Biology subjects

Pedersen, L.

Publications and source records attributed to Pedersen, L..

10 recordsLinked to original sources

bioRxiv2026

Injectable Electrospun Hydrogel with Antimicrobial, pH Sensing Nanoparticles for Local Infection Control and Monitoring

Most antimicrobial drug candidates currently in development are derivatives of established antibiotic classes. In contrast, antimicrobial heteroatom-doped carbon quantum dot (COD) nanoparticles vastly differ from their chemical antibiotic counterparts and exhibit potent antibacterial activity and favourable biocompatibility, representing a promising alternative strategy, particularly for topical applications. Here, we report the incorporation of cobalt-doped carbon quantum dots (Co-CODs) into injectable, biocompatible hydrogels capable of both sensing pH and eliminating bacteria. Ultrasmall Co-CODs demonstrated broad-spectrum activity against gram-positive Methicillin-resistant Staphylococcus aureus (MRSA) and Gram-negative Pseudomonas aeruginosa (PAO1), mediated by membrane hyperpolarisation and reactive oxygen species (ROS) induced membrane damage. The particles showed negligible effect on primary fibroblast and endothelial cell viability at concentrations that were bactericidal to MRSA. Polymeric hydrogels were fabricated via electrospinning of chitosan, polyvinylpyrrolidone (PVP), and polyvinyl alcohol (PVA) polymer blends incorporating Co-COD and pH-responsive HPTS particles. This approach provided accurate measurement of environmental pH within the physiological range observed across healthy and chronic wounds. In vivo, the injectable hydrogels exhibited robust antimicrobial efficacy against MRSA without impairing wound closure relative to untreated controls, while also reducing inflammatory immune responses in infected tissues. Collectively, these findings demonstrate the potential of ultrasmall metal-doped CODs for infection control and their integration into 3D matrices as multifunctional theragnostic platforms. ToC (<60 words describe the main results)Ultrasmall antimicrobial carbon nanoparticles were incorporated into polymeric hydrogels containing a pH-responsive probe. This platform enabled detection across a physiologically relevant pH range of 5.0-6.5, spanning conditions associated with both healthy healing and chronically infected wounds. The hydrogel demonstrated strong antibacterial activity by generating damaging reactive oxygen species, and, in mice, effectively controlled infection while reducing pro-inflammatory immune responses. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=171 SRC="FIGDIR/small/736887v1_ufig1.gif" ALT="Figure 1"> View larger version (41K): org.highwire.dtl.DTLVardef@1a52b32org.highwire.dtl.DTLVardef@b6eed2org.highwire.dtl.DTLVardef@1f94143org.highwire.dtl.DTLVardef@12b9ff3_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOScheme 1:C_FLOATNO Antimicrobial nanoparticle-doped hydrogel glows in alkaline wound conditions which are representative of chronic infections. Once in the wound bed, the hydrogel removes all MRSA infection, reducing inflammatory macrophage (iNOS) and neutrophil (MPO) populations, and restores healthy wound collagen deposition. C_FIG

bioengineering↗

bioRxiv2026

BAG6 and RNF126 are broadly involved in protein quality control of non-native missense protein variants

Protein quality control (PQC) degradation is a vigorous and selective system that limits the accumulation of harmful, non-native and aggregation-prone proteins. Specific PQC pathways have been described for misfolded ER proteins, aberrant translational products and mislocalized proteins. However, many components involved in PQC of structurally unstable cytosolic proteins are unknown despite such proteins being a common consequence of pathogenic coding variants. Here, we present results from a genome-wide CRISPR knockout screen to identify components involved in PQC of the Parkin R42P variant. We find that HSP90 and STIP1 stabilize Parkin, while the BAG6 chaperone and E3 ubiquitin ligase RNF126 are critical for PQC degradation. Variant abundance by massively parallel sequencing (VAMP-seq) reveal >1000 Parkin variants, including several variants linked to autosomal recessive juvenile Parkinsonism, are BAG6 targets. Pathogenic missense variants in phenylalanine hydroxylase (PAH) and the tumor suppressor FLCN are also stabilized in BAG6 and RNF126 knockout cells. We propose that BAG6 and RNF126 are broadly involved in PQC and may represent targets for the development of therapeutics for protein misfolding diseases.

biochemistry↗

bioRxiv2024

Acetic acid induces osmotic imbalances in drug-resistant bacteria synergistically enhancing cobalt-doped carbon quantum dots bactericidal efficiency

When pathogenic bacteria colonise a wound, they can create an alkaline ecological niche which selects for their survival by creating an inflammatory environment which restricts healthy wound healing to proceed. To aid healing, wound acidification has been exploited to disrupt this process and stimulate fibroblast growth, increase wound oxygen concentrations, minimise proteolytic activity and re-stimulate the host immune system. Within this study, we have developed unique cobalt doped carbon quantum dot nanoparticles which work together with mild acetic acid creating a potent synergistic antimicrobial therapy. The acidic environment alters the osmotic balance of microorganisms forcing them to swell and speed up the internalisation of the ultra-small particles. The particles hyperpolarise the bacterial membranes and generate damaging peroxidase species resulting in cellular lysis. In mice, cobalt doped carbon quantum dots remove MRSA infection while allowing wounds to heal at equivalent rates to uninfected wounds. This work demonstrates how synergistic antimicrobial treatment strategies can be successfully used to combat antimicrobial resistant infections.

microbiology↗

bioRxiv2023

Deep mutational scanning reveals a tight correlation between protein degradation and toxicity of thousands of non-native aspartoacylase protein variants

When the structural stability of a protein is compromised, the protein may form non-native interactions with other cell proteins and thus becomes a hazard to the cell. To mitigate this danger, destabilized proteins are targeted by the cellular protein quality control (PQC) network, which either corrects the folding defect or targets the protein for degradation. However, the details of how the protein folding and degradation systems collaborate to combat potentially toxic non-native proteins are unknown. To address this issue, we performed systematic studies on destabilized variants of the cytosolic aspartoacylase, ASPA, where loss-of-function variants are linked to Canavans disease, an autosomal recessive and lethal neurological disorder, characterized by the spongy degeneration of the white matter in the brain. Using Variant Abundance by Massively Parallel sequencing (VAMP-seq), we determined the abundance of 6152 out of the 6260 ([~]98%) possible single-site missense and nonsense ASPA variants in cultured human cells. The majority of the low abundance ASPA variants are degraded through the ubiquitin-proteasome system (UPS) and become toxic upon prolonged expression. Variant cellular abundance data correlates with predicted thermodynamic stability, evolutionary conservation, and separates most known disease-linked variants from benign variants. Systematic mapping of degradation signals (degrons) shows that inherent primary degrons in ASPA are located in buried regions, and reveals that the wild-type ASPA C-terminal region functions as a degron. Collectively, our data can be used to interpret Canavans disease variants and also offer mechanistic insight into how ASPA missense variants are targeted by the PQC system. These are essential steps towards future implementation of precision medicine for Canavans disease.

molecular biology↗

bioRxiv2023

Cytomegalovirus promotes proliferation and survival of prostate cancer cells and constitutes a therapeutic target

Metastatic prostate cancer is incurable and new therapeutic targets and drugs are needed. Viruses are associated with several cancer types, but their connection to prostate cancer is unclear. Here we show that human herpes virus cytomegalovirus (CMV) infection is common in the healthy prostate epithelium as well as in prostate cancer, with 85% of tumors being infected to varying degrees. The CMV gene locus UL122-UL123 upheld viral genome persistence in endogenously CMV infected prostate cancer cell lines. CMV promoted prostate cancer cell viability independently of androgen receptor status and anti-androgen resistance, partly through CMV UL97 and the androgen signaling pathway. DNA intercalation mitigated CMV infection and reduced CMV-dependent tumor size in xenotransplantation experiments. The anti-herpes drug aciclovir showed modest effects, but the well tolerated CMV UL97 kinase inhibitor maribavir partly mimicked CMV loss by inducing apoptosis and attenuating proliferation, resulting in reduced tumor growth in vivo. We conclude that CMV infects prostate cells in vivo and alters core prostate cancer cell properties, suggesting that it can be therapeutically targeted to improve prostate cancer outcomes.

cancer biology↗

bioRxiv2022

Angelman syndrome patient neuron screen identifies a potent and selective clinical ASO targeting UBE3A-ATS with long lasting effect in cynomolgus monkey

Angelman syndrome (AS) is a severe neurodevelopmental disorder caused by the loss of neuronal E3 ligase UBE3A with no available treatment. Restoring UBE3A levels via downregulation of the paternally cis-acting long non-coding antisense transcript (UBE3A-ATS) is a potential disease modifying. Developing molecules targeting human UBE3A-ATS is challenging because it is expressed only in neurons and lacks animal species sequence conservation. To overcome this, we performed a library screen of locked-nucleic acid (LNA)-modified antisense oligonucleotides (ASOs) on AS patient-derived neurons, identifying initial sequences. Further optimization led to the identification of the ASO, RO7248824, which selectively and potently reduces UBE3A-ATS, while concomitantly upregulating the UBE3A mRNA and protein. These properties held true in both human AS patient- and neurotypical-, as well as cynomolgus monkey-derived neurons. In vivo use of tool molecules in wild-type (WT) and AS Ube3am-/p+ mice, revealed a steep relationship between UBE3A-ATS knock-down and UBE3A mRNA/protein upregulation, whereby an almost 90% downregulation was needed to achieve a 50% upregulation, respectively. This relationship was confirmed in cynomolgus monkeys. Whereby, repeated lumbar intrathecal administrations of RO7248824 was well tolerated without adverse in-life effects or tissue pathology and produced a robust, long lasting (up to 3 months) paternal reactivation of UBE3A mRNA/protein across key monkey brain regions. Our results demonstrate that AS human pluripotent stem cell neurons serve as an excellent translational tool and furthermore LNA-modified ASOs exhibit excellent drug-like properties. Sustained efficacy translated to infrequent, intrathecal dosing and serves as the basis for the ongoing clinical development of RO7248824 for AS. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=131 SRC="FIGDIR/small/495066v1_ufig1.gif" ALT="Figure 1"> View larger version (24K): org.highwire.dtl.DTLVardef@1c2a97eorg.highwire.dtl.DTLVardef@1059954org.highwire.dtl.DTLVardef@95835aorg.highwire.dtl.DTLVardef@1e2adea_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOGraphical abstract.C_FLOATNO From AS patient blood to a neuronal screen, identifies clinical ASO with excellent in vivo properties. (1) Patients were recruited. (2) Whereby blood was reprogrammed into hIPSC and subsequently differentiated into neurons. (3) ASOs were designed and screened on human neurons to downregulate the UBE3A-ATS likely via directed RNase H Cleavage of Nascent Transcripts. (4a) RO7248824 was identified that potently and selective reduces UBE3A-ATS, concomitantly with upregulating the UBE3A sense transcript and protein which was used for in vitro pk/pd. (4b) In parallel tool murine ASO were used demonstrate in vivo POC.(5) Pivotal nonhuman primate studies to monitor safety and predict the human dose. (6) RO7248824 is in AS clinical trial. C_FIG One Sentence SummaryFrom angelman syndrome human neuron screen to cynomolgus monkey proof of concept identifies the clinical molecule RO7248824

neuroscience↗

bioRxiv2022

Identifying interactions in omics data for clinical biomarker discovery

The identification of predictive biomarker signatures from omics data for clinical applications is an active area of research. Recent developments in assay technologies and machine learning (ML) methods have led to significant improvements in predictive performance. However, most high-performing ML methods suffer from complex architectures and lack interpretability. Here, we present the application of a novel symbolic-regression-based algorithm, the QLattice, on a selection of clinical omics data sets. This approach generates parsimonious high-performing models that can both predict disease outcomes and reveal putative disease mechanisms. Due to their high performance, simplicity and explicit functional form, these biomarker signatures can be readily explained, thereby making them attractive tools for high-stakes applications in primary care, clinical decision making and patient stratification.

bioinformatics↗

bioRxiv2020

High dimensional immunotyping of the obese tumor microenvironment reveals model specific adaptation

Obesity is a disease characterized by chronic low-grade systemic inflammation and has been causally linked to the development of 13 cancer types. Several studies have been undertaken to determine if tumors evolving in obese environments adapt differential interactions with immune cells and if this can be connected to disease outcome. Most of these studies have been limited to single cell lines and tumor models and analysis of limited immune cell populations. Given the multicellular complexity of the immune system and its dysregulation in obesity, we applied high-dimensional suspension mass cytometry to investigate how obesity affects tumor immunity. We used a 36-marker immune-focused mass cytometry panel to interrogate the immune landscape of orthotopic syngeneic mouse models of pancreatic and breast cancer. Unanchored batch correction was implemented to enable simultaneous analysis of tumor cohorts to uncover the immunotypes of each cancer model and reveal remarkably model-specific immune regulation. In the E0771 breast cancer model, we demonstrate an important link to obesity with an increase in two T cell suppressive cell types and a decrease in CD8 T-cells.

cancer biology↗

bioRxiv2020

C/EBPB-dependent Adaptation to Palmitic Acid Promotes Stemness in Hormone Receptor Negative Breast Cancer

Epidemiological studies have established a positive association between obesity and the incidence of postmenopausal breast cancer. Moreover, it is known that obesity promotes stem cell-like properties of breast cancer cells. However, the cancer cell-autonomous mechanisms underlying this correlation are not well defined. Here we demonstrate that obesity-associated tumor formation is driven by cellular adaptation rather than expansion of pre-existing clones within the cancer cell population. While there is no correlation with specific mutations, cellular adaptation to obesity is governed by palmitic acid (PA) and leads to enhanced tumor formation capacity of breast cancer cells. This process is governed epigenetically through increased chromatin occupancy of the transcription factor CCAAT/enhancer-binding protein beta (C/EBPB). Obesity-induced epigenetic activation of C/EBPB regulates cancer stem-like properties by modulating the expression of key downstream regulators including CLDN1 and LCN2. Collectively, our findings demonstrate that obesity drives cellular adaptation to PA drives tumor initiation in the obese setting through activation of a C/EBPB dependent transcriptional network. SignificanceCellular adaptation to obesity-induced palmitic acid drives tumor initiation through activation of a C/EBPB-dependent transcriptional network. This highlights a cell-autonomous mechanistic connection between obesity and postmenopausal hormone receptor negative breast cancer.

cancer biology↗

bioRxiv2019

Golgi-localized PAQR4 mediates Anti-apoptotic Ceramidase Activity in Breast Cancer

The metabolic network of sphingolipids plays important roles in cancer biology. Prominent sphingolipids include ceramides and sphingosine-1-phosphate that regulate multiple aspects of growth, apoptosis and cellular signaling. Although many significant enzymatic regulators of the sphingolipid pathway have been described in detail, the list is currently incomplete. Here, we applied a systemic approach to identify and molecularly define progestin and adipoQ receptor family member IV (PAQR4) as a Golgi-localized ceramidase. We find PAQR4 to be [~]5 fold upregulated in breast cancer compared to matched control tissue and that its overexpression correlate with disease-specific survival rates in breast cancer. PAQR4 is a seven transmembrane protein, and depletion of PAQR4 leads to cellular apoptosis through accumulation of ceramides. Our findings establish PAQR4 as Golgi-localized ceramidase required for cellular growth in breast cancer.

cancer biology↗