Biology subjects

White, A.

Publications and source records attributed to White, A..

At least 19 recordsLinked to original sources

bioRxiv2026

L-DOPA Rescues Reach Height but Not Trajectory Area in a Bimanual String-Pulling Behavior in Parkinsonian Rats

While gross motor changes in Parkinson's disease, bradykinesia, hypokinesia, difficulty initiating movement, have been well studied in rodent models of the disease, limb movements, and especially bimanual coordination deficits, are more difficult to study in these animal models. Here we describe a novel bimanual string-pulling task that can be used to generate a rich repertoire of behaviors that require limb and bimanual coordination in rats with unilateral 6-hydroxydopamine (6-OHDA) lesion. We show that 6-OHDA lesion significantly reduces string speed, pulling bout duration, paw speed especially during reaching, and reduces the area of paw trajectories during pulling. However, it does not affect the variability around that movement trajectory. We also show that levodopa (L-DOPA) treatment restores many of these measures but not all. L-DOPA restores paw speed and string-pulling speed and fully restores paw reach height and pulling bout duration, but has no effect on trajectory area. Together, our results demonstrate that dopamine depletion differentially effects features of this bimanual coordination task, that L-DOPA mostly, but not fully, restores string pulling performance, and opens up a new avenue for measuring the effect of Parkinson's disease treatments on motor movement, allowing for better assessment of how effectively treatments restore motor activity.

neuroscience↗

bioRxiv2026

Increased EV yield and bioactivity of matrix-bound nanovesicles compared to conditioned culture medium-derived extracellular vesicles

Aim: Extracellular vesicles (EVs) are nanoparticles secreted by cells for cell-cell communication functions, such as wound repair, but low yields often limit their use. Several isolation methods have been explored to increase EV yield from conditioned culture medium (liquid-EVs); however, few studies compare isolation techniques and yield between liquid-EVs and matrix-bound nanovesicles (MBVs), a novel EV subtype embedded within the extracellular matrix. Methods: We isolate liquid-EVs and MBVs from mesenchymal stem cells (MSC) using size exclusion chromatography (SEC) and ultracentrifugation (UC) across various timepoints (14, 21, 24, 30 days). EVs are characterized by their yield, size, morphology, protein concentration, surface marker expression (CD9, CD81, ALIX), zeta potential, and influence on fibroblast wound closure. Results: We find that isolation method influences yield, where both SEC isolated liquid-EVs and MBVs yield higher particle counts and protein compared to UC. Interestingly, we find that regardless of isolation method, MBVs have a significantly higher yield than liquid-EVs from the same culture (15.6-fold higher using UC and 7.49-fold higher using SEC). Culturing for 24 days yielded the greatest number of MBV particles and protein. We performed a fibroblast scratch assay to assess bioactivity and found that liquid-EVs decreased wound closure compared to a medium control, whereas MBVs did not. Conclusion: Our work suggests SEC maximizes particle and protein yields for MSC-EVs. By achieving much higher yields of MBVs compared to liquid-EVs, and their promise as a wound repair strategy, we offer an alternative EV choice when EV yields are an issue towards translation.

bioengineering↗

bioRxiv2026

Metabolic regulation of cytokine responses in diffuse large B-cell lymphoma

Aberrant communication between cells of the immune system can drive disease progression. Cytokines form the central pilar of immune cell communication and are well established factors in lymphomagenesis. An increasing body of evidence suggests that immunometabolism is tightly connected to cytokine production. However, the exact link between metabolism and cytokine responses during lymphomagenesis remains largely unknown. Here, we used established cell models representing the most common form of B-cell lymphoma, diffuse large B-cell lymphoma (DLBCL), to study the effect of metabolism on cytokine production. We found that stimulation or inhibition of the glycolysis pathway could attenuate IL-6, IL-10 and TNFa; production by DLBCL. Furthermore, we found that two different subtypes of DLBCL displayed distinct metabolic responses to IL-4. In summary, our work suggests that metabolic pathways could be involved in controlling cytokine production in DLBCL, and paves the road for further research aimed at finding specific metabolic targets that can be exploited for therapeutic intervention.

cancer biology↗

bioRxiv2026

Complex epidemiological dynamics driven by the combination of host spatial structure and seasonal forcing

Spatial population structure and seasonality are both central to the spread of many infectious diseases of plants, animals and humans. While seasonal forcing in transmission often plays an important role in epidemiological models of a wide range of infectious disease, and we now have some theoretical understanding of the dynamical impacts of spatial structure, the combined effects of these two ubiquitous processes has not been examined in detail. Here, we develop a novel model to explore the combined influence of spatial structure and temporal variability on disease dynamics. Spatial structure is represented using a lattice-based approach with near-neighbour interactions, while temporal variability is included through regular, seasonal, variation of the transmission rate. We use bifurcation analysis of a pair approximation of the full spatial model to identify the parameter regimes associated with qualitatively distinct dynamical behaviours. The model exhibits a remarkably wide range of complex dynamics, including limit cycles, quasi-periodic cycles, multi-year cycles, chaotic dynamics and bistability between these different states. In particular, complex dynamics occur when reproduction is predominantly local, with the dynamics depending critically on the amplitude of the seasonal transmission rate. We show how high transmission rates, high birth rates and in particular low recovery rates are requirements for complex dynamics. We predict that SI-type disease interactions in plant pathogen systems will show complex dynamics even with relatively global transmission dynamics.

ecology↗

bioRxiv2026

Gene-metabolite networks reveal physiological trade-offs but not transcriptional co-regulation between carotenoids and dry matter in cassava (Manihot esculenta) roots

Provitamin A biofortification of cassava (Manihot esculenta) is constrained by a negative genetic correlation between total carotenoid (TC) and dry matter (DM) contents, but its underlying biological mechanism remains unclear. We examined this relationship in 24 African, Latin American, and hybrid cassava genotypes by measuring gene expression and metabolites in inner and outer storage root layers that varied spatially in carotenoid accumulation, enabling comparisons across and within genotypes. TC, and particularly upstream cis-carotenes, were negatively associated with DM after accounting for genotype, and this relationship strengthened across developmental timepoints, consistent with a physiological component of the trade-off. Gene-metabolite co-expression networks constructed from genetic, non-genetic, and overall phenotypic trait components showed no significant topological overlap between carotenoid- and starch-related gene sets, indicating that the TC/DM relationship is not driven by transcriptional co-regulation of the main pathways, although individual associations between carotenoids and carbohydrate-related genes suggested possible indirect metabolic links. Instead, TC accumulation was most strongly associated with regulatory, stress-, redox-, and plastid-related genes, enriched for heme-binding and oxidoreductase functions. These findings suggest that the TC/DM trade-off is not a fixed constraint, and identify candidate regulators of carotenoid content for future functional validation to support cassava provitamin A biofortification. HighlightGenetic, spatial, and developmental variation in cassava storage roots implicate cis-carotenes, but not direct transcriptional regulation of the carotenoid and starch pathways, in the trade-off between carotenoids and dry matter.

plant biology↗

bioRxiv2026

Functional remodeling of the parasubthalamic nucleus drives alcohol drinking escalation in dependence

The neurocircuitry changes mediating the development and maintenance of an alcohol use disorder are complex and dynamic. The parasubthalamic nucleus (PSTN), a small nucleus of the posterior lateral hypothalamus best known for suppressing appetite, is interconnected with brain regions disrupted in addiction; yet its potential role in the regulation of alcohol consumption had never been examined. Here we show that the PSTN exerts potent control over alcohol drinking in mice. Remarkably, the influence of endogenous PSTN activity on voluntary alcohol consumption switches from inhibitory to stimulatory upon induction of alcohol dependence. Among PSTN cells, Crh neurons represent a unique subpopulation that promotes alcohol drinking and fires more in dependent mice. Alcohol intake escalation driven by PSTN Crh neurons involves thalamic output and behavioral disinhibition. Based on our results, PSTN Crh neurons could represent a critical node in the brain circuitry overactive in alcohol addiction driven by reward seeking in humans.

neuroscience↗

bioRxiv2026

Altered Crosstalk of Bacterial Lipopolysaccharide with Immune Cells in Colorectal Cancer Compared to Paired Adjacent Intestinal Tissue

Commensal bacteria play a crucial role in modulating human immune responses in the intestine. Under homeostatic conditions, gut microbiota are tightly regulated by interactions with the mucosal immune system. However, colorectal cancer (CRC) is characterized by an imbalance in bacterial composition and bacterial translocation across the intestinal barrier. The spatial distribution of bacteria and their interactions with immune cells in CRC tumors are poorly understood. By applying 3D light-sheet imaging, spatial transcriptomics, and imaging mass cytometry to patient-derived CRC and adjacent tissue, bacterial lipopolysaccharide (LPS) is visualized alongside immune cells and vessels. The results show regional bacterial LPS accumulation and colocalization with distinct immune cell subsets. In CRC-adjacent tissue, bacterial LPS is mainly associated with CD11c+ dendritic cells, CD15+ neutrophils, and CD163+ macrophages. In matched CRC tissue, the number and LPS colocalization of CD163+ macrophages and CD11c+ dendritic cells decreased, while CD15+ neutrophils and their colocalization with LPS increased. Notably, immune cell composition and immune cell-bacteria interactions differ between tumor and adjacent tissue, offering insights into host-microbiota dynamics and mechanistic interactions.

cancer biology↗

bioRxiv2026

Mutagenic and carcinogenic potency determinations for NDMA support the cumulative dose assumption underpinning the less-than-lifetime Threshold of Toxicological Concern

The management of N-nitrosamine impurities challenges pharmaceutical development and regulation worldwide. Because most medicinal exposures are shorter than lifetime and absolute impurity exclusion is impossible, reliable approaches to define duration-specific intake limits are essential. On the premise that carcinogenic risk is proportional to cumulative dose, the Less-Than-Lifetime (LTL) Threshold of Toxicological Concern (TTC) framework defines progressively lower intake limits for mutagenic impurities over longer exposures. However, N-nitrosamines are currently treated as a cohort of concern, necessitating compound-specific evaluation placing reliance on in vivo mutagenicity assays for impurity qualifications. To better understand durational potency relationships and the application domain of the LTL-TTC, we apply benchmark dose (BMD) modelling to cumulative-dose-scaled transgenic rodent (TGR), error-corrected sequencing and rodent carcinogenicity datasets for N-nitrosodimethylamine (NDMA) obtained from the published literature. For TGR, cumulative-dose scaling better resolved liver as the most sensitive organ and reduced interstudy variability: liver BMDs spanned [~]80-fold in daily-dose units but only [~]20-fold when scaled to cumulative dose. Among closely-matched mouse liver gavage studies, cumulative-dose BMDs only varied by [~]2.5-fold across 1 to 28-day treatment regimens. Error-corrected sequencing also demonstrated parity, with acute-dose regimens producing mutation burdens near-identical (< 1.2-fold) to those cumulated from 28-day repeat-dose regimens. Comparable results were obtained from carcinogenicity datasets confirming proportionality-of-effect to cumulative dose. These findings empirically support the validity of the LTL-TTC concept. More broadly, they demonstrate that short-term in vivo mutagenicity assays can serve as reliable surrogates for lifetime carcinogenicity studies, strengthening the scientific and regulatory basis for duration-adjusted acceptable intakes for N-nitrosamine impurities.

pharmacology and toxicology↗

bioRxiv2026

Human CD1c-autoreactive T cells recognise Mycobacterium tuberculosis-infected antigen-presenting cells and display cytotoxic effector programmes

Tuberculosis (TB), caused by Mycobacterium tuberculosis (Mtb), remains the leading cause of death from infection globally, yet the contribution of non-classical T-cell pathways to human immunity remains poorly defined. CD1c-autoreactive T-cells, which recognise self-lipids presented by the antigen-presenting molecule CD1c, are frequent in human blood, but their role during infection is unclear. Here, we investigate how CD1c-expressing antigen-presenting cells (APCs) and Mtb infection shape CD1c-autoreactive T-cell responses using engineered human APC systems, complemented by single-cell transcriptomic profiling to define the ex vivo phenotypic landscape of these T-cells. CD1c is present within human TB granulomas, whereas Mtb down-modulates CD1c expression on infected APCs, consistent with an immune evasion strategy. CD1c-autoreactive T-cells respond more strongly to Mtb-infected CD1c+ APCs than to uninfected cells, exhibiting enhanced activation, cytotoxicity, and diverse cytokine secretion via CD1c-dependent recognition. Under in vitro conditions, these T-cells reduce relative Mtb burden in infected phagocytes. Single-cell RNA-sequencing reveals cytotoxic effector-memory programmes and expression of antimicrobial molecules, providing a mechanistic basis for these responses. Together, these findings define a human CD1c-restricted T-cell response to Mtb-infected APCs and identify autoreactive CD1c-restricted T-cells as a candidate cellular axis for lipid-directed immunity in TB.

immunology↗

bioRxiv2026

Daily HIV pre-exposure prophylaxis enhances monocyte activation and effector function and reprogrammes cellular metabolism.

BackgroundPre-exposure prophylaxis (PrEP) with tenofovir/emtricitabine (TDF/FTC) is highly effective for HIV prevention. While antiretroviral therapy (ART) is linked to chronic inflammation in people living with HIV, its direct effects on immune phenotype, function, and metabolism in HIV-negative individuals remain unclear. MethodsGay, bisexual, and other men who have sex with men (gbMSM) on daily TDF/FTC PrEP underwent immunophenotyping and single-cell metabolic profiling using SCENITH. Cytokine and chemokine responses were measured ex vivo and after lipopolysaccharide or Mycobacterium tuberculosis stimulation. These were compared with a demographically similar PrEP-naive cohort, with five individuals followed 6-9 months after PrEP initiation. FindingsMonocytes from people taking PrEP (n=15; median 533 days) exhibited higher activation marker expression (HLA-DR, CD14) ex vivo and enhanced IL-1{beta} and TNF after bacterial challenge compared with PrEP-naive individuals (n=11). Longitudinal follow-up indicated that PrEP initiation increased monocyte activation markers (HLA-DR, CD14, CD40, TNFRI/II) and cytokine production (IL-1{beta}, TNF, GM-CSF, IFN-{gamma}, Granzyme B, MIP-1). Reduced glucose dependency was observed in monocytes, CD56dim NK cells and CD4+ T cells 6-9 months after PrEP initiation. InterpretationDaily TDF/FTC promotes monocyte activation, enhances pro-inflammatory responses, and reprogrammes immune cell metabolism, highlighting ARTs potential to modulate immune-mediated inflammatory pathways in HIV-negative individuals. FundingTrinity Translational Medicine Institute, Trinity College Dublin, Dublin, The Association of Physicians of Great Britain and Ireland, Health Research Board Ireland. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=85 SRC="FIGDIR/small/698427v1_ufig1.gif" ALT="Figure 1"> View larger version (28K): org.highwire.dtl.DTLVardef@d48088org.highwire.dtl.DTLVardef@1428926org.highwire.dtl.DTLVardef@13a4facorg.highwire.dtl.DTLVardef@144d1f1_HPS_FORMAT_FIGEXP M_FIG C_FIG Research in ContextO_ST_ABSEvidence before this studyC_ST_ABSDespite effective viral suppression with antiretroviral therapy (ART), people living with HIV (PLWHIV) experience persistent immune activation and chronic inflammation that increase their risk of age-associated comorbidities. The extent to which ART itself contributes to this dysregulated immune state remains unclear, as HIV infection confounds most studies. Pre-exposure prophylaxis (PrEP) with tenofovir disoproxil fumarate and emtricitabine (TDF/FTC) offers a unique opportunity to examine the direct immunological effects of ART in HIV-negative individuals. However, few studies have explored how PrEP influences immune cell activation, effector function, or cellular metabolism in the absence of viral infection. Added value of this studyThis study is the first to characterise how daily PrEP with TDF/FTC modulates innate immune activation and cellular metabolism independently of HIV infection. We show that PrEP enhances monocyte activation and effector cytokine production while reprogramming metabolic pathways to reduce glucose dependency in monocytes, NK cells, and CD4 T cells. These findings reveal previously unrecognised immunometabolic effects of ART in HIV-negative individuals, providing mechanistic insight into how ART exposure can shape immune homeostasis in the absence of infection. Implications of all the available evidenceOur findings, together with existing data from PLWHIV, suggest that ART itself can remodel immune and metabolic pathways, potentially contributing to both beneficial and detrimental outcomes. ART-induced immunometabolic reprogramming may underlie persistent inflammation and the early onset of comorbidities observed in treated HIV infection, while also enhancing innate responsiveness to bacterial pathogens such as Mycobacterium tuberculosis. Understanding these mechanisms may inform future strategies to optimise ART regimens and mitigate inflammation-associated complications.

immunology↗

bioRxiv2025

Ligand-responsive groove remodelling in human and macaque CD1d reveals a conserved MHC-like gating mechanism

CD1d presents lipid antigens to invariant natural killer T (iNKT) cells. We determined a high-resolution crystal structure of human CD1d bound to -galactosylceramide (-GalCer) at 1.76 [A], enabling detailed investigation of ligand-sensitive conformational flexibility at Phe84, a conserved aromatic residue that caps the F' groove. Electron density at Phe84 revealed multiple side-chain conformations, suggestive of ligand-induced plasticity. Molecular dynamics simulations indicated that the canonical rotamer is energetically favoured in the absence of a stabilising groove-occupying ligand. To assess conservation of this putative gating mechanism, we solved the first CD1d structure from a non-human primate, rhesus macaque CD1d--GalCer, at 1.83 [A] resolution. In contrast to the human complex, Phe84 in macaque CD1d adopted a fixed conformation. As this aromatic residue is conserved across CD1 isoforms and CD1d-expressing species, and mirrors gating residues in MHC class I that regulate peptide accommodation, our findings support a shared evolutionary strategy for managing antigen diversity. These data provide critical insight into the mechanisms of antigen presentation by CD1 molecules. Significance StatementThis study reveals that Phe84, a conserved aromatic residue in CD1d, may act as a ligand-responsive gate modulating F' groove accessibility. This conditional plasticity could enable binding of structurally diverse lipid antigens and appears conserved across CD1 isoforms. The mechanism parallels class I MHC, where gating residues regulate peptide presentation, suggesting an evolutionarily shared strategy for accommodating antigen diversity.

immunology↗

bioRxiv2025

Imaging-based temporal dynamics of electrophile-induced NRF2 signaling in liver cells identifies adaptive versus adverse repeated exposure conditions.

The activation of stress responses upon chemical exposure is critical to restore cellular homeostasis. One of these pivotal pathways is the oxidative stress response activated by NRF2 under control of sensor KEAP1. Soft electrophiles are known to bind with KEAP1 and consequently activate NRF2. However, the understanding of the NRF2 activation dynamics and influence on cellular fate during prolonged repeated exposure conditions is still lacking. Therefore, we accurately mapped the NRF2 activation dynamics upon single or repeated exposures using HepG2 BAC GFP reporters combined with live cell confocal imaging. In a 2D set-up, a concentration-dependent NRF2 activation and subsequent SRXN1 induction upon exposure to sulforaphane or CDDO-Me was observed. The level of NRF2 activation upon sulforaphane exposure highly correlated with cytotoxicity induction. Reactivation of NRF2 upon a second exposure without a recovery period was lower compared to initial exposure, yet resulted in a strong and sustained upregulation of SRXN1. In contrast, inclusion of recovery periods did allow for strong NRF2 and SRXN1 upregulation. In 3D, increased SRXN1 upregulation was observed upon a second exposure with sulforaphane after recovery up to 6 days compared to the first exposure, while similar or lower SRXN1 induction was observed after secondary CDDO-Me treatment. In conclusion, NRF2 activation dynamics and subsequently SRXN1 induction is highly chemical, concentration and exposure duration dependent. Recovery periods allows cells to adapt and initiate a secondary NRF2 response. Together this allowed for further understanding of NRF2 dynamics and cellular fate upon repeated exposures contributing to improving chemical safety testing.

pharmacology and toxicology↗

bioRxiv2025

Developmental benzopyrene exposure alters stress hormones, neurotransmitters and behavioral responses of mice dependent on Cyp1 genotype

Benzo[a]pyrene (BaP) is a prototypical polycyclic aromatic hydrocarbon (PAH) produced during combustion processes and when grilling foods. Epidemiological studies indicate exposure to PAHs during pregnancy lead to learning and memory deficits as well as behavioral problems that persist into adolescence. Studies in rodents and zebrafish have frequently reported anxiolytic effects of BaP exposure in adult animals and in developmental studies. We conducted sequential experiments of Cyp1a1(-/-) and Cyp1b1(-/-) knockout mice compared with wild type C57BL/6J mice to determine if genotype changes the response to developmental BaP exposure. We treated pregnant dams from gestational day 10 to postnatal day 25 (P25) with BaP in corn oil-soaked cereal or the corn oil vehicle and tested one male and one female offspring beginning at P60. We found increased exploratory behavior in the elevated zero maze for Cyp1a1(-/-) knockout mice, but no significant differences in Cyp1b1(-/-) knockouts. In contrast, Cyp1b1(-/-) knockout mice buried fewer marbles in a second test of anxiety-like behavior. There were no significant differences when Cyp1a1(-/-) knockout mice were tested. BaP decreased immobility time in Cyp1a1(-/-) knockouts in the forced swim test, but increased immobility time in wild type and Cyp1b1(-/-) knockout mice. We measured plasma corticosterone levels at baseline and following the forced swim test and monoamine neurotransmitters at the end of behavioral testing. BaP treatment increased corticosterone in wild type mice, but decreased it in Cyp1a1(-/-) knockout mice. Both BaP-exposed and corn oil control Cyp1b1(-/-) knockout mice had higher corticosterone levels compared with wild type mice. Dopamine and serotonin signaling were altered in the hypothalamus dependent on genotype, treatment and sex. Together, these data suggest that both CYP1A1 and CYP1B1 have a normal role in brain functioning or development, and that CYP1 genotype alters the response to developmental BaP exposure in behavioral and biochemical tests related to stress, anxiety and depression. HighlightsO_LIBaP-exposed Cyp1a1(-/-) mice had lower corticosterone and decreased immobility in the forced swim test C_LIO_LIBaP exposure increased FST immobility in wild type and Cyp1b1(-/-) mice C_LIO_LICyp1a1(-/-) and Cyp1b1(-/-) knockout mice showed less anxiety-like behavior C_LIO_LIDevelopmental BaP exposure altered corticosterone levels dependent on Cyp1 genotype C_LIO_LIGenotype, treatment and sex all impacted neurotransmitter levels in the hypothalamus C_LIO_LIGenetic differences in CYP enzymes altered susceptibility to developmental BaP exposure C_LI

pharmacology and toxicology↗

bioRxiv2025

Myelin Decompaction in Mice Given Anesthetics during Magnetic Resonance Imaging

AbstractThe objective of this secondary analysis of a prior investigation was to determine if prolonged exposure to the anesthetics isoflurane and dexmedetomidine during MRI was associated with a higher proportion of axons with myelin decompaction. 16 mice underwent an MRI protocol in which they had prolonged exposure to isoflurane and dexmedetomidine, while 10 mice did not undergo this protocol. All mice were sacrificed and electron microscope images were taken of various brain regions including the right prefrontal cortex (anterior cingulate and prelimbic area), the nucleus accumbens, the amygdala, and the ventral hippocampus.. Proportion of decompacted axons was calculated for each mouse, and an inter-rater reliability score of 80% was achieved. Welchs t-tests were used to test the hypothesis that mice undergoing MRI with prolonged anesthesia had greater levels of myelin decompaction than mice that did not experience prolonged anesthesia. Mice with prolonged anesthetic exposure during MRI had significantly higher proportions of decompacted axons than mice that did not experience prolonged anesthesia (p-value of 0.00003642). Prolonged exposure to anesthetics, particularly isoflurane, may be associated with myelin decompaction. These findings, if replicated, have potential to impact future anesthesia use in clinical work and scientific research. Significance StatementProlonged exposure to the anesthetics isoflurane and dexmedetomidine during brain imaging may lead to myelin decompaction in adult rodents. Myelin is a protective sheath around nerve fibers that ensures efficient transmission of electrical signals in the nervous system. Decompaction of myelin can disrupt these signals, potentially leading to neurological issues. This discovery is significant because it highlights potential risks associated with these anesthetics, which are commonly used in fMRI studies of rodents and in veterinary and medical procedures.

neuroscience↗

bioRxiv2025

Innate Immune Remodeling Drives Therapy Resistance via Macrophage-NK Cell Crosstalk.

The dynamic evolution of the immune tumor microenvironment (TME) during targeted therapy is a critical yet poorly understood determinant of treatment response and resistance. While most studies compare immune states before and after treatment, temporal immune changes during therapy remain largely uncharacterized, limiting development of effective combination strategies. Here, we investigated immune dynamics throughout targeted therapy using mouse melanoma models that recapitulate human therapeutic responses. Single-cell RNA sequencing (scRNA-seq) identified a previously unrecognized inflection point where the inflamed TME during tumor regression, characterized by robust NK cell infiltration, transitions to an immune-excluded state upon onset of drug-tolerant residual disease. We uncovered a unique macrophage subset (F4/80hiCCL5MHCIICD63) that orchestrates NK cell recruitment through CCR2/5 signaling during regression. Depletion of these macrophages using LysM-cre;iDTR mice significantly reduced NK cell infiltration. Specifically during residual disease, pharmacological inhibition of Ptpn22, a phosphatase that negatively regulates immune activation, reprogrammed macrophages, restored NK cell recruitment and enhanced therapeutic efficacy. Extending these findings to human cancer, longitudinal scRNA-seq analysis of melanoma and lung cancer patient samples revealed dynamic NK cell infiltration during targeted therapy, establishing a direct link between innate immune remodeling and treatment outcome. Unlike prior prognostic studies assessing immune states at single time points, our results provide mechanistic evidence of a temporal relationship between NK cell infiltration and therapeutic efficacy. Together, these findings position immune evolution as a driver of acquired resistance and identify macrophage-NK cell crosstalk as a therapeutically actionable axis to overcome immune exclusion and improve targeted therapy across multiple cancer types. One Sentence SummaryCancer therapy resistance emerges from a dynamic evolution of the tumor microenvironment, characterized by macrophage-driven NK cell infiltration during initial tumor regression, followed by exclusion of NK cells during residual disease, highlighting macrophage-NK cell interactions as a promising therapeutic target to improve clinical outcomes.

cancer biology↗

bioRxiv2025

Protein kinase CK2 alpha prime as a dual modulator of immune signaling and synaptic dysfunction in Tauopathy

Tauopathies are a group of neurodegenerative diseases characterized by tau accumulation, neuroinflammation, and synaptic dysfunction, yet effective treatments remain elusive. Protein Kinase CK2 has been previously associated with different aspects of tau pathology but genetic evidence for the contribution of CK2 to tauopathy remained lacking. Here, we show CK2, one of the two catalytic subunits of CK2, as a novel regulator of tau-mediated neurodegeneration. We found that CK2 expression is elevated in postmortem brains of dementia patients and in the hippocampus of PS19 tauopathy mice, especially in neurons and microglia. Using genetic haploinsufficiency in PS19 mice, we demonstrated that reduced CK2 levels significantly decrease phosphorylated tau and total tau burden in the hippocampus and cortex. CK2 depletion also attenuated microglial activation, pro-inflammatory cytokine production, and microglia synaptic engulfment, enhanced synaptic gene expression, synaptic density, and LTP. Importantly, CK2 depletion rescued cognitive deficits assessed in the Barnes maze. These effects appear to be mediated through both neuronal and glial functions and may involve CK2-dependent modulation of tau-associated phosphorylation and neuroinflammatory and immune signaling pathways. One Sentence summaryThis study highlights CK2 as a key node at the intersection of tau pathology, synaptic dysfunction, and neuroimmune signaling.

neuroscience↗

bioRxiv2025

The Role of Pace of Life in Animal Social Networks

The fast-slow continuum is a key axis of variation in life history strategies that captures the evolutionary trade-off between allocating in lifespan versus reproduction. It has been suggested that social behaviour, and therefore network structure, may vary across the fast-slow continuum, but formal theory remains scarce. We develop a novel mathematical model to examine how the rate of demographic replacement may influence emergent social network structures in natural populations. We additionally consider variation in social preferences and modes of social inheritance. Our key finding is that more rapid demographic replacement can substantially constrain the structure of dynamic social networks. For species with longer generation times, network structures are primarily determined by social preferences, while for shorter generation times they are primarily determined by mechanisms of social inheritance. By considering how demographic replacement can constrain social network organisation, our work provides important insights into social evolutionary ecology.

ecology↗

bioRxiv2025

Fleming: An AI Agent for Antibiotic Discovery in Mycobacterium Tuberculosis

Antibiotic development is challenged by high costs and failure rates. Artificial intelligence (AI) holds promise to overcome these challenges by predicting inhibitory properties of novel compounds, generating new candidates, and contextualizing property predictions in the biological background. Fleming is an integrative AI agent that explores novel chemical space to identify lead compounds meeting multiple criteria. The discriminative and generative AI models for Mycobacterium tuberculosis (Mtb) inhibition were trained on a set of 114,900 diverse compounds and fragments based on in vitro growth inhibition. We combined both models as well as molecular optimization, ADMET prediction and literature search functions to make Fleming an integrated agent for Mtb preclinical lead identification. Fleming has 17% higher discrimination between known Mtb leads and leads for other diseases than a generic LLM agent along with 13% higher discrimination than molecular property prediction alone on challenging ADMET tasks. Fleming demonstrates an 83% in vitro hit rate of predicted inhibition and a 100% hit rate of de novo generative design. Flemings generative designs also demonstrate an 83% rate of favorable ADMET profiles. Fleming is an integrative AI agent able to explore new regions of the chemical space to select lead compounds that simultaneously meet several desirable criteria.

bioinformatics↗