treatments. Therefore, a percentage of LGG patients experience tumor relapse and malignant progression to high-grade glioma which leads to fatal outcomes. In part, malignant progression is potentiated by the immunosuppressive stromal component of the tumor microenvironment (TME) underscored by M2-macrophages and a paucity of cytotoxic T cells. As a result, first-line immunotherapies have failed to improve outcomes for patients with progressive high-grade gliomas. Here, we report the efficacy of an in vivo approach that demonstrates the potential for a novel cell-mediated innate immunotherapy designed to abrogate immunosuppressive mechanisms within the glioma TME and enhance the recruitment of activated effector T cells. A single dose of engineered bone marrow-derived myeloid cells that release Interleukin-2 (GEMys-IL2) was used systemically to treat mice with LGG tumors systemically. Our results demonstrate that GEMys-IL2 efficiently crossed the blood brain barrier (BBB), infiltrated the glioma microenvironment, and reprogrammed the infiltrating immune cell composition and transcriptome. In addition, GEMys-IL2 impaired tumor progression and extended survival in a LGG immunocompetent mouse model. In conclusion, we demonstrated that GEMys-IL2 have a therapeutic effect in vivo, thus supporting its potential application as a novel immunotherapy that warrants further investigation.

cancer biology↗

bioRxiv2022

Amplicon structure creates collateral therapeutic vulnerability in cancer

Although DNA amplifications in cancers frequently harbor passenger genes alongside oncogenes, the functional consequence of such co-amplifications and their impact for therapy remains ill-defined. We discovered that passenger co-amplifications can create amplicon structure-specific collateral vulnerabilities. We present the DEAD-box helicase 1 (DDX1) gene as a bona fide passenger co-amplified with MYCN in cancers. Survival of cancer cells with DDX1 co-amplifications strongly depends on the mammalian target of rapamycin complex 1 (mTORC1). Mechanistically, aberrant DDX1 expression inhibits the tricarboxylic acid cycle through a previously unrecognized interaction with dihydrolipoamide S-succinyltransferase, a component of the alpha-ketoglutarate dehydrogenase complex. Cells expressing aberrant DDX1 levels compensate for the metabolic shift by enhancing mTORC1 activity. Consequently, pharmacological mTORC1 inhibition triggered cell death specifically in cells harboring the DDX1 co-amplification. This work highlights a significant contribution of passenger gene alterations to the therapeutic susceptibility of cancers. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=130 SRC="FIGDIR/small/506647v2_ufig1.gif" ALT="Figure 1"> View larger version (34K): org.highwire.dtl.DTLVardef@58b27dorg.highwire.dtl.DTLVardef@12e2fccorg.highwire.dtl.DTLVardef@1440f33org.highwire.dtl.DTLVardef@141e933_HPS_FORMAT_FIGEXP M_FIG C_FIG

cancer biology↗

bioRxiv2021

Strigo-D2 - a bio-sensor for monitoring the spatio-temporal pattern of strigolactone signaling in intact plants

Strigolactones (SLs) are a class of plant hormones modulating developmental programs in response to endogenous and exogenous stimuli and mediating biotic interactions. However, a comprehensive view on the spatio-temporal pattern of SL signaling has not been established and tools for a systematic in planta analysis do not exist. Here, we present Strigo-D2, a genetically encoded ratiometric SL signaling sensor, allowing the examination of SL signaling distribution with cellular resolution and its rapid response to altered SL levels in intact plants. By monitoring the abundance of a truncated and fluorescently labeled SUPPRESSOR OF MAX2 1-LIKE 6 (SMXL6) protein, a proteolytic target of the SL signaling machinery, we show that all cell types investigated have the capacity to respond to changes in SL levels but with very different dynamics. In particular, SL signaling is pronounced in vascular cells but low in guard cells and the meristematic region of the root. We also show that other hormones leave Strigo-D2 activity unchanged indicating that initial SL signaling steps work in isolation from other hormonal signaling pathways. Specificity and spatio-temporal resolution of Strigo-D2 underline the value of the sensor for monitoring SL signaling in a broad range of biological contexts and with highly instructive analytical depth.

plant biology↗

bioRxiv2021

Directed Evolution of AAV Targeting Primate Retina by Intravitreal Injection Identifies R100, a Variant Demonstrating Robust Gene Delivery and Therapeutic Efficacy in Non-Human Primates

Targeted AAV vectors are needed for safe and efficient delivery to and transduction of specific tissue target(s) in patients. Effective intravitreal delivery for retina gene therapy is not feasible with wildtype AAV. We employed directed evolution in nonhuman primates (NHP) to discover an AAV variant (R100) for intravitreal treatment of multiple target cells in the primate retina. R100 demonstrated superior transduction of human retinal cells compared to wildtype AAV. Furthermore, three R100-based gene therapeutics demonstrated safety, delivery, and durable pan-retinal expression of intracellular or secreted transgenes throughout the NHP retina following intravitreal administration. Finally, efficacy of R100-mediated delivery of therapeutic transgenes was demonstrated in patient-derived retinal cells (monogenic diseases) and in an NHP model of pathogenic retinal angiogenesis.

bioengineering↗

bioRxiv2018

Mapping of TNTs using Correlative Cryo-Electron Microscopy Reveals a Novel Structure

The harmonious orchestration of intercellular communication is essential for multicellular organisms. One mechanism by which cells communicate is through long, actin-rich membranous protrusions, called tunneling nanotubes, that allow for the intercellular transport of various cargoes, including viruses, organelles, and proteins between the cytoplasm of distant cells in vitro and in vivo. Over the last decade, studies have focused on their functional role but information regarding their structure and the differences with other cellular protrusions such as filopodia, is still lacking. Here, we report the structural characterization of tunneling nanotubes using correlative light- and cryo-electron microscopy approaches. We demonstrate their structural identity compared to filopodia by showing that they are comprised of a bundle of functional individual Tunneling Nanotubes containing membrane-bound compartments and allowing organelle transfer.

cell biology↗

bioRxiv2016

Ancient hybridization and strong adaptation to viruses across African vervet monkey populations

Vervet monkeys (genus Chlorocebus, also known as African green monkeys), are highly abundant in savannahs and riverine forests throughout sub-Saharan Africa. They are amongst the most widely distributed nonhuman primates, show considerable phenotypic diversity, and have long been an important biomedical model for a variety of human diseases1 and in vaccine research2-4. They are particularly interesting for HIV/AIDS research as they are the most abundant natural hosts of simian immunodeficiency virus (SIV), a close relative of HIV. Here we present the first genome-wide survey of polymorphism in vervets, using sequencing data from 163 individuals sampled from across Africa and the Caribbean islands where vervets were introduced during the colonial era. We find high diversity, within and between taxa, and clear evidence that taxonomic divergence was reticulate rather than following a simple branching pattern. A scan for diversifying selection across vervet taxa yields gene enrichments much stronger than in similar studies on humans5. In particular, we report strong and highly polygenic selection signals affecting viral processes -- in line with recent evidence that proposes a driving role for viruses in protein evolution in mammals6. Furthermore, selection scores are highly elevated in genes whose human orthologs interact with HIV, and in genes that show a response to experimental SIV infection in vervet monkeys but not in rhesus macaques, suggesting that part of the signal reflects taxon-specific adaptation to SIV. Intriguingly, rather than affecting genes with antiviral and inflammatory-related functions7, selection in vervets appears to have primarily targeted genes involved in the transcriptional regulation of viruses, and in particular those that are harmful only under immunodeficiency, suggesting adaptation to living with SIV rather than defense against infection.

evolutionary biology↗