Biology subjects

Murray, A.

Publications and source records attributed to Murray, A..

At least 19 recordsLinked to original sources

bioRxiv2026

Integration of Neuroimaging and Histopathology in a Squirrel Monkey Model of Spontaneous Cerebral Amyloid Angiopathy and Amyloid-Related Imaging Abnormalities

Cerebral amyloid angiopathy (CAA) is a prevalent cerebrovascular pathology in AD and contributes to amyloid-related imaging abnormalities (ARIA), a major complication of current anti-amyloid immunotherapy. Despite its growing clinical importance, critical gaps remain in the development of reliable biomarkers for antemortem diagnosis of CAA. Squirrel monkeys (SQMs) are a valuable non-human primate model with translational relevance due to their universal propensity to develop abundant CAA and spontaneous ARIA in geriatric animals. The present study employed R2*, the apparent transverse relaxation rate, which is sensitive to susceptibility-related tissue properties, including iron content and blood oxygenation levels, to monitor age-related brain pathology in SQMs with varying CAA severity. Young, early geriatric, and late geriatric SQMs underwent 7T MRI using a dual-purpose T2*-w 3D multi-gradient-echo sequence for high-resolution anatomy and quantitative R2* mapping, alongside T2-w/FLAIR imaging. Whole-brain and gray matter R2* increased with age. In contrast, white matter R2* showed an initial increase followed by a late-life reversal, likely reflecting age-related changes in myelin integrity, tissue microstructure, and tissue water content. MRI-histopathology correlation linked T2*-w MRI hypointensities to CAA-positive iron-laden vessels associated with perivascular inflammation and, in some cases, hemosiderin deposits. Here we confirmed the occurrence of ARIA-H and ARIA-E events in geriatric animals. SQMs provided a valuable opportunity to examine the underlying pathology of spontaneous ARIA-E, revealing distinctive tissue signatures associated with its manifestation. ARIA-E hyperintensities were characterized by reactive gliosis and BBB disruption, whereas more advanced lesions exhibited perivascular lymphocytic infiltration and evidence of myelin and axonal injury. The current study presents compelling evidence linking R2* alterations with CAA severity and ARIA-related tissue injury, providing a foundation for further advancing early detection of CAA, ARIA risk assessment, and treatment strategies.

neuroscience↗

bioRxiv2026

RSV & rhinovirus coinfection order dictates outcome via type III interferon-mediated interference in infant respiratory epithelium

Coinfection with respiratory syncytial virus (RSV) and rhinovirus (RV) is the most frequently detected coinfection in infants, yet mechanisms governing viral interference and disease outcome remain poorly understood. Although infection order is a key determinant of coinfection outcome involving RSV, influenza, rhinovirus, and SARS-CoV-2, its role in RSV/RV coinfections has not been defined. Using infant-derived human nasal organoids at air-liquid interface, we demonstrate that coinfection order fundamentally determines the outcome of RSV/RV interactions. An initial RSV infection almost completely inhibits secondary RV coinfection, whereas primary RV infection only partially impairs a subsequent RSV coinfection. These distinct outcomes are accompanied by divergent temporal antiviral and pro-inflammatory responses. Mechanistically, we identify type III interferons as a sufficient mediator of RSV-induced restriction of RV, establishing a host-driven mechanism of viral interference. In contrast, partial impairment of RSV following RV infection occurs through an interferon-independent mechanism. Despite marked differences, RSV/RV coinfections do not exacerbate epithelial injury or innate immune responses beyond that induced by RSV alone, indicating RSV is the dominant driver of pathology in coinfections. Collectively, our data establishes coinfection order as a critical determinant of RSV/RV outcome and reveals novel and mechanistic insight into critical viral-host interactions in the infant nasal epithelium.

microbiology↗

bioRxiv2026

RSV Infects the Human Nasal Epithelium via the Basolateral Route with Distinct Subgroup Infectivity and Basal Cell Tropism

Respiratory syncytial virus (RSV) causes millions of lower respiratory tract infections (LRTIs) in young children, older adults, and immunocompromised populations every year. RSV infection initiates in the upper respiratory tract and can progress to the lower airways resulting in bronchiolitis, pneumonia, and even death. RSV primarily infects epithelial cells apically, but we hypothesized that basolateral exposure of the respiratory epithelium could provide an alternative mechanism of infection that contributes to LRTI development. Using a human nose organoid-air liquid interface (HNO-ALI) model, we performed apical and basolateral inoculations with contemporaneous RSV strains (RSV/A/ON and RSV/B/BA) representing the two RSV subgroups (A and B) in both adult and infant derived HNO-ALIs. Basolateral RSV exposure resulted in delayed viral replication and apical release compared to apical infection. A statistically significant difference in basolateral infection frequency was observed between RSV/B/BA and RSV/A/ON (81.3% versus 25%). Basolateral infection selectively targeted a rare basal cell population, while preserving epithelial integrity. Using undifferentiated HNO-ALIs, we determined for the first time that Krt23+ activated basal cells (ABCs) are uniquely susceptible to RSV infection, a finding we confirmed in fully differentiated HNO-ALIs. Together, our findings show that RSV can infect the respiratory epithelium from the basolateral side by initially targeting a rare subset of basal cells before spreading apically to ciliated cells. Moreover, RSV/B/BA may have an advantage over RSV/A/ON in utilizing the basolateral infection route. These findings highlight an alternative RSV infection pathway and could be a potential mechanism for RSV spread to the lower airways. ImportanceUnderstanding the pathogenesis of RSV is essential to understanding and preventing acute and long-term sequelae from infection. The canonical understanding of RSV infection is that the virus infects and is restricted to the apical ciliated cells upon inhalation or fomite exposure. We demonstrate that an alternative route of infection - the basolateral route, can be utilized by RSV to infect the apical ciliated cells of the respiratory epithelium. We also show for the first time a novel difference in infectivity between the two contemporaneous RSV strains (RSV/A/ON and RSV/B/BA). In addition, we describe a rare basal subset-the Krt23+ activated basal cells that are uniquely susceptible to RSV thus expanding the known cellular tropism of RSV. Infection of basal cells can impact airway differentiation, homeostasis, and remodeling. Overall, our findings expand on the pathogenesis of RSV and indicate there are alternative mechanisms of infection and cell populations that are susceptible to RSV.

microbiology↗

bioRxiv2026

BRD4 represses developmental and neuronal genes through interactions with polycomb complexes

BRD4 is best known as a transcriptional co-activator, yet heterozygous loss-of-function variants cause craniofacial and neurodevelopmental abnormalities through unclear mechanisms. Using human embryonic stem cells and neural organoids as an in vitro model of human embryonic brain development, we show that BRD4 represses polycomb-regulated developmental and neuronal genes. BRD4 co-occupies bivalent promoters with PRC1.6 and directly interacts with PCGF6 and RING1B through its C-terminal domain. H3K23ac contributes to BRD4 recruitment through BD2, linking acetylated chromatin recognition to polycomb-associated repression. Acute BRD4 depletion alters PRC1.6 occupancy, reduces ubiquitination of H2AK119 and rapidly increases developmental gene transcription. In neural organoids, BRD4 BD2 mutations alter neuronal cell composition and increase expression and chromatin accessibility associated with neuronal transcription-factor programmes. These findings establish BRD4 as a context-dependent chromatin regulator that prevents premature activation of developmental genes and provide mechanistic insight into BRD4-associated neurodevelopmental disorders.

molecular biology↗

bioRxiv2026

Abnormal neuronal and synaptic morphology in Down syndrome brains reproduces in 2D and 3D human cellular models

Down syndrome (DS) is the most common autosomal aneuploidy compatible with postnatal survival and is caused by full or partial trisomy of chromosome 21. In this study, human isogenic induced pluripotent stem cells (iPSCs) were differentiated into 2D neurons and cortico-striatal assembloids (hCSAs). Abnormal neuronal morphology was observed: trisomic (T21) neurons formed aggregates of cell bodies interconnected with thick neurite bundles radiating outwards, connected and overlapped with other neurons in between the bundles while disomic (D21) neurons were evenly distributed across the surface and formed strong neuronal networks. Detailed analysis revealed significantly shorter neurites with larger diameter, fewer branches, and fewer terminal points in T21 neurons compared to D21 neurons in both 2D cultures and hCSAs. We observed similar phenotypes in foetal and postnatal human brain tissue. Furthermore, we observed abnormal mitochondrial morphology with an excess of some mitochondrial proteins (AIF, TOMM20), abnormal synaptic morphology and significantly lower expression of both presynaptic and postsynaptic markers (SYN-1, PSD95 and GEPH) throughout in vitro differentiation of T21 neurons. Finally, our data showed that T21 spheroids were significantly smaller throughout in vitro differentiation compared to D21 spheroids. T21 spheroids also exhibited significantly higher expression of neural stem cells (SOX2), significantly lower expression of proliferating cells (Ki67) and significantly higher expression of apoptotic cells (CCaspase-3). Overall, our study demonstrates that T21 leads to abnormal neuronal morphology in both 2D neurons and hCSAs, consistent with observations in the human brain.

neuroscience↗

bioRxiv2025

Redefining Ovarian Fibrosis Through Comparative Analysis of Collagen Architecture

Short abstractOvarian fibrosis is a known pathology of reproductive aging, becoming a growing concern for infertility and complex ovarian diseases. In research, mouse and human ovary samples are utilized, though distinct differences between species warrant validation of architectural phenotypes to accurately define its pathology. Using polarized light microscopy and orientation analysis of collagen fibers in mouse and human ovaries, we define ovarian fibrosis as the accumulation and/or anisotropic organization of fibrillar collagen within the ovarian stroma and/or cortex.

cell biology↗

bioRxiv2025

BRCA mutation alters the stromal landscape in normal ovaries

For BRCA mutation (BRCA+) carriers, the risk of ovarian cancer can be as high as 59% compared with 1.4% for the general population. While the impact of BRCA mutations on epithelial cell transformation has been extensively studied, we hypothesize that these mutations cause structural changes that prematurely transform the ovary into a rich metastatic niche that supports the early onset of ovarian cancer. Analysis of collagen content and organization in human ovaries revealed increased coherence associated with fibrosis in premenopausal BRCA+ ovaries relative to those without a BRCA mutation. Brca1 deficiency and haploinsufficiency in murine ovarian fibroblasts triggered the expression of hallmarks of senescence, including Cdkn2a (p16) and acidic {beta}-galactosidase activity. Brca1-deficient fibroblasts also acquired an antigen-presenting myofibroblastic phenotype, characterized by expression of MHC-II molecules, -SMA and extracellular matrix components, suggesting the capacity to modulate immune activity and drive structural changes resembling fibrosis. These results provide insight into the mechanisms contributing to accelerated ovarian aging in BRCA+ carriers. TeaserBRCA mutation promotes fibroblast hyperactivity and senescence that changes the stromal architecture of the ovarian niche.

molecular biology↗

bioRxiv2025

Non-autonomous PMK-1/p38 MAPK signaling ensures homeostatic downregulation of germline stem cell proliferation in C. elegans

Stem cell underproliferation leads to tissue loss while over proliferation favors hyperplasia and tumorigenesis. Stem and progenitor proliferation rates are therefore usually coupled to the needs for their differentiated cellular progenies in the tissue(s) they serve. We used the C. elegans hermaphrodite reproductive system to understand how germline stem cell (GSC) proliferation is linked to sperm availability and oocyte usage. We developed a forward genetic screening method to identify genes required for the homeostatic downregulation of GSC proliferation when oocytes are not used, where germline homeostasis defective (ghd) mutants grow benign differentiated germline tumors. We provide evidence that the TIR-1/SARM1 metabolic sensor works together with the NIPI-3/TRIB1 pseudokinase to activate a canonical PMK-1/p38 MAPK signaling cascade in the somatic gonad, shut down the extracellular regulated kinase MPK-1/ERK, and couple GSC proliferation to oocyte needs. Similar multi-tissue signaling modules could underlie homeostatic stem cell regulation and prevent benign tumorigenesis in humans.

cell biology↗

bioRxiv2025

MOAST: Mechanism of Action Similarity Tool

Determining the mechanism of action (MOA) for natural products remains a significant bottleneck in drug discovery, particularly for researchers with limited computational resources or small compound libraries. Traditional approaches require screening large numbers of annotated compounds alongside unknowns, which is cost-prohibitive, or depend on complex machine learning models that need substantial computational resources and large datasets. Here, we present a dissertation chapter excerpt: MOAST (Mechanism of Action Similarity Tool), a BLAST-inspired computational workflow that addresses these limitations by providing rapid MOA hypotheses for newly screened compounds. This chapter investigates two complementary approaches: a kernel density estimation (KDE) method providing statistical significance measures and E-values for MOA class membership, and a CatBoost machine learning classifier for multi-class prediction with ranked outputs. Using cytological profiling data from HeLa and A549 cell lines, MOAST achieved 22% accuracy for the top 5 predictions among [~] 300 MOA classes, with the CatBoost classifier reaching 10% balanced accuracy--significantly better than the [~] 3% reported in literature. The tool suggests a 0.8 prediction probability threshold for trustworthy results and demonstrates robust performance across multiple feature reduction strategies. MOAST provides a practical, accessible solution that bridges traditional phenotypic screening and modern computational approaches, making MOA determination feasible for researchers with limited resources while maintaining statistical rigor and interpretability.

bioinformatics↗

bioRxiv2025

Synaptic and intrinsic membrane defects disrupt early neural network dynamics in Down syndrome

Down syndrome, caused by trisomy 21, affects around six million people worldwide and features learning, memory and language deficits. However, the mechanisms underlying trisomy 21 neurophenotypes involving human cortical circuitry are unknown. By characterising developing neural network dynamics and single cell excitability profiles, with synaptic and voltage-dependent ion channel behaviour, using an isogenic induced pluripotent stem cell- derived neuronal model, we show that trisomy 21 impairs the activity and development of cortical circuitry. This is caused by deficient glutamatergic synaptic connectivity and by aberrant intrinsic membrane properties involving K+ and Na+ channels culminating in spike firing defects that weaken neural network activity and disrupt the synchrony of developing neurons. We also identify transiently activated A-type K+ channels, specifically Kv4.3 channels, as a key orchestrator for Down syndrome during neurodevelopment. Overall, these excitability changes will significantly contribute towards the aberrant neurophenotypes observed later on in life.

neuroscience↗

bioRxiv2024

Potent antitumor activity of a designed interleukin-21 mimic

Long-standing goals of cancer immunotherapy are to activate cytotoxic antitumor T cells across a broad range of affinities while dampening suppressive regulatory T (Treg) cell responses, but current approaches achieve these goals with limited success. Here, we report a de novo IL-21 mimic, 21h10, designed to have augmented stability and high signaling potency in both humans and mice. In multiple animal models and in ex vivo human melanoma patient derived organotypic tumor spheroids (PDOTS), 21h10 showed robust antitumor activity. 21h10 generates significantly prolonged STAT signaling in vivo compared with native IL-21, and has considerably stronger anti-tumor activity. Toxicities associated with systemic administration of 21h10 could be mitigated by TNF blockade without compromising antitumor efficacy. In the tumor microenvironment, 21h10 induced highly cytotoxic antitumor T cells from clonotypes with a range of affinities for endogenous tumor antigens, robustly expanding low-affinity cytotoxic T cells and driving high expression of interferon- (IFN-) and granzyme B compared to native IL-21, while increasing the frequency of IFN-+ Th1 cells and reducing that of Foxp3+ Tregs. As 21h10 has full human/mouse cross-reactivity, high stability and potency, and potentiates low-affinity antitumor responses, it has considerable translational potential.

biochemistry↗

bioRxiv2024

Accurate de novo design of high-affinity protein binding macrocycles using deep learning

The development of macrocyclic binders to therapeutic proteins typically relies on large-scale screening methods that are resource-intensive and provide little control over binding mode. Despite considerable progress in physics-based methods for peptide design and deep-learning methods for protein design, there are currently no robust approaches for de novo design of protein-binding macrocycles. Here, we introduce RFpeptides, a denoising diffusion-based pipeline for designing macrocyclic peptide binders against protein targets of interest. We test 20 or fewer designed macrocycles against each of four diverse proteins and obtain medium to high-affinity binders against all selected targets. Designs against MCL1 and MDM2 demonstrate KD between 1-10 M, and the best anti-GABARAP macrocycle binds with a KD of 6 nM and a sub-nanomolar IC50 in vitro. For one of the targets, RbtA, we obtain a high-affinity binder with KD < 10 nM despite starting from the target sequence alone due to the lack of an experimentally determined target structure. X-ray structures determined for macrocycle-bound MCL1, GABARAP, and RbtA complexes match very closely with the computational design models, with three out of the four structures demonstrating Ca RMSD of less than 1.5 [A] to the design models. In contrast to library screening approaches for which determining binding mode can be a major bottleneck, the binding modes of RFpeptides-generated macrocycles are known by design, which should greatly facilitate downstream optimization. RFpeptides thus provides a powerful framework for rapid and custom design of macrocyclic peptides for diagnostic and therapeutic applications.

biochemistry↗

bioRxiv2024

3D nanoscale architecture of the respiratory epithelium reveals motile cilia-rootlets-mitochondria axis of communication

A major frontier in single cell biology is decoding how transcriptional states result in cellular-level architectural changes, ultimately driving function. A remarkable example of this cellular remodelling program is the differentiation of airway stem cells into the human respiratory multiciliated epithelium, a tissue barrier protecting against bacteria, viruses and particulate matter. Here, we present the first isotropic three-dimensional map of the airway epithelium at the nanometre scale unveiling the coordinated changes in cellular organisation, organelle topology and contacts, occurring during multiciliogenesis. This analysis led us to discover a cellular mechanism of communication whereby motile cilia relay mechanical information to mitochondria through striated cytoskeletal fibres, the rootlets, to promote effective ciliary motility and ATP generation. Altogether, this study integrates nanometre-scale structural, functional and dynamic insights to elucidate fundamental mechanisms responsible for airway defence.

cell biology↗

bioRxiv2024

Sequence-specific targeting of intrinsically disordered protein regions

Intrinsically disordered proteins and peptides play key roles in biology, but the lack of defined structures and the high variability in sequence and conformational preferences has made targeting such systems challenging. We describe a general approach for designing proteins that bind intrinsically disordered protein regions in diverse extended conformations with side chains fitting into complementary binding pockets. We used the approach to design binders for 39 highly diverse unstructured targets and obtain designs with pM to 100 nM affinities in 34 cases, testing [~]22 designs per target (including polar targets). The designs function in cells and as detection reagents, and are specific for their intended targets in all-by-all binding experiments. Our approach is a major step towards a general solution to the intrinsically disordered protein and peptide recognition problem.

biochemistry↗

bioRxiv2024

Diffusing protein binders to intrinsically disordered proteins

Proteins which bind intrinsically disordered proteins (IDPs) and intrinsically disordered regions (IDRs) with high affinity and specificity could have considerable utility for therapeutic and diagnostic applications. However, a general methodology for targeting IDPs/IDRs has yet to be developed. Here, we show that starting only from the target sequence of the input, and freely sampling both target and binding protein conformation, RFdiffusion can generate binders to IDPs and IDRs in a wide range of conformations. We use this approach to generate binders to the IDPs Amylin, C-peptide and VP48 in a range of conformations with Kds in the 3 -100nM range. The Amylin binder inhibits amyloid fibril formation and dissociates existing fibers, and enables enrichment of amylin for mass spectrometry-based detection. For the IDRs G3bp1, common gamma chain (IL2RG) and prion, we diffused binders to beta strand conformations of the targets, obtaining 10 to 100 nM affinity. The IL2RG binder colocalizes with the receptor in cells, enabling new approaches to modulating IL2 signaling. Our approach should be widely useful for creating binders to flexible IDPs/IDRs spanning a wide range of intrinsic conformational preferences.

biochemistry↗

bioRxiv2024

A ribosome-associating chaperone mediates GTP-driven vectorial folding of nascent eEF1A

Eukaryotic translation elongation factor 1A (eEF1A) is a highly abundant, multi-domain GTPase. Post-translational steps essential for eEF1A biogenesis are carried out by bespoke chaperones but co-translational mechanisms tailored to eEF1A folding remain unexplored. Here, we find that the N-terminal, GTP-binding domain of eEF1A is prone to co-translational misfolding and using computational approaches, yeast genetics, and microscopy analysis, we identify the conserved yet uncharacterized yeast protein Ypl225w as a chaperone dedicated to solving this problem. Proteomics and biochemical reconstitution reveal that Ypl225ws interaction with ribosomal eEF1A nascent chains depends on additional binding of Ypl225w to the UBA domain of nascent polypeptide-associated complex (NAC). Lastly, we show by orthogonal chemical genetics that Ypl225w primes eEF1A nascent chains for their subsequent binding to GTP and release from Ypl225w. Our work establishes eEF1A as a model system for chaperone-dependent co-translational folding and unveils a novel mechanism for GTP-driven folding on the ribosome.

biochemistry↗

bioRxiv2023

Whole genome sequencing analysis identifies rare, large-effect non-coding variants and regions associated with circulating protein levels

The role of non-coding rare variation in common phenotypes is largely unknown, due to a lack of whole-genome sequence data, and the difficulty of categorising non-coding variants into biologically meaningful regulatory units. To begin addressing these challenges, we performed a cis association analysis using whole-genome sequence data, consisting of 391 million variants and 1,450 circulating protein levels in [~]20,000 UK Biobank participants. We identified 777 independent rare non-coding single variants associated with circulating protein levels (P<1x10-9), after conditioning on protein-coding and common associated variants. Rare non-coding aggregate testing identified 108 conditionally independent regulatory regions. Unlike protein-coding variation, rare non-coding genetic variation was almost as likely to increase as decrease protein levels. The regions we identified overlapped predicted tissue-specific enhancers more than promoters, suggesting they represent tissue-specific regulatory regions. Our results have important implications for the identification, and role, of rare non-coding variation associated with common human phenotypes.

genetics↗

bioRxiv2023

The autonomic effects of transcutaneous auricular nerve stimulation at different sites on the external auricle of the ear

Transcutaneous auricular nerve stimulation (tANS) applied to specific parts of the external ear has positive health effects in both healthy volunteers and patient groups. However, due to differences between studies in ear stimulation sites and extent of effect on autonomic variables, it is challenging to determine what part of the external ear is the optimum site for electrode placement. This study investigated the autonomic effects of bilateral tANS at four different sites on the external auricle of the ear: tragus, cymba concha, helix and earlobe. tANS was performed using modified surface electrodes connected to a transcutaneous electrical nerve stimulation (TENS) machine. Participants (n = 24) each underwent four sessions where a 15 minute period of stimulation (pulse width: 200 s; pulse frequency: 30 Hz; current: adjusted to sensory threshold) was applied bilaterally to either the tragus, cymba concha, helix or earlobe. Heart rate and blood pressure were continuously recorded during 10-minute baseline, 15-minute stimulation and 10-minute recovery periods. Heart rate variability (HRV) was derived. Results showed that regardless of site, stimulation significantly influenced measures of HRV. Baseline LF/HF ratio predicted change in LF/HF ratio during stimulation for each site and for all sites combined. Response (i.e. change in LF/HF ratio between baseline and stimulation) was closely linked with measures reflecting starting autonomic function. This demonstrates the importance of evaluating how autonomic function is modulated by tANS in individual participants (as well as the whole group). These findings have key implications for adopting a tailored approach when considering the therapeutic/clinical applications of tANS.

neuroscience↗