Biology subjects

Jacobsen, S.

Publications and source records attributed to Jacobsen, S..

11 recordsLinked to original sources

bioRxiv2026

Noradrenergic infraslow rhythm during sleep is the critical link between heart-rate dynamics and memory consolidation

Recent work shows that the brains arousal system remains active during sleep, with rhythmic locus coeruleus (LC) activity shaping sleep architecture and supporting memory consolidation. The LC releases norepinephrine (NE) in infraslow ([~]0.02 Hz) bouts that gate NREM sleep spindles. Here, we demonstrate that heart rate (HR) fluctuations during NREM are tightly phase-locked to these NE rhythms, identifying the LC as a key driver of very-low-frequency HR variability (VLF-HRV), an understudied autonomic signal. Using optogenetics, transient LC inhibition blunts HR slowing, whereas LC activation produces rapid HR acceleration, directly linking LC output to cardiac control during sleep. We further show that infraslow HR variability is a cross-species marker of spindle-dependent memory processing. In mice, the amplitude of HR decelerations during NREM correlate with spindle activity and subsequent memory performance. Remarkably, human sleepers show the same pattern: stronger VLF-HR fluctuations during NREM correspond to increased spindle expression and better overnight memory retention. These findings reveal a mechanistic pathway through which LC activity modulates autonomic physiology during sleep and identify infraslow HR variability as a non-invasive marker of brainstem function and memory-promoting sleep. Because LC degeneration occurs early in neurodegenerative disease, sleep-derived HR metrics may provide a scalable indicator of emerging neuromodulatory dysfunction.

neuroscience↗

bioRxiv2023

Eukaryotic RNA-guided endonucleases evolved from a unique clade of bacterial enzymes

RNA-guided endonucleases form the crux of diverse biological processes and technologies, including adaptive immunity, transposition, and genome editing. Some of these enzymes are components of insertion sequences (IS) in the IS200/IS605 and IS607 transposon families. Both IS families encode a TnpA transposase and TnpB nuclease, an RNA-guided enzyme ancestral to CRISPR-Cas12. In eukaryotes and their viruses, TnpB homologs occur as two distinct types, Fanzor1 and Fanzor2. We analyzed the evolutionary relationships between prokaryotic TnpBs and eukaryotic Fanzors, revealing that a clade of IS607 TnpBs with unusual active site arrangement found primarily in Cyanobacteriota likely gave rise to both types of Fanzors. The wide-spread nature of Fanzors imply that the properties of this particular group of IS607 TnpBs were particularly suited to adaptation and evolution in eukaryotes and their viruses. Experimental characterization of a prokaryotic IS607 TnpB and virally encoded Fanzor1s uncovered features that may have fostered coevolution between TnpBs/Fanzors and their cognate transposases. Our results provide insight into the evolutionary origins of a ubiquitous family of RNA-guided proteins that shows remarkable conservation across domains of life.

molecular biology↗

bioRxiv2023

Multi-omic temporal landscape of plasma and synovial fluid-derived extracellular vesicles using an experimental model of equine osteoarthritis

Extracellular vesicles contribute to osteoarthritis pathogenesis through their release into joint tissues and synovial fluid. Limited studies have profiled extracellular vesicles in osteoarthritic biofluids, such as plasma and synovial fluid. Due to the potential involvement in osteoarthritis pathogenesis, synovial fluid-derived extracellular vesicles have the potential to be direct biomarkers in the causal pathway of disease but also enable understanding of their role in disease progression. Utilizing a temporal model of early osteoarthritis, we defined the changes in matched synovial fluid and plasma-derived extracellular vesicle small non-coding RNA and protein cargo using small RNA sequencing and mass spectrometry proteomics. We explored the data with a multi-omic approach including time series clustering, factor analysis and gene enrichment interrogation. Chondrocyte signalling induced by temporal synovial fluid-derived extracellular vesicles derived from the model were analysed using luciferase-based transcription factor activity assays. Extracellular vesicle protein cargo appears to be more important during osteoarthritis progression than small non-coding RNA cargo. Cluster analysis revealed plasma-extracellular vesicles represented a time-dependant response to osteoarthritis induction, were principally derived from protein cargo and were associated with supramolecular complexes. Clusters for synovial fluid-derived extracellular vesicles were associated with an initial osteoarthritis response and represented immune/inflammatory pathways. Factor analysis revealed that plasma-derived extracellular vesicles correlated with day post induction and were primarily composed of proteins which may modulate lipid metabolism in osteoarthritis. Synovial fluid-derived extracellular vesicles significant factors represented intermediate filament and supramolecular complexes reflecting tissue repair responses to osteoarthritis induction. There was a significant interaction between time and osteoarthritis for cAMP response element, Nuclear factor-kappa B response element, serum response element and serum response factor response element reporters with a trend for osteoarthritis synovial fluid-derived EVs at later time points to have a more pronounced effect. Local and systemic osteoarthritis-associated changes in extracellular vesicle cargo profiles in this in vivo model provided a unique opportunity to understand their role in disease propagation and progression and may represent novel biomarkers to stage osteoarthritis.

molecular biology↗

bioRxiv2023

Protein Assembly Modulation: A New Approach to ALS Therapeutics

Amyotrophic Lateral Sclerosis (ALS) is a neurodegenerative disease with a complex, multifactorial pathophysiology, most commonly manifest as loss of motor neurons. We introduce a new mechanism of ALS pathogenesis via a novel drug-like small molecule series that targets protein disulfide isomerase (PDI) within a previously unappreciated transient and energy-dependent multi-protein complex. This novel drug was found to have activity in cellular models for both familial and sporadic ALS, as well as in transgenic worms, flies, and mice bearing a diversity of human genes with ALS-associated mutations. These compounds were initially identified as modulators of human immunodeficiency virus (HIV) capsid assembly in cell-free protein synthesis and assembly (CFPSA) systems, with demonstrated antiviral activity in cell culture. Their advancement as ALS-therapeutics, and the subsequent separation of activity against HIV and ALS in chemical subseries through structure-activity-relationship optimization, may provide insights into the molecular mechanisms governing pathophysiology of disordered homeostasis relevant to ALS.

neuroscience↗

bioRxiv2022

Temporal Extracellular Vesicle Protein Changes following Intraarticular Treatment with Integrin α10β1-selected Mesenchymal Stem Cells in Equine Osteoarthritis

Equine osteoarthritis is a heterogeneous, degenerative disease of the musculoskeletal system with multifactorial causation, characterised by a joint metabolic imbalance. Extracellular vesicles are nanoparticles involved in intracellular communication. Mesenchymal stem cell (MSC) therapy is a form of regenerative medicine that utilises their properties to repair damaged tissues. Despite its wide use in veterinary practice, the exact mechanism of action of MSCs is not fully understood. The aim of this study was to determine the synovial fluid extracellular vesicle protein cargo following integrin 10{beta}1-selected mesenchymal stem cell treatment in an experimental model of equine osteoarthritis with longitudinal sampling. Adipose tissue derived, integrin 10-MSCs were injected into the osteoarthritis afflicted joint after 18 days post surgery. Sixty-nine synovial fluid samples were collected via aseptic arthrocentesis at day 0, 18, 21, 28, 35, and 70. Synovial fluid was hyaluronidase treated and extracellular vesicles isolated using differential ultracentrifugation. Extracellular vesicles were characterised using the Exoview human tetraspanin chip. Extracellular vesicle concentration, surface marker identification, fluorescent microscopy and tetraspanin colocalization analysis was undertaken, in conjunction with nanoparticle tracking analysis. For proteomics, extracellular vesicle pellets were suspended in urea lysis buffer. Samples were reduced, alkylated and digested on SP3 beads with trypsin/LysC. A data independent acquisition mode was utilised for nano liquid chromatography tandem mass spectrometry analysis on a Triple TOF 6600 mass spectrometer. A total of 442 proteins were identified across all samples, with 48 proteins differentially expressed (FDR[≤] 0.05) between control and osteoarthritis treated with MSCs.. The most significant pathways following functional enrichment analysis of the differentially abundant protein dataset were serine endopeptidase activity (p=0.023), complement activation (classical pathway) (p=0.023), and collagen containing extracellular matrix (p=0.034). To date this is the first study to quantify the global extracellular vesicle proteome in synovial fluid following MSC treatment of osteoarthritis. Changes in the proteome of the synovial fluid-derived EVs following MSC injection suggest EVs may play a role in mediating the effect of cell therapy through altered joint homeostasis and an improved phenotype.

molecular biology↗

bioRxiv2022

Small non-coding RNA landscape of extracellular vesicles from a post-traumatic model of equine osteoarthritis

Extracellular vesicles comprise an as yet inadequately investigated intercellular communication pathway in the field of early osteoarthritis. We hypothesised that small non-coding RNA expression pattern in synovial fluid and plasma would change during progression of experimental osteoarthritis. In this study, we used small RNA sequencing to provide a comprehensive overview of the temporal expression profiles of small non-coding transcripts carried by EVs derived from plasma and synovial fluid for the first time in a post-traumatic model of equine osteoarthritis. Additionally, we characterised synovial fluid and plasma-derived extracellular vesicles with respect to quantity, size, and surface markers. The differential expression of seven microRNAs in plasma and synovial fluid-derived extracellular vesicles; miR-451, miR-25, miR-215, miR-92a, miR-let-7c, miR-486-5p, miR-23a and four snoRNAs; U3, snord15, snord46, snord58 represent potential biomarkers for early OA. Bioinformatics analysis of the differentially expressed microRNAs in synovial fluid highlighted that in early OA these related to the inhibition of cell cycle, cell cycle progression, DNA damage and cell proliferation but increased cell viability, and differentiation of stem cells. Plasma and synovial fluid-derived extracellular vesicle small non-coding signatures have been established for the first time in a temporal model of osteoarthritis. These could serve as novel biomarkers for the evaluation of osteoarthritis progression or act as potential therapeutic targets.

molecular biology↗

bioRxiv2021

The mRNA-LNP platform's lipid nanoparticle component used in preclinical vaccine studies is highly inflammatory

Vaccines based on mRNA-containing lipid nanoparticles (LNPs) are a promising new platform used by two leading vaccines against coronavirus disease in 2019 (COVID-19). Clinical trials and ongoing vaccinations present with very high protection levels and varying degrees of side effects. However, the nature of the reported side effects remains poorly defined. Here we present evidence that LNPs used in many preclinical studies are highly inflammatory in mice. Intradermal injection of these LNPs led to rapid and robust inflammatory responses, characterized by massive neutrophil infiltration, activation of diverse inflammatory pathways, and production of various inflammatory cytokines and chemokines. The same dose of LNP delivered intranasally led to similar inflammatory responses in the lung and resulted in a high mortality rate. In summary, here we show that the LNPs used for many preclinical studies are highly inflammatory. Thus, their potent adjuvant activity and reported superiority comparing to other adjuvants in supporting the induction of adaptive immune responses likely stem from their inflammatory nature. Furthermore, the preclinical LNPs are similar to the ones used for human vaccines, which could also explain the observed side effects in humans using this platform.

immunology↗

bioRxiv2020

A paired liver biopsy and plasma proteomics study reveals circulating biomarkers for alcohol-related liver disease

Existing tests for detecting liver fibrosis, inflammation and steatosis, three stages of liver disease that are still reversible are severely hampered by limited accuracy or invasive nature. Here, we present a paired liver-plasma proteomics approach to infer molecular pathophysiology and to identify biomarkers in a cross-sectional alcohol-related liver disease cohort of nearly 600 individuals. Metabolic functions were downregulated whereas fibrosis-associated signaling and novel immune responses were upregulated, but only half of tissue proteome changes were transmitted to the circulation. Machine learning models based on our biomarker panels outperformed existing tests, laying the foundation for a generic proteomic liver health assessment.

biochemistry↗

bioRxiv2019

Describing the fecal metabolome in cryogenically collected samples from healthy participants.

IntroductionThe chemical composition of feces plays an important role in human metabolism. Metabolomics and lipidomics are valuable tools for screening the metabolite composition in feces. Here we set out to describe fecal metabolite composition in healthy participants in frozen stools.\n\nMethodsFrozen stool samples were collected from 10 healthy volunteers and cryogenically drilled in four areas along the specimen. Polar metabolites were analyzed using derivatization followed by two-dimensional gas chromatography and time of flight mass spectrometry. Lipids were detected using ultra high-performance liquid chromatography coupled with quadruple time-of-flight mass spectrometry. The technical variation threshold was set to 30% in pooled quality control samples and metabolite variation was then assessed in four areas per specimen. A data-generated network using metabolites found in all areas was computed for healthy participants.\n\nResults2326 metabolic features were detected. Out of a total of 298 metabolites that were annotated we report here 185 that showed a technical variation of x< 30%. These metabolites included amino acids, fatty acid derivatives, carboxylic acids and phenolic compounds. Lipids predominantly belonged to the groups of diacylglycerols, triacylglycerols and ceramides. Metabolites varied between sampling areas (14%-80%). A network using metabolites present in all areas showed two main clusters, DAG lipids and phenyllactic acid.\n\nConclusionsIn feces from healthy participants, the main groups detected were phenolic compounds, ceramides, diacylglycerols and triacylglycerols. Metabolite levels differed considerably depending on the sampling area.\n\n\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=52 SRC=\"FIGDIR/small/708685v1_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (16K):\norg.highwire.dtl.DTLVardef@17db665org.highwire.dtl.DTLVardef@51e140org.highwire.dtl.DTLVardef@19b55d7org.highwire.dtl.DTLVardef@120d399_HPS_FORMAT_FIGEXP M_FIG C_FIG

systems biology↗

bioRxiv2018

Inactive USP14 and inactive UCHL5 cause accumulation of distinct ubiquitinated proteins in mammalian cells

USP14 is a cysteine-protease deubiquitinase associated with the proteasome and plays important catalytic and allosteric roles in proteasomal degradation. USP14 inhibition has been considered a therapeutic strategy for accelerating degradation of aggregation-prone proteins in neurodegenerative diseases and for inhibiting proteasome function to induce apoptotic cell death in cancers. Here we studied the effects of USP14 inhibition in mammalian cells using small molecule inhibitors and an inactive USP14 mutant C114A. Neither the inhibitors nor USP14 C114A changed the level of TDP-43, tau or -synuclein in HEK293T cells. However, USP14 C114A led to an accumulation of ubiquitinated proteins, which were isolated by ubiquitin immunoprecipitation and identified by mass spectrometry. Among these proteins we confirmed that ubiquitinated {beta}-catenin was accumulated in the cells expressing USP14 C114A with biochemistry and molecular biology experiments. The proteasome binding of USP14 C114A is required for its effect on ubiquitinated proteins. UCHL5 is the other cysteine-protease deubiquitinase associated with the proteasome. Interestingly, the inactive mutant of UCHL5 C88A also caused an accumulation of ubiquitinated proteins in HEK293T cells but did not affect {beta}-catenin. Using ubiquitin immunoprecipitation and mass spectrometry, we identified the accumulated ubiquitinated proteins in UCHL5 C88A expressing cells which are mostly distinct from those accumulated in USP14 C114A expressing cells. Among the identified proteins are well established proteasome substrates and proteasome subunits. Together our data suggest that USP14 and UCHL5 can deubiquitinate distinct substrates at the proteasome and regulate the ubiquitination of the proteasome itself which is tightly linked to its function.

molecular biology↗

bioRxiv2017

Epigenome-wide association in adipose tissue from the METSIM cohort identifies novel loci and the involvement of adipocytes and macrophages in diabetes traits

Most epigenome-wide association studies to date have been conducted in blood. However, metabolic syndrome is mediated by a dysregulation of adiposity and therefore it is critical to study adipose tissue in order to understand the effects of this syndrome on epigenomes. To determine if natural variation in DNA methylation was associated with metabolic syndrome traits, we profiled global methylation levels in subcutaneous abdominal adipose tissue. We measured association between 32 clinical traits related to diabetes and obesity in 201 people from the Metabolic Syndrome In Men cohort. We performed epigenome-wide association studies between DNA methylation levels and traits, and identified associations for 13 clinical traits in 21 loci. We prioritized candidate genes in these loci using eQTL, and identified 18 high confidence candidate genes, including known and novel genes associated with diabetes and obesity traits. Using methylation deconvolution, we examined which cell types may be mediating the associations, and concluded that most of the loci we identified were specific to adipocytes. We determined whether the abundance of cell types varies with metabolic traits, and found that macrophages increased in abundance with the severity of metabolic syndrome traits. Finally, we developed a DNA methylation based biomarker to assess type II diabetes risk in adipose tissue. In conclusion, our results demonstrate that profiling DNA methylation in adipose tissue is a powerful tool for understanding the molecular effects of metabolic syndrome on adipose tissue, and can be used in conjunction with traditional genetic analyses to further characterize this disorder.

genetics↗