Biology subjects

Vegvari, A.

Publications and source records attributed to Vegvari, A..

At least 19 recordsLinked to original sources

bioRxiv2026

The mitochondrial transaminase GOT2 supports Japanese encephalitis virus replication in neuronal cells

Japanese encephalitis virus (JEV) is the leading cause of viral encephalitis in Asia, yet the host pathways that sustain its replication in the central nervous system remain poorly defined, and no antiviral therapies exist. Here we combine time-resolved transcriptomics and proteomics in mouse neuroblastoma (Neuro-2a) cells with time-resolved proteomics of infected mouse brain, integrated using directionality-penalized p-value merging. JEV infection was accompanied by progressive induction of interferon-stimulated proteins and by changes in the abundance of enzymes of central carbon and energy metabolism, spanning the tricarboxylic acid cycle, glycolysis, oxidative phosphorylation and glutaminolysis. Temporal clustering of the brain proteome linked oxidative phosphorylation remodelling to a dependence on glutamine metabolism. Glutamine antagonism with DON reduced viral RNA, whereas glycolytic inhibition and AKT modulation did not significantly alter it under the conditions tested. Silencing of the mitochondrial transaminase GOT2 reduced JEV RNA, viral protein, and infectious virus production in human SH-SY5Y cells. Our findings identify a glutamine-GOT2 axis as a metabolic dependency of JEV and a candidate host-directed antiviral target.

microbiology↗

bioRxiv2026

Lysine methyltransferase SET7 links cardiometabolic risk to endothelial dysfunction by dysregulating mRNA splicing and eNOS-CaM interaction

BACKGROUNDLysine methyltransferase SET7 activates gene expression through mono- methylation of histone H3 at lysine 4 (H3K4me1) and modulates protein function via mono- methylation of non-histone proteins (Kme1). However, its role and molecular targets in endothelial dysfunction associated with cardiometabolic disorders remain unknown. METHODSEndothelial-specific Setd7 knockout (Setd7EC-KO) mice were generated and endothelial function assessed in WT and Setd7EC-KO mice after high-fat diet (HFD). Human aortic endothelial cells (HAECs) were used to investigate SET7 expression and function under metabolic stress. SET7-dependent histone and non-histone targets were identified by proteomic and ChIP analyses. Insights from these datasets guided the design of bioinformatic, molecular, and functional studies to define their regulatory mechanisms. Clinical relevance was evaluated in human arteries. RESULTSHFD selectively increased endothelial SET7 expression in WT mouse aortas. Despite comparable metabolic abnormalities, Setd7EC-KO mice were protected from HFD- induced endothelial dysfunction, oxidative stress, and inflammation. In HAECs, high glucose emerged as the strongest inducer of SET7 expression, promoting pro-inflammatory and pro- oxidant gene expression, monocyte adhesion, and ROS generation. These effects were reproduced by overexpression of catalytically active SET7 and reversed by its inhibition or silencing. Proteomic and ChIP analyses revealed that SET7-dependent H3K4me1 activates transcription of spliceosome components, linking aberrant mRNA splicing to endothelial inflammation and oxidative stress. Moreover, Kme1-proteomics identified endothelial nitric oxide synthase (eNOS) as a direct SET7 substrate. Bioinformatic analyses and mutagenesis experiments demonstrated that SET7-mediated mono-methylation of eNOS at K494 disrupts calmodulin (CaM) binding and impairs NO synthesis. These molecular signatures were also observed in internal mammary arteries from patients with vascular disease and hyperglycemia. CONCLUSIONSSET7 drives endothelial dysfunction through a dual mechanism: 1) H3K4me1-dependent activation of splicing machinery triggering inflammation and oxidative stress, and 2) eNOS mono-methylation at K494 reducing NO bioavailability. Targeting SET7 may therefore represent a promising avenue to safeguard endothelial homeostasis in cardiometabolic disease. GRAPHIC ABSTRACTA graphic abstract is available for this article.

molecular biology↗

bioRxiv2026

Defining Quality Control Standards for Single-Cell Proteomics by Inter-Laboratory Benchmarking

Single-cell proteomics can quantify thousands of proteins from individual mammalian cells, yet the absence of community-wide quality control limits biological interpretability. Here, the HUPO Single Cell Initiative presents the first inter-laboratory single-cell proteomics benchmarking study across seven laboratories using standardized 384-well plates acquired on Orbitrap Astral and timsTOF Ultra2 instruments. Centralized analysis across six DIA software tools revealed that software choice impacts identification depth and quantitative accuracy more than instrument vendor. Multi-layered quality control enabled the detection of cell-leakage during sorting, LC misconfiguration, column degradation and site-specific pipetting failures. Inter-lab quantitative correlations were strongest between instruments of the same vendor relative to cross-platform comparisons. Sequential correction for plate identity and well position recovered clean cell-type separation for confident downstream differential expression analysis. This study provides a data-driven quality control framework spanning plate design to batch correction for reproducible single-cell proteomics across laboratories and platforms.

biochemistry↗

bioRxiv2026

Multi-omics uncovers interaction in the vaginal microbiome and a type II secretion/Tad pilus system in Gardnerella vaginalis

The vaginal microbiome is a critical determinant of womens health. We investigated the genetic basis of common vaginal microbiome species and their biofilm formation. Genomic analysis of Gardnerella vaginalis (Gv) revealed a fundamental phylogenetic split correlating with high- versus low-biofilm phenotypes, driven by clade-specific genomic islands and allelic variants. In a dual-species coculture model of five key vaginal bacteria, Gv achieved numerical dominance, triggering extensive, asymmetric proteomic reprogramming in partner species while showing limited shifts itself. Proteins from biofilm-associated modules showed functional divergence, supported by AI-predicted structural variations in a type II secretion/Tad pilus system, which is first discovered from Gv strains. Integrated metabolomics identified a methyl-{beta}-carboline compound that is elevated in cocultures containing Prevotella bivia (Pb). This compound acts as a potent and selective inhibitor of Gv and Pb biofilms, sparing Lactobacillus crispatus. This work establishes a direct genomic basis for Gv virulence and demonstrates how interspecies interactions govern community dynamics and antimicrobial metabolite production. HighlightsO_LIComprehensive genomic resource comparing with high-quality long-read whole genomes and reference Gardnerella vaginalis and Lactobacillus iners strains. C_LIO_LIIntegrated multi-omics and functional analysis on the most common vaginal microbiome species using 16S rRNA gene sequencing, proteomics, metabolomics, and in vitro assays. C_LIO_LIKey phenotypes quantified, including biofilm formation and polymicrobial interactions. C_LIO_LIConserved Type II Secretion/Tad Pilus System identified across all Gardnerella vaginalis strains, with AI-predicted structural modeling. C_LIO_LIEvaluation of growth inhibition using metabolites against a panel of relevant microbes, including vaginal microbes and opportunistic pathogens. C_LI

microbiology↗

bioRxiv2026

MitoSAM-dependent lipoylation controls postnatal heart development via metabolic remodeling

The neonatal heart undergoes a rapid metabolic transition from fetal glycolysis to oxidative phosphorylation, requiring coordinated metabolic remodeling. Mechanisms driving this transition remain unclear. Here, we demonstrate that sufficient mitochondrial S-adenosylmethionine (mitoSAM), imported via the solute carrier Slc25a26, is essential for this shift by sustaining the lipoylation of 2-oxoacid dehydrogenases, critical for TCA cycle activation. Proteomic and metabolomic profiling revealed that reduced mitoSAM availability impaired lipoylation, blocking TCA cycle function and restricting nucleotide synthesis, while mitochondrial gene expression and respiratory capacity remained largely intact. In vivo EdU labeling showed persistent cardiomyocyte proliferation imposing further strain on nucleotide pools. Supplementation with medium-chain triglycerides during the suckling-to-weaning transition restored metabolic function and normalized cardiac growth and morphology. Our data reveal a critical developmental window in which mitoSAM-dependent lipoylation ensures heart maturation.

biochemistry↗

bioRxiv2026

ISG15-USP18 signaling restrains viperin-dependent metabolic antiviral restriction

Type I interferon (IFN-I) responses are tightly regulated to balance antiviral defense with cellular homeostasis. In humans, interferon-stimulated gene 15 (ISG15) functions as a critical negative regulator of IFN-I signaling by stabilizing the IFN negative regulator USP18, yet the functional consequences of ISG15 deficiency remain elusive. Here, we show that the loss of ISG15 exaggerates the JAK-STAT activation and, downstream, amplifies multiple ISGs including the nucleotide-modifying enzyme RSAD2 (viperin). Our quantitative proteomics, genetic reconstitution, and signaling analyses establish that defective USP18 stabilization skews the IFN response towards viperin expression. This amplified ISG network promotes viperin-catalyzed accumulation of the antiviral nucleotide analog ddhCTP, resulting in enhanced inhibition of viral RNA synthesis and the replication of Crimean-Congo hemorrhagic fever virus and SARS-CoV-2. Together, these findings demonstrate an ISG15-USP18-viperin axis that can be targeted to boost the metabolic antiviral restriction.

microbiology↗

bioRxiv2025

Towards a species search engine: KISSE offers a rigorous statistical framework for bone collagen tandem mass spectrometry data

DNA and bone collagen are two key sources of resilient molecular markers used to identify species from their remains. Collagen is more stable than DNA, and thus it is preferred for ancient and degraded samples. Current mass spectrometry-based collagen sequencing approaches are empirical and lack a rigorous statistical framework. Based on the well-developed approaches to protein identification in shotgun proteomics, we introduce a first approximation of the species search engine (SSE). Our SSE named KISSE is based on a species-specific library of collagenous peptides that uses both peptide sequences and their relative abundances. The developed statistical model can identify the species and the probability of correct identification, as well as determine the likelihood of the analyzed species not being in the library. We discuss the advantages and limitations of the proposed approach and the possibility of extending it to other tissues.

zoology↗

bioRxiv2025

Acute high-dose irradiation of human primary ovarian cells reveals a shift in transcriptomics profile and impairment in cell-cell adhesion

STUDY QUESTIONHow do human cortical (cPOCs) and medullary (mPOCs) primary ovarian cells respond to acute X-ray exposure? SUMMARY ANSWERAcute high-dose X-ray exposure causes a shift in cPOCs and mPOCs transcriptomic profiles and impairs significantly their cell-cell adhesion ability. WHAT IS KNOWN ALREADYRadiotherapy is a leading cancer treatment, due to its effectiveness in targeting malignant cells. However, it can also affect healthy cells, potentially causing organ dysfunction, among which ovaries. When targeted radiotherapy is not feasible, fertility preservation is recommended to avoid premature ovarian insufficiency. In addition, the effects of irradiation on ovarian somatic cells remain poorly understood. STUDY DESIGN, SIZE, DURATIONOvarian tissue was obtained from patients undergoing gender-affirming surgery at Karolinska University Hospital Huddinge, Sweden. The ovarian tissue was separated into cortex and medulla, then individually dissociated into single-cell suspensions using mechanical and enzymatic methods. Monolayer cultures from cPOCs and mPOCs were exposed to a single dose of 10 Gy X-ray irradiation or left unexposed as paired controls. Following irradiation, the cells were cultured at various time-points for further molecular and morphological evaluation. PARTICIPANTS/MATERIALS, SETTING, METHODSOvarian tissue from 8 patients (age 23-36 years) was used. Dissociated cPOCs and mPOCs were cultured to 80% confluence and irradiated with 10 Gy (1.33 Gy/min), with non-irradiated controls. Cellular ATP and mitochondrial activity were assessed, followed by immunofluorescence staining for canonical irradiation-induced effects in cells: DNA damage, apoptosis and cell cycle progression. Bulk RNA-sequencing was performed on controls and irradiated samples. Libraries were prepared using the Illumina Stranded mRNA Prep Ligation protocol and sequenced on Illumina NovaSeq6000 platform. Genes were considered to be differentially expressed under the cut-off of false discovery rate (FDR) < 0.05. Subsequently, affected biological pathway was predicted using all expressed genes ranked by log2 fold change again hallmark gene sets. To further investigate the potential upstream regulators, transcription factor enrichment analysis were performed based on DEGs. To assess changes at protein level, we mapped the proteomic profile using liquid chromatography-tandem mass spectrometry. Peptides were considered to be differentially expressed (DEPs) under the cut-off of p-value < 0.01. Finally, we measured the ability of cPOCs and mPOCs to form 3D aggregates after seeding irradiated and non-irradiated cells on Biosilk scaffolds. MAIN RESULTS AND THE ROLE OF CHANCEFollowing irradiation, ATP levels and mitochondrial activity in cPOCs and mPOCs were comparable to controls, indicating minimal irradiation impact on cell viability and proliferation. Immunofluorescence analysis confirmed the modulation of canonical pathways, such as DNA damage, apoptosis and cell cycle in both cPOCs and mPOCs. Transcriptomic analysis showed that cPOCs and mPOCs at 1 h post-irradiation clustered together with the related 1 h control. However, a shift in transcriptomic profile was observed after 4 h and even more after 24 h post-irradiation in both cPOCs and mPOCs. Gene set enrichment analysis (GSEA) indicated upregulation of the p53 pathway at 4 h and 24 h post-irradiation, alongside downregulation of MYC targets, E2F targets, the G2/M checkpoint and mTORC1 pathway. Gene pattern analysis showed irradiation-dependent trends related to extracellular matrix (ECM) organisation, p53-mediated apoptotic mechanisms and chromosome segregation during the 24 h period following irradiation. Additionally, transcription factor enrichment analysis based on DEGs suggested p53 and MYC as potential upstream regulators. On a proteomic level, DEPs associated with ECM organisation and cytoskeleton formation were detected at 4 and 24 h post-irradiation. Finally, X-ray exposure hindered the cell-cell adhesion ability of both cPOCs and mPOCs, leading to impaired formation of Silk-Ovarioids. LARGE SCALE DATAThe RNA sequencing count matrix is deposited in Gene Expression Omnibus (GEO) with accession number GSE291604. The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PXD061796. The code used for the analysis can be found at https://github.com/tialiv/X-Ovary. LIMITATIONS, REASONS FOR CAUTIONThe ovarian tissue was obtained from gender-affirming surgery patients who received androgen treatment before removal. Even though unlikely, this hormonal treatment might influence ovarian environment and alter cellular response to irradiation. Additionally, in this study the impact of X-ray exposure was assessed on a monolayer cell model, thus limiting the extrapolation power of our results to ovary in vivo. Lastly, the impact of irradiation was focused on the somatic cell populations that are essential for ovarian function. Further studies are needed to investigate the effects of X-ray exposure on ovarian follicles and their function. WIDER IMPLICATIONS OF THE FINDINGSUnderstanding the roles of MYC, p53 and cell adhesion factors in response to irradiation could guide the development of future ovarian protective strategies. These findings lay the foundation for further studies on ovarian tissue protection and fertility preservation in cancer patients. STUDY FUNDING/COMPETING INTEREST(S)This work was funded by the European Unions HORIZON 2020 research and innovation programme (MATER) under the Marie Skodowska-Curie Actions (grant agreement No: 813707), the Estonian Research Council (grants PRG1076 and PSG608), the Orion Research Foundation sr personal grant, the Research grant from the Center for Innovative Medicine (CIMED) and the Karolinska Institutet Consolidator Grant.

cell biology↗

bioRxiv2025

Disrupted α-ketoglutarate homeostasis trains monocyte-derived macrophages towards M2-like phenotype in long-term treated HIV-infection

Cells of the myeloid lineage, particularly monocytes and macrophages, are central to HIV pathogenesis, contributing to viral persistence and immune regulation during suppressive therapy. We hypothesized that metabolic reprogramming and altered chemokine signaling in people with HIV (PWH) on long-term ART impair monocyte trafficking and macrophage polarization. Using single-cell RNA sequencing, immunophenotyping, and metabolic modeling, we identified altered receptor expression and disrupted metabolic flux linked to reduced monocyte migration. Plasma secretome profiling revealed a nonclassical inflammatory microenvironment, while integrative multi-omics and single-cell proteomics of monocyte-derived macrophages (MDMs) demonstrated metabolic rewiring of the Glycolysis-TCA Anaplerosis Axis, orchestrated in part by elevated -ketoglutarate (AKG). Differentiation with PWH serum or AKG, skewed MDMs toward an M2-like phenotype, and enhanced HIV susceptibility. Together, these systems-level and mechanistic analyses reveal that metabolic training drives macrophage dysfunction in well-treated PWH, sustaining low-grade inflammation and highlighting potential therapeutic targets.

systems biology↗

bioRxiv2024

Characterization of HLA-DR immunopeptidome of bronchoalveolar lavage cells in patients with newly diagnosed rheumatoid arthritis and healthy current-smoker controls

Evidence suggests that self-tolerance is breached in the lung prior to the clinical onset of rheumatoid arthritis (RA) in the joints. The human leukocyte antigen DR (HLA-DR) shared epitope (SE) represents the strongest genetic risk factor for sero-positive RA. However, to our knowledge, the HLA-DR immunopeptidome of the RA lung and its link to HLA-DR genotype has not been investigated to date. The objective of this study was to optimize the methods for characterizing the HLA-DR immunopeptidome of lung immune cells and apply it to newly diagnosed RA patients versus current-smoker healthy controls, as well as to investigate the connection with the HLA-DR genotype. The HLA-DR immunopeptidome method was improved to facilitate characterization from as few as 6 million bronchoalveolar lavage (BAL) cells per subject, consisting primarily of alveolar macrophages. This method was applied to newly diagnosed RA patients naive to treatment (n=9, LURA cohort), as well as healthy current-smoker controls (n=10, COSMIC cohort). For five of the RA patients, a 6-month follow-up after initiation of the standard-of-care treatment regime was also included. After isolation and purification, peptide samples were separated by nano-flow liquid chromatography coupled to an Orbitrap mass spectrometer equipped with ion mobility device (FAIMS). Mass spectra acquired in data dependent acquisition mode were then searched against a human proteome database. Subsequently, the identified peptides were deconvoluted to their predicted binding HLA-DR allele using MHCMotifDecon based on the sequenced genotype of the individual. An optimized sample preparation and analytic method enabled the detection of over 23,000 peptides from over 3,000 source proteins with between 1,000 and 5,000 peptides identified per sample. Notably, the application of FAIMS with three compensation voltages allowed for efficient transfer of 2+, 3+, and 4+ peptide ions while removing singly charged background ions. Hierarchical clustering revealed that the immunopeptidome was more driven by the HLA-DR genotype than by RA disease or sex. However, since the HLA-DR genotype is a strong risk factor for RA, these results are convoluted. When deconvoluting the peptides to their predicted binding allele, the HLA-DRB1 alleles *01:01, *04:01, *04:04, *04:05, *04:07, and *10:01 were consistently assigned more peptides than other alleles. Except for *04:07 these alleles belong to the SE risk factor alleles, providing a potential explanation between HLA-SE and RA pathogenesis. Native peptides from known citrullinated and non-modified RA autoantigens (such as -enolase and calreticulin) were detected and validated as binders in prediction algorithms. No significant differences were found between base line and follow-up (post-treatment) samples from RA patients. Taken together, this data characterizes the HLA-DR immunopeptidome in the lung of early RA in an unprecedented manner, which together with future immunogenicity studies will help our understanding of the connection between the lung and the pathogenesis of RA. Finally, more peptides predicted to bind to SE alleles and *04:07 compared to other alleles demands further study on the relative expression of HLA-DR alleles and presentation mechanisms to understand the implications for RA.

immunology↗

bioRxiv2024

Tissue-specific responses to TFAM and mtDNA copy number manipulation in prematurely ageing mice

Somatic mitochondrial DNA (mtDNA) mutations are heavily implicated as important drivers of ageing and age-related diseases. Their pathological effect can be partially counteracted by increasing the absolute amount of wild-type mtDNA via moderately upregulating TFAM, a protein important for mtDNA packaging and expression. However, strong TFAM overexpression can also have detrimental effects as it results in hypercompaction of the mtDNA and subsequent impairment of mtDNA gene expression. In this study, we have experimentally addressed the propensity of moderate TFAM modulation to improve the premature ageing phenotypes of mtDNA mutator mice, carrying random mtDNA mutations. Surprisingly, we detect tissue-specific endogenous compensatory mechanisms acting in mtDNA mutator mice which largely affects the outcome of TFAM modulation. Accordingly, moderate overexpression of TFAM can have both negative and beneficial effects in different tissues of mtDNA mutator mice. We see a similar behavior for moderate TFAM reduction, which improves brown adipocyte tissue homeostasis, while other tissues are largely unaffected. Our findings highlight that regulation of copy number and gene expression of mtDNA is complex and cause tissue-specific effects that should be considered when modulating TFAM levels. Additionally, we suggest that TFAM is not the sole determinant of mtDNA copy number in situations where oxidative phosphorylation (OXPHOS) is compromised but other important players must be involved.

genetics↗

bioRxiv2024

microRNA and non-targeted proteome analysis of liquid biopsies from the distal lung collected by Particles in Exhaled Air (PExA) reveals presence from extracellular vesicles

Background. Early detection and longitudinal follow-up are essential for timely diagnosis and treatment for lung diseases. Currently, invasive methods are often required to examine the distal parts of the lungs. The growing need to explore the bio-molecular mechanisms in various lung diseases highlights the importance of non-invasive methods. The use of particles in exhaled air (PExA), a non-invasive technique for sampling of epithelial lining fluid from distal airways, is gaining attention. MicroRNAs (miRNAs) are crucial in modulating protein expression both intracellularly and intercellularly, often transported via extracellular vesicles. Dysregulated miRNAs have been linked to many pulmonary diseases, and their relative stability, especially when encapsulated in EVs, makes them promising biomarkers. Here we report for the first time multi-modal analysis of miRNAs and proteins in PExA, offering an opportunity to study the role of miRNAs in the pathophysiology of respiratory diseases in a non-invasive manner. Methods. Exhaled particles were collected from healthy subjects using the PExA 2.0 instrument utilizing the optimized PExA breathing maneuver. PExA samples collected on different types of impaction membranes were analyzed using a non-targeted mass spectrometry-based proteomics workflow optimized for single-cell detection, and a miRNAseq workflow optimized for low input starting material. Technical validation of a subset of the detected miRNAs was performed using custom-designed miRCURY LNA miRNA PCR assays. Pathway enrichment analyses for the detected proteins were performed using STRING. Results. Proteomic analysis consistently identified over 50 proteins across multiple types of impaction membranes, sample dilution series, and individuals down to a single PEx sPOT (24ng starting material). We observed a significant enrichment of proteins associated with extracellular vesicles, including blood microparticles, and secretory granules. miRNA-seq revealed 39 mature miRNAs, the majority of which have been previously reported to be detected in the airways. Some were also reported to be secreted by primary human airway epithelial cells via extracellular vesicles. miRNA-125b and the members of the let-7 family were among the most abundant miRNAs detected. Fluorometric assays showed significant RNase activity in both PExA and other lung-related samples, such as bronchoalveolar lavage fluid, suggesting that this activity originates from the airways and is independent of the sampling techniques used. The workflow for extraction and processing of the PExA collection membrane, tested with abundant synthetic miRNAs and analyzed using the miRCURY LNA miRNA PCR assay, yielded results comparable to control samples, indicating that the membrane material does not interfere with the assay. Conclusions. Using PExA, we identified several miRNAs reported to be dysregulated in pulmonary disorders. The enrichment of extracellular secretory components in the core protein list, along with the elevated RNAse activity in the respiratory tract, suggest that the detected miRNAs may be encapsulated within extracellular vesicles. These miRNAs are of particular interest due to their potential role in intercellular communication. Our findings suggest that PExA holds a potential as a non-invasive tool for studying extracellular vesicle-mediated miRNA cargo in the small airways.

physiology↗

bioRxiv2024

Mouse PAW: reverse-translating the FINGER multimodal lifestyle intervention enhances synaptic plasticity and cognition in adult wild type female mice

BackgroundTargeting multiple risk factors through preventive interventions can halt the onset or progression of dementia. The clinical efficacy of this approach was shown in the multimodal FINGER trial, yet knowledge of the underlying biological mechanisms is limited. In the current study, we applied for the first time a multimodal lifestyle intervention in mice to study effects on cognition and associated molecular pathways. MethodsWe have established a novel experimental model, the lifestyle intervention PAW (Prevention of Alzheimers by a Multimodal Lifestyle Protocol - Working-mechanisms for Memory Gains) in mice. In this model, we combined different modalities of intervention aiming to achieve synergistic effects. The animals were given access to running wheels (voluntary exercise), Fortasyn Connect (a medical food that slows disease progression in early Alzheimers disease), and they were subjected to cognitive training in an IntelliCage environment (PAW group). To separately investigate the effects of pharmacological vascular management as a preventive measure, another group of mice was given Atorvastatin and Enalapril (cholesterol and blood pressure lowering pharmaceuticals, respectively) dosed in the diet (Pharma group). Control mice were housed in normal conditions. We included 12 wild type C57BL/6J female mice 6.5 months of age per group. The full intervention lasted for 8 weeks. Blood pressure was measured at baseline and the end of the intervention. All mice underwent a battery of behavioural testing after the eight weeks of intervention. Hippocampi were dissected for proteomics analysis. ResultsDuring the intervention, the PAW group actively participated in the intervention by learning the different cognitive training programs and by using the running wheels. At the end of the intervention, the PAW group showed a lowering of blood pressure to a similar extent as in the Pharma group (systolic 158 mmHg to 139 mmHg, p = 0.003, and 163 mmHg to 136 mmHg, p = 0.042, respectively). Furthermore, the PAW group displayed a better short-term spatial working memory compared to the control group as assessed by the spontaneous alternation in the Y maze test (66.5% and 56.7%, respectively, p = 0.036). Proteomic analysis of the hippocampi and downstream bioinformatic analysis revealed that several pathways were upregulated in the PAW mice including synaptogenesis (Z = 4.27, p = 1.26E-18) and glutamate binding, activation of AMPA receptors and synaptic plasticity (Z = 3.74, p = 3.16E-19). ConclusionsOur findings suggest that the PAW model effectively mimics the clinical effects of multimodal lifestyle dementia prevention, and further demonstrates the activation of hippocampal-specific molecular drivers of memory gains.

neuroscience↗

bioRxiv2024

Silk-Ovarioids: Establishment and characterization of human ovarian primary cells 3D-model system

In vitro models that mimic ovaries are crucial for elucidating the biological mechanisms underlying follicle activation and growth. Three-dimensional (3D) systems are particularly relevant because they can replicate the heterogeneity and cell-cell communication between different ovarian cell types. However, complex models using human ovarian primary cells have not yet been established. In this study, we developed and characterized long-term cultured 3D models of primary ovarian somatic cells isolated from adult tissues, using Biosilk as a scaffold. We successfully established both ovarian cortex- and medulla-derived 3D systems, termed Silk-Ovarioids. The presence of key ovarian somatic cell types - including granulosa, stromal, endothelial, and perivascular cells - was confirmed by transcriptomics, proteomics, and immunostaining. Notably, Silk-Ovarioids exhibited the formation of a pro-angiogenic hypoxic core, as evidenced by the development of vessel-like structures after six weeks of culture. The Silk-Ovarioids demonstrated low intra-batch variability and long-term culture stability, underscoring their potential as a robust step towards creating a bioengineered, patient-specific artificial ovary.

cell biology↗

bioRxiv2024

TISSUE-SPECIFIC METABOLOMIC REPROGRAMMING DETERMINES THE DISEASE PATHOPHYSIOLOGY OF SARS-COV-2 VARIANTS IN HAMSTER MODEL

Despite significant effort, a clear understanding of host tissue-specific responses and their implications for immunopathogenicity against the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variant infection has remained poorly defined. To shed light on the interaction between organs and specific SARS-CoV-2 variants, we sought to characterize the complex relationship among acute multisystem manifestations, dysbiosis of the gut microbiota, and the resulting implications for SARS-CoV-2 variant-specific immunopathogenesis in the Golden Syrian Hamster (GSH) model using multi-omics approaches. Our investigation revealed increased viremia in diverse tissues of delta-infected GSH compared to the omicron variant. Multi-omics analyses uncovered distinctive metabolic responses between the delta and omicron variants, with the former demonstrating dysregulation in synaptic transmission proteins associated with neurocognitive disorders. Additionally, delta-infected GSH exhibited an altered fecal microbiota composition, marked by increased inflammation-associated taxa and reduced commensal bacteria compared to the omicron variant. These findings underscore the SARS-CoV-2-mediated tissue insult, characterized by modified host metabolites, neurological protein dysregulation, and gut dysbiosis, highlighting the compromised gut-lung-brain axis during acute infection. TeaserIn hamsters at acute infection, SARS-CoV-2 variant-specific metabolic responses and gut dysbiosis dysregulate synaptic transmission proteins.

systems biology↗

bioRxiv2024

Gel-Assisted Proteome Position Integral Shift (GAPPIS) Assay Returns Molecular Weight to Shotgun Proteomics and Identifies Novel Caspase 3 Substrates

Here we present a high-throughput virtual top-down proteomics approach that restores the molecular weight (MW) information in shotgun proteomics, and demonstrate its utility in studying proteolytic events in programmed cell death. With Gel-Assisted Proteome Position Integral Shift (GAPPIS), we quantified over 7000 proteins in staurosporine-induced apoptotic HeLa cells and identified 84 proteins exhibiting in a statistically significant manner at least two of the following features: 1) a negative MW shift; 2) an elevated ratio in a pair of a semi-tryptic and tryptic peptide, 3) a negative shift in the standard deviation of MW estimated for different peptides, and 4) a negative shift in skewness of the same data. Of these proteins, 58 molecules were novel caspase 3 substrates. Further analysis identified the preferred cleavage sites consistent with the known caspase cleavages after the DXXD motif. As a powerful tool for high-throughput MW analysis simultaneously with the conventional expression analysis, GAPPIS assay can prove useful in studying a broad range of biological processes involving proteolytic events.

biochemistry↗

bioRxiv2023

Multifaceted proteome analysis at solubility, redox, and expression dimensions for target identification

Multifaceted interrogation of the proteome deepens the system-wide understanding of biological systems; however, mapping the redox changes in the proteome has so far been significantly more challenging than expression and solubility/stability analyses. Here, we devise the first high- throughput redox proteomics approach integrated with expression analysis (REX) and combine it with Proteome Integral Solubility Alteration (PISA) assay. The whole PISA-REX experiment with up to four biological replicates can be multiplexed into a single tandem mass tag TMTpro set. For benchmarking this compact tool, we analyzed HCT116 cells treated with auranofin, showing great improvement compared with previous such studies. Then we applied PISA-REX to study proteome remodeling upon stimulation of human monocytes by interferon . We also studied the proteome changes in plasmacytoid dendritic cells isolated from wild type vs. Ncf1- mutant mice treated with interferon , showing that NCF1 deficiency enhances the STAT1 pathway and modulates the expression, solubility and redox state of interferon-induced proteins. Providing comprehensive multifaceted information on the proteome, the compact PISA-REX has the potential to become an industry standard in proteomics and to open new windows into the biology of health and disease.

biochemistry↗

bioRxiv2023

Genomic adaptation underlies nutrient-driven reprogramming in the malaria-causing parasite

Parasites often depend on metabolic adaptation to the host environment. An adaptive feature of malaria-causing parasites is digestion of hemoglobin (HB) to acquire amino acids (AAs). Here we describe a link between nutrient availability and translation elongation-dependent regulation of gene expression as an adaptive strategy. We show that, unexpectedly, tRNA expression in P. falciparum does not match the decoding need as tRNAs decoding AAs that are rare in HB are lowly expressed. This discrepancy renders codons of HB-rare AAs inefficiently decoded and transcripts levels negatively correlated with the requirement of HB-rare AAs for protein synthesis, which are consistent with poor codon optimality causing co-translational mRNA decay. Intriguingly, proliferation-related genes have evolved to require a high level of HB-rare AAs in their encoded proteins, thereby allowing the parasite to control its proliferation by repressing protein synthesis of these genes during nutrient stress. We conclude that the parasite modulates translation elongation by maintaining a discordant tRNA profile as a mechanism to exploit variations in AA-composition among genes as an adaptation strategy.

microbiology↗