Biology subjects

Shine, J.

Publications and source records attributed to Shine, J..

At least 19 recordsLinked to original sources

bioRxiv2026

Mapping the response of primary human chondrocytes to an osteoarthritis-relevant stimulus by single-cell RNA sequencing

Objective: To determine how fibronectin fragment (Fn-f), a matrikine that induces an osteoarthritis (OA)-like phenotype, reshapes chondrocyte states and transcriptional programs at single-cell resolution. Design: Primary human ankle chondrocytes from two cadaveric donors without OA were treated with PBS or purified recombinant Fn-f for 18 hours and profiled by single-cell RNA sequencing. Transcriptional states were characterized by marker genes and functional enrichment, compared with classifications used for OA chondrocytes, and evaluated for Fn-f-dependent changes in abundance and transcriptional programs. Results: Five transcriptionally distinct populations were identified with features that matched previous classifications of effector, inflammatory, pre-hypertrophic/fibrochondrocyte, reparative, and homeostatic chondrocytes. Fn-f markedly redistributed cells among these states, enriching inflammatory chondrocytes while reducing effector and reparative populations. Within transcriptional states, Fn-f differentially altered matrix/cartilage, inflammatory, and stress/immediate-early programs. These responses did not uniformly correspond to assigned subtype identities, demonstrating that transcriptional programs can be dynamically deployed across chondrocyte states. Conclusions: Controlled perturbations of healthy chondrocytes complement observational OA atlases by resolving stimulus-dependent changes in chondrocyte state abundance and transcriptional programs. Discordance between subtype annotations and dynamic functional programs further highlights the need for harmonized definitions of chondrocytes across phenotypic states.

genetics↗

bioRxiv2026

Sex differences in senescence burden within human osteoarthritic synovial fibroblasts

ObjectiveCellular senescence has been shown to underlie many age-related diseases, including osteoarthritis (OA). In addition to age, biological sex is an OA risk factor with females at greater risk of hand and knee OA. We profiled the senescence burden in OA human synovial fibroblasts while accounting for these factors to understand how senescence may contribute to the increased burden of OA in females. MethodsSynovial fibroblasts were isolated from tissue obtained at knee arthroplasty for OA from 10 male and 10 female donors. Single cell multiplexed immunofluorescence imaging was used to profile the senescence burden in samples age-matched to account for the differences in chronological age. Clustering was performed using stability and generalizability scoring. ResultsIndependent of chronological age, OA synovial fibroblasts from female donors showed higher levels of senescence associated proteins p16, p21, p53, phospho-p65, IL-6, and IL-8. Assessment of oxidative stress associated proteins NRF2, SEPP1, NQO1 and TXNIP indicated a lower capacity for female cells to respond to oxidative stress. Clustering analysis revealed male and female enriched clusters. The female-enriched clusters showed higher levels of senescence-associated proteins and an increased oxidative stress response. ConclusionsOA synovial fibroblasts from female donors demonstrated higher levels of senescence associated markers, lower ability to respond to oxidative stress, and increased senescence with increasing age. These findings indicate that female synovial fibroblasts are more likely to show markers of senescence and oxidative stress, suggesting senescence can contribute to the increased incidence of osteoarthritis in women.

cell biology↗

bioRxiv2026

Human hip osteoarthritis-associated Chadl variant induces intervertebral disc degeneration in mice

Chondroadherin-like (CHADL), a small leucine-rich proteoglycan, plays a role in ECM assembly and chondrocyte differentiation. CHADL has been implicated in osteoarthritis (OA) due to the discovery of a rare frameshift variant (rs532464664) that confers one of the highest genetic risks for hip OA reported to date. In this study, we characterized the skeletal phenotypes of two mouse models of Chadl loss-of-function, a global null and an 8bp insertion that mimics the human frameshift variant. Surprisingly, while there was a slight increase in knee OA at 12 months, there were no genotype-based differences in knee or hip OA in aged mice. Interestingly, histological assessment revealed phenotypic changes in the intervertebral discs of mutant mice, along with increased disc height index, suggesting altered motion-segment biomechanics. Polarized imaging showed dysregulated collagen turnover in the annulus fibrosus (AF), evidenced by changes in the proportions of thin and intermediate fibers. There was decreased abundance of the nucleus pulposus (NP) marker CA3 and decreased staining for ECM proteins in the AF of mutants. CHADL loss affected vertebral trabecular architecture, cortical thickness, and mineral density. This study highlights an unrecognized role of CHADL in fine-tuning ECM homeostasis and health of the intervertebral disc and vertebral bone.

cell biology↗

bioRxiv2026

Gradients in excitability generate hippocampal waves and shape their interactions with cortex

Travelling waves are a prominent feature of hippocampal activity, but the mechanisms determining their propagation and influence on the cerebral cortex remain unclear. Using a biophysically-grounded model of neural activity evolving across hippocampal and cortical surfaces, we show that spatial gradients in external in-put or neural excitability are a sufficient mechanism for the emergence of travelling waves along the long axis of the hippocampus. These waves emerge only above a critical gradient threshold, propagate with biologically-plausible velocities and exhibit frequency-dependent reversals in direction across slow and fast theta regimes. When coupled to the cerebral cortex, anterior-to-posterior hippocampal waves selectively reorganise globally synchronous cortical activity into metastable travelling waves, whereas posterior-to-anterior hippocampal waves do not, revealing a directional asymmetry in hippocampal-cortical communication. Conversely, cortical waves aligned with large-scale functional gradients induce structured hippocampal waves, revealing complementary direction specific effects across the two systems. These analyses identify structured excitability gradients as a principle governing wave propagation in the hippocampus and suggest how wave-to-wave interactions may coordinate complex cortical and hippocampal interactions during mnemonic and perceptual processes.

neuroscience↗

bioRxiv2026

CRISPR-mediated engineering of bovine satellite cells for Alpha-Gal Syndrome-compatible cultivated meat

Alpha-gal Syndrome (AGS) is a potentially life-threatening allergy caused by an IgE-mediated immune response to galactose--1,3-galactose (alpha-gal), a carbohydrate epitope present in most mammalian meats. Currently, strict avoidance of mammalian meat remains the primary management strategy for affected individuals, and alpha-gal-free beef is not commercially available. Here, we leverage cultivated meat as a biotechnology plat-form to address this unmet clinical need by engineering alpha-gal-free bovine muscle cells. Using CRISPR/Cas9 genome editing, we disrupted GGTA1, the gene encoding 1,3-galactosyltransferase, in immortalized bovine satellite cells (iBSCs). High-efficiency editing produced clonal GGTA1 knockout iBSCs harboring a homozygous frameshift mutation. Flow cytometry and immunofluorescence confirmed loss of the alpha-gal epitope, while bulk RNA-seq indicated minimal disruption of global gene expression and preserved myogenic differentiation capacity. Importantly, lysates from GGTA1 knockout iBSCs elicited substantially reduced basophil activation in assays using plasma from a patient with AGS, indicating reduced basophil activation consistent with reduced allergenic potential. Together, these findings establish a proof of concept for engineering AGS-compatible cultivated meat and demonstrate the potential of cultivated meat technologies to address human health challenges. HIGHLIGHTS{circ} CRISPR/Cas9-mediated disruption of GGTA1 eliminated alpha-gal from bovine satellite cells {circ}GGTA1 knockout cells retained myogenic identity and differentiation capacity {circ}GGTA1 knockout reduced basophil activation in an alpha-gal syndrome immune assay {circ}Genome-edited bovine cells provide a proof of concept for AGS-compatible cultivated meat

bioengineering↗

bioRxiv2026

Inferring norepinephrine dynamics from partial observations reveals the temporal structure of elevations during arousal

Hemodynamic artifacts present a significant challenge for two-photon fluorescence imaging of genetically encoded reporters, particularly when the timescale of relevant measurements matches those of vascular dynamics. This is an acute challenge for sensors in which the hemodynamic artifact is of comparable magnitude to the biological signal of interest. However, standard correction methods, such as isobestic recording or repeated experiments, are often impractical. Here we introduce a tiered framework for inferring norepinephrine (NE) dynamics across varying levels of recording information. First, we verify that dual-channel recording using an inert fluorescent reporter alongside the neuromodulator indicator enables direct hemodynamic correction within the same recording session. For contexts in which a dedicated reference channel is unavailable, we trained an LSTM-based model that predicts and removes hemodynamic contributions post-hoc from the recorded NE signal and behavioral variables. Finally, we show that key features of NE dynamics can be recovered from behavioral variables alone, providing an estimate of neuromodulatory state even when fluorescence recordings are unavailable. These methods enabled simultaneous multi-spectral measurements of axonal activity and neuromodulator release via simultaneous two-photon imaging of LC noradrenergic axons and extracellular NE in the same field of view. Cortical NE signals are graded with respect to behavioral intensity, scaling with both locomotion duration and pupil dilation amplitude. As expected, axonal activity precedes increases in ambient NE levels, but NE peaks later within a run and remains elevated after axonal activity has subsided, suggesting that extracellular NE integrates LC output over time rather than tracking instantaneous LC firing. Together, these findings demonstrate that accurate hemodynamic correction is essential for interpreting NE dynamics, and reveal a clearer view of the temporal structure of cortical norepinephrine signaling.

neuroscience↗

bioRxiv2026

Comparative whole-genome analyses of articular chondrocytes and skin fibroblasts reveal distinct genome instability landscapes in mesenchymal cell types

DNA damage lesions can result in mutations and genome rearrangements that are associated with cellular aging and diseases. The landscape of somatic mutations in individual tissue and cell types are dictated by their unique physiological states, cellular functions, mutagenic exposures, and efficiency of DNA repair. Articular chondrocytes and skin fibroblasts are two cell types of mesodermal origin with distinct exposure to internal and external sources of DNA damage. While somatic genome instability features of skin fibroblasts have been well detailed, knowledge about mechanisms underlying genome changes in chondrocytes is scarce. Here, we took a whole-genome sequencing approach to evaluate the load, sources, and patterns of genome changes in 18 primary human chondrocyte clones from donors with and without osteoarthritis (OA). Findings in chondrocyte clones largely agreed with a recent study of 100 single-cell sequenced chondrocytes. We compared genome changes in chondrocytes with clonally-expanded human skin fibroblasts sequenced in our previous studies. We demonstrated that skin fibroblasts show a higher burden of somatic mutations, with an increased rate of mutation accumulation per cell division. Motif-centered analyses of mutation catalogues identified only endogenous sources of mutations in chondrocytes, as opposed to skin fibroblasts which also showed a heavy burden of UV-induced mutations. Spontaneous deamination of meCpG and mutagenesis by exposure to small epoxides and SN2 electrophiles showed higher mutagenic activities in chondrocytes compared to skin fibroblasts. Chondrocytes showed ubiquitous prevalence of indels in homonucleotide runs of [≥]5 bases, while skin fibroblasts showed high contributions of UV-associated deletions of [≥]5bp not in repeats. Structural variants in rearrangement hotspots colocalized with human common fragile sites in skin fibroblasts, but not in chondrocytes. Together, our study comprehensively recorded genome instability features in chondrocytes and highlighted the unique mutagenesis landscapes of two mesenchymal cell types.

genetics↗

bioRxiv2025

How human aging disrupts the head direction network: evidence from VR experiments and mechanistic models

Navigational deficits during aging can severely limit mobility and reduce quality of life. While research on the underlying neural mechanisms has primarily focused on medial temporal lobe dysfunction, the head-direction (HD) system--a core component of the mammalian navigation circuit--remains largely unexplored in the context of aging. We established an immersive virtual reality paradigm that provides direct behavioral read-outs of HD signals. In addition, we developed a biologically inspired HD model, which accommodates noise sources that simulate age-related neural changes. Compared to younger adults, older participants exhibited larger angular errors, and a brief delay increased their heading uncertainty. In addition, our novel ring-attractor architecture shows that synaptic noise and small-scale neuronal loss replicate the magnitude and dynamics of the age-related deficits observed behaviorally. Together, these behavioral and computational findings provide the first evidence that aging compromises the fidelity and stability of the HD system. By pinpointing noise accumulation and neuron attrition as mechanistic contributors, our study significantly advances the understanding of spatial navigation deficits in old age, and it highlights novel targets for interventions aimed at preserving navigational abilities and quality of life.

neuroscience↗

bioRxiv2025

Harmonized Protocol for Segmentation of the Hippocampal Tail on High-Resolution in vivo MRI from the Hippocampal Subfields Group (HSG)

The hippocampus is a heterogeneous structure with cytoarchitectonically distinct subfields that exhibit heterogeneous lifespan trajectories and are differentially susceptible to diseases. Advances in high-resolution imaging have accelerated research on these structures, yet variability in segmentation protocols limits cross-study comparability. The Hippocampal Subfields Group (HSG) is an international consortium addressing this challenge by developing a reliable, accessible, and freely available segmentation protocol for high-resolution T2-weighted 3 tesla MRI scans (http://www.hippocampalsubfields.com). Here, we present the harmonized protocol for the posterior portion of the hippocampus (the "tail"), complementing the previously established "body" protocol, and with an anterior "head" protocol under development. The tail protocol provides standardized definitions of the external boundaries for the posterior-most extent of the hippocampus, facilitating consistent segmentation from surrounding tissues. The research community was extensively involved through an online survey that incorporated comprehensive protocol details, feasibility assessments, tutorial videos, and illustrative segmentations. Through this collaborative process, consensus emerged to exclude subfield labeling in the hippocampal tail due to limited visibility of internal landmarks and substantial anatomical variability in this region. All proposed boundary guidelines were deemed clear and agreed upon via a Delphi procedure. The harmonized tail protocol has high intra-(Averaged ICC(2,1) > 0.98; Averaged Dice Similarity Coefficient = 0.92) and inter-rater reliability (Averaged ICC(2,k) > 0.98; Averaged Dice Similarity Coefficient = 0.86) and offers a practical framework for replicable segmentation. By establishing standardized guidelines, this protocol enhances comparability of findings across developmental, aging, and clinical research and is compatible with ongoing technological advances.

neuroscience↗

bioRxiv2025

Altered coding of environmental boundaries in human aging: an fMRI study

Aging is associated with changes in spatial memory and navigation, yet the mechanisms underlying these changes are not yet fully understood. Environmental boundaries are among the most salient and reliable spatial cues, supporting both spatial memory and orientation. Here, we investigated how aging affects the use and the neural representation of boundary information during a virtual object location memory task. Healthy young and older adults navigated a square virtual environment while undergoing functional magnetic resonance imaging, allowing us to assess moment-to-moment encoding of distance to environmental boundaries in the entorhinal cortex and subiculum. Behaviorally, both age groups showed more accurate memory for objects located near boundaries, but this effect was amplified in older adults, whose spatial precision declined more steeply with increasing distance from boundaries. Older adults also exhibited a stronger bias to recall objects closer to boundaries. Analysis of navigation behaviour revealed that older adults followed boundary-oriented paths regardless of target location, whereas young adults flexibly adapted their navigation based on spatial context. Neurally, older adults--but not young adults--showed significant blood-oxygen-level-dependent modulation by boundary distance in the entorhinal cortex and subiculum, with activity decreasing as participants moved farther from boundaries. This effect was most pronounced in low-performing older adults and was associated with stronger behavioral boundary bias, suggesting a maladaptive reliance on proximity-based cues. Together, our results provide converging behavioral and neural evidence that aging alters the use and representation of boundary information, with downstream effects on spatial memory. Altered boundary processing may represent a key mechanism contributing to age-related declines in spatial cognition.

neuroscience↗

bioRxiv2025

A unified model of cortico-hippocampal interactions through neural field theory

Numerous physical systems evolve on curved manifolds whose geometry constrains their dynamics. The human brain provides a canonical example, with large-scale neural activity evolving on distinct anatomical surfaces such as the cortex and hippocampus. Within each structure, intrinsic feedback loops and manifold geometry shape characteristic neural rhythms. However, core cognitive functions of the brain arise from reciprocal interactions between these spatially distinct neural structures. Here, we introduce a general framework for geometry-constrained coupling between spatially extended dynamical systems evolving on separate manifolds. Using quasi-conformal mapping, we construct neighbourhood-preserving interactions that enable continuous neural activity on distinct geometries to interact while preserving local neighbourhood structure. Applying this framework to neural activity evolving on cortical and hippocampal surfaces, we show that increasing inter-manifold coupling reorganises system dynamics, producing frequency shifts, mode interactions, and coupling-driven instabilities consistent with critical transitions. These effects reproduce key features of large-scale brain activity, including topographically organised synchronisation between cortex and hippocampus during healthy cognition and critical transitions to seizure-like spectral dynamics. These results identify inter-manifold coupling as a core influence on dynamics in the human brain and highlight the broader role of geometry-constrained coupling on emergent dynamics in complex spatially extended systems.

neuroscience↗

bioRxiv2025

Brain-heart coupling shapes large scale brain dynamics

Functional brain networks reconfigure to support adaptive behaviour, balancing integration and segregation. These dynamics are influenced by neuromodulatory arousal, reflected in heart rate (HR) fluctuations. We leverage intracranial EEG (iEEG), functional MRI (fMRI), and HR recordings during emotional movie viewing to probe neurocardiac contributions to large-scale network dynamics. Network dynamics using high-frequency iEEG activity (60-140 Hz), an established marker of neuronal firing, reveal that greater network integration tracks elevated HR, while segregation aligns with lower HR. However, we observe an inverted relationship between HR and network dynamics in a separate fMRI dataset utilising the same movie, and replicate this in another independent fMRI dataset. Biophysical modelling of BOLD from iEEG reproduces the iEEG-HR findings, suggesting neurovascular transformation may obscure neural-cardiac links in fMRI. These results link large-scale network dynamics to physiological arousal through HR driven adrenergic-cholinergic neuromodulation and highlight the complex interplay between neural activity, autonomic regulation, and haemodynamics.

neuroscience↗

bioRxiv2025

Seeing through the Static: Reduced Imagery Vividness in Aphantasia is Associated with Impaired Temporal Lobe Signal Complexity

Aphantasia is the inability to experience mental imagery in full wakefulness without any prominent perceptual deficits. Visual aphantasia is associated with differences in distributed brain networks, but its neurobiological underpinnings remain a mystery. We rationalised that aphantasia may arise due to impairments in the top-down control over visual imagination. We expected that this in turn would prevent the brains of aphantasic subjects from differentiating neural activity encoding the contents of imagination from the background noise of resting activity, particularly within the ventral temporal lobes. To test this hypothesis, we re-analysed functional magnetic resonance imaging data collected from aphantasics (n = 23) and controls (n = 20) during a simple perception and imagery task. We used two measures of informational complexity to quantify the complexity of the spatial pattern of thresholded BOLD signal in the participants temporal lobes during visual imagery. This spatial complexity was lower in aphantasics than controls during blocks of imagery, but not during perception (P < 0.05). We then performed dynamic functional connectivity analyses on the same data to demonstrate that the higher-order networks of aphantasics coupled abnormally with the temporal lobes during imagery (P < 0.05). These results provide a novel perspective, reframing aphantasia as an inability of the visual system to selectively activate regions encoding object-specific visual categories above background levels of noise.

neuroscience↗

bioRxiv2024

Response splicing QTLs in primary human chondrocytes identifies putative osteoarthritis risk genes

Osteoarthritis affects millions worldwide, yet effective treatments remain elusive due to poorly understood molecular mechanisms. While genome-wide association studies (GWAS) have identified over 100 OA-associated loci, identifying the genes impacted at each locus remains challenging. Several studies have mapped expression quantitative trait loci (eQTL) in chondrocytes and colocalized them with OA GWAS variants to identify putative OA risk genes; however, the degree to which genetic variants influence OA risk via alternative splicing has not been explored. We investigated the role of alternative splicing in OA pathogenesis using RNA-seq data from 101 human chondrocyte samples treated with PBS (control) or fibronectin fragment (FN-f), an OA trigger. We identified 590 differentially spliced genes between conditions, with FN-f inducing splicing events similar to those in primary OA tissue. We used CRISPR/Cas9 to mimic an SNRNP70 splicing event observed in OA and FN-f-treated chondrocytes and found that it induced an OA-like expression pattern. Integration with genotyping data revealed 7,188 splicing quantitative trait loci (sQTL) affecting 3,056 genes. While many sQTLs were shared, we identified 738 and 343 condition-specific sQTLs for control and FN-f, respectively. We identified 15 RNA binding proteins whose binding sites were enriched at sQTL splice junctions and found that expression of those RNA binding proteins correlated with exon inclusion. Colocalization with OA GWAS identified 6 putative risk genes, including a novel candidate, PBRM1. Our study highlights the significant impact of alternative splicing in OA and provides potential therapeutic targets for future research.

genetics↗

bioRxiv2024

Thalamic Control Over Laminar Cortical Dynamics Across Conscious States

The human brain must support both stable and flexible neural dynamics in order to adapt to changing contexts that are inherently non-linear. The thalamus has been linked to the coordination of these opposing dynamical regimens in the cerebral cortex, however existing methodological approaches have not integrated sufficient neurobiological details with a sensitive measure of neural dynamics that permits sensitivity to time-series non-linearities. Inspired by the field of fluid dynamics, we use a novel approach to show that spontaneous fMRI data exhibits non-trivial fluctuations in predictability over time, akin to a river that has sections of smooth and predictable (laminar) versus rough and unpredictable (non-laminar) fluid flow. We use a combination of pharmacological fMRI, macaque electrophysiology and a large-scale biophysical model of the thalamocortical system to provide robust evidence that the thalamus provides versatile control over globally linear dynamics in the cerebral cortex that characterize conscious states.

neuroscience↗

bioRxiv2024

Phylogenetically-Preserved Multiscale Neuronal Activity: Iterative Coarse-Graining Reconciles Scale-Dependent Theories of Brain Function

Brain recordings collected at different resolutions support statistically distinct signatures of information processing, leading to scale-dependent theories of brain function. Here, we demonstrate that these disparate neural-coding signatures emerge from the same multiscale functional organisation of neuronal activity across calcium-imaging recordings collected from the whole brains of zebrafish and nematode, as well as sensory regions of the fly, mouse, and macaque brain. Network simulations show that hierarchical-modular structural connectivity facilitates multiscale functional coordination, enhancing information processing benefits such as a maximal dynamic range. Finally, we demonstrate that this cross-scale organisation supports distinct behavioural states across species by reconfiguring functional affiliation and temporal dynamics at the mesoscale. Our findings suggest that self-similar scaling of neuronal activity is a universal principle that reconciles scale-dependent theories of brain function, facilitating both efficiency and resiliency while enabling significant reconfiguration of mesoscale cellular ensembles to accommodate behavioural demands.

neuroscience↗

bioRxiv2024

A network correspondence toolbox for quantitative evaluation of novel neuroimaging results

Decades of neuroscience research has shown that macroscale brain dynamics can be reliably decomposed into a subset of large-scale functional networks, but the specific spatial topographies of these networks and the names used to describe them can vary across studies. Such discordance has hampered interpretation and convergence of research findings across the field. To address this problem, we have developed the Network Correspondence Toolbox (NCT) to permit researchers to examine and report spatial correspondence between their novel neuroimaging results and sixteen widely used functional brain atlases, consistent with recommended reporting standards developed by the Organization for Human Brain Mapping. The atlases included in the toolbox show some topographical convergence for specific networks, such as those labeled as "default" or "visual". Network naming varies across atlases, particularly for networks spanning frontoparietal association cortices. For this reason, quantitative comparison with multiple atlases is recommended to benchmark novel neuroimaging findings. We provide several exemplar demonstrations using the Human Connectome Project task fMRI results and UK Biobank independent component analysis maps to illustrate how researchers can use the NCT to report their own findings through quantitative evaluation against multiple published atlases. The NCT provides a convenient means for computing Dice coefficients with spin test permutations to determine the magnitude and statistical significance of correspondence among user-defined maps and existing atlas labels. The NCT also includes functionality to incorporate additional atlases in the future. The adoption of the NCT will make it easier for network neuroscience researchers to report their findings in a standardized manner, thus aiding reproducibility and facilitating comparisons between studies to produce interdisciplinary insights.

neuroscience↗

bioRxiv2024

Response eQTLs, chromatin accessibility, and 3D chromatin structure in chondrocytes provide mechanistic insight into osteoarthritis risk

Osteoarthritis (OA) poses a significant healthcare burden with limited treatment options. While genome-wide association studies (GWAS) have identified over 100 OA-associated loci, translating these findings into therapeutic targets remains challenging. Integrating expression quantitative trait loci (eQTL), 3D chromatin structure, and other genomic approaches with OA GWAS data offers a promising approach to elucidate disease mechanisms; however, comprehensive eQTL maps in OA-relevant tissues and conditions remain scarce. We mapped gene expression, chromatin accessibility, and 3D chromatin structure in primary human articular chondrocytes in both resting and OA-mimicking conditions. We identified thousands of differentially expressed genes, including those associated with differences in sex and age. RNA-seq in chondrocytes from 101 donors across two conditions uncovered 3782 unique eGenes, including 420 that exhibited strong and significant condition-specific effects. Colocalization with OA GWAS signals revealed 13 putative OA risk genes, 10 of which have not been previously identified. Chromatin accessibility and 3D chromatin structure provided insights into the mechanisms and conditional specificity of these variants. Our findings shed light on OA pathogenesis and highlight potential targets for therapeutic development. Highlights{circ} Comprehensive analysis of sex- and age-related global gene expression in human chondrocytes revealed differences that correlate with osteoarthritis {circ}First response eQTLs in chondrocytes treated with an OA-related stimulus {circ}Deeply sequenced Hi-C in resting and activated chondrocytes helps connect OA risk variants to their putative causal genes {circ}Colocalization analysis reveals 13 (including 10 novel) putative OA risk genes

genetics↗