Biology subjects

Hall, C.

Publications and source records attributed to Hall, C..

At least 19 recordsLinked to original sources

bioRxiv2026

Stoichiometric m6A regulation of YY1 orchestrates the metabolic switch during cardiac development

Chemical modifications of RNA provide an additional regulatory layer essential for development. N6A methyladenosine (m6A) is the most abundant internal mRNA mark, but how site specificity, stoichiometry, and cellular context together determine mRNA fate remains unclear. Here, we define these rules in cardiogenesis by combining single-molecule nanopore direct RNA sequencing (DRS) with a CRISPRdCas13 epitranscriptomic editing platform in human induced pluripotent stem cells and a conditional Mettl14 cardiac knockout in mice, integrated with multiomics, to map m6A sites and quantify stoichiometry. We uncover a bimodal m6A code in which low versus high modification ratios are associated with opposite mRNA and protein outcomes. We further show that Mettl14 loss causes developmental cardiomyopathy and embryonic lethality by disrupting the glycolysis to oxidative phosphorylation (OXPHOS) metabolic switch, and identify an m6A YY1 (Yin Yang 1) axis that post transcriptionally controls OXPHOS genes. Finally, targeted installation of m6A at defined sites using CRISPR/dCas13 reveals that m6A effects on YY1 are strongly locus and context dependent. Together, these findings establish m6A as a site and stoichiometry dependent regulatory code interpreted by cellular context to direct cardiac metabolic maturation. These principles are likely to extend to other developmental and physiological contexts in which precise control of metabolic state and gene dosage is required.

developmental biology↗

bioRxiv2026

Nerve injury triggers nociceptive hypersensitivity with interhemispheric divergence in haplodeficient GAD67-GFP mice

Nerve injury causes an imbalance of glutamatergic excitation over GABAergic inhibition, contributing thereby to lasting neuropathic pain. Transgenic GAD67-GFP knock-in reporter mice were developed to visualize GABAergic interneurons. The knock-in into glutamate decarboxylase (GAD67) causes haploinsufficiency that manifest in low GABA levels. In this model, we studied if diminished GABA exacerbates neuropathic pain after nerve injury. Adolescent male and female GAD67-GFP knock-in mice were subjected to Spared Sciatic Nerve Injury (SNI). At baseline, nociception and thermal preferences were equal but after SNI, GAD67-GFP mice developed thermal allodynia which was not detected in wildtype littermates. At the electrophysiology level, SNI caused a partial decrease in the excitability in layer 2/3 pyramidal neurons in the projection-hemisphere in wildtype mice. This effect was exacerbated in GAD67-GFP, affecting both sides, and was accompanied with imbalance of field-potential (FP) amplitudes between projection and non-projection hemisphere, which did not occur in wildtype mice. The results suggest that GABA deficiency can be compensated to protect from hyperexcitability at baseline, but it cannot be further upscaled, ultimately leading to network hyperactivity after injury. Metabolomic studies confirmed the moderate loss of GABA in ipsi- and contralateral cortex and lumbar spinal cord of GAD67-GFP mice and failure to raise GABA in the ipsilateral dorsal horn after injury. Carnosine, cystathionine, and glutathione, three important anti-oxidative metabolites, were co-reduced with GABA suggesting that GABAergic activity and anti-oxidative capacity are interconnected and failure of this axis contributes to neuropathic "pain".

neuroscience↗

bioRxiv2026

PPM1B utilizes a trinuclear metal architecture for phosphatase activity

The metal-dependent protein phosphatase (PPM/PP2C) family regulates innate immune and cell death pathways through reversible phosphorylation. Although these enzymes contain a conserved third Mg2+/Mn2+ ion (M3) that is essential for activity, its chemical role in phosphate hydrolysis has remained unclear. Here, we report studies that reveal PPM1B promotes cell death during Pseudomonas aeruginosa infection and utilizes a trinuclear metal center in which M3 directly coordinates the substrate phosphate, positioning it for in-line SN2 hydrolysis. In addition to substrate orientation, M3 positions a water molecule to protonate the departing alkoxide, stabilizing the leaving-group. Functionally, M3 substitutes for the arginine clamp in phosphoprotein phosphatases (PPP), revealing that these evolutionarily distinct phosphatase families have converged on the same chemical strategy through fundamentally different catalytic architectures. Together, these findings define a three-metal mechanism in PPM phosphatases and identify the M3 site as a rare and potentially druggable feature for immune and infectious diseases.

biochemistry↗

bioRxiv2026

Altered stem cell properties of human hematopoietic stem and progenitor cells based on bone region location

The bone marrow microenvironment forms a highly specialized niche that houses hematopoietic stem and progenitor cells (HSPCs). Within bone, two anatomically distinct regions, the medullary cavity and the trabecular compartment, differ in their cellular and physical composition, with the potential to differentially regulate influence on resident HSPCs. We hypothesized that HSPCs enriched from the medullary cavity (BM) and trabeculae (TB) represent functionally distinct populations. Contrary to this, functional assessment of HSPCs revealed comparable cellular outputs between BM- and TB-derived HSPCs. To investigate whether microenvironmental signaling contributes to functional regulation, we examined the effects of extracellular vesicles (EVs) isolated from medullary BM and TB. Notably, TB-derived EVs inhibited cell cycle progression, directing HSPCs toward a quiescent state. Together, these findings demonstrate that while isolated BM- and TB-derived HSPCs exhibit similar cell-intrinsic properties, EVs enriched from the TB specifically promote HSPC quiescence, supporting a protective regulatory role for the trabecular microenvironment.

cell biology↗

bioRxiv2025

Disruption of the Wnt-antagonist Apc in the pituitary stem cells drives the development of adamantinomatous craniopharyngioma.

Adamantinomatous craniopharyngiomas (aCPs) are complex intracranial neoplasms that generally arise in the sellar and suprasellar region of the brain which affect the endocrine and nervous systems causing severe sequelae. Activating mutations resulting in degradation-resistant forms of {beta}-catenin (CTNNB1) have been shown to be the main driver for many of these neoplasms. However, the underlying genetic driver for a proportion of these tumours is still unknown. Using murine transgenic models, we show that genetic disruption of the Wnt-antagonist and tumour suppressor, adenomatous polyposis coli (Apc), within the pituitary progenitors/stem cells, leads to pituitary tumours that closely resemble human aCPs. These tumours present classic histopathological hallmarks of aCPs, such as large deposits of wet keratin, stellar-reticular-like cells, large cystic components and clusters of accumulating nucleo-cytoplasmic {beta}-catenin that are slow-dividing and exhibit a secretory phenotype. We show that a hypomorphic allele of Apc is sufficient for tumour development, indicating that disruption of Apc function can lead to aCP formation. Moreover, we identify that bi-allelic loss of Apc in the Sox2+ve pituitary stem cells is sufficient to initiate tumour formation, indicating that Sox2+ve stem cells are the cell origin of these Apc-driven aCPs. Transcriptomic analyses of early tumour-initiating cells revealed that Apc-driven clusters of accumulating {beta}-catenin undergo senescence-associated secretory phenotype (SASP), which is p21-mediated and results in secretion of inflammasome, angiosome and developmental growth factors. Our data unequivocally show a causal role for the disruption of the tumour suppressor Apc as a primary driver of aCPs independent of mutations in {beta}-catenin. We provide murine models representing a novel genetic subtype of human aCPs offering insights into aCP pathogenesis. Our work reinforces the importance of genetic testing for mutations in APC in patients with aCPs and identifies a potential need to screen patients with familial adenomatous polyposis (FAP) or spectrum of APC-pathogenic syndromes for aCPs in early life.

cancer biology↗

bioRxiv2025

Chaperone AIP Couples mTORC1 Activation and Catabolic Metabolism During Neonatal Development

To grow and divide cells must tightly coordinate anabolic programs with the availability of nutrients and growth factors. This balance is especially critical during postnatal development, when biosynthetic and energetic demands are high, and nutrient supply and neonates have to adapt to periods of fasting. These conditions place acute stress on the proteostasis network, making autophagy essential for nutrient recycling. We found that the chaperone aryl hydrocarbon receptor-interacting protein (AIP) supports both arms of this metabolic balance: promoting anabolic PI3K-AKT signaling for mTORC1 activation and enabling catabolic processes such as proteasomal degradation and autophagy. Loss of AIP causes a severe neonatal metabolic disorder, where affected infants fail to thrive postnatally. Our findings establish AIP as a central regulator of neonatal metabolic adaptation and cellular homeostasis. One Sentence SummaryAIP integrates nutrient sensing and protein recycling to sustain neonatal survival.

developmental biology↗

bioRxiv2025

Chronic intestinal immune activation reveals separable impacts of inflammation and barrier loss on hallmarks of ageing.

Inflammaging is considered a driver of age-associated pathology across tissues. Similarly, intestinal permeability is a feature of ageing and underlies a range of inflammatory and age-related diseases. Increased intestinal permeability has been described as both a cause and a consequence of inflammation. Both intestinal permeability and inflammation are closely associated with microbial dysbiosis, epithelial dysplasia and mortality but dissecting the complex interplay between these phenotypes remains challenging. Here we genetically induce intestinal immune activation in Drosophila and stratify animals by their intestinal barrier status using the Smurf assay. We demonstrate that intestinal immune activation and barrier failure have distinct impacts on the microbiota. Further, intestinal immune activation drives intestinal barrier failure and mortality even in the absence of the microbiota. Importantly, immune-induced intestinal barrier failure takes time to develop and is closely associated with the onset of mortality. Our work adds to building evidence that the impact of intestinal permeability on the microbiota and on animal health needs to be considered independently of its relationship with inflammation.

physiology↗

bioRxiv2025

Enriching for Extracellular Vesicles from Human Bone

Extracellular vesicles (EVs) are nano-sized membrane-bound structures thought to be secreted by all cells and increasingly recognized as key mediators of intercellular communication. Established EV isolation protocols for bodily fluids-primarily focus on blood with limited insights into methods optimized for EVs from other hematopoietic regions. In this study, we present a novel protocol for the isolation and enrichment of EVs from human trabecular bone and bone marrow. This method employs a two-step purification strategy, combining iodixanol density cushion (IDC) ultracentrifugation with size exclusion chromatography (SEC), and enables EV recovery from fresh tissue hours after collection. Importantly, this approach facilitates the enrichment of bone-derived EVs without the need for enzymatic digestion or long-term culture, preserving native EV populations. This protocol offers a valuable tool for researchers investigating EVs derived from the diverse cellular constituents of the bone microenvironment.

cell biology↗

bioRxiv2025

The kinase domain of RIPK3 tunes its scaffolding functions

The pro-inflammatory programmed cell death pathway, necroptosis, relies on phosphorylation of the terminal effector, MLKL, by RIPK3. RIPK3-deficient mice or those harboring the kinase-inactivating mutation, RIPK3K51A, are ostensibly normal in the absence of challenge, indicating that RIPK3 and its kinase activity are dispensable for development. However, another kinase-inactivating mutation, RIPK3D161N, results in embryonic lethality in mice due to widespread apoptosis. As a result, the RIPK3D161N mutation is thought to confer a toxic gain-of-function. Here, to further explore the impacts of RIPK3 inactivation, we compared the stability and cellular interactions of RIPK3D161N and RIPK3K51A to a third previously-uncharacterized kinase-dead variant, RIPK3D143N. Here, we show that RIPK3K51A was unstable and did not associate with RIPK1, RIPK3D161N was unstable but interacted with RIPK1, whereas RIPK3D143N was stable and bound RIPK1 in a manner comparable to wild-type RIPK3. Thus, all three variants scaffold differently, suggesting that the assembly of cell death machinery by RIPK3 is finely tuned, not just by its kinase activity, but also by the conformation of its kinase domain. Physiologically, Ripk3D143N/D143N mice exhibited a partially penetrant lethality in utero. However, once born, Ripk3D143N/D143N mice were fertile and phenotypically indistinguishable from wild-type mice in the absence of challenge, with RIPK3D143N mutation protecting mice lacking intestinal epithelial Caspase-8 from necroptotic ileitis. Our studies support the idea that RIPK3 is a nexus between apoptotic and necroptotic signaling, and highlight the importance of considering kinase domain conformation in RIPK3 inhibitor development.

biochemistry↗

bioRxiv2025

Retroelement co-option disrupts the cancer transcriptional programme

BackgroundTranscriptional activation of otherwise repressed endogenous retroelements (RTEs) is a hallmark of cancer, shaping tumour progression and immunogenicity by multifaceted, yet incompletely understood mechanisms. MethodsWe used an extended pan-cancer transcriptome assembly to identify potential effects of RTEs on the genes near or within which they have integrated. These were subsequently verified in test cases by further analysis of transcriptional profiles in cancer patient data, and by in vitro studies involving restoration of gene activity, and proliferation and migration assays in cancer cell lines. ResultsWe report that cancer-specific transcriptional activation of RTEs causes frequent reduction or loss of gene function. Exonisation and alternative splicing of RTEs creates non-functional RNA and protein isoforms and derepressed RTE promoter activity initiates antisense transcription, both at the expense of the canonical isoforms. Contrary to theoretical expectation, transcriptionally activated RTEs affect genes with established tumour-promoting function, including the common essential RNGTT and the lung cancer-promoting CHRNA5 genes. Furthermore, the disruptive effect of RTE activation on adjacent tumour-promoting genes is associated with slower disease progression in clinical data, whereas experimental restoration of gene activity enhances tumour cell in vitro growth and invasiveness ConclusionsThese findings underscore the gene-disruptive potential of seemingly innocuous germline RTE integrations, unleashed only by their transcriptional utilisation in cancer. They further suggest that such metastable RTE integrations are co-opted as sensors of the epigenetic and transcriptional changes occurring during cellular transformation and as executors that disrupt the function of tumour-promoting genes.

genomics↗

bioRxiv2024

Tuning Insulin Receptor Signaling Using De Novo Designed Agonists

Binding of insulin to the insulin receptor (IR) induces conformational changes in the extracellular portion of the receptor that lead to activation of the intracellular kinase domain and the AKT and MAPK pathways, and downstream modulation of glucose metabolism and cell proliferation. We reasoned that designed agonists that induce different conformational changes in the receptor might induce different downstream responses, which could be useful both therapeutically and to shed light on how extracellular conformation is coupled to intracellular signaling. We used de novo protein design to first generate binders to individual IR extracellular domains, and then to fuse these together in different orientations and with different conformational flexibility. We describe a series of synthetic agonists that signal through the IR that differ from insulin and from each other in the induction of receptor autophosphorylation, MAPK activation, intracellular trafficking, and cell proliferation. We identify designs that are more potent than insulin causing much longer lasting reductions in glucose levels, and that retain signaling activity on disease-causing receptor mutants that do not respond to insulin. These results inform our understanding of how changes in receptor conformation and dynamics are transmitted to downstream signaling, and our synthetic agonists have considerable therapeutic potential for diabetes and severe insulin resistance syndromes. HighlightsO_LIComputational design yielded super agonists, partial agonists, and antagonists of IR. C_LIO_LIDe novo agonists induce a distinct IR active conformation. C_LIO_LIDesigned agonists tune IR signaling by modulating conformational dynamics of activated IR. C_LIO_LIDesigned agonists are more potent than insulin, reducing glucose levels longer and activating disease-causing IR mutants. C_LI

bioengineering↗

bioRxiv2024

The consequences of mismatched buffers in spectral cell sorting

Although spectral flow cytometry has become a ubiquitous tool for cell analysis, the use of spectral cytometry on cell sorters requires additional considerations arising from the unique requirements of sorting workflows. Here, we show that care should be taken when ascertaining the purity of a sort on a spectral cell sorter, as the mismatch of buffers used for initial sample suspension and the buffers used for sort collection can affect the unmixing of the data, potentially giving rise to erroneous purity check results.

cell biology↗

bioRxiv2024

DNA polymerase Lambda is anchored within the NHEJ synaptic complex via Ku70/80

Non-homologous end joining (NHEJ) is the predominant pathway by which double-strand DNA breaks (DSBs) are repaired in mammals. To enable final break closure, various NHEJ end-processing factors respond to the chemistry of the damaged DNA ends. Amongst these factors is DNA polymerase lambda (Pol {lambda}), a member of the Pol X family. How members of the Pol X family engage with the NHEJ complex is unknown. Here, we present cryo-EM structures of Pol {lambda} in complex with the Ku70/80 DSB sensor whilst engaged with the DNA-PK holoenzyme in a long-range synaptic complex. These structures reveal a specific interaction site between Ku70/80 and the Pol {lambda} BRCT domain. The functionality of this interaction is assessed by generating point mutations on either side of the Pol {lambda} BRCT:Ku70/80 interface. Using these mutants in two orthogonal assays in cells (live protein recruitment at biphoton laser-damaged nuclear sites and transfection with an original gap-filling reporter plasmid) defines the molecular basis and essentiality of the BRCT domain for the recruitment and activity of the Pol {lambda} within the NHEJ complex. Ultimately, these data explain the role of this interaction in cell survival to DSBs. Finally, we propose a unified model for the interaction of the three Pol X family members bearing BRCT domains with the same site of Ku70/80.

biochemistry↗

bioRxiv2024

Biallelic Loss of Molecular Chaperone Molecule AIP Results in a Novel Severe Multisystem Disease Defined by Defective Proteostasis

Children born with deleterious biallelic variants of the chaperone aryl hydrocarbon receptor interacting protein (AIP) have a novel pediatric metabolic disease presenting a severe, complex clinical phenotype characterized by failure to develop following birth. Analysis of Aip knockout mouse embryonic fibroblasts and patient-derived dermal fibroblasts revealed that AIP was required to support proteostasis; including proteasome activity, induction of autophagy and lysosome function. aip knockout zebrafish, recapitulated the phenotype of the children; dying at an early stage of development when autophagy is required to adapt to periods of starvation. Our results demonstrate that AIP plays a crucial role in initiating autophagy and maintaining proteostasis in vitro and in vivo. One Sentence SummaryHomozygous loss of the chaperone AIP results in a novel pediatric disease exhibiting multiple features of a lysosomal storage disease.

molecular biology↗

bioRxiv2024

Population sequencing for diversity and transmission analyses

Genomic diversity in a pathogen population is the foundation for evolution and adaptations in virulence, drug resistance, pathogenesis, and immune evasion. Characterizing, analyzing, and understanding population-level diversity is also essential for epidemiological and forensic tracking of sources and revealing detailed pathways of transmission and spread. For bacteria, culturing, isolating, and sequencing the large number of individual colonies required to adequately sample diversity can be prohibitively time-consuming and expensive. While sequencing directly from a mixed population will show variants among reads, they cannot be linked to reveal allele combinations associated with particular traits or phylogenetic inheritance patterns. Here, we describe the theory and method of how population sequencing directly from a mixed sample can be used in conjunction with sequencing a very small number of colonies to describe the phylogenetic diversity of a population without haplotype reconstruction. To demonstrate the utility of population sequencing in capturing phylogenetic diversity, we compared isogenic clones to population sequences of Burkholderia pseudomallei from the sputum of a single patient. We also analyzed population sequences of Staphylococcus aureus derived from different people and different body sites. Sequencing results confirm our ability to capture and characterize phylogenetic diversity in our samples. Our analyses of B. pseudomallei populations led to the surprising discovery that the pathogen population is highly structured in sputum, suggesting that for some pathogens, sputum sampling may preserve structuring in the lungs and thus present a non-invasive alternative to understanding colonization, movement, and pathogen/host interactions. Our analyses of S. aureus samples show how comparing phylogenetic diversity across populations can reveal directionality of transmission between hosts and across body sites, demonstrating the power and utility for characterizing the spread of disease and identification of reservoirs at the finest levels. We anticipate that population sequencing and analysis can be broadly applied to accelerate research in a broad range of fields reliant on a foundational understanding of population diversity. Author SummaryThe ability to characterize diversity in a single bacterial population (i.e., a single host or even a single body site) is critical for understanding adaptation and evolution, with far-reaching implications on disease treatment and prevention that include revealing patterns of spread and persistence. While the scientific community has made great strides in sequencing methods to characterize single colonies and entire communities, there is a dearth of studies at the population level. This is because 1) the need to culture and sequence a sufficiently representative number of isogenic colonies is prohibitive, and 2) the theoretical foundation for characterizing a population by sequencing a single sample (as is done for microbiome and metagenomic analyses) has not been developed. Here, we introduce this theoretical foundation and validate its applicability by characterizing a lung infection caused by Burkholderia pseudomallei. We also demonstrate the utility of this method in determining the directionality of spread of Staphylococcus aureus between people and across body sites within the same host (a level of spatial resolution that has not been previously performed). We anticipate that this work will open the door to a host of new studies and discoveries across a diverse set of microbiological fields.

evolutionary biology↗

bioRxiv2024

Effect of muscarinic blockade on the speed of attention shifting and learning

The study aimed to investigate to what extent blockade of muscarinic receptors affects the speed of endogenous versus exogenous attentional shift times, and how it affects learning induced improvements of attention shift times. Subjects viewed an array of 10 moving clocks and reported the time a clock indicated when cued. Target clocks were indicated by peripheral or central cues, including conditions of pre-cuing. This allowed assessing shift times when attention was pre-allocated, when peripheral cues triggered exogenous attention shifts, and when central cues triggered endogenous attention shifts. In study 1, each subject participated in 2 sessions (scopolamine/placebo), whereby the order of drug intake was counterbalanced across subjects, and subjects were blinded to conditions. Scopolamine/placebo was administered before a psychophysical experiment was conducted. In study 2, the effect of muscarinic blockade on learning induced improvements of attention shift times was investigated. Here scopolamine/placebo was administered immediately after the first (of two) psychophysical sessions, whereby a given subject either received scopolamine or placebo pills. Confirming previous results, we show that pre-cuing resulted in the fastest shift times, followed by exogenous cuing, with endogenous attentional shifts being slowest. Scopolamine application increased attentional shift times across all 3 conditions compared to placebo, but in a dose dependent manner. Additionally, blockade of muscarinic receptors immediately after the first session reduced learning dependent improvement of attention shift times. These results demonstrate that muscarinic receptors play an important role in attention shifting, and they contribute to learning of attention shifting.

neuroscience↗

bioRxiv2023

Spatiotemporal modeling reveals high-resolution invasion states in glioblastoma

Diffuse invasion of glioblastoma cells through normal brain tissue is a key contributor to tumor aggressiveness, resistance to conventional therapies, and dismal prognosis in patients. A deeper understanding of how components of the tumor microenvironment (TME) contribute to overall tumor organization and to programs of invasion may reveal opportunities for improved therapeutic strategies. Towards this goal, we applied a novel computational workflow to a spatiotemporally profiled GBM xenograft cohort, leveraging the ability to distinguish human tumor from mouse TME to overcome previous limitations in analysis of diffuse invasion. Our analytic approach, based on unsupervised deconvolution, performs reference-free discovery of cell types and cell activities within the complete GBM ecosystem. We present a comprehensive catalogue of 15 tumor cell programs set within the spatiotemporal context of 90 mouse brain and TME cell types, cell activities, and anatomic structures. Distinct tumor programs related to invasion were aligned with routes of perivascular, white matter, and parenchymal invasion. Furthermore, sub-modules of genes serving as program network hubs were highly prognostic in GBM patients. The compendium of programs presented here provides a basis for rational targeting of tumor and/or TME components. We anticipate that our approach will facilitate an ecosystem-level understanding of immediate and long-term consequences of such perturbations, including identification of compensatory programs that will inform improved combinatorial therapies.

cancer biology↗

bioRxiv2023

An immunohistochemical atlas of necroptotic pathway expression

Necroptosis is a lytic form of regulated cell death reported to contribute to inflammatory diseases of the gut, skin and lung, as well as ischemic-reperfusion injuries of the kidney, heart and brain. However, precise identification of the cells and tissues that undergo necroptotic cell death in vivo has proven challenging in the absence of robust protocols for immunohistochemical detection. Here, we provide automated immunohistochemistry protocols to detect core necroptosis regulators - Caspase-8, RIPK1, RIPK3 and MLKL - in formalin-fixed mouse and human tissues. We observed surprising heterogeneity in protein expression within tissues, whereby short-lived immune barrier cells were replete with necroptotic effectors, whereas long-lived cells lacked RIPK3 or MLKL expression. Local changes in the expression of necroptotic effectors occurred in response to insults such as inflammation, dysbiosis or immune challenge, consistent with necroptosis being dysregulated in disease contexts. These methods will facilitate the precise localisation and evaluation of necroptotic signaling in vivo. HighlightsO_LI13 automated immunohistochemistry protocols for detecting the necroptotic pathway C_LIO_LINecroptotic pathway expression is confined to fast-cycling immune barriers C_LIO_LINecroptotic pathway expression changes at sites of immunoinflammatory challenge C_LIO_LIImmunodetection of necrosomes in IBD patients is a putative new diagnostic tool C_LI

cell biology↗