Biology subjects

Davies, J.

Publications and source records attributed to Davies, J..

At least 19 recordsLinked to original sources

bioRxiv2026

Median raphe input to dorsal CA1 shapes VIP interneuron recruitment and novelty-guided spatial memory

Vasoactive intestinal peptide-expressing interneurons (VIP-INs) gate hippocampal inhibition during novel experience, but the long-range signals that engage these cells remain poorly understood. Here we identify median raphe (MnR) projections as a brainstem pathway that tunes dorsal CA1 VIP-IN recruitment through coordinated glutamatergic and serotonergic mechanisms. Anatomical mapping and optogenetic recordings showed that MnR axons innervate multiple VIP-IN subtypes, while transcriptomic and pharmacological analyses revealed fast glutamatergic excitation together with serotonin receptor-dependent modulation of synaptic and intrinsic responsiveness. In vivo calcium imaging showed that novelty preferentially recruited a speed-coupled VIP-IN ensemble, and inhibition of MnR input selectively reduced the magnitude of this response. A hippocampal circuit model linked this pathway to dendritic disinhibition and place-cell recruitment. Behaviorally, inhibition of MnR input preserved exploratory engagement but disrupted the organization of spatial sampling and impaired object-location memory. Thus, MnR input organizes hippocampal disinhibition to support novelty-guided exploration and memory encoding.

neuroscience↗

bioRxiv2026

Cell-free pathway prototyping enables cost-effective biomanufacturing of 1,2,4-butanetriol at the 1-L scale

Biomanufacturing offers sustainable alternatives to chemical synthesis under lower temperatures and pressures than traditional catalytic methods. However, the slow pace and iterative engineering bottlenecks of cell strain development restrict the feasible biological design space. Cell-free systems circumvent these constraints, providing a flexible and high-throughput screening approach to accelerate pathway prototyping and enzyme optimization but are not typically used for manufacturing scale-up. To understand the scalability of cell-free biosynthesis, we establish an end-to-end fully cell-free architecture to discover, develop, and scale the biosynthesis of 1,2,4-butanetriol (BT), a high-value industrial platform chemical. First, we systematically screened ~150 enzymes across the 4-step pathway from xylose to BT to identify highly active homologs for each reaction. Next, we applied statistical Design of Experiments to optimize reaction formulations for cost and titer. Finally, the maximum-titer and minimum-cost formulations were scaled up across five orders of magnitude, from 10-{micro}L to 1-L reactions. This resulted in peak volumetric productivities of ~1 g/L/h and yields over 13 g of BT in a single 1-L reaction, with raw substrate costs totaling just $3.00 per liter. This work expands the diversity of enzymes tested for BT synthesis and establishes a blueprint for advancing industrial biochemical manufacturing fully in vitro.

synthetic biology↗

bioRxiv2026

Spatial atlas of the ovary identifies molecular events in primordial follicle activation in humans

The human ovarian reserve is established prenatally, when granulosa cells encapsulate germ cells to form a pool of quiescent primordial follicles, that ultimately determines the female reproductive and endocrine lifespan. From birth to menopause, subsets of these quiescent follicles, located in the thin outer ovarian cortex, are activated and undergo a growth programme with progressive inward migration to the inner cortex, before either undergoing atresia or, during reproductive age, ovulation. Disruption of this process may lead to infertility, metabolic disorders and early menopause, yet early follicle development remains largely poorly understood. Here, we generate the most comprehensive single-cell and spatial multiomics atlas of the human pre- and postnatal ovarian cortex, integrating transcriptomic and chromatin profiles from over four million cells obtained from fetal and newly profiled pediatric and adult donors. We resolve the early granulosa cell trajectory at unprecedented resolution and identify a retinoic acid-associated regulatory switch accompanying follicle activation. We further show that stromal fibroblasts are not homogeneous, but instead form a dynamic scaffold establishing previously unrecognised morphogen and paracrine gradients that organise the cortex into functional niches supporting quiescent, growing, and atretic follicles. Finally, we identify ovarian lipid associated macrophages (oLAMs) that localise around follicles and are likely to support tissue remodelling during folliculogenesis. Together, this atlas provides a foundational blueprint for human ovarian development and homeostasis, and provides a framework for improving strategies in fertility preservation and in vitro follicle maturation.

cell biology↗

bioRxiv2026

Preserved CD4+ T cell helper function and coordinated antiviral immunity in people with HBV/HIV co-infection on long-term therapy

Background & AimsPeople with HBV/HIV co-infection on antiretroviral therapy achieve higher rates of HBV functional cure than those with HBV mono-infection, yet the immunological basis remains poorly characterised. HBV-specific CD4+ T cell responses are critical for viral control and functional cure but have been scarcely examined in HBV/HIV co-infection. Our previous studies in HBV/HIV co-infection demonstrated preserved stem-like CD8+ T cells and NK cell functional responses, but whether CD4+ T cell helper function is similarly maintained is unknown. MethodsWe analysed CD4+ T cell responses in 72 participants (HBV n=26, HBV/HIV n=24, HIV n=22) on suppressive antiviral therapy, using multiparameter flow cytometry, virus-specific CD4+ T cell functional assays and proliferation assays. ResultsPeople with HBV/HIV co-infection had significantly higher HBV envelope- and core-specific CD4+ T cell responses, with IL-2 production particularly discriminating between groups. CD4+ T cell responses to CEF (CMV, EBV, and Influenza) were comparable, confirming antigen specificity. Granzyme B-expressing cytotoxic CD4+ T cells and TCF-1+CD127+PD-1+CD4+ T cells were enriched in co-infection. CD4+ and CD8+ T cell responses were more frequently coordinated within donors in co-infection than in mono-infection (envelope 83% vs 50%; core 94% vs 60%), where they were more often uncoupled. IL-2 producing CD4+ T cells correlated with CD8+ T cell responses and the CD4:CD8 ratio in co-infection. HBV-specific proliferative capacity was enhanced in co-infection. ConclusionsPeople with HBV/HIV co-infection mount functional HBV-specific CD4+ T helper responses that are coordinated with CD8+ T cell immunity at the individual level. Together with our prior findings of preserved NK and CD8+ T cell responses in this cohort, these data identify treated HBV/HIV co-infection as a setting of integrated, rather than compromised, antiviral immunity. Impact and ImplicationsPeople with HBV/HIV co-infection can achieve HBV functional cure more frequently than people with HBV mono-infection, but the immune mechanisms remain unclear. This study shows that treated HBV/HIV co-infection is characterised by functional HBV-specific CD4 helper responses and coordinated CD4/CD8 antiviral immunity. These responses were most strongly associated with the CD4:CD8 ratio, a routinely available clinical marker, rather than with CD4 count alone. These findings argue that people with HBV/HIV co-infection should be prioritised in, not excluded from, HBV cure immunotherapy trials. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=90 SRC="FIGDIR/small/730166v1_ufig1.gif" ALT="Figure 1"> View larger version (24K): org.highwire.dtl.DTLVardef@89be79org.highwire.dtl.DTLVardef@13836bborg.highwire.dtl.DTLVardef@1915698org.highwire.dtl.DTLVardef@cc286c_HPS_FORMAT_FIGEXP M_FIG C_FIG

immunology↗

bioRxiv2026

A key role for chromosome compartment interactions in directing Xist RNA localisation

X-chromosome inactivation, the mechanism for dosage compensation in mammals, is orchestrated by the long non-coding RNA Xist which localises across the X chromosome in cis. The basis for in cis localisation remains poorly understood. To investigate in situ Xist localisation, we established MCPH1-deficient cell models that retain compacted interphase chromosomes, enabling visualisation of individualised chromosome territories. We find that Xist RNA is directed to sites around the periphery of compacted chromosome territories, and moreover that these sites correlate closely with A1-sub-compartments on the X chromosome. We further show that peripheral positioning of A1-sub-compartments occurs on all chromosomes and is a hallmark of early prophase. A key role for compartment interactions in Xist localisation is further supported by analysis of MCPH1-deficient models where Xist is overexpressed (from the X chromosome or an autosomal Xist transgene), and following depletion of HNRNPU, a key factor that anchors Xist RNA to chromosome territories.

genetics↗

bioRxiv2026

Structural and biochemical characterization of a novel inhibitor of NMNAT1, the gatekeeper of nuclear NAD+ biosynthesis

Nicotinamide adenine dinucleotide (NAD+) is crucial for cellular functions including DNA repair and metabolism. Nicotinamide mononucleotide adenylyltransferase (NMNAT) enzymes catalyze the final step of NAD+ synthesis from NMN and ATP. There are three NMNAT isoforms: NMNAT1, NMNAT2, and NMNAT3, located in the nucleus, cytoplasm, and mitochondria, respectively. Nuclear NAD+ promotes disease progression in NAD+-dependent cancers, and it is hypothesized that targeting NMNAT1 with small-molecule inhibitors could be an effective therapeutic strategy. Here, we identify an NMNAT1 inhibitor from a bioactive compound screen and report its effects on NAD+ levels and the viability of NMNAT1-dependent cancer cell lines. The compound AMI-1 is a known inhibitor of Protein Arginine N-Methyltransferase 1, and we find that it also inhibits NMNAT1 with similar potency. Additionally, we determined a cryo-EM structure of NMNAT1 bound to AMI-1 and revealed its mechanism of inhibition. This provides proof of principle for inhibiting NMNAT1 to target NAD+ metabolism in dependent cancers, while also highlighting that caution is warranted when interpreting studies using AMI-1 as a PRMT1 inhibitor, given its effect on NAD+ through NMNAT1. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=64 SRC="FIGDIR/small/716846v1_ufig1.gif" ALT="Figure 1"> View larger version (16K): org.highwire.dtl.DTLVardef@139e792org.highwire.dtl.DTLVardef@923869org.highwire.dtl.DTLVardef@1b5aa1borg.highwire.dtl.DTLVardef@1b2d797_HPS_FORMAT_FIGEXP M_FIG C_FIG

biochemistry↗

bioRxiv2026

Light-inducible proximity labelling in vivo captures sex-specific RNA at excitatory synapses

Local RNA regulation is essential for synaptic plasticity, yet the full repertoire of RNA species and associated isoforms within specific synaptic compartments in vivo has yet to be determined. Existing RNA profiling approaches lack the spatial and temporal precision needed to resolve RNA repertoires restricted to cell-type specific synaptic compartments. To overcome this challenge, we developed PSD-95-Halo-seq, a light-induced proximity labelling technique that, when combined with long-read sequencing, selectively captures all post-synaptic full length RNA species in the excitatory post-synaptic compartment. Here, we applied this approach to investigate sex differences in RNA expression within excitatory synapses following exposure to an associative fear learning task in C57/Bl6 mice. We found dramatic sex differences in pseudogene and protein coding RNA expression, which are most abundant in females, with males exhibiting multiple noncoding RNA classes, including lncRNA, snoRNA, and rRNA. Females generally showed more 3' UTR expression, and there was widespread differential exon usage following fear conditioning, including 179 isoforms in males, 69 in females, with no significant gene-level differential expression, indicating that behavioural state modifies sex-specific isoform usage rather than overall transcript abundance. Our discovery that synaptic RNA composition is dynamic, sexually dimorphic, and profoundly shaped by experience, offers new insight into previously inaccessible mechanisms underlying sex differences in fear-related learning and memory. PSD-95-Halo-seq is therefore a powerful method for the precise spatiotemporal identification of compartment-and cell-type-specific RNA. One sentence take-awaySynapse-targeted proximity labelling and Long-Read sequencing demonstrate that excitatory post-synapses encode experience through sex-specific, isoform-level RNA remodeling.

neuroscience↗

bioRxiv2025

Tracking GAD-specific T-cell expansions in Type 1 diabetes by intradermal GAD-Alum challenge

Identifying and monitoring autoreactive T cells that drive beta cell destruction remains a major obstacle to developing effective immunotherapies for type 1 diabetes (T1D). These cells are extremely rare in peripheral blood and cannot be accessed directly from the pancreas. We used intradermal injection of GAD-Alum to recruit GAD-specific T cells to accessible sites in the skin and skin-draining lymph nodes (LNs), sampled by skin suction blisters and ultrasound-guided LN aspiration. Peripheral blood samples obtained before GAD injection were restimulated with GAD in vitro to detect reactive CD4+ T cells. Re-expression of selected T cell receptors (TCRs) confirmed antigen specificity. Up to 70% of T cells at the skin injection site were clonally-expanded and 4 of 14 (28%) re-expressed TCRs were GAD-reactive. In draining LNs 1 of 14 (4%) clonally-expanded TCRs was GAD-reactive, representing [~]0.08% of all T-cells. GAD-reactive cells across compartments displayed Th1 and Th17-associated transcription signatures. These results demonstrate the intradermal autoantigen challenge, coupled with scRNAseq, enables direct identification and molecular profiling of autoreactive T cells in vivo. This minimally invasive approach provides a powerful platform for tracking antigen-specific specific T cells to monitor disease activity and evaluate immune interventions in T1D.

immunology↗

bioRxiv2025

Neuronal excitability is permanently altered by activity manipulation during an embryonic critical period in Drosophila

Neuronal intrinsic excitability provides the baseline that homeostatic mechanisms act to preserve, yet the processes that establish a baseline remain poorly defined. Developmental critical periods (CPs) are thought to play a central role, but the link between early activity and long-term intrinsic properties is not well characterised. To address this, we used the genetic tractability of the Drosophila larval locomotor circuit to manipulate individual neurons during an embryonic CP. Following optogenetic excitation or inhibition, during the CP, we assessed intrinsic excitability of the same neurons in third-instar larvae (i.e. [~]5 days thereafter). We compared an excitatory premotor interneuron (A27h), an inhibitory premotor interneuron (A31k), and a motor neuron (aCC). Both interneurons exhibited anti-homeostatic responses: excitatory perturbation increased intrinsic excitability, while inhibitory perturbation decreased it, effects that persisted throughout larval development. In contrast, motor neurons showed no significant changes under the same conditions, revealing cell type-specific sensitivity to early activity. These findings build on the general principles of the functional relationships between CP activity and neuronal excitability and how intrinsic excitability is not passively set but actively shaped during these windows, with long-lasting, neuron-specific consequences. More broadly, our results highlight how developmental perturbations can alter the excitatory-inhibitory balance of mature neural circuits that may contribute to the aetiology of neurodevelopmental disorders.

neuroscience↗

bioRxiv2025

Splenic granulopoiesis and S100A9 drive resistance to checkpoint inhibitors conferred by liver metastases

Here, we investigate why liver metastases reduce the efficacy of immune checkpoint inhibitors (CPI). The poor prognosis of patients with liver metastases is associated with a systemic increase in neutrophils. Using experimental models, we confirm that mice with liver metastases respond poorly to CPI, have elevated neutrophils and suppress the response of subcutaneous lesions to CPI. We demonstrate that liver metastases, acting partly via IL-6, boost granulopoiesis in the spleen and promote the generation of immature S100A9hi neutrophils that suppress T-cell proliferation. Human liver metastases exhibit a similar increase in S100A9hi neutrophils. Neutrophil depletion attenuates the growth of liver metastases, but not subcutaneous metastases. Moreover, genetic deletion of S100A9 enables liver metastases to be effectively treated with CPI, and prevents liver metastases from suppressing the response in subcutaneous metastases. Thus, we document how liver metastases specifically change splenic granulopoiesis leading to changes in the microenvironment of non-hepatic lesions, and how targeting a key neutrophil protein restores the efficacy of CPI.

immunology↗

bioRxiv2025

A mobile circular DNA element drives memory-related processes in mice

Extrachromosomal circular DNAs (ecDNAs) are double stranded, closed loop DNA molecules that act independently of the genome. Here we report the discovery of a brain-enriched ecDNA, ecCldn34d, that regulates the transcriptional state of plasticity-related genes and is temporally associated with the stability of fear memories. ecDNA therefore represents a novel class of mobile DNA elements that are involved in experience-dependent neuroadaptation.

neuroscience↗

bioRxiv2025

Pan-cancer analysis in the real-world setting uncovers immunogenomic drivers of acquired resistance post-immunotherapy

Immune checkpoint blockade (ICB) has revolutionised cancer therapy, yet resistance -- both primary and acquired -- remains a significant obstacle, affecting the majority of patients. Here, we leveraged a large-scale, real-world clinicogenomic dataset to systematically explore the molecular underpinnings of ICB resistance in the post-progression setting. Analysing over 5,000 pan-cancer patients with clinical and pre-/post-treatment genomic and transcriptomic data, we identify distinct immunogenomic drivers of acquired vs. primary ICB resistance. Post-ICB progression, acquired resistance showed extended survival compared to primary resistance across all cancer types. The acquired resistance clinical phenotype was paralleled by a universally immune-inflamed, albeit dysfunctional, tumour microenvironment (TME) at the onset of acquired resistance, with sustained or ICB-induced inflammatory and interferon responses. We confirm previously described mechanisms of acquired resistance, including B2M loss-of-function (LoF) in non-small cell lung cancer (NSCLC), and identify novel potential mediators, including LoF of TGFBR2 in NSCLC, CYLD in head and neck cancer, and RUNX1 in triple negative breast cancer. Further supporting their involvement in resistance, these acquired ICB alterations associated with immune-escaped TMEs, characterised by active immunomodulatory oncogenic signalling, hyperproliferation and invasiveness, or altered tumour metabolism. These findings emphasise the heterogeneity of molecular drivers of acquired resistance to ICB within and across cancers, and highlight the potential for personalised therapeutic interventions post-progression to improve patient outcomes.

cancer biology↗

bioRxiv2025

Papaver S-determinants trigger an integrated network of mitochondrially derived ROS and disruption of energy metabolism in incompatible pollen tubes

Many plants use self-incompatibility (SI) mechanisms to prevent inbreeding by inhibiting pollen tube growth in "self" pistils. In Papaver rhoeas, SI is triggered by allele-specific interaction between the pollen and pistil S-determinants, activating a Ca2+-dependent signalling network that leads to rapid reactive oxygen species (ROS) production and eventual programmed cell death (PCD) in incompatible pollen tubes. Expression of the Papaver pollen S-determinant (PrpS) in Arabidopsis thaliana recapitulates Papaver SI when challenged with the cognate pistil ligand (PrsS). Using roGFP2-Orp1, a genetically encoded hydrogen peroxide (H2O2) sensor, combined with measurements of mitochondrial metabolism we have revealed a complex SI response. Within minutes, elevated cytosolic Ca2+ ([Ca2+]cyt) and cytosolic acidification converge to trigger mitochondrial H2O2 production (with consequent cytosolic and plastid H2O2 increase), membrane depolarisation, decreased respiration rate, and ATP depletion. In parallel, oxidative inactivation of cytosolic GAPDH inhibits glycolytic flux, resulting in decreased TCA cycle intermediates and providing a feedback loop to enhance mitochondrial disruption. Preceding production of mitochondrially-sourced ROS, we show that SI rapidly arrests pollen tube growth via inactivation of plasma membrane localised NADPH oxidase (RBOH) mediated superoxide production. Our findings provide new insights into how different ROS signatures from NADPH oxidase and mitochondria drive distinct processes. We demonstrate that mitochondrial disruption is an early and central event in the SI-response, likely driven by positive feedback loops involving altered Ca2+ signalling, cytosolic pH and ROS. Our findings provide novel insights into how SI rapidly disrupts energy metabolism in pollen tubes through interconnected signalling networks centred on mitochondria prior to PCD.

plant biology↗

bioRxiv2025

Expanded adaptive NKG2C+ NK cells exhibit potent ADCC and functional responses against HBV-infected hepatoma cell lines

BackgroundHepatitis B virus (HBV) infection remains a significant global health challenge, leading to chronic liver disease and hepatocellular carcinoma (HCC). Natural killer (NK) cells play an important role in the clearance of HBV-infected cells, but their efficacy is often compromised during chronic infection. Adaptive NK cells, characterised by NKG2C expression and enhanced functional responses, represent a promising therapeutic avenue for enhancing anti-HBV immunity and responses to HBV-driven cancers. MethodsWe applied an established protocol, involving K562-HLA-E expressing feeder cells and cytokines (IL-2), for the expansion of adaptive NK cells from cryopreserved T- and B cell depleted peripheral blood mononuclear cells (PBMCs) derived from donors with chronic HBV infection alone or with Human Immunodeficiency Virus (HIV) co-infection. We evaluated the adaptive profile of expanded NK cells, their antibody-dependent cellular cytotoxicity (ADCC) capacity and functional responses against hepatoma cell lines in the presence or absence of HBV infection. ResultsExpanded NK cells achieved >97% purity, with the NKG2C positive population exhibiting a mean 100-fold expansion. These cells demonstrated a predominantly adaptive phenotype with high surface expression of NKG2C and cytotoxic potential (Granzyme B). They maintained high levels of CD16 surface expression and upregulated CD2, essential for ADCC. Functionally, expanded adaptive NK cells showed enhanced ADCC capacity and functional responses to K562 targets, naive, HBV integrant-expressing, and de novo infected hepatoma cell lines. TGF-{beta} preconditioning induced tissue-resident features (CD103, CD49a) in expanded adaptive NK cells, while preserving their adaptive phenotype and functionality, enhancing their potential for liver targeted immunotherapy. Further, expanded adaptive NK cells demonstrated minimal reactivity against autologous activated T cells, suggesting limited off-target effects. ConclusionsOur study demonstrates the first successful expansion of adaptive NK cells with robust functional responses from donors with chronic viral infection. This approach creates opportunities for NK cell-based therapies alone or in combination with monoclonal antibodies contributing to HBV functional cure strategies and the treatment of HBV-driven cancers.

immunology↗

bioRxiv2025

Male mice prefer to live on their own

Around the world, guidance for the management of laboratory mice recommends social housing (1-3). However, fighting in male mice represents a major animal welfare and scientific issue. Despite the risks of stress and injury and associated welfare costs of incage aggression, we currently prioritise group housing. In this study we first validated a trans-species behavioural biomarker of affective state for mice using a chronic corticosterone model of depression. We next used the same methods to quantify affective state in male mice, group or singly housed in conventional versus individually ventilated cages (IVCs). The results revealed group housed male mice are in a negative affective state similar to that induced by chronic corticosterone treatment. IVC housing was also associated with a more negative affective state. These studies provide an objective assessment of the welfare costs of different housing conditions for male mice.

animal behavior and cognition↗

bioRxiv2025

ABHD11 inhibition drives sterol metabolism to modulate T cell effector function and alleviate autoimmunity

Chronic inflammation in autoimmunity is driven by T cell hyperactivation. This unregulated response to self is fuelled by heightened metabolic programmes, which offers a promising new direction to uncover novel treatment strategies. /{beta}-hydrolase domain-containing protein 11 (ABHD11) is a mitochondrial hydrolase that maintains the catalytic function of -ketoglutarate dehydrogenase (-KGDH), and its expression in CD4+ T cells has been linked to remission status in rheumatoid arthritis (RA). However, the importance of ABHD11 in regulating T cell metabolism and function - and thus, the downstream implication for autoimmunity - is yet to be explored. Here, we show that pharmacological inhibition of ABHD11 dampens cytokine production by human and mouse T cells. Mechanistically, the anti-inflammatory effects of ABHD11 inhibition are attributed to increased 24,25-epoxycholesterol (24,25-EC) biosynthesis and subsequent liver X receptor (LXR) activation, which arise from a compromised TCA cycle. The impaired cytokine profile established by ABHD11 inhibition is extended to two patient cohorts of autoimmunity. Importantly, using a murine model of accelerated type 1 diabetes (T1D), we show that targeting ABHD11 suppresses cytokine production in antigen-specific T cells and delays the onset of diabetes in vivo. Collectively, our work provides pre-clinical evidence that ABHD11 is an encouraging drug target in T cell-mediated autoimmunity. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=200 SRC="FIGDIR/small/643996v1_ufig1.gif" ALT="Figure 1"> View larger version (59K): org.highwire.dtl.DTLVardef@bb3fcborg.highwire.dtl.DTLVardef@1594fc8org.highwire.dtl.DTLVardef@84e078org.highwire.dtl.DTLVardef@1ad023e_HPS_FORMAT_FIGEXP M_FIG C_FIG

immunology↗

bioRxiv2025

Single-cell mass cytometry maps the evolution of immune cell signatures predictive of acute graft-versus-host disease

Allogeneic haematopoietic stem-cell transplantation (AHST) can cure patients with many diseases, but harmful acute graft-versus-host disease (aGvHD) remains a challenge. Many immune cells are implicated in the pathogenesis and control of alloreactive T-cell responses causing aGvHD, but the functionally dominant cells at different times remain unknown. Using mass cytometry to simultaneously assess alloreactive and immunoregulatory cell populations after AHST, we identified a robust early immune signature predictive of aGvHD rich in CD4 effector memory T-cells and deficient in functionally allosuppressive NK cells. Additionally, network analysis identified a heterogeneous immunoregulatory cell group (IRCG) that more accurately predicted aGVHD than any individual cell populations or established serum biomarkers. Immune signatures preceding aGvHD evolved over time, with qualitative and quantitative changes in both the alloreactive T-cell compartment and the constituent components of the IRCG. In mapping how alloreactive and immunoregulatory cell populations evolve temporally, we provide mechanistic insight into dynamic control of alloreactivity supporting development of time-sensitive targeted strategies to reduce aGvHD. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=184 HEIGHT=200 SRC="FIGDIR/small/640331v1_ufig1.gif" ALT="Figure 1"> View larger version (50K): org.highwire.dtl.DTLVardef@12bb519org.highwire.dtl.DTLVardef@7e9dbcorg.highwire.dtl.DTLVardef@a5b041org.highwire.dtl.DTLVardef@1d69a82_HPS_FORMAT_FIGEXP M_FIG C_FIG

immunology↗

bioRxiv2025

Cell-type-specific DNA methylation dynamics in the prenatal and postnatal human cortex

The human cortex undergoes extensive epigenetic remodelling during development, although the precise temporal and cell-type-specific dynamics of DNA methylation remain incompletely understood. In this study, we profiled genome-wide DNA methylation across human cortex tissue from donors aged 6 post-conception weeks (pcw) to 108 years of age. We observed widespread, developmentally regulated, changes in DNA methylation, with pronounced shifts occurring during early- and mid-gestation that were distinct from age-associated modifications in the postnatal cortex. Using fluorescence-activated nuclei sorting (FANS), we optimized a protocol for the isolation of SATB2-positive neuronal nuclei, enabling the identification of cell-type-specific DNA methylation trajectories in developing neuronal and non-neuronal populations. Developmentally dynamic DNA methylation sites were significantly enriched near genes implicated in autism and schizophrenia, supporting a role for epigenetic dysregulation in neurodevelopmental disorders. Our findings underscore the prenatal period as a critical window of epigenomic plasticity in the central nervous system with important implications for understanding the genetic basis of neurodevelopmental phenotypes.

genomics↗