Biology subjects

Bennett, D.

Publications and source records attributed to Bennett, D..

At least 19 recordsLinked to original sources

bioRxiv2026

LIF is a pro-algesic mediator in human and mouse models of arthritis-related pain

Purpose: Emerging clinical and experimental data suggest that JAK inhibitors (JAKi) are effective in reducing pain in Rheumatoid Arthritis (RA). We recently showed that JAK/STAT signalling cytokines, specifically IL-6, LIF and IL-11, are present in the RA joint and can act directly on human induced pluripotent stem cell (iPSC) derived sensory neurons by increasing their STAT3 phosphorylation (pSTAT3) levels and expression of select pain-relevant genes. In this study, we determined that LIF is the most consequential cytokine out of the three, altering neuronal signalling, outgrowth and pain-like behaviours in in vitro and in vivo models of arthritis. Methods: Human iPSC-derived sensory neurons were stimulated with RA synovial fluid (SF) or with cytokine-treated RA synovial fibroblast conditioned media (CM) in the absence or presence of anti-cytokine antibodies. pSTAT3 and pSTAT1 levels, and gene expression patterns, were assessed by Western blot and RNA-sequencing (RNA-seq). The immortalised dorsal root ganglion (DRG)-derived cell line (HD 10.6) was assessed for LIF-induced JAK/STAT signalling in addition to neurite outgrowth assays as a functional readout of the sensory neurons. Lastly, mouse models were used to assess pain-related behaviours in vivo. Results: LIF was found to be consistently present in the SF from painful joints from individuals with inflammatory arthritis. Western blotting revealed that the addition of RA SF to iPSC-derived sensory neurons led to LIF-dependent induction of pSTAT3 and pSTAT1, while RNA-seq demonstrated that LIF alters the transcriptome of sensory neurons more prominently than IL-6 and IL-11, up-regulating signature genes related to peripheral neuron sensitization, such as TRPV1, NTRK1, BDNF, HRH1 and SCN10A. Similarly, cytokine-treated fibroblast conditioned media was shown to induce neuronal pSTAT3 and pSTAT1 and upregulate expression of BDNF, HRH1 and VGF in a LIF-dependent manner. Additionally, the immortalised dorsal root ganglion (DRG)-derived cell line (HD 10.6), which also exhibited LIF-induced pSTAT1 and pSTAT3, showed increased neurite outgrowth after axotomy when treated with LIF. Finally, in a mouse model of inflammatory arthritis, LIF was shown to be significantly increased in the affected joint. Furthermore, intraarticular injection of LIF into a healthy mouse knee resulted in increased responsiveness to painful pressure stimuli in that joint. Conclusions: Our data indicate that LIF may be a pro-algesic mediator and a possible therapeutic target to improve pain management in individuals living with inflammatory arthritis.

neuroscience↗

bioRxiv2026

Non-instrumental information has limited effects on bet size in risky decisions

Recent research has suggested that the availability of non-instrumental information about the outcome of a risky choice increases risk appetite. In this study, we aimed to perform a conceptual replication of these findings and to examine the cognitive mechanisms underlying this effect. Across two experiments (N = 150, 102), we presented participants with mathematically fair gambles and allowed them to choose the size of their bet. Between trials, we varied the presence of non-instrumental information that would reveal the outcome ahead of time. In both experiments, we did not find consistent evidence for an effect of the availability of non-instrumental information on bet size. These findings suggest that the previously reported effects of non-instrumental information on risk appetite may have been an idiosyncratic feature of experimental design, rather than a more general phenomenon that characterises human decision making under risk.

animal behavior and cognition↗

bioRxiv2026

Task-Based Value Generalization Correlates With Positive Overgeneralization and Bipolar Symptoms

Positive overgeneralization -- the tendency to generalize from specific successes to broad expectations of future reward -- has been linked to vulnerability to mania. Because positive overgeneralization has only been assessed using self-report measures, we have limited insight into the underlying cognitive process. Here, we introduce a behavioral paradigm that quantifies how reward generalizes to novel stimuli, and characterize individual generalization profiles by fitting psychometric functions to choice data. In an online transdiagnostic study (N = 163), broader task-based generalization was associated with both higher self-reported positive overgeneralization and subclinical bipolar traits. Response times provided converging evidence: a smaller increase in response time as stimuli became less similar to the rewarded stimulus was associated with higher positive overgeneralization. In computational simulations, we show that self-efficacy, operationalized as the relative weight placed on the best and worst available future actions, shapes generalization, with more weight on the best possible action broadening the spread of expected reward to similar states. Together, these findings show that positive overgeneralization can be measured behaviorally, and identify one computational factor that may determine how broadly reward generalizes.

neuroscience↗

bioRxiv2026

Tabular foundation model predicts alternative lengthening of telomeres (ALT) and identifies SMARCAL1 as a target in ALT-driven cancers

Alternative lengthening of telomeres (ALT) is a telomerase-independent pathway used by aggressive cancers to maintain their replicative immortality. Because ALT is absent from normal human cells, it is an appealing target for cancer therapy, but the lack of ability to determine ALT status at scale has hindered discovery. Here, we developed ALTitude, a machine learning method from a tabular foundation model that infers ALT from cell line whole genome sequencing data, without need for paired germline analysis. We deployed ALTitude across the DepMap, doubling the number of known ALT+ cancer models. Systematic integration of ALTitude with CRISPR-Cas9 screens yielded the selective dependency on SMARCAL1 in ALT+ cell lines, where we show it stabilizes the ALT phenotype. Acute depletion of SMARCAL1 leads to G2/M arrest, mitotic catastrophe, and cell death. These data provide a valuable resource for studying ALT-related genomic features and present SMARCAL1 as a therapeutic target for ALT+ malignancies.

cancer biology↗

bioRxiv2026

Enhanced Hi-C Capture Analysis reveals complex regulatory architecture at the PICALM-EED locus for Alzheimer Disease

ObjectiveBoth the phosphatidylinositol binding clathrin assembly protein gene (PICALM) and the embryonic ectoderm development gene (EED) have been implicated as causal genes driving a genome-wide association for Alzheimer disease (AD) risk. We employed a new virtual approach using genome-wide chromatin interactions (Hi-C) called enhanced Hi-C Capture Analysis (eHiCA) to identify the genes and regulatory regions that are driving this important AD risk association. MethodsHi-C data from the frontal cortex of eight AD patients, as well as inducible pluripotent stem cell-derived microglia and spheroids of AD and control patients were used. We applied 14 eHiCA baits each containing a GWAS SNP to identify the cis regulatory interactions in this GWAS locus at a 5kb resolution. ResultsThe baits derived from the GWAS associated haplotype primarily interacted with the PICALM promoter and the large cis-regulatory elements cluster (CREe) lying upstream of the EED promoter. The EED promoter interacts with PICALM gene body and promoter region but not directly with the associated risk haplotype. Although the AD-associated variants segregate together as a haplotype in the population, each bait exhibited distinct functional chromatin interactions. InterpretationThe PICALM gene is the primary driver of the association in microglia along with the CREe locus. Different SNPs in a segregating haplotype can display different physical Hi-C interactions. This study demonstrates that eHiCA can help resolve the casual genes driving complex GWAS associations, opening new pathways to study Alzheimer disease and other disorders.

genomics↗

bioRxiv2025

mfSuSiE enables multi-cell-type fine-mapping and multi-omic integration of chromatin accessibility QTLs in aging brain.

Molecular quantitative trait locus (QTL) studies increasingly profile chromatin accessibility, histone modifications, DNA methylation, RNA modifications such as N6-methyladenosine (m6A), and transcription across multiple cell types using high-throughput sequencing, generating dense base-pair-resolved measurements. The conventional approach of testing each variant against each molecular feature independently suffers from severe multiple testing burden and ignores linkage disequilibrium and spatial correlation. Existing fine-mapping methods only partially address these challenges and are sub-optimal for analyzing such datasets: multivariate approaches such as mvSuSiE jointly analyze multiple molecular contexts but are designed for a single trait value per context and cannot accommodate thousands of base-resolution measurements per context, while functional approaches such as fSuSiE model spatial structure across thousands of measurements but analyze each context separately. Here, we introduce mfSuSiE, which integrates multivariate analysis with wavelet-based functional regression to jointly fine-map thousands of base-resolution traits across multiple cell types. In simulations, mfSuSiE identified causal variants and affected molecular features more accurately than fSuSiE, while mvSuSiE cannot be applied to this type of data. Applied to single-nucleus chromatin accessibility data from six brain cell types from postmortem aging human brains, mfSuSiE substantially increased discovery and resolution, with substantial power gains for cell types with limited samples. Multi-cell-type analysis revealed extensive sharing of regulatory effects on chromatin accessibility (caQTL). Importantly, mfSuSiE produces Bayesian inference compatible with the SuSiE framework, enabling systematic multi-omic integration. Applied to Alzheimers disease loci, we integrated caQTL with expression QTLs, epigenomic QTLs, and GWAS, observing regulatory patterns suggesting complex mechanisms at loci including EARS2, CHRNE, SCIMP, and RABEP1.

genetics↗

bioRxiv2025

Fair-weather friends: Unequal partnerships between Parastagonospora nodorum and Pyrenophora tritici-repentis define disease dynamics in wheat

Parastagonospora nodorum and Pyrenophora tritici-repentis are the causal agents of septoria nodorum blotch and tan spot of wheat, respectively. Though these fungal phytopathogens have been found to frequently cohabitate the same leaf, their interaction dynamics in the manifestation of disease remain poorly understood due to limitations in species-specific detection methods. We developed a digital PCR based model targeting conserved regions of the -tubulin gene, enabling biomass quantification of both pathogens during infection. Field surveys revealed up to two in three symptomatic infections involved both pathogens, with co-infected plants showing significantly higher individual pathogen biomass than single-species infections. Host plants in the field with moderate resistance to both pathogens were found to be significantly more necrotic under co-infection, with individual pathogen biomass up to twice that observed value for single infections. However, like fair-weather friends the partnership between these two pathogens seems to be conditional.When P. tritici-repentisestablished first, secondary P. nodorumcolonisationled to a breakdown of host resistance. Conversely, when P. nodorum established on the host first, it suppressed P. tritici-repentis colonisation regardless of host resistance. To our knowledge this is the first description of asymmetric priority effects overcoming host resistance in a plant pathosystem. Resistance breeding strategies evaluating single pathogen challenges may inadvertently select for cultivars vulnerable to sequential co-infection, necessitating integrated disease complex approaches for durable resistance development.

microbiology↗

bioRxiv2025

Improved genome assembly of double haploid Prunus persica siblings Lovell 2D and Lovell 5D and the peach NLRome

Prunus persica (peach) has long served as a model fruit tree for studying phenological events. It has a relatively small genome and exhibits tremendous plasticity in climate tolerances due to the high variation of chill requirements, bloom times, and fruit ripening times. The peach variety Lovell 2D was used to generate one of the first high-quality genome assemblies for a tree species, using Sanger sequencing of genetic-map ordered BAC clones. A key to the high quality of this early assembly was the use of a doubled haploid variety, which eliminates the challenges posed by mixed haplotypes. Here, we re-sequenced and assembled the Lovell 2D genome along with a doubled haploid sibling Lovell 5D using 3rd generation technologies. The resulting genomes were significantly more contiguous than the current Lovell 2D reference genome (ver2.0 updated in 2017) and are closer to the estimated total genome size for peach (265Mb). In addition, new gene, transposable element (TE), and Nucleotide-binding domain and Leucine-rich repeat receptor (NLR) annotations were performed to enhance the integrity and utility of the genome. These updated peach doubled-haploid reference assemblies will provide the research community with an improved reference genome for genomics-guided studies and breeding efforts.

genomics↗

bioRxiv2025

Genetic and functional analysis of unproductive splicing using LeafCutter2

Alternative splicing commonly generates unproductive mRNA transcripts that harbor premature termination codons1, leading to their degradation by nonsense-mediated decay (NMD). These events reduce overall protein expression levels of affected genes, potentially contributing to gene regulation and disease mechanisms. Here, we present LeafCutter2, which enables identification and quantification of unproductive splicing from short-read RNA-seq data. LeafCutter2 requires minimal gene annotations (start and stop codons) to annotate NMD-inducing splicing events, and identifies differential unproductive splicing between groups, providing insights into its contributions to differential gene expression. Moreover, LeafCutter2 enables mapping of unproductive splicing quantitative trait loci (u-sQTLs), which often colocalize with expression QTLs and GWAS loci. Applying LeafCutter2 to RNA-seq data across human and 6 non-human species, we uncovered a broad landscape of unproductive splicing, which varies widely across tissues. Strikingly, we observed a conserved developmental-stage-specific increase in unproductive splicing during testis maturation across all species. In Alzheimers disease (AD), we analyzed RNA-seq data from the AD Functional Genomics consortium FunGen-xQTL project and identified unproductive splicing events in 18 AD risk genes, including TSPAN14, PICALM, and CASS4, likely mediating genetic effects on disease risk. We performed an integrative analysis using gene expression QTLs, protein expression QTLs, and AD GWAS data, showing that unproductive splicing provides unique regulatory insights beyond traditional approaches. Thus, LeafCutter2 represents a powerful tool for understanding the functional impact of alternative splicing on gene expression and disease mechanisms.

genomics↗

bioRxiv2025

Permissive central tolerance plus defective peripheral checkpoints licence pathogenic memory B cells in CASPR2-antibody encephalitis

Autoimmunity affects 10% of the population. Within this umbrella, autoantibody-mediated diseases targeting one autoantigen provide a unique opportunity to comprehensively understand the developmental pathway of disease-causing B cells and autoantibodies. While such autoreactivities are believed to be generated during germinal centre reactions, the roles of earlier immune checkpoints in autoantigen-specific B cell tolerance are poorly understood. We address this concept in patients with CASPR2-autoantibody encephalitis and healthy controls. In both groups, comparable and high ([~]0.5%) frequencies of unmutated CASPR2-reactive naive B cells were identified. By contrast, CASPR2-reactive memory B cells were exclusive to patients, and their B cell receptors demonstrated affinity-enhancing somatic mutations with heterogenous binding kinetics. These effector molecules possessed epitope-dependent pathogenic effects in vitro neuronal cultures and in vivo. The unmutated common ancestors of these memory B cells showed a distinctive balance between strong CASPR2 reactivity and very limited binding across the remaining human proteome. Our results are the first to propose mechanisms underlying autoantigen-specific tolerance in humans. We identify permissive central tolerance, defective peripheral tolerance and heterogenous autoantibody binding properties as sequential pathogenic steps which licence CASPR2-directed pathology. By leveraging the basic immunobiology, we rationally direct tolerance-restoring approaches in CASPR2-antibody diseases. This paradigm is applicable across autoimmune conditions.

immunology↗

bioRxiv2024

Identification of SLC45A4 as a pain gene encoding a neuronal polyamine transporter.

Polyamines are regulatory metabolites with key roles in transcription, translation, cell signalling and autophagy1. They are implicated in multiple neurological disorders including stroke, epilepsy and neurodegeneration and can regulate neuronal excitability through interactions with ion channels2. Polyamines have been linked to pain showing altered levels in human persistent pain states and modulation of pain behaviour in animal models3. However, the systems governing polyamine transport within the nervous system remain unclear. In undertaking a Genome Wide Association Study (GWAS) of chronic pain intensity in the UK-Biobank we found significant association with variants mapping to the SLC45A4 gene locus. In the mouse nervous system SLC45A4 expression is enriched in all sensory neuron sub-types within the dorsal root ganglion including nociceptors. Cell-based assays show that SLC45A4 is a selective plasma membrane polyamine transporter, whilst the cryo-EM structure reveals a novel regulatory domain and basis for polyamine recognition. Mice lacking SLC45A4 show normal mechanosensitivity but reduced sensitivity to noxious heat and algogen induced tonic pain that is associated with reduced excitability of peptidergic nociceptors. Our findings thus establish a role for neuronal polyamine transport in pain perception and identify a new target for therapeutic intervention in pain treatment.

neuroscience↗

bioRxiv2024

Targeting complement C3a receptor resolves mitochondrial hyperfusion and subretinal microglial activation in progranulin-deficient frontotemporal dementia

Mutations in progranulin (GRN) cause frontotemporal dementia (GRN-FTD) due to deficiency of the pleiotropic protein progranulin. GRN-FTD exhibits diverse pathologies including lysosome dysfunction, lipofuscinosis, microgliosis, and neuroinflammation. Yet, how progranulin loss causes disease remains unresolved. Here, we report that non-invasive retinal imaging of GRN-FTD patients revealed deficits in photoreceptors and the retinal pigment epithelium (RPE) that correlate with cognitive decline. Likewise, Grn-/- mice exhibit early RPE dysfunction, microglial activation, and subsequent photoreceptor loss. Super-resolution live imaging and transcriptomic analyses identified RPE mitochondria as an early driver of retinal dysfunction. Loss of mitochondrial fission protein 1 (MTFP1) in Grn-/- RPE causes mitochondrial hyperfusion and bioenergetic defects, leading to NF-kB-mediated activation of complement C3a-C3a receptor signaling, which drives further mitochondrial hyperfusion and retinal inflammation. C3aR antagonism restores RPE mitochondrial integrity and limits subretinal microglial activation. Our study identifies a previously unrecognized mechanism by which progranulin modulates mitochondrial integrity and complement-mediated neuroinflammation.

neuroscience↗

bioRxiv2024

Activation loop phosphorylation of Cdk11 is restrained by PNUTS-PP1 and regulates Cdk11 activity and function

Organisation of the transcription cycle is facilitated by the reversible phosphorylation of the C-terminal domain of RNA Polymerase II (RNAPII-CTD) and its accessory factors. The PNUTS-PP1 protein phosphatase is crucial for mRNA synthesis and processing, yet the complete spectrum of its physiological targets in these processes remain elusive. Here, using quantitative phosphoproteomics, we discover that Cdk11, in addition to various spliceosomal and RNA processing factors, associates with PNUTS, and that disruption of PP1-binding results in hyperphosphorylation of Cdk11 at an evolutionarily conserved Serine residue, seven amino acid residues C-terminal to DFG residues in the activation loop. In vitro experiments reveal a role for Ser DFG+7 in modulating Cdk11 kinase activity towards RNAPII-CTD Ser5. Making use of a novel technique to conditionally disrupt PP1 binding, we show that PNUTS-PP1 normally serves to restrain Cdk11 phosphorylation in vivo. Mutational analysis shows that cdk11 is not only essential for survival but also plays a widespread role in regulating normal mRNA expression and splicing. Notably, we find that a phosphomimetic mutation in cdk11 exhibits distinct biological effects compared to loss of cdk11 function, including defective processing of intronic small nucleolar RNAs, diminished intronic RNA Pol II velocity, and a decrease in intergenic transcription. These findings underscore physiologically significant roles of Cdk11 dephosphorylation by PNUTS-PP1 in the regulation of mRNA transcription and processing.

molecular biology↗

bioRxiv2024

The fine-tuning of synapse development by oxidative stress and autophagy requires presynaptic ATM kinase

Two processes held in delicate balance during the fine tuning of synapse development are oxidative stress and autophagy: each can promote synapse expansion yet in excess are toxic. How this balance is maintained is not fully understood. While ataxia-telangiectasia mutated (ATM) is recognized as a key regulator of the DNA damage response, there is increasing evidence of a neuronal-specific role for this ubiquitous kinase and deficiency causes early-onset neurodegeneration. We report a requirement for presynaptic Drosophila ATM (dATM) in neurodevelopment that is independent of its functions in the DNA damage response. Reduction of presynaptic dATM expression causes hypersensitivity to raised oxidative stress and a failure to induce autophagy which leaves mitochondria in excess in neurons. We demonstrate that presynaptic dATM coordinates autophagy through the conserved ATM-AMPK axis. Similarly to mammalian ATM, neuronal dATM is predominantly cytosolic and forms synaptic foci. dATM also colocalizes with autophagosomes. We propose a model wherein dATM responds to increased reactive oxygen species resulting from heightened neuronal activity by activating autophagy to induce synaptic growth, while protecting the neuron from excitotoxicity and oxidative stress.

developmental biology↗

bioRxiv2023

A Molecular Basis of Human Brain Connectivity

Neuroimaging is commonly used to infer human brain connectivity, but those measurements are far-removed from the molecular underpinnings at synapses. To uncover the molecular basis of human brain connectivity, we analyzed a unique cohort of 98 individuals who provided neuroimaging and genetic data contemporaneous with dendritic spine morphometric, proteomic, and gene expression data from the superior frontal and inferior temporal gyri. Through cellular contextualization of the molecular data with dendritic spine morphology, we identified hundreds of proteins related to synapses, energy metabolism, and RNA processing that explain between-individual differences in functional connectivity and structural covariation. By integrating data at the genetic, molecular, subcellular, and tissue levels, we bridged the divergent fields of molecular biology and neuroimaging to identify a molecular basis of brain connectivity. One-Sentence SummaryDendritic spine morphometry and synaptic proteins unite the divergent fields of molecular biology and neuroimaging.

neuroscience↗

bioRxiv2023

The ENCODE4 long-read RNA-seq collection reveals distinct classes of transcript structure diversity

The majority of mammalian genes encode multiple transcript isoforms that result from differential promoter use, changes in exonic splicing, and alternative 3 end choice. Detecting and quantifying transcript isoforms across tissues, cell types, and species has been extremely challenging because transcripts are much longer than the short reads normally used for RNA-seq. By contrast, long-read RNA-seq (LR-RNA-seq) gives the complete structure of most transcripts. We sequenced 264 LR-RNA-seq PacBio libraries totaling over 1 billion circular consensus reads (CCS) for 81 unique human and mouse samples. We detect at least one full-length transcript from 87.7% of annotated human protein coding genes and a total of 200,000 full-length transcripts, 40% of which have novel exon junction chains. To capture and compute on the three sources of transcript structure diversity, we introduce a gene and transcript annotation framework that uses triplets representing the transcript start site, exon junction chain, and transcript end site of each transcript. Using triplets in a simplex representation demonstrates how promoter selection, splice pattern, and 3 processing are deployed across human tissues, with nearly half of multitranscript protein coding genes showing a clear bias toward one of the three diversity mechanisms. Evaluated across samples, the predominantly expressed transcript changes for 74% of protein coding genes. In evolution, the human and mouse transcriptomes are globally similar in types of transcript structure diversity, yet among individual orthologous gene pairs, more than half (57.8%) show substantial differences in mechanism of diversification in matching tissues. This initial large-scale survey of human and mouse long-read transcriptomes provides a foundation for further analyses of alternative transcript usage, and is complemented by short-read and microRNA data on the same samples and by epigenome data elsewhere in the ENCODE4 collection.

genomics↗

bioRxiv2023

How far are we from personalized gene expression prediction using sequence-to-expression deep neural networks?

Introductory Paragraph Deep learning methods have recently become the state-of-the-art in a variety of regulatory genomic tasks1-6 including the prediction of gene expression from genomic DNA. As such, these methods promise to serve as important tools in interpreting the full spectrum of genetic variation observed in personal genomes. Previous evaluation strategies have assessed their predictions of gene expression across genomic regions, however, systematic benchmarking is lacking to assess their predictions across individuals, which would directly evaluates their utility as personal DNA interpreters. We used paired Whole Genome Sequencing and gene expression from 839 individuals in the ROSMAP study7 to evaluate the ability of current methods to predict gene expression variation across individuals at varied loci. Our approach identifies a limitation of current methods to correctly predict the direction of variant effects. We show that this limitation stems from insufficiently learnt sequence motif grammar, and suggest new model training strategies to improve performance.

bioinformatics↗

bioRxiv2022

Mouse behaviour on the trial-unique non-matching-to-location (TUNL) touchscreen task reflects a mixture of distinct working memory codes and response biases

The trial-unique non-matching to location (TUNL) touchscreen task shows promise as a translational assay of working memory deficits in disorders including autism, ADHD, and schizophrenia. Although it is commonly assumed that the TUNL task predominantly measures spatial working memory in rodents, this proposition has not previously been tested. In this project, we used computational modelling of behaviour from mice performing the TUNL task (total N = 163 mice across three datasets; 158,843 total trials). Contrary to common assumptions, behaviour on the TUNL task did not exclusively reflect spatial working memory. Instead, choice behaviour was explained as a mixture of both retrospective (spatial) working memory and prospective working memory for an intended behavioural response, as well as animal-specific response biases. We suggest that these findings can be understood within a resource-rational cognitive framework, and propose several task-design principles that we predict will maximise spatial working memory and minimise alternative behavioural strategies.

animal behavior and cognition↗