Biology subjects

Baker, C.

Publications and source records attributed to Baker, C..

At least 19 recordsLinked to original sources

bioRxiv2026

Collateral Immune Cell Signaling Compromises the Efficacy of T-cell Engaging Therapies for Cardiac Fibrosis

Cardiac fibrosis is causally linked to heart failure progression and survival. Currently, there are no approved treatments that directly target cardiac fibrosis. Recent studies have identified a subset of activated cardiac fibroblasts distinct from myofibroblasts that are marked by fibroblast activation protein (FAP) expression, emerge in the injured and diseased heart through inflammatory signaling, and contribute to fibrosis. Using a genetic mouse model, we demonstrate the potential benefits of FAP+ fibroblast depletion following myocardial infarction. Unexpectedly, while FAP targeted bispecific T-cell engaging antibodies (BiTE(R) molecules) effectively eliminate FAP+ fibroblasts from the heart, they surprisingly lead to accelerated deterioration of cardiac function, enhanced remodeling, and increased scar size. FAP BiTE(R) molecules elicit a robust cytokine response within the heart with prominent activation of interferon gamma (IFNg) and CD40 ligand pathways. Target cell killing was independent of IFNg; and CD40L signaling and blockade of these pathways was sufficient to unmask the protective therapeutic effects of FAP+ fibroblast depletion. Mechanistically, we reveal that IFNg; signaling to fibroblasts drives the differentiation of an independent lineage of activated fibroblasts not typically found in the infarcted heart, which are responsible for the harmful effects of FAP BiTE(R) molecules. Collectively, these findings highlight a previously unrecognized cardiac liability of BiTE(R) molecules and inform the design of the next generation of therapeutics.

immunology↗

bioRxiv2026

Forecasting high pathogenicity avian influenza with a stochastic mechanistic model: performance and lessons for Australia

High pathogenicity avian influenza (HPAI) H5N1 clade 2.3.4.4b has caused a global panzootic with unprecedented impacts on wildlife and livestock, making evidence-based disease mitigation and outbreak response critical. In this paper, we describe a spatiotemporal mechanistic model of infectious disease dynamics developed for the HPAI Modelling Challenge and its implications for forecasting and policy in Australia. To emulate emergency response conditions, we adapted an existing model for rapid deployment rather than developing a bespoke model. We refined the model iteratively across the challenge to better analyse the provided outbreak data. Throughout the challenge, we accurately forecast temporal trends and local outbreak spread, but could not predict rarer, long-distance dispersal events. The challenge ended before HPAI H5N1 was first detected in Australia (June 2026), providing a critical opportunity to test our response modelling readiness for an incursion in wildlife and potential spillover into commercial poultry. Our experience identifies three key considerations for Australia's HPAI H5N1 preparedness: targeted enhancements to our model to improve forecast precision and enable scenario-based policy evaluation; the critical value of pre-existing modelling infrastructure for rapid emergency response; and sustained collaboration between research and policy institutions to align modelling capabilities with outbreak response requirements.

bioinformatics↗

bioRxiv2026

Losses of TMC and CIB neurosensory genes in schizophoran flies at the PETM

The K-Pg extinction ended the world of non-avian dinosaurs 66 Mya and ushered in the Age of Mammals. During the [~]10 My of recovery, Schizophora, an immensely successful group of flies, appeared, flourished and diversified. This large radiation produced over half of all dipteran families ([~]78/150), including the family for Drosophila, the model genetic powerhouse. In the context of this evolutionary radiation, we investigate the loss of two of three highly conserved, neurosensory transmembrane channel (TMC) genes. Here, we show that these genes were separately lost across multiple diverging schizophoran lineages of the early Paleogene, suggesting a powerful environmental driver was involved. We also show that unlinked genes encoding the calcium- and integrin-binding (CIB) subunits of the missing TMC complexes were lost during the same time frame. Because the lost genes encode complexes involved in thermal nociception, we propose the external driver was likely the Paleocene- Eocene thermal maximum (PETM), a 200 ky interval of elevated global temperatures occurring 56 Mya, slightly before the earliest schizophoran fossil from 53 Mya. These results suggest that gene loss may have been adaptive for most schizophoran lineages to emerge past the hothouse Earth of the PETM.

evolutionary biology↗

bioRxiv2026

Autonomous computational prioritisation of colorectal cancer vulnerabilities via multi-scale AI swarms

The acceleration of automated scientific discovery has been fundamentally bottlenecked by the epistemic gap between the semantic reasoning of large language models (LLMs) and the complex, non-linear reality of mammalian biology. While recent multi-agent frameworks have achieved autonomous hypothesis generation and in vitro experimental analysis, they frequently lack the rigorous statistical constraints required for multi-scale clinical translation. Furthermore, while algorithmic clinical digital twins successfully forecast biological states, they often rely on opaque latent spaces, sacrificing mechanistic interpretability for predictive accuracy. Here, we introduce the Multi-Scale Autonomous Discovery Engine (Octopus), a neuro-symbolic framework that unites a fully localised, privacy-preserving multi-agent swarm with regularised predictive algorithmic environments. Rather than stopping at isolated cellular assays, the system autonomously prioritises therapeutic hypotheses against in vitro CRISPR dependency data (CCLE), traces feature attribution cascades using XGBoost SHAP vectors, and orthogonally translates emergent vulnerabilities in silico to predict in vivo mammalian tumour trajectory (PDX) and human overall survival (Marisa). In a fully unsupervised sweep of colorectal cancer transcriptomes, the pipeline autonomously prioritised Insulin-like Growth Factor 2 (IGF2) as a predictive biomarker for 5-Fluorouracil sensitivity. The discovery maintained significance after rigorous Benjamini-Hochberg false discovery rate correction (q = 0.0292, Log-Rank p = 0.0007) and successfully predicted significant in vivo tumour volume shrinkage in an independent mouse cohort (Mixed-Effects LMM p = 0.0373). By bridging agentic hypothesis generation with statistically bounded clinical survival, this framework establishes a verifiable, local paradigm for the automated computational prioritisation of biomedical discoveries.

cancer biology↗

bioRxiv2026

IL1β/IL1R1/IRAK4 Drives Inflammatory Ovarian Cancer Seeding at the inflamed sites and Is Reversed by an IRAK4 inhibitor UR241-2

Inflammation-driven tumor implantation, such as port-site metastasis (PSM) following laparoscopic gynecologic surgery and peritoneal seeding during post-surgical recurrence, represents an aggressive clinical problem that remains poorly understood and lacks targeted therapies. To address this, we developed a non-surgical Mesothelium-Inflammation/Injury-Metastasis (MIM) model and investigated the role of the IL-1{beta}/IL1R1/MYD88/IRAK1/4 axis and NLRP3 in epithelial ovarian cancer (EOC) seeding at inflamed or injured sites. This model created by a needle injury recapitulates inflammation-driven peritoneal seeding and mimics PSM and inflammation associated dissemination in peritoneum during recurrence. Seeding was dependent on Il1r1 but not Nlrp3, despite its role in regulating IL-1{beta} production, as Il1ra-/- and Nlrp3-/- mice phenocopied wild-type C57BL/6 mice. Given the limited antitumor efficacy of IL-1{beta}-targeting agents such as Anakinra and Canakinumab, we focused on IRAK4 as a therapeutic target. IRAK4 knockdown significantly prolonged survival, reduced tumor cell adhesion, downregulated E-cadherin and Wnt4, and induced S-phase/mitotic arrest. This led to the development of UR241-2, a small-molecule IRAK4 inhibitor, which was validated through molecular simulations, hotspot analysis, nanoBRET, global kinome profiling, and NF-{kappa}{beta} reporter assays. UR241-2 inhibited NF-{kappa}{beta} nuclear translocation and blocked IL-1{beta}-induced IRAK4 phosphorylation. UR241-2 exhibited favorable drug-like properties, including absence of CYP or hERG inhibition, and acceptable CaCo-2 permeability, plasma protein binding, microsomal stability, and pharmacokinetics. In vivo, UR241-2 reduced SKOV3 xenograft growth, suppressed mesothelial seeding, and increased MHC-II macrophages and activated neutrophils in syngeneic high-grade epithelial ovarian HGS3 tumors. RNA-seq revealed enrichment of neutrophil activation signatures and suppression of extracellular matrix (ECM) gene programs. Together, these findings establish a role for the IL-1{beta}/IL1R1/IRAK4 axis in inflammation-driven PSM and peritoneal seeding and ECM regulation in EOC, and demonstrate that IRAK4 inhibition activates antitumor immune responses, providing a therapeutic strategy to block metastatic seeding and improve tumor control.

cancer biology↗

bioRxiv2026

Noncoaxial Transcatheter Aortic Valve Deployment Creates Cusp-Specific Thrombogenic Microenvironments Through Altered Sinus Hemodynamics

BackgroundTranscatheter aortic valve replacement has transformed the management of aortic stenosis; however, adverse outcomes such as leaflet thrombosis and hypoattenuating leaflet thickening remain clinically significant concerns. Flow disturbances resulting from valve canting may alter local hemodynamics and promote thrombogenic conditions. We investigated how modest transcatheter heart valve canting alters cusp-specific sinus flow and washout and promotes localized thrombogenic microenvironments associated with leaflet surface thrombus formation using particle image velocimetry, a physiologic blood loop, and tissue analysis. MethodsA patient-derived aortic root model was used to evaluate the hemodynamic and thrombogenic effects of THV canting at -10{degrees} (anti-curvature), 0{degrees} (neutral), and +10{degrees} (along-curvature). High-resolution particle image velocimetry quantified sinus flow fields and washout characteristics, and complementary whole-blood loop experiments enabled histologic assessment of leaflet-associated thrombus formation. ResultsCanting redistributed systolic jet orientation and sinus recirculation in a direction-dependent manner while preserving global hemodynamic measurements. The most spatially constrained cusp showed the largest increase in stasis and the slowest washout. In the right coronary cusp, anti-curvature canting increased the fraction of sinus area with velocity magnitude <0.05 m/s to 92% versus 43% in neutral and 10% in along-curvature deployments, and prolonged neo-sinus (T90) washout to 4.7 cycles versus 2.9 and 1.8 cycles, respectively. Histology localized surface-adherent platelet/fibrin thrombus to these poorly washed regions, most prominently on the right coronary cusp leaflet in anti-curvature deployments. Left and noncoronary cusp responses shifted with tilt direction, indicating redistribution rather than uniform worsening of thrombogenic conditions. ConclusionsEven modest noncoaxial deployment is sufficient to create sinus-resolved throm-bogenic microenvironments that are not captured by global gradient or effective orifice area. Deployment configuration is therefore a modifiable determinant of post-TAVR leaflet throm-bosis risk and may contribute to HALT.

bioengineering↗

bioRxiv2026

Single-nuclei RNA-sequencing uncovers sexually divergent exercise signatures partially mimicked by TFEB overexpression in mouse skeletal muscle

Exercise induces extensive, cell-type-specific transcriptional remodeling in skeletal muscle to support metabolic flexibility and adaptation. However, the regulatory mechanisms underlying these transcriptional programs, and the extent to which they differ between sexes, remain poorly defined. We previously reported that lifelong, muscle-specific overexpression of human Transcription Factor E-B (cTFEB;HSACre transgenic mice) recapitulates many adaptive features of endurance training in both sexes, leading to profound geroprotective effects during aging even in the absence of exercise. Here, we profile transcriptional adaptations to voluntary wheel running (VWR) and TFEB-overexpression at single-nucleus resolution in young male and female mouse tibialis anterior muscle. This represents, to our knowledge, the first integrated analysis of exercise and TFEB signaling using sex as a biological variable. Using robust bioinformatic and single-nuclei RNA-sequencing approaches, we profiled six muscle-resident cell populations and uncover previously unrecognized, sex-dependent signaling nodes governing exercise-associated metabolic plasticity. TFEB activation and endurance training by VWR elicit strongly correlated transcriptional programs enriched for lipid metabolism, mitochondrial remodeling, and immune modulation, establishing TFEB-overexpression as a partial exercise mimetic. In general, female muscle exhibited enhanced extracellular matrix and lipid-associated responses to endurance training and TFEB overexpression, whereas males preferentially engaged in angiogenic and oxidative networks, revealing distinct sex-specific, sex-dimorphic, or sex-agnostic regulatory routes to metabolic flexibility. Integration with independent multi-omics datasets from endurance-trained rats (MoTrPAC) confirms the conservation of TFEB-exercise transcriptional convergence in skeletal muscle across species and potentially muscle types. Together, these findings define TFEB as a regulator of exercise transcriptional programs and reveal sex-specific molecular frameworks that drive metabolic adaptation in skeletal muscle. Furthermore, the resulting sex-resolved, single-nucleus transcriptional atlas provides a unique resource for the field, enabling comparative, mechanistic, and hypothesis-driven exploration of exercise-responsive skeletal muscle regulatory networks across sexes.

physiology↗

bioRxiv2025

Epicardial contributions to fibro-inflammatory signaling in a Pkp2-deficient arrhythmogenic cardiomyopathy model

BackgroundArrhythmogenic Cardiomyopathy (ACM) is an inherited disease that is characterized by lethal ventricular arrhythmias stemming from myocyte dysfunction. ACM is associated with considerable subepicardial fibrosis and inflammation with right ventricle predominance. Most cases of gene positive ACM are caused by a desmosome protein mutation, with plakophilin-2 (Pkp2) mutations being most common. We hypothesized Pkp2-deficiency in epicardium-derived cells (EPDCs) contributes to fibro-inflammatory signaling and ACM pathogenesis. MethodsWe developed transgenic mice that lack Pkp2 in cardiomyocytes (Pkp2-cKO) or in both cardiomyocyte and EPDC (Pkp2-ceKO) via the tissue-specific expression of tamoxifen-inducible Cre recombinase. Non-myocyte populations were isolated 21 days post-tamoxifen injection for single cell RNA-sequencing (scRNA-seq). Immunohistochemistry, flow cytometry, qRT-PCR, and echocardiography were used to interrogate cardiac physiology and cellular composition. ResultsWe identified a population of epicardium-derived fibroblasts characterized by the expression of Ccl2, Ccl7, Thbs1, and Ptx3 that accumulated upon Pkp2 deletion. While pro-inflammatory EPDCs are found in Pkp2-cKO mice, they become significantly enriched in Pkp2-ceKO mice. Pro-inflammatory fibroblasts acquired the senescence-associated secretory phenotype (SASP), correlating with elevated Senescence Associated (SA)-{beta}gal staining in the right ventricle. Gene expression, flow cytometry, and histological data also revealed an exaggerated inflammatory response in Pkp2-ceKO mice, that progresses from right to bi-ventricular predominance. Importantly, macrophages and B cells accumulate in both Pkp2-cKO and Pkp2-ceKO mice compared to controls. Antibody-mediated B cell depletion delays the early inflammatory and fibrosis response but did not significantly alter end-stage cardiac physiology. ConclusionPkp2 deletion in EPDC facilitates the emergence of a fibro-inflammatory phenotype that may contribute to ACM pathogenesis.

cell biology↗

bioRxiv2025

Neutrophil TLR2 signaling promotes lipid accumulation and vascular plaque growth

Neutrophils are short-lived cells that are produced by the billions every day to circulate throughout the body and surveil all tissues. They are a key component of the innate immune system that play essential roles in antimicrobial immunity, but can also instigate sterile inflammatory diseases like gout and cancer. Immunometabolic paradigms that were developed by studying T cells and macrophages establish that cellular metabolic programming dictates immune function. Neutrophils have long been known as glucose-reliant and highly glycolytic. But surprising neutrophil heterogeneity has recently been described, and roles for lipids have been reported in both granulopoiesis and mature neutrophil effector function. Therefore, we set out to uncover how neutrophils acquire lipids from their environment and how this influences their functionality in the context of lipotoxicity. We found that neutrophils take up both free fatty acids and complex lipoproteins, but that their uptake is regulated through different signaling pathways. Neutrophil lipoprotein uptake is inducible by certain TLR2 signals, and this causes neutrophils to depolymerize their actin fibers and stop moving. Using a mouse model of atherosclerosis, we show that neutrophils in the plaque are lipid-laden and that neutrophil-deficient mice are protected from atherosclerotic plaque growth. Lipoprotein uptake causes neutrophils to recruit macrophages, conditional ablation of TLR2 on neutrophils prevents their lipid uptake and storage, and these mice are also protected against atherosclerosis. Our work highlights an important understudied role for lipids in neutrophil biology, and the importance of studying different lipid classes and different signaling pathways in neutrophils as compared to other myeloid populations.

immunology↗

bioRxiv2025

Multi-season analysis reveals hundreds of drought-responsive genes in sorghum

Persistent drought affects global crop production and is becoming more severe in many parts of the world in recent decades. Deciphering how plants respond to drought will facilitate the development of flexible mitigation strategies. Sorghum bicolor L. Moench (sorghum), a major cereal crop and an emerging bioenergy crop, exhibits remarkable resilience to drought. To better understand the molecular traits that underlie sorghums remarkable drought tolerance, we undertook a large-scale sorghum gene expression profiling effort, totaling nearly 1,500 transcriptome profiles, across a 3-year field study with replicated plots in Californias Central Valley. This study included time-resolved gene expression data from roots and leaves of two sorghum genotypes, BTx642 and RTx430, with different pre-flowering and post-flowering drought-tolerance adaptations under control and drought conditions. Quantification of genotype-specific drought tolerance effects was enabled by de novo sequencing, assembly, and annotation of both BTx642 and RTx430 genomes. These reference-quality genomes were used to construct a pan-gene set for characterizing conserved and genotype-specific expression. By integrating time-resolved transcriptomic responses to drought in the field across three consecutive years, we identified a set of drought-responsive genes that responded similarly in all three years of our field study. This expansive dataset represents a unique resource for sorghum and drought research communities and provides a methodological framework for the integration of multi-faceted time-resolved transcriptomic datasets.

genomics↗

bioRxiv2025

A global map for introgressed structural variation and selection in humans

Genetic introgression from Neanderthals and Denisovan has shaped modern human genomes; however, introgressed structural variants (SVs [≥]50 base pairs) remain challenging to discover. We integrated high-quality phased assemblies from four new Papua New Guinea (PNG) genomes with 94 published assemblies of diverse ancestry to infer an archaic introgressed SV map. Introgressed SVs are overall enriched in genes (44%, n=1,592), including critical genomic disorder regions, and most abundant in PNG. We identify 11 centromeres likely derived from archaic hominins, adding unexplored diversity to centromere genomics. Pangenome genotyping across 1,363 samples reveals 16 candidate adaptive SVs, many associated with immune-related genes and their expression, in the PNG. We hypothesize that archaic SV introgression contributed to reproductive success, underscoring introgression as a significant force in human adaptive evolution.

evolutionary biology↗

bioRxiv2025

IL-1β/IRAK4 Axis Promotes Ovarian Tumor Development at the Mesothelium Injury Sites

Epithelial ovarian cancer (EOC) cells seed at mesothelial inflammation or injury sites. Lack of animal models recapitulating tumor cells seeding at inflamed sites in EOC hinders mechanistic studies and therapy developments. Here, we developed a non-surgical MIM (Mesothelium Inflammation/Injury Metastasis) model that recapitulates tumor cell seeding at inflamed sites. This model captures temporal changes in tumor immune microenvironment and tumor growth allowing for deeper mechanistic and preclinical therapeutic studies of EOC in-vivo. We show here that HGS-3 high-grade murine serous EOC cells seed at needle-induced injury sites in mesothelium/peritoneal wall, forming tumors both internally and protruding outward. Using MIM model, we found that deletion of IL1R1 in mice reduced EOC cell seeding at mesothelium injury/inflamed site in WT but not IL1ra-deficient mice. Treatment of MiM mice with a novel IRAK4 inhibitor we recently developed (UR241-2) revealed an essential role for IRAK4 signaling downstream IL-1{beta}/IL-1R1 in fostering an anti-tumor inflammatory environment, and reduced tumor burden. We conclude that IRAK4 inhibitors can be more effective than IL-1/IL-1R1 targeting agents to control metastasis and peritoneal tumors, an unmet medical need in EOC recurrence. Downregulation of extracellular matrix (ECM), upregulation of neutrophil activation genes, reduced cell adhesion and migration exhibit how UR241-2 corrects ECM and immune disorders in EOC, making it less conducive to metastasis and tumorigenesis.

cancer biology↗

bioRxiv2024

Neural and behavioral reinstatement jointly reflect retrieval of narrative events

When recalling past events, patterns of gaze position and neural activity resemble those observed during the original experience. We hypothesized that these two phenomena, known as gaze reinstatement and neural reactivation, are linked through a common process that underlies the reinstatement of past experiences during memory retrieval. Here, we tested this proposal based on the viewing and recall of a narrative movie, which we assessed through fMRI, deep learningbased gaze prediction, and language modeling of spoken recall. In line with key predictions, gaze behavior adhered to the same principles as neural activity; it was event-specific, robust across individuals, and generalized across viewing and recall. Additionally, gaze-dependent brain activity overlapped substantially across tasks. Collectively, these results suggest that retrieval engages mechanisms that direct our eyes during natural vision, reflecting common constraints within the functional organization of the nervous system. Moreover, they highlight the importance of considering behavioral and neural reinstatement together in our understanding of remembering.

neuroscience↗

bioRxiv2024

Transcripts with high distal heritability mediate genetic effects on complex metabolic traits

Although many genes are subject to local regulation, recent evidence suggests that complex distal regulation may be more important in mediating phenotypic variability. To assess the role of distal gene regulation in complex traits, we combined multi-tissue transcriptomes with physiological outcomes to model diet-induced obesity and metabolic disease in a population of Diversity Outbred mice. Using a novel high-dimensional mediation analysis, we identified a composite transcriptome signature that summarized genetic effects on gene expression and explained 30% of the variation across all metabolic traits. The signature was heritable, interpretable in biological terms, and predicted obesity status from gene expression in an independently derived mouse cohort and multiple human studies. Transcripts contributing most strongly to this composite mediator frequently had complex, distal regulation distributed throughout the genome. These results suggest that trait-relevant variation in transcription is largely distally regulated, but is nonetheless identifiable, interpretable, and translatable across species.

genetics↗

bioRxiv2024

Cortical state contributions to response variability in the early visual cortex: A system identification approach

Neurons in the early visual cortex respond selectively to multiple features of visual stimuli, but they respond inconsistently to repeated presentation of the same visual stimulus. Such trial-to-trial response variabilities are often treated as noise and addressed by simple trial-averaging to obtain the stimulus-driven response, though this approach is insufficient to fully remove the response variability. More importantly, response variability may primarily be caused by non-sensory factors, particularly by variations in cortical state. Here we recorded and analyzed neuronal spiking activity in response to natural images from areas 17 and 18 of cats, along with local population neuronal signals, i.e. local field potentials (LFPs) and multi-unit activity (MUA). Single neurons showed highly varying degrees of trial-to-trial response variability, even when recorded simultaneously. We used a variability ratio (VR) measure to quantify the trial-wise differences in neural responses, and two cortical state indicative measures, a global fluctuation index (GFI) calculated using MUA, and a synchrony index (SI) calculated from LFP signals. We propose a compact convolutional neural network model with parallel pathways, to capture the stimulus-driven activity and the cortical state-driven response variabilities. The stimulus-driven pathway is comprised of a spatiotemporal filter, a parametric rectifier and a Gaussian map, and the cortical state-driven pathway contains temporal filters for MUA and LFPs. The model parameters are fit to best predict the spiking activity of each neuron. The fitted model performed with a significantly higher accuracy in predicting neural responses compared to a basic model with a stimulus-driven pathway alone. The neurons with higher response variability benefited more from the cortical state-driven pathway compared to less variable neurons. These results show that different neurons may differ greatly in their variability and in the degree of their relationship to indicators of cortical state fluctuations. Author SummaryNeuronal responses in the early visual cortex to repeated presentation of an identical stimulus can be highly variable across trials. The variable portion of these neuronal responses can in some cases be as large as the stimulus-driven response. The cortical state fluctuations that may underlie the response variabilities can vary continuously during a data recording session, and these dynamics are associated with population response signals such as local field potentials and multi-unit activity. Here we demonstrate that a model combining these cortical signals along with a visual stimulus processing pathway can predict single neurons responses significantly better than a model containing a stimulus-driven pathway alone. This improvement in predictive performance is heterogeneous across cortical neurons, and is much greater in neurons that exhibit greater trial-wise response variabilities. Overall, this work provides insights to understanding how visual cortex neurons not only respond to visual stimuli, but also interact with non-sensory events such as cortical state fluctuations.

neuroscience↗

bioRxiv2024

Brief encounters with real objects modulate medial parietal but not occipitotemporal cortex

Humans are skilled at recognizing everyday objects from pictures, even if we have never encountered the depicted object in real life. But if we have encountered an object, how does that real-world experience affect the representation of its photographic image in the human brain? We developed a paradigm that involved brief real-world manual exploration of everyday objects prior to the measurement of brain activity with fMRI while viewing pictures of those objects. We found that while object-responsive regions in lateral occipital and ventral temporal cortex were visually driven and contained highly invariant representations of specific objects, those representations were not modulated by this brief real-world exploration. However, there was an effect of visual experience in object-responsive regions in the form of repetition suppression of the BOLD response over repeated presentations of the object images. Real-world experience with an object did, however, produce foci of increased activation in medial parietal and posterior cingulate cortex, regions that have previously been associated with the encoding and retrieval of remembered items in explicit memory paradigms. Our discovery that these regions are engaged during spontaneous recognition of real-world objects from their 2D image demonstrates that modulation of activity in medial regions by familiarity is neither stimulus nor task-specific. Overall, our results support separable coding in the human brain of the visual appearance of an object from the associations gained via real-world experience. The richness of object representations beyond their photographic image has important implications for understanding object recognition in both the human brain and in computational models.

neuroscience↗

bioRxiv2024

Disruption of mitochondrial folate metabolism leads to mitochondrial DNA leakage and activation of apoptotic or inflammatory pathways

Folate-mediated one-carbon metabolism (FOCM) is required for the biosynthesis of purines, thymidylate (dTMP), and methionine. Maintenance of adequate cellular dTMP levels is essential to preserve the integrity of the nuclear and mitochondrial genomes. Inadequate dTMP production leads to uracil misincorporation into mitochondrial DNA (mtDNA) and impaired mitochondrial function. However, the mechanisms whereby uracil in mtDNA impairs mitochondrial function are uncharacterized. The release of mtDNA into the cytosol acts as a damage-associated molecular pattern (DAMP), resulting in inflammation and cell death. Previously, we reported that disrupting mitochondrial dTMP synthesis through serine hydroxymethyltransferase 2 (Shmt2) heterozygosity increases uracil in mtDNA and impairs mitochondrial function in mice. This study aimed to investigate whether impairment of mitochondrial FOCM through Shmt2 disruption leads to the release of mtDNA into the cytosol. Shmt2+/- MEF cells showed a > 2-fold increase in cytosolic mtDNA leakage compared to Shmt2+/+ cells (p<0.05). There was no significant difference in total mtDNA content between Shmt2+/+ and Shmt2+/- MEF cells. MEFs with decreased Shmt2 expression activated apoptosis by the ratio of cleaved caspase-3 to caspase-3. In addition, SHMT2 knock-out (SHMT2 KO) haploid chronic myeloid leukemia (HAP1) cells also exhibited increased cytosolic mtDNA content compared to the wild-type (WT) HAP1 cells. HAP1 lacking Shmt2 expression activated the cGAS/STING pathway, but suppressed apoptosis, compared to WT HAP1 cells. This study demonstrates that decreased Shmt2 expression leads to cytosolic mtDNA leakage and that the downstream effects of mtDNA leakage vary by cell type.

biochemistry↗

bioRxiv2024

Causal network perturbation analysis identifies known and novel type-2 diabetes driver genes

The molecular pathogenesis of type 2 diabetes mellitus (T2DM) involves environmental and genetic factors that remain poorly understood. Increased insulin resistance leads to pancreatic {beta}-islet cell exhaustion and failure, leading to more severe T2DM. As such, targeting {beta}-cell dysfunction is an attractive pathway for T2DM treatment. Single-cell RNA sequencing can help identify differentially expressed genes (DEGs) that may contribute to disease-associated pathophysiology, but cannot capture the full spectrum of disease pathophysiology, as some genes that are not differentially expressed may still play important roles in disease progression or mechanisms. As such, we investigated single-cell gene expression changes in {beta}-cells from healthy (C57BL/6J) and diabetic (NZO/HlLtJ) mice fed with normal or high-fat, high-sugar diet (HFHS) across the spectrum of T2DM development (prediabetic, mild or severely diabetic) using an innovative integration of the causal network perturbation assessment (ssNPA) framework with meta-cell transcriptome analysis to identify driver genes for T2DM. By generating a reference causal network and conducting in silico perturbations, we identified three classes of genes implicated in T2DM pathophysiology: (1) DEGs that were not perturbed (e.g, Igf2bp2 strongly linked to {beta} cell dysfunction and glucose regulation), (2) perturbed non-DEGs (e.g., Glp1r a therapeutic target of modern diabetes drugs) that were perturbed, and (3) DEGs that were perturbed (e.g., Pdx1 a master {beta} cell transcription factor), and validated some of the targets using the KOMP database. Together, these results show that each analytic layer captures complementary mechanisms underlying T2DM severity, and their synthesis provides a more complete view of the disease pathophysiology.

bioinformatics↗