Biology subjects

Larsen, M. R.

Publications and source records attributed to Larsen, M. R..

At least 19 recordsLinked to original sources

bioRxiv2026

The Glycoproteome of Loxosceles Venom Reveals an Expanded Landscape of Animal Toxins

Spider venoms of the genus Loxosceles constitute a complex mixture of bioactive proteins and peptides associated with the major clinical manifestations of loxoscelism. Although significant advances have been made in the proteomic characterization of these toxins, studies addressing post-translational modifications, particularly glycosylation, and their potential impact on venom properties remain scarce. Here, we investigated the occurrence and characteristics of N-glycosylation in the venoms of Loxosceles gaucho, Loxosceles intermedia, and Loxosceles laeta. Using two-dimensional electrophoresis combined with glycoprotein-specific staining and LC-MS/MS, we identified glycosylation in different proteins biologically relevant to envenomation, predominantly belonging to the phospholipase D family, with distinct profiles among the species analyzed. Bottom-up glycoproteomic analysis of crude venoms using Byonic and a customized sequence database identified 88 N-glycosylated peptide sequences, primarily associated with lyases and hydrolases. Extensive microheterogeneity was detected at individual glycosylation sites, with paucimannosidic structures predominating alongside oligomannose and hybrid/complex N-glycans. Complementary enzyme-linked lectin assays supported the presence of distinct carbohydrate epitopes, including mannose, galactose, and N-acetylgalactosamine containing structures, and revealed 2,6-sialic acid-reactive motifs in two species. These findings establish N-glycosylation as an additional layer of molecular heterogeneity in Loxosceles venoms and provide a foundation for investigating its potential contribution to toxin properties and venom diversity.

biochemistry↗

bioRxiv2026

STEP-PTMs: Sequential TMT-based Enrichment and Profiling of Post-Translational Modifications

Comprehensive characterization of protein abundance and multiple post-translational modifications (PTMs) from the same biological samples is essential for understanding cellular regulation and PTM crosstalk but remains analytically challenging. Here, we present STEP-PTM (Sequential Tag-based Enrichment of Post-Translational Modifications), a modular TMT-multiplexed workflow that enables integrated quantitative analysis of the proteome, metabolome and multiple PTM classes from a single peptide preparation. Proteins are digested, isobarically labeled using tandem mass tags (TMT), and combined into a single multiplexed peptide pool prior to sequential PTM enrichment, thereby minimizing technical variability, reducing sample requirements and facilitating direct quantitative integration across datasets. STEP-PTM supports flexible sequential enrichment of phosphopeptides, peptides containing free and reversibly modified cysteines, sialylated N-linked glycopeptides, lysine-acetylated peptides and S-palmitoylated peptides, while preserving non-modified peptides for global proteome analysis. PTM-specific database searches further improve identification confidence and quantitative accuracy, and the modular workflow can readily be adapted by incorporating or omitting enrichment modules according to the biological question. Application of STEP-PTM to TMT16-plex cerebral brain organoids enabled the quantification of 10,413 proteins, 2,969 metabolites, 19,655 phosphopeptides, 28,876 peptides containing reversibly modified cysteines, 9,723 peptides containing free cysteines, 1,716 intact sialylated N-linked glycopeptides and 771 lysine-acetylated peptides from the same biological samples. We further demonstrate the applicability of the workflow to multiple mouse tissues, highlighting its broad utility for integrated systems-level characterization of protein expression and PTM regulation across diverse biological models.

biochemistry↗

bioRxiv2026

GPMAW Glyco-Search: An Integrated Workflow for Identification and Validation of Intact Sialylated N-Glycopeptides

Comprehensive analysis of intact sialylated N-glycopeptides remains challenging because of their low abundance, extensive structural heterogeneity, and limited peptide backbone fragmentation during tandem mass spectrometry. Here, we present an integrated workflow for high-confidence identification of intact sialylated N-glycopeptides that combines selective TiO2 enrichment, dual LC-MS/MS analysis of intact and deglycosylated glycopeptides, and the GPMAW glyco-search platform based on high-accuracy mass mapping. Unlike most conventional glycoproteomics search engines, GPMAW uses experimentally identified deglycopeptides to constrain glycan assignment before matching intact glycopeptide precursor masses to candidate glycan compositions. Identifications were validated using diagnostic oxonium ions, glycopeptide-associated Y-ion fragments, and an experimentally derived glycopeptide score. In addition, GPMAW integrates an interactive spectrum annotation interface that enables rapid manual validation of candidate identifications through visualization of annotated Y-ion series, oxonium ions, and peptide fragments, allowing individual assignments to be readily accepted or rejected. The workflow was optimized using bovine fetuin, validated on standard glycoproteins, and applied to depleted human plasma, where more than 2800 unique intact sialylated N-glycopeptides were identified across hundreds of glycosites and glycoproteins. Moreover, more than 1000 unique N-glycopeptides were identified from only 1 L of plasma. Comparative analysis demonstrated that GPMAW glyco-search identified more confidently assigned intact sialylated N-glycopeptides than three widely used N-glycoproteomics search engines while maintaining high reproducibility and low false-positive rates following manual validation. Together, this workflow provides a robust, flexible, and accessible platform for large-scale, high-confidence characterization of intact N-glycopeptides and establishes experimentally constrained glycan composition assignment combined with interactive spectrum validation as an effective strategy for reducing ambiguity in N-glycoproteomics. HighlightsO_LIThe program "GPMAW glyco-search" enables high-accuracy mass mapping for confident identification of intact N-glycopeptides. C_LIO_LIIntegrated workflow combining TiO2 enrichment, dual LC-MS/MS of intact and deglycosylated glycopeptides and GPMAW glyco-search for intact sialylated N-glycopeptides. C_LIO_LIOptimized TiO2 enrichment provides >95% selective enrichment of sialylated N-glycopeptides from complex biological samples. C_LIO_LIInteractive spectrum annotation and Y-ion-based scoring enable rapid manual validation and high-confidence glycopeptide identification. C_LIO_LIGPMAW glyco-search confidently identified more intact sialylated N-linked glycopeptides compared to three established glycoproteomics search engines. C_LI

biochemistry↗

bioRxiv2026

Patient-Derived Air-Liquid Interface Forebrain Organoids Reveal Functional Synaptic Deficits in Schizophrenia

Schizophrenia (SCZ) is a severe and debilitating neurodevelopmental disorder with lifelong impact on everyday life. Disruptions in synapse functions play a key role in its complex and poorly understood etiological and pathological mechanisms. Here, we investigated both the molecular composition and the spontaneous and stimulated functional properties of synapses in neural organoids from SCZ individuals. Air-liquid interface forebrain organoids (ALI-FOs) were generated from induced pluripotent stem cells (iPSCs) derived from three individuals with SCZ and three healthy controls. At day 170 synaptosomes were enriched and analyzed by data-independent acquisition mass spectrometry to profile the proteome, alongside with TMT-labeled phosphoproteomics both before and after acute KCl-induced depolarization. In parallel, we characterized the PTMome of the surrounding cellular environment, comprising phosphorylation, peptides with free and reversibly modified cysteines, and sialylated N-linked glycopeptides. Functional glutamatergic and GABAergic activity was assessed using calcium imaging to capture spontaneous neuronal signaling. Both conditions exhibited mature synaptic structures, while growth cones were observed only in SCZ-derived ALI-FOs, indicative of ongoing or delayed synaptogenesis. Proteomic analysis of synaptosome preparations revealed 358 differentially regulated proteins between SCZ and controls and 125 phophoproteins with altered phosphorylation, which clustered into three major categories: (1) synaptogenesis and synapse signaling; (2) cytoskeleton and cell junctions; (3) growth cone dynamics and neurite outgrowth. Analysis of the PTMs in the surrounding cellular environment revealed regulation of key regulatory mechanisms in 526 proteins, supporting the synaptic alterations observed. Notably, components of the Wnt signaling pathway were consistently dysregulated across both the synaptosome preparation and the PTMome in SCZ-derived ALIFOs as compared to controls. Depolarization-induced phospho-signaling revealed SCZ-specific response enriched in synaptic vesicle trafficking pathways. Together, these findings provide new insights into early synaptic alterations in SCZ, highlighting changes not only in protein composition, but more in protein regulatory mechanisms underlying synaptic signaling.

neuroscience↗

bioRxiv2026

Protein-state dysregulation and sex-specific neurodevelopmental signatures in schizophrenia forebrain organoids

Schizophrenia is highly heritable, yet the molecular mechanisms linking genetic risk to abnormal human brain development remain poorly understood. To address this, we generated dorsal forebrain organoids from 17 individuals with idiopathic schizophrenia and 17 age- and sex-matched controls and profiled them across multiple molecular layers, including single-nucleus transcriptomics, quantitative proteomics, metabolomics and deep post-translational modification (PTM) analysis. The organoids reproducibly modelled early cortical development and showed largely similar cellular composition between schizophrenia and control groups. Surprisingly, transcriptomic differences were relatively limited, with the strongest cell-type-specific changes observed in Cajal-Retzius neurons. In contrast, proteomic and particularly PTM-level analyses revealed widespread molecular disruption affecting pathways involved in neuronal migration, neurite development, synaptic function, protein kinase signalling, extracellular matrix organisation and lipid metabolism. Many of the earliest disease-associated changes emerged at the level of protein phosphorylation, consistent with altered neuronal maturation and neurite dynamics. At later developmental stages, schizophrenia organoids showed reduced abundance of synaptic proteins, fewer synaptic puncta and evidence of dysregulated retinoic acid and YAP1 signalling. Notably, most disease-associated alterations occurred independently of changes in transcript or protein abundance, indicating that key aspects of schizophrenia biology are encoded in protein state rather than expression level. These findings identify sex-specific dysregulation of protein state as a major molecular feature of schizophrenia and demonstrate the value of multi-layer proteomic approaches for uncovering disease mechanisms missed by transcriptomics alone.

neuroscience↗

bioRxiv2026

Dysregulation of miRNAs Drives Premature GABAergic Maturation and Early Neurodevelopmental Defects in Schizophrenia

BackgroundSchizophrenia (SCZ) is a severe neurodevelopmental disorder with numerous genetic risk loci. However, little is known about the molecular alterations that occur during brain development in SCZ, particularly regarding the role of microRNA (miRNA) mediated regulatory mechanisms. This gap in knowledge is largely due to the limited availability of developing human brain tissue. Patient-derived brain organoids offer a promising alternative model. Here we use 3D dorsal forebrain organoids (DFOs) to investigate miRNA dysregulation in SCZ. MethodsDFOs were generated from human induced pluripotent stem cells (hiPSCs) derived from six SCZ patients and five matched controls and cultured for 120 days. Multi-omics analyses, immunohistochemistry, and in situ hybridization were employed to characterize molecular and spatial features. ResultsDFOs recapitulated key molecular hallmarks of human cortical development. Nineteen miRNAs were differentially expressed in SCZ: nine associated with neural progenitor proliferation were downregulated and ten linked to neuronal differentiation and synaptic maturation were upregulated, reflecting a compressed developmental timeline. Among 77 dysregulated mRNAs, 55 were predicted miRNA targets. SCZ DFOs exhibited significant upregulation of GABAergic pathway genes accompanied by altered expression of their regulatory miRNAs, indicating premature GABAergic lineage specification. The disrupted miRNA-mRNA network converged on glutamatergic and dopaminergic development, synaptic organization, and extracellular matrix remodeling. ConclusionDysregulated miRNAs in SCZ DFOs disrupt neuronal differentiation, excitatory-inhibitory balance, and early circuit formation, implicating miRNA-mediated post-transcriptional regulation as a key mechanism linking molecular alterations to cellular and network-level deficits in SCZ.

cell biology↗

bioRxiv2026

Modulation of Cysteine modifications upon short time T-cell activation

T cell activation is initiated by rapid and tightly regulated signaling events that rely on reversible post-translational modifications to ensure speed, specificity, and fidelity. While phosphorylation is well established as a central regulator of T cell receptor signaling, the contribution of cysteine-based modifications remains poorly defined at a systems level. Due to their redox-sensitive thiol side chains, cysteine residues can undergo rapid and reversible chemical modifications, enabling them to function as molecular switches that modulate protein structure, activity, and interactions during signal transduction. Engagement of the TCR induces localized redox signaling, primarily through mitochondrial and NADPH oxidase-derived H2O2, leading to selective and reversible oxidation of reactive cysteine residues. These redox events act as spatially and temporally controlled signaling mechanisms rather than global oxidative stress, transiently reshaping phosphorylation-dependent networks through modulation of redox-sensitive kinases, phosphatases, and adaptor proteins. Specificity is conferred by peroxiredoxin-, thioredoxin-, and glutathione-dependent redox control systems that fine-tune cysteine reactivity. In addition, redox-dependent modulation of cysteine residues within zinc-coordinating motifs suggests a coupled redox-zinc signaling axis during T cell activation, where transient redistribution of zinc from cysteine-rich zinc-finger proteins may further regulate kinase activity and transcriptional programs downstream of TCR engagement. Here, we present a quantitative, time-resolved proteomic strategy to systematically interrogate cysteine dynamics during the earliest phases of human T cell activation. By combining cysteine-specific phosphonate adaptable tagging, thiol-disulfide exchange chromatography and TMT-based multiplexed mass spectrometry, we quantified 25,324 free cysteine-containing peptides and 14,853 reversibly modified cysteine peptides across seconds-to-minutes following TCR stimulation. This comprehensive cysteine proteome revealed rapid remodeling of cysteine redox states as early as 30 seconds after activation of T-cells. Functionally, regulated cysteines were enriched in core signaling pathways, including kinases, phosphatases, transcription factors, and nuclear zinc-finger proteins. Notably, key TCR signaling components such as Lck, CD45, ZAP-70, Akt, NFATC3, and RASGRP1 exhibited dynamic cysteine modulation. Together, these findings establish cysteine redox dynamics as a pervasive and functionally relevant regulatory layer in T cell activation, positioning cysteine modification alongside phosphorylation as a central component of immune signal transduction.

systems biology↗

bioRxiv2025

An ancestral transmembrane transcription factor couples cell envelope regulation and the SOS response in Caulobacter crescentus

The DNA damage (SOS) response in bacteria involves derepression of a set of genes in order to activate mechanisms to tolerate stress, repair DNA and slow down cell division. While some of these genes are well characterized, many genes exist which are clearly induced by DNA damage but for which the function is unclear. In Caulobacter crescentus, the toxin-antitoxin (TA) system higBA and a closely associated downstream transcription factor (higX) are strongly induced as part of the SOS response, but the role of higX is unknown. We show that, unexpectedly, HigX functions independently of HigBA as a cell membrane-associated regulator and is toxic when overexpressed in filamentous cells. ChIP-Seq indicated that it binds to several promoters associated with cell envelope regulation. In cells with the SOS response constitutively activated, HigX was overproduced, but at the same time was unable to bind the majority of its target promoters. higX was highly conserved in genomic context among many alpha-proteobacteria, while higBA was only found upstream of it in a small number of Caulobacter genomes, including the universal laboratory strain C. crescentus NA1000. Compositional analysis suggested that higBA originated from a foreign source, while higX is likely ancestral to the alpha-proteobacteria. Our data support a model where dysregulation of HigX production and activity in filamentous {Delta}lexA cells contributes to cell envelope instability and antibiotic sensitivity. Thus, the protective effect of inhibiting cell division during the SOS response in order to repair the DNA, carries the hidden cost of interference with HigX-mediated cell envelope maintenance. Author summaryThe DNA damage (SOS) response in bacteria is key for their survival in harsh conditions, but the genes which are induced by this response and the molecular mechanisms involved are variable between different bacteria. We investigated the function of an uncharacterized SOS-induced gene in Caulobacter crescentus (higX) and found that it is a membrane-localized DNA binding protein, but that it did not help survival in DNA damage. Instead, it negatively affected cell viability when induced, unlike other SOS response genes. Genomic analysis showed that higX is highly conserved among alphaproteobacteria, but it is only under SOS control in a small number of genomes (including Caulobacter crescentus) where a toxin-antitoxin system and its SOS-regulatory promoter have been inserted upstream. This work uncovers HigX as a novel factor in cell envelope regulation, and shows that loss of cell shape regulation, eg. in filamentous {Delta}lexA cells, can influence the ability of transmembrane transcription factors to bind to their target genes.

microbiology↗

bioRxiv2025

Extracellular vesicles from morphine-exposed prefrontal cortex carry transcriptomic and proteomic signatures of synaptic dysfunction

Extracellular vesicles (EVs) released by neurons and glial cells mediate intercellular communication in the brain and regulate synaptic function, neuronal survival, and neuropathological processes. Although chronic opioid exposure induces widespread neuroadaptations, the contribution of brain-derived EVs (BDEVs) to these processes remains largely unknown. Here, we isolated BDEVs from the prefrontal cortex of rats chronically exposed to morphine and performed integrative transcriptomic and proteomic analyses of their molecular cargo. Total RNA sequencing combined with unbiased proteomics revealed that morphine profoundly reprograms the BDEV transcriptome and proteome, enriching pathways related to synaptic plasticity, endoplasmic reticulum (ER) stress, mitochondrial dysfunction, and neurodegeneration. Among the most prominent alterations, the synaptic regulator ARC was consistently modulated at the mRNA level, while the ER stress marker HSPA5 was altered at both mRNA and protein levels. Functional assays further demonstrated that BDEVs derived from morphine-treated rats were sufficient to reconfigure transcriptional programs in naive cortical neurons, affecting genes associated with synaptic remodeling and excitability. Collectively, these findings provide the first evidence that chronic opioid exposure reprograms BDEV cargo in a brain region critical for addiction and that these vesicles can propagate transcriptional reorganization to recipient neurons. BDEVs thus emerge as active mediators of morphine-induced neuroadaptations and as potential targets for biomarker discovery and therapeutic intervention in opioid use disorder.

neuroscience↗

bioRxiv2025

MrgD Receptor Modulates Neurotransmission in the Nigrostriatal Pathway

The Mas-related G protein-coupled receptor D (MrgD) is primarily known for its role in peripheral nociception and, more recently, as a receptor for alamandine, influencing cardiovascular function and exhibiting antidepressant-like effects. However, its function within the central nervous system, particularly in motor and reward-related circuits, remains largely unexplored. Here, we investigate the role of MrgD in the nigrostriatal pathway using proteomic approaches focused on post-translational modifications in MrgD-knockout (KO) mice. Integrated proteomic, phosphoproteomic, and N-glycoproteomic analyses revealed significant alterations in synaptic vesicle-associated proteins, pointing to impaired neurotransmission in the nigrostriatal system of KO mice. These molecular findings were supported by neurotransmitter quantification and functional assays demonstrating impaired synaptic vesicle exocytosis. Pharmacodynamic analyses showed that MrgD modulates synaptic exocytosis in an agonist-selective manner, being responsive to alamandine but not {beta}-alanine. Furthermore, behavioral analyses revealed increased locomotor activity and compulsive-like behavior in MrgD-deficient mice, without impairments in short- or long-term memory. Together, these findings uncover a new role for MrgD beyond its involvement in nociception, highlighting this receptor as a potential therapeutic target for neurological disorders involving motor hyperactivity and compulsivity.

neuroscience↗

bioRxiv2025

Differential Proteomic Analysis of DEN-Induced Hepatocellular Carcinoma in Male and Female Balb/c Mice Reveals Novel Gender Specific Markers

BackgroundHepatocellular carcinoma (HCC) is one of the leading causes of hepatic malignancy with a higher prevalence in males compared to females, however, the distinct underlying mechanisms contributing to this disparity remain poorly understood. MethodsIn this study, we aimed to investigate comparative proteome profiling of a diethylnitrosamine (DEN) induced HCC model in male and female Balb/c mice. We extracted proteins from liver tissue of DEN treated male and female mice and their corresponding controls and subjected them to mass spectrometry and subsequent bioinformatics analyses. ResultsWe identified 170 and 233 differentially expressed proteins (DEPs) in female and male mice, respectively. We identified chemical carcinogenesis and cortical cytoskeleton as the shared pathways between the two groups. In addition, we identified distinct signaling pathways in DEN-treated male and female mice. Female mice showed enrichment in oxidative phosphorylation, fatty acid biosynthesis, metabolism and degradation and cytochrome P450 clusters. In contrast, in male mice, these pathways were enriched in cholesterol metabolism, coagulation and mRNA processing. Further, we identified top ten genes ranked by highest maximal clique centrality, by protein-protein interaction analysis of differentially expressed proteins (DEPs) in both sexes. Of these hub genes, female mice showed upregulation of NDUFA8 and ATP5H and were associated with poor patient survival. On the other hand, In DEN-treated male mice upregulation of FGG, FGA, HPX and SERPINC1 were associated with poor survival. ConclusionIn conclusion, our research provides gender-specific proteomic signatures in DEN-induced HCC. The identification of proteins associated cholesterol metabolism and coagulation in males, and mitochondrial complex I proteins in females as prognostic markers suggests novel therapeutic targets that may inform gender-tailored treatment strategies for HCC. Simple SummaryHepatocellular carcinoma (HCC) is a common and deadly liver cancer that affects men more than women. To understand the biological reasons behind this difference, we developed a liver cancer model in male and female mice using a chemical called diethylnitrosamine (DEN). We then studied the proteins involved in tumor development using advanced techniques like mass spectrometry and bioinformatics. We found that different sets of proteins and biological pathways were active in males and females. In males, ribosomal and RNA-binding proteins were linked to worse survival, while in females, mitochondrial proteins were more important. These findings suggest that men and women may need different strategies for diagnosing and treating HCC, and they offer new gender-specific targets for future therapies.

cancer biology↗

bioRxiv2025

Isolation and characterization of synaptic structures from human neural organoids

Human neural organoids (NOs) provide a powerful platform for investigating synaptic development and dysfunction during early neurodevelopment. However, methodologies for isolating functional synaptic structures from these models remain limited. Here, we present a differential centrifugation protocol enabling the enrichment of growth cone particles (GCPs) and immature synaptosomes from air-liquid interface cerebral organoids (ALI-COs) at distinct developmental stages (day 90 and 150). Notably, the method avoids density gradients, requires minimal starting material while maintaining reproducibility across human and murine tissues. Quantitative proteomic profiling revealed significant enrichment of growth cone markers (e.g. GAP43) and classical synaptosomal proteins (e.g. PCLO, BSN, SYN1). Transmission electron microscopy (TEM) confirmed the presence of membrane-enclosed GCPs with fibrous content and mitochondria in day 90 isolates, and immature synaptosomes containing synaptic vesicles on day 150. Functional viability of both types of synaptic structures was demonstrated through KCl-induced depolarization, which triggered phosphorylation changes in growth cone proteins (GAP43, MARCKS, MARCKSL1), cytoskeletal regulators (DCLK1, SHTN1, MARK4, MAP1B) and protein kinases (CAMK2G, PRKCE) in day 90 GCPs, as well as classical synaptic vesicle cycle proteins (SYN1, DNM1, RPH3A) at day 150. Overall, this study establishes a centrifugation-based protocol for isolating growth cones and immature synapses from human organoids, capturing key stages of synaptic development and enabling scalable, patient-compatible models to study synaptic function and dysfunction in neurodevelopmental and neurodegenerative disorders.

neuroscience↗

bioRxiv2025

High-throughput assessment of exercise-induced adaptations and muscle function in health and ageing

Exercise improves metabolic health, enhances insulin sensitivity, and preserves muscle function, making it a core intervention to combat age-related decline and metabolic disorders. However, large-scale genetic and pharmacological screens to uncover exercise-induced adaptations remain challenging in mammalian models due to their complexity and cost. Here, we present the ClimbMaster, a fully automated, computer-controlled platform for assessing exercise-induced adaptations and physical performance in the fruit fly Drosophila. The system uses repeated climbing exercises to simulate endurance training, enabling precise measurements of climbing speed and endurance across different conditions and life stages. Using the ClimbMaster, we demonstrate that exercise improves endurance, promotes fat loss, and enhances insulin-mediated glucose uptake and modulates insulin sensitivity in muscle, highlighting key conserved features of exercise physiology between flies and mammals. We also show that rapamycin, a TOR inhibitor, mitigates age-related performance decline. This platform enables high-throughput screens to investigate genetic and environmental factors influencing muscle health, aging, and insulin resistance, providing a scalable and versatile tool for the identification of novel therapeutic targets to improve healthspan and physical performance.

physiology↗

bioRxiv2024

Optimizing PSC culture for generating neural organoids

Cerebral organoids generated according to unguided protocols produce neural tissue with exceptional cell diversity and fidelity to in vivo. However, with only minimal extrinsic intervention, the importance of high quality starting material becomes paramount. Better understanding of what constitutes a high quality stem cell line and how to maintain those properties throughout prolonged culture is therefore a crucial foundation for successful organoid differentiation. In this study, we investigate the proteome and phospho-proteome of human pluripotent stem cells to uncover the mechanisms that drive neural organoid competence. We identify aberrant cell-extracellular matrix interaction and increased oxidative metabolism as hallmarks of poor neural differentiators. Drawing on the proteomic data and published literature, we optimise culturing conditions by using improved coating matrix, sustained supply of the key growth factor FGF2 and reducing oxidative stress. These adjustments improve brain organoid generation across all tested cell lines, though with varying degrees of efficiency. This work highlights the importance of optimal culture conditions to best support stem cells, ultimately enhancing the quality of brain organoids produced.

cell biology↗

bioRxiv2024

Temporal proteomic and PTMomic atlas of cerebral organoid development

Cerebral organoids (CBOs) are generated from pluripotent stem cells that undergo neuroectoderm specification and neuronal differentiation in three dimensions. The developing neurons in CBOs migrate and self-organize into cerebral cortex-like layers, mimicking human brain development. CBOs develop according to intrinsic signaling mechanisms and offer unique insights into mechanisms of early human brain development. This process requires coordinated spatiotemporal regulation of protein expression and function, where the latter can be achieved by post-translational modifications (PTMs) on proteins. Despite the importance of proteins in brain development and function, profiling of protein abundance and the involvement of PTMs in CBO development remain underexplored. To gain insight into protein and PTM abundance in CBOs, we performed a high-resolution temporal analysis of CBOs up to day 200 using proteomics, PTMomics and metabolomics. We quantified more than 9,300 proteins and various neurodevelopmentally relevant PTMs (including phosphorylation, lysine acetylation, sialylated N-glycosylation, and cysteine modifications). We demonstrate that protein abundance and dynamic PTMs show significant temporal changes during CBO development related to neuronal differentiation and energy metabolism, whereas calcium signaling is mainly regulated by dynamic PTMs. We further show that synaptic protein content correlated with neurotransmitter levels, and we detected astroglia beyond day 100. Lastly, comparative analysis showed proteomic similarities between CBOs and human fetal brain tissue, supporting the physiological relevance of CBOs. Overall, our study presents a temporal atlas of protein and PTM abundance in CBOs and provides a valuable resource for studying neurodevelopment in neural organoids.

neuroscience↗

bioRxiv2024

Lipidomic and Proteomic Insights from Extracellular Vesicles in Postmortem Dorsolateral Prefrontal Cortex Reveal Substance Use Disorder-Induced Brain Changes

Substance use disorder (SUD) significantly increases the risk of neurotoxicity, inflammation, oxidative stress, and impaired neuroplasticity. The activation of inflammatory pathways by substances may lead to glial activation and chronic neuroinflammation, potentially mediated by the release of extracellular particles (EPs), such as extracellular condensates (ECs) and extracellular vesicles (EVs). These particles, which reflect the physiological, pathophysiological, and metabolic states of their cells of origin, might carry molecular signatures indicative of SUD. In particular, our study investigated neuroinflammatory signatures in SUD by isolating EVs from the dorsolateral prefrontal cortex (dlPFC) Brodmanns area 9 (BA9) in postmortem subjects. We isolated BA9-derived EVs from postmortem brain tissues of eight individuals (controls: n=4, SUD: n=4). The EVs were analyzed for physical properties (concentration, size, zeta potential, morphology) and subjected to integrative multi-omics analysis to profile the lipidomic and proteomic characteristics. We assessed the interactions and bioactivity of EVs by evaluating their uptake by glial cells. We further assessed the effects of EVs on complement mRNA expression in glial cells as well as their effects on microglial migration. No significant differences in EV concentration, size, zeta potential, or surface markers were observed between SUD and control groups. However, lipidomic analysis revealed significant enrichment of glycerophosphoinositol bisphosphate (PIP2) in SUD EVs. Proteomic analysis indicates downregulation of SERPINB12, ACYP2, CAMK1D, DSC1, and FLNB, and upregulation of C4A, C3, and ALB in SUD EVs. Gene ontology and protein-protein interactome analyses highlight functions such as cell motility, focal adhesion, and acute phase response signaling that is associated with the identified proteins. Both control and SUD EVs increased C3 and C4 mRNA expression in microglia, but only SUD EVs upregulated these genes in astrocytes. SUD EVs also significantly enhanced microglial migration in a wound healing assay.This study successfully isolated EVs from postmortem brains and used a multi-omics approach to identify EV-associated lipids and proteins in SUD. Elevated C3 and C4 in SUD EVs and the distinct effects of EVs on glial cells suggest a crucial role in acute phase response signaling and neuroinflammation.

neuroscience↗

bioRxiv2024

Angiotensin-(1-5) is a Potent Endogenous Angiotensin AT2-Receptor Agonist

BackgroundThe renin-angiotensin system involves many more enzymes, receptors and biologically active peptides than originally thought. With this study, we investigated whether angiotensin-(1-5) [Ang-(1-5)], a 5-amino acid fragment of angiotensin II, has biological activity, and through which receptor it elicits effects. MethodsThe effect of Ang-(1-5) (1{micro}M) on nitric oxide release was measured by DAF-FM staining in human aortic endothelial cells (HAEC), or Chinese Hamster Ovary (CHO) cells stably transfected with the angiotensin AT2-receptor (AT2R) or the receptor Mas. A potential vasodilatory effect of Ang-(1-5) was tested in mouse mesenteric and human renal arteries by wire myography; the effect on blood pressure was evaluated in normotensive C57BL/6 mice by Millar catheter. These experiments were performed in the presence or absence of a range of antagonists or inhibitors or in AT2R-knockout mice. Binding of Ang-(1-5) to the AT2R was confirmed and the preferred conformations determined by in silico docking simulations. The signaling network of Ang-(1-5) was mapped by quantitative phosphoproteomics. ResultsKey findings included: (1) Ang-(1-5) induced activation of eNOS by changes in phosphorylation at Ser1177eNOS and Tyr657eNOS and thereby (2) increased NO release from HAEC and AT2R-transfected CHO cells, but not from Mas-transfected or non-transfected CHO cells. (3) Ang-(1-5) induced relaxation of preconstricted mouse mesenteric and human renal arteries and (4) lowered blood pressure in normotensive mice - effects which were respectively absent in arteries from AT2R-KO or in PD123319-treated mice and which were more potent than effects of the established AT2R-agonist C21. (5) According to in silico modelling, Ang-(1-5) binds to the AT2R in two preferred conformations, one differing substantially from where the first five amino acids within angiotensin II bind to the AT2R. (6) Ang-(1-5) modifies signaling pathways in a protective RAS-typical way and with relevance for endothelial cell physiology and disease. ConclusionsAng-(1-5) is a potent, endogenous AT2R-agonist.

pharmacology and toxicology↗

bioRxiv2024

HR3/RORα-mediated cholesterol sensing regulates TOR signaling

Cells and organisms adjust their growth based on the availability of cholesterol, which is essential for cellular functions. However, the mechanisms by which cells sense cholesterol levels and translate these into growth signals are not fully understood. We report that cholesterol rapidly activates the master growth-regulatory TOR pathway in Drosophila tissues. We identify the nuclear receptor HR3, an ortholog of mammalian ROR, as an essential factor in cholesterol-induced TOR activation. We demonstrate that HR3 binds cholesterol and promotes TOR pathway activation through a non-genomic mechanism acting upstream of the Rag GTPases. Similarly, we find that ROR is necessary for cholesterol-mediated TOR activation in human cells, suggesting that HR3/ROR represents a conserved mechanism for cholesterol sensing that couples cholesterol availability to TOR-pathway activity. These findings advance our understanding of how cholesterol influences cell growth, with implications for cholesterol-related diseases and cancer. HighlightsO_LICholesterol leads to dynamic TOR pathway activation, driving systemic growth C_LIO_LIHR3 in Drosophila binds cholesterol and couples its availability to TOR activation C_LIO_LIHR3 acts upstream of Rag GTPases to activate TOR in response to lysosomal cholesterol C_LIO_LIMammalian HR3 ortholog ROR is required for cholesterol-induced TOR activation C_LI

cell biology↗