Biology subjects

Riley, J.

Publications and source records attributed to Riley, J..

13 recordsLinked to original sources

bioRxiv2026

AAV-DJ Enables Targeted Gene Modulation in Human Ovarian Cells

Study question: Can adeno-associated viruses (AAVs) efficiently and safely transduce human primary granulosa cells and human ovarian stromal fibroblasts to modulate the expression of genes involved in follicle recruitment and ovarian microenvironment regulation? Summary answer: AAVs can efficiently transduce human primary granulosa cells and human ovarian stromal cells with low toxicity, with the serotype DJ (AAV-DJ) demonstrating superior performance. AAVs enable targeted modulation of ovarian genes such as AMHR2 in human primary granulosa cells and TGF{beta}1 in human ovarian stromal cells, supporting the feasibility of gene-based approaches to improve ovarian function. What is known already: Infertility affects approximately 15% of couples, with diminished oocyte quality and quantity being major contributors, particularly with advanced reproductive age. Assisted reproductive technologies rely primarily on hormonal stimulation and do not directly target molecular pathways governing folliculogenesis or the ovarian microenvironment. Animal studies suggest that gene therapy using AAVs offers a promising strategy for tissue-specific and durable gene modulation, yet its application in human ovarian cells remains largely unexplored. Study design, size, duration: This was an experimental laboratory study using primary human granulosa cells from patients undergoing in vitro fertilization (IVF) and ovarian stromal cells obtained from post-pubertal patients who donated surplus ovarian tissue from ovarian tissue cryopreservation procedures for research. Sixteen AAV serotypes were evaluated for transduction efficiency, toxicity, and expression dynamics, followed by functional gene knockdown studies using AAV-DJ-based shRNA vectors. Participants/materials, setting, methods: Primary human granulosa cells and ovarian stromal cells were isolated from follicular aspirates and ovarian tissue, respectively. Cells were transduced with GFP-expressing AAV serotypes at varying multiplicities of infection (MOIs), incubation times, and culture days to assess transduction efficiency and cytotoxicity. Lead serotypes were further evaluated in dose-response studies. Functional gene modulation was assessed using AAV-DJ-mediated shRNA knockdown of AMHR2 in granulosa cells and TGF{beta}1 in stromal cells, quantified by RT-qPCR, immunofluorescence, and western blotting. Main results and the role of chance: Six of sixteen AAV serotypes (AAV2, AAV3, AAV6, AAV9, AAV-DJ, and AAV-X1.1) achieved greater than 10% transduction efficiency in human primary granulosa cells. Among these, AAV-DJ demonstrated the highest efficiency across all MOIs tested, reaching up to 48% transduction at 100,000 MOI, significantly outperforming AAV2 and AAV9. Toxicity increased with viral dose for all serotypes but remained comparable across vectors, with AAV-DJ exhibiting higher efficiency with comparable toxicity. The AAV-DJ-shRNA-AMHR2 construct produced a significant reduction in expression of AMHR2 mRNA by ~81% (p<0.05) in human primary granulosa cells as well as at the protein level in HEK293T-AMHR2-ZsGreen engineered cells (~85% knockdown, p<0.01). In human ovarian stromal cells, AAV-DJ preferentially transduced EMILIN1 and ACTA2-positive fibroblast and myofibroblast-like cells and enabled robust knockdown of TGF{beta}1 at both transcript (~89% knockdown, p<0.05) and protein levels (~67% knockdown, p<0.0001) using AAV-DJ-shRNA-TGF{beta}1 construct. Limitations, reasons for caution: These experiments were performed in vitro using primary human ovarian cells, which may not fully recapitulate the in vivo ovarian environment. Functional reproductive outcomes were not assessed, and future studies will be required to evaluate the effects of gene modulation on folliculogenesis and fertility. Wider implications of the findings: These findings establish AAV-DJ as a promising vector for targeted gene modulation in human ovarian cells. This approach introduces a novel framework for addressing infertility and ovarian function by directly targeting molecular pathways involved in follicle recruitment and ovarian stromal signaling, potentially enhancing current assisted reproductive technologies.

developmental biology↗

bioRxiv2026

Multimodal profiling establishes ovarian fibrosis as a measurable and targetable hallmark of human reproductive aging

ABSTRACT Ovarian aging underpins infertility, systemic morbidity, and mortality in women. Stromal fibrosis is implicated in ovarian aging but has not been defined in the human ovary in situ. We integrated shear wave elastography (SWE), extracellular matrix (ECM) neoepitope fingerprinting, and singlecell RNA sequencing of follicular fluid aspirates within the same individual to comprehensively profile ovarian fibrosis. In an age-stratified cohort (<33 and >37 years; N=32), age predicted ovarian stiffness, while mean stiffness was independently associated with reduced oocyte yield and follicular efficiency. ECM profiling revealed a dynamic fibrotic index favoring formation over degradation products. Single-cell transcriptomics demonstrated an age-associated fibroinflammatory stromal program enriched in pro-fibrotic pathways with stromal-immune crosstalk. In a larger validation cohort (25-45 years; N=100), age was similarly associated with ovarian stiffness. Thus, ovarian fibrosis is a quantifiable hallmark of human reproductive aging and represents a robust potential non-invasive biomarker and target for therapeutic intervention.

cell biology↗

bioRxiv2026

A look inside the net: freshwater turtles assort with conspecifics in feeding aggregations

Non-avian reptiles have been assumed to be non-social for many years, yet recent studies show diverse social behaviours in squamates, crocodilians, and turtles. Here, we investigate social structure within feeding aggregations of three freshwater turtle species caught in baited traps in a coastal marsh over 12 years. In 488 instances in which traps contained turtles, 45% contained multiple individuals, and these aggregations were strongly positively assorted by species. midland painted turtles (Chrysemys picta) and Blandings turtles (Emydoidea blandingii) were captured with conspecifics more often than expected in a non-social null model. Snapping turtles (Chelydra serpentina), the largest species in this study, were caught with conspecifics at rates consistent with the non-social null model, and were avoided by heterospecifics. This suggests that species differences play a role in how feeding aggregations are structured, with painted and Blandings turtles driving positive species assortment while avoiding snapping turtles around food sources. We did not detect significant intraspecific sex assortment in any of the three species, nor did turtle body size strongly affect the probability of aggregating with conspecifics at the perceived food source in the traps. Our study illustrates how long-term monitoring data can be used to investigate social structure in wild populations, an approach that may be valuable for species of conservation concern. Significance StatementReptile sociality has been historically overlooked, but recent work has revealed intriguing social behaviours in non-avian reptiles. We investigated associations among three species of freshwater turtle, captured in baited traps over 12 years of trapping. Turtles in these feeding aggregations grouped with their own species more often than expected by chance. This result was driven by the two smaller-bodied species (midland painted turtle and Blandings turtle), which were more likely to be caught with conspecifics than with other species. In contrast, the largest species (snapping turtle) showed no evidence of attraction to other snapping turtles, and midland painted turtles and Blandings turtles showed avoidance of the larger snapping turtles. Our analyses illustrate how long-term monitoring data can be used to uncover previously unrecognized social behaviour in turtles and other species in which behaviour is difficult to observe directly.

animal behavior and cognition↗

bioRxiv2025

Small molecule inhibitors of the NorA multidrug efflux pump potentiate antibiotic activity by binding the outward-open conformation

Antibiotic resistance is among the greatest threats of the modern era. Multidrug efflux pumps expel antibiotics from bacterial cells and present a particular challenge by conferring resistance to a broad range of antibiotic classes; however, there is currently a lack of potent and selective inhibitors. Here, we report the discovery of IMP-2380, a drug-like chemical probe for the multidrug efflux pump NorA that delivers low-nanomolar potentiation of ciprofloxacin activity in vitro and activity in an in vivo S. aureus infection model. A phenotypic high-throughput screen for inhibitors of the ciprofloxacin-activated SOS DNA repair pathway in methicillin-resistant Staphylococcus aureus (MRSA) identified hit compounds targeting NorA, and subsequent optimization established IMP-2380 as the most potent NorA inhibitor discovered to date. The structure of NorA bound to IMP-2380 was solved by cryo-electron microscopy at 2.52 [A] resolution, revealing that the small molecule locks the pump in the outward-open conformation. This closes the inner face and prevents antibiotics binding from the cytosol, providing an explanation for the exceptional potency of IMP-2380 and structure-activity relationship across the series. IMP-2380 represents an in vivo active NorA inhibitor, functioning via a structurally defined outward-open binding mode, and will enable future exploration of NorA as a druggable target to combat antibiotic resistance.

biochemistry↗

bioRxiv2024

Caspase-2 kills cells with extra centrosomes

Centrosomes are membrane-less organelles that orchestrate a wide array of biological functions by acting as microtubule organizing centers. Here, we report that caspase-2-driven apoptosis is elicited in blood cells failing cytokinesis and that extra centrosomes are necessary to trigger this cell death. Activation of caspase-2 depends on the PIDDosome multi-protein complex and priming of PIDD1 at extra centrosomes is necessary for this pathway. Accordingly, loss of its centrosomal adapter, ANKRD26, allows for cell survival and unrestricted polyploidization in response to cytokinesis failure. Mechanistically, cell death is initiated upstream of mitochondria via caspase-2-mediated processing of the BCL2 family protein BID, driving BAX/BAK-dependent mitochondrial outer membrane permeabilization (MOMP). Remarkably, BID-deficient cells enforce apoptosis by engaging p53-dependent pro-apoptotic transcriptional responses initiated by caspase-2. Consistently, BID and MDM2 act as shared caspase-2 substrates, with BID being kinetically favored. Our findings document that the centrosome limits its own unscheduled duplication by the induction of PIDDosome-driven mitochondrial apoptosis to avoid potentially pathogenic polyploidization events.

cell biology↗

bioRxiv2023

Aberrant Wnt activation in recurrent genetically variant human pluripotent stem cells impairs cardiomyocyte differentiation and phenotype

Human pluripotent stem cell (hPSC)-derived cardiomyocytes have emerged as powerful tools for disease modelling and cell therapy. The production of cardiomyocytes from hPSCs typically requires expanding large numbers of hPSCs and maintaining them in culture for extended periods of time. This in turn predisposes hPSCs to the acquisition of non-random genetic changes, including recurrent gains of chromosome 1q. Here, we show that gain of chromosome 1q in hPSCs affects both the efficiency of differentiation to cardiomyocytes and phenotype of the differentiated cells. Mechanistically, we show that aberrant activation of the Wnt signalling pathway underpins the skewed differentiation of variant 1q hPSCs. Collectively, our data demonstrates that the presence of genetically variant cells in cultures is a significant concern for production of hPSC-derived cardiomyocytes for research or clinical applications. Further, our results suggest new approaches for removing genetically variant cells for future clinical applications.

cell biology↗

bioRxiv2023

Mitochondrial outer membrane integrity regulates a ubiquitin-dependent NF-κB inflammatory response

Mitochondria are often essential for apoptosis through mitochondrial outer membrane permeabilization (MOMP). This central event enables cytochrome c release leading to caspase activation and rapid cell death. Recently, MOMP has been shown to be inherently pro-inflammatory, for instance, by enabling mitochondrial DNA-dependent activation of cGAS-STING signalling. Alongside having emerging functions in health and disease, MOMP associated inflammation can also elicit anti-tumour immunity. Nonetheless, how MOMP triggers inflammation and how the cell counteracts this remains poorly defined. We find that upon MOMP, mitochondria are ubiquitylated in a promiscuous manner targeting proteins localised to both inner and outer mitochondrial membranes. Mitochondrial ubiquitylation serves to recruit the essential adaptor molecule, NEMO, leading to activation of pro-inflammatory NF-{kappa}B signalling. We find that disruption of mitochondrial outer membrane integrity through different means leads to engagement of a similar pro-inflammatory signalling platform. Thus, mitochondrial integrity directly controls inflammation, such that permeabilised mitochondria initiate NF-{kappa}B signalling. This event may be important for the various pathophysiological functions of MOMP-associated inflammation.

cell biology↗

bioRxiv2023

In utero pulse injection of isotopic amino acids quantifies protein turnover rates during murine fetal development

Protein translational control is highly regulated step in the gene expression program during mammalian development that is critical for ensuring that the fetus develops correctly and that all of the necessary organs and tissues are formed and functional. Defects in protein expression during fetal development can lead to severe developmental abnormalities or premature death. Currently, quantitative techniques to monitor protein synthesis rates in a developing fetus (in utero) are limited. Here, we developed a novel in utero stable isotope labeling approach to quantify tissue-specific protein dynamics of the nascent proteome during mouse fetal development. Fetuses of pregnant C57BL/6J mice were injected with isotopically labeled lysine (Lys8) and arginine (Arg10) via the vitelline vein at various gestational days. After treatment, fetal organs/tissues including brain, liver, lung, and heart were harvested for sample preparation and proteomic analysis. We show that the mean incorporation rate for injected amino acids into all organs was 17.50 {+/-} 0.6%. By analyzing the nascent proteome, unique signatures of each tissue were identified by hierarchical clustering. In addition, the quantified proteome-wide turnover rates (kobs) were calculated between 3.81E-5 and 0.424 hour-1. We observed similar protein turnover profiles for analyzed organs (e.g., liver versus brain), however, their distributions of turnover rates vary significantly. The translational kinetic profiles of developing organs displayed differentially expressed protein pathways and synthesis rates which correlated with known physiological changes during mouse development.

systems biology↗

bioRxiv2020

Implantation and Gastrulation Abnormalities Characterize Early Embryonic Lethal Mouse Lines

The period of development between the zygote and embryonic day 9.5 in mice includes multiple developmental milestones essential for embryogenesis. The preeminence of this period of development has been illustrated in loss of function studies conducted by the International Mouse Phenotyping Consortium (IMPC) which have shown that close to one third of all mouse genes are essential for survival to weaning age and a significant number of mutations cause embryo lethality before E9.5. Here we report a systematic analysis of 21 pre-E9.5 lethal lines generated by the IMPC. Analysis of pre- and post-implantation embryos revealed that the majority of the lines exhibit mutant phenotypes that fall within a window of development between implantation and gastrulation with few pre-implantation and no post-gastrulation phenotypes. Our study provides multiple genetic inroads into the molecular mechanisms that control early mammalian development and the etiology of human disease, in particular, the genetic bases of infertility and pregnancy loss. We propose a strategy for an efficient assessment of early embryonic lethal mutations that can be used to assign phenotypes to developmental milestones and outline the time of lethality.

developmental biology↗

bioRxiv2020

Tyrosine phosphorylation of ACLY regulates lipid metabolism and oncogenesis in ALK positive Anaplastic Large Cell Lymphoma

A fundamental requirement for growth of rapidly proliferating cells is metabolic adaptation to promote synthesis of biomass1. ATP citrate lyase (ACLY) is a critical enzyme responsible for synthesis of cytosolic acetyl-CoA, the key building component for de novo fatty acid synthesis and links vital pathways such as carbohydrate and lipid metabolism2. The mechanisms of ACLY regulation are not completely understood and the regulation of ACLY function by tyrosine phosphorylation is unknown. Here we show using mass-spectrometry-driven phosphoproteomics and metabolomics that ACLY is phosphorylated and functionally regulated at an evolutionary conserved residue, Y682. Physiologic signals promoting rapid cell growth such as epidermal growth factor stimulation in epithelial cells and T-cell receptor activation in primary human T-cells result in rapid phosphorylation of ACLY at Y682. In vitro kinase assays demonstrate that Y682 is directly phosphorylated by multiple tyrosine kinases, including ALK, ROS1, SRC, JAK2 and LTK. Oncogenically activating structural alterations such as gene-fusions, amplification or point mutations of ALK tyrosine kinase result in constitutive phosphorylation of ACLY in diverse forms of primary human cancer such as lung cancer, anaplastic large cell lymphoma (ALCL) and neuroblastoma. Expression of a phosphorylation-defective ACLY-Y682F mutant in NPM-ALK+ ALCL decreases ACLY activity and attenuates lipid synthesis. Metabolomic analyses reveal that ACLY-Y682F expression results in increased {beta}-oxidation of 13C-oleic acid-labeled fatty acid with increased labeling of +2-citrate (p<0.01) and +18-oleyol carnitine (p<0.001). Similarly, oxygen consumption rate (OCR) is significantly increased in cells expressing ACLY-Y682F (p<0.001). Moreover, expression of ACLY-Y682F dramatically decreases cell proliferation, impairs clonogenicity and abrogates tumor growth in vivo. Our results reveal a novel mechanism for direct ACLY regulation that is subverted by multiple oncogenically-activated tyrosine kinases in diverse human cancers. These findings have significant implications for novel therapies targeting ACLY in cancer and metabolism.

cancer biology↗

bioRxiv2019

A Topological Data Analysis Network Model of Asthma Based on Blood Gene Expression Profiles

Stratified medicine requires discretisation of disease populations for targeted treatments. We have developed and applied a discrete Morse theory clustering algorithm to a Topological Data Analysis (TDA) network model of 498 gene expression profiles of peripheral blood from asthma and healthy participants. The Morse clustering algorithm defined nine clusters, BC1-9, representing molecular phenotypes with discrete phenotypes including Type-1, 2 & 17 cytokine inflammatory pathways. The TDA network model and clusters were also characterised by activity of glucocorticoid receptor signalling associated with different expression profiles of glucocorticoid receptor (GR), according to microarray probesets targeted to the start or end of the GR mRNAs 3 UTR; suggesting differential GR mRNA processing as a possible driver of asthma phenotypes including steroid insensitivity.

molecular biology↗

bioRxiv2018

Activated BAX/BAK enable mitochondrial inner membrane permeabilisation and mtDNA release during cell death

During apoptosis, pro-apoptotic BAX and BAK are activated, causing mitochondrial outer membrane permeabilisation (MOMP), caspase activation and cell death. However, even in the absence of caspase activity, cells usually die following MOMP. Such caspase-independent cell death is accompanied by inflammation that requires mitochondrial DNA (mtDNA) activation of cGAS-STING signaling. Because the mitochondrial inner membrane is thought to remain intact during apoptosis, we sought to address how matrix mtDNA could activate the cytosolic cGAS-STING signaling pathway. Strikingly, using super-resolution imaging, we show that mtDNA is efficiently released from mitochondria following MOMP. In a temporal manner, we find that following MOMP, BAX/BAK-mediated mitochondrial outer membrane pores gradually widen over time. This allows extrusion of the mitochondrial inner membrane into the cytosol whereupon it permeablises allowing mtDNA release. Our data demonstrate that mitochondrial inner membrane permeabilisation can occur during cell death in a BAX/BAK-dependent manner. Importantly, by enabling the cytosolic release of mtDNA, inner membrane permeabilisation underpins the immunogenic effects of caspase-independent cell death.

cell biology↗

bioRxiv2017

Contribution of the β-glucosidase BglC to the Onset of the Pathogenic Lifestyle of Streptomyces scabies

Common scab disease on root and tuber plants is caused by Streptomyces scabies and related species which use the cellulose synthase inhibitor thaxtomin A as main phytotoxin. Thaxtomin production is primarily triggered by the import of cello-oligosaccharides. Once inside the cell, the fate of the cello-oligosaccharides is dichotomized into i) fueling glycolysis with glucose for the saprophytic lifestyle through the action of {beta}-glucosidase(s) (BG), and ii) eliciting the pathogenic lifestyle by inhibiting the CebR-mediated transcriptional repression of thaxtomin biosynthetic genes. Here we investigated the role of scab57721 encoding a putative BG (BglC) in the onset of the pathogenicity of S. scabies. Enzymatic assays showed that BglC was able to release glucose from cellobiose, cellotriose and all other cello-oligosaccharides tested. Its inactivation resulted in a phenotype opposite to what was expected as we monitored reduced production of thaxtomin when the mutant was cultivated on media containing cello-oligosaccharides as unique carbon source. This unexpected phenotype could be attributed to the highly increased activity of alternative intracellular BGs, probably as a compensation of bglC inactivation, which then prevented cellobiose and cellotriose accumulation to reduce the activity of CebR. In contrast, when the bglC null mutant was cultivated on media devoid of cello-oligosaccharides it instead constitutively produced thaxtomin. This observed hypervirulent phenotype does not fit with the proposed model of the cello-oligosaccharide-mediated induction of thaxtomin production and suggests that the role of BglC in the route to the pathogenic lifestyle of S. scabies is more complex than currently presented.

microbiology↗