Biology subjects

Thomas, M.

Publications and source records attributed to Thomas, M..

At least 37 records · Page 2Linked to original sources

bioRxiv2026

miR-202 drives medaka fertility by targeting antagonistic Yap-dependent transcriptional regulators tead3b and vgll4b in a sex-dependent manner

How miRNAs can sometimes drive major organism-level phenotypes by targeting a single gene and by triggering limited changes in mRNA levels remains poorly understood, especially in vertebrates. In medaka, the knockout of miR-202-5p, a gonad-specific miRNA in vertebrates, leads to impaired male and female fertility, including drastically reduced egg production and low developmental success. Here we show that miR-202-5p drives gamete formation by targeting antagonist Yap-dependent transcriptional regulators tead3b and vgll4b in a sex-dependent manner. Disruption of the miR-202-5p binding site in the 3UTR of tead3b, but not vgll4b, results in a significant decrease in female fertility. In contrast, disrupting miR-202-5p target site in the 3UTR of vgll4b, but not tead3b, results in impaired male fertility. In females, 3D ovary imaging and RNA-seq analysis of isolated ovarian follicles revealed that disrupting miR-202-5p binding to the 3 UTR of tead3b results in a polycystic ovarian syndrome (PCOS)-like phenotype and the expression of many PCOS-associated marker, including androgen signaling and estrogen metabolism genes. In males, disrupting miR-202-5p binding to the 3UTR of vgll4b triggers severe phenotypes, including reduced sperm motility and abnormal testicular development. No effects on sex ratio were observed, indicating that miR-202-5p drives gamete formation by regulating mechanisms acting down-stream of the sex-determining cascade. The analysis of miR-202-5p target sites in 3 UTRs suggests long-term conservation of antagonistic TEAD and VGLL targeting across vertebrate species, including mammals. Together, our results show that miR-202-5p drives fertility by leveraging antagonistic Yap-dependent transcriptional regulators in a sex dependent manner.

genetics↗

bioRxiv2026

Identification of miR-187 as a modulator of early oogenesis and female fecundity in medaka

MicroRNAs (miRNAs) are known regulators of ovarian function in vertebrates, yet their physiological roles in fish reproduction remain poorly understood. Here, we identified miR-187 as one of the most ovarian-enriched miRNAs in medaka (Oryzias latipes) and we uncovered its function in vivo using CRISPR/Cas9-mediated gene inactivation. miR-187-3p is expressed in oocytes and granulosa cells in the ovary, and in discrete brain areas. Its loss-of-function leads to a significant reduction in female fecundity. High-resolution 3D imaging of whole ovaries revealed that mir-187 mutants accumulate early stage I follicles and show reduced progression to later stages, indicating a defect in early follicle recruitment and growth. Transcriptomic profiling of mutant ovaries revealed extensive gene-expression remodeling, including downregulation of key regulators of steroidogenesis, Wnt/{beta}-catenin signaling, and TGF-{beta} pathways, and upregulation of genes associated with early follicle activation and immature somatic cell states. Using an expression-based target-prediction pipeline, we identified several putative miR-187-3p targets, including nr6a1a (gcnf) and dpagt1, two genes previously implicated in oocyte differentiation and female fertility in mammals. Together, our results demonstrate that miR-187 acts as a previously unrecognized regulator of early folliculogenesis and female reproductive capacity in medaka, expanding the repertoire of miRNAs with essential in vivo roles in teleost oogenesis and female fecundity. AUTHOR SUMMARYSuccessful fish reproduction depends on the continuous production of oocytes within the ovary. This process depends on the coordinated development of germ cells and the supporting somatic cells. Although microRNAs (miRNAs) are known to post-transcriptionally regulate gene expression, their physiological roles in the fish ovary and female reproduction remain poorly understood. In this study, we used the medaka to investigate the function of miR-187, a miRNA strongly enriched in the ovary. By generating a CRISPR/Cas9 knockout line, we showed that females lacking miR-187 produce fewer eggs and display defects in early follicle development. Using whole-ovary 3D imaging, we found that mutant females accumulate early follicles that fail to progress through normal growth stages. Transcriptomic analyses revealed broad gene-expression changes affecting pathways involved in follicle activation, somatic cell maturation, and ovarian signaling. Our results demonstrate that miR-187 is a previously unrecognized regulator of early folliculogenesis and female fecundity in medaka. This work expands the landscape of miRNA-mediated regulation in the ovary and highlights the importance of post-transcriptional mechanisms in controlling reproductive success in teleosts. Grant supportThe DYNAMO project (French National Research Agency, ANR-18-CE20-0004). The OVOPAUSE project (French National Research Agency, ANR-22-CE45-00017-02). The IMMO project (INRAE Metaprogramme DIGIT-BIO).

developmental biology↗

bioRxiv2025

Early-Life Commensal Lung Bacteria Shape Immune Responses and RSV Susceptibility in Neonatal Mice

The lung mucosa during the neonatal period and early infancy is especially susceptible to respiratory syncytial virus (RSV) infection. Respiratory disease severity is strongly influenced by the age at first exposure, which may also affect the trajectory of airway function. Early life represents a critical window for lung development and initial microbiota colonization, both of which shape mucosal immune responses to RSV. The contribution of early lung-colonizing bacterial strains to the establishment of the lung microbiota and susceptibility to RSV infection in neonatal mice remains poorly characterized. In the present study, we showed that early-life primo-colonizing bacterial strains in the mouse lung differentially induce innate immune responses and influence RSV susceptibility in ex vivo models using lung explants and alveolar macrophages (AMs). We identified a specific bacterial strain (strain 17) whose prior exposure enhances type I interferon (IFN-I) responses in AMs upon RSV infection and reduces viral replication both ex vivo and in vivo in lung tissues. Intranasal administration of this strain during early life prevented the development of immunopathological responses upon RSV reinfection in adult mice. Finally, using a translational human airway epithelium model, we demonstrated that pre-exposure to strain 17 restricts RSV spread without cytotoxicity, likely via enhanced {beta}-defensin 2 production. These findings highlight the potential of early-life microbiota modulation as a promising intervention for preventing RSV disease and its long-term respiratory consequences. Author summaryRespiratory syncytial virus (RSV) is a major cause of severe respiratory infections in newborns and infants, a period during which the lungs and immune system are still maturing. Simultaneously, the respiratory tract undergoes its first microbial colonization by so-called primo-colonizing bacteria -- the first bacterial species to establish themselves on neonatal lower respiratory mucosal surfaces. These early microbial pioneers may play an unsuspected role in shaping how the immature immune system responds to viral threats. In this study, we investigated whether these early lung-colonizing strains influence RSV susceptibility. Using neonatal mouse models, lung explants, and alveolar macrophages, we found that distinct bacterial strains trigger markedly different innate immune responses. Prior exposure to one strain in particular, strain 17, was associated with enhanced type I interferon responses, reduced viral replication, and protection against harmful inflammation upon RSV reinfection later in life. In a human airway epithelium model, pre-exposure to strain 17 also restricted RSV spread without tissue damage, potentially through increased {beta}-defensin 2 production. These findings provide proof-of-concept that the bacterial strains establishing in the neonatal lung can influence future immune reactivity and antiviral responses, and suggest that early-life respiratory microbiota modulation could represent a promising strategy to prevent severe RSV disease.

immunology↗

bioRxiv2025

Robust Colonization of Nasal Microbiota Across the Respiratory Tract and the Gut Modulates Innate Immune Response in a Germ-Free Pig Model

The use of antibiotics in swine production has contributed to improved health and growth rates but also led to significant challenges, including the emergence of antibiotic-resistant bacteria and disruptions in the microbiome. This study employs a germ-free pig model to investigate the transplantation of the nasal microbiome into the respiratory tract, exploring its potential to colonize multiple body sites and its impact on host immunity. Using germ-free piglets inoculated with nasal microbiota from healthy donors, we examined the dynamics of microbial community formation across the respiratory and gastrointestinal tracts and assessed the effects of antibiotic intervention. Our findings reveal that specific taxa, predominantly from the phyla Proteobacteria and Firmicutes, cross colonized both respiratory as well as gastrointestinal tract. This cross- colonization highlights the adaptability of nasal microbiota and suggests a significant role in modulating host immunity through the gut-lung axis. The administration of the antibiotic tulathromycin on day 11 post-inoculation altered both nasal and gut microbiota compositions, reducing microbial diversity and impacting immune gene expression and cytokine profiles. These results underscore the complex interactions within the gut-lung axis and emphasize the implications of antibiotic use on microbial health and host immunity. Understanding these interactions provides crucial insights into alternative strategies for managing health in swine production without relying on antibiotics. Our study advocates for a reevaluation of antibiotic practices and supports the development of microbiome-centered interventions in swine health management.

microbiology↗

bioRxiv2025

Monoaminergic neurons share transcriptional identity across Bilaterian animals

The evolutionary conservation of cell types over deep time has long been theorised but remains difficult to demonstrate. Monoaminergic neurons, which produce molecules such as serotonin and dopamine, are central to animal behaviour and cognition, yet their evolutionary origins remain unresolved. Here, we analysed single-cell transcriptomes from 16 metazoan species spanning eight phyla. Using a novel integration method, Orthogroup Recoding, together with experimental validation, we show that monoaminergic neurons form consistent transcriptional clusters across Bilateria. These clusters share a regulatory signature involving conserved transcription factors, including homologues of Fev, Lmx1b, Fer2, Insm, and Isl, suggesting a common regulatory program. This signature extends beyond the brain including other monoaminergic cells, such as the gut enterochromaffin cells and larval sensory neurons. By contrast, non-bilaterian lineages lack the coordinated expression of the transcription factors and the biosynthetic machinery that regulate monoamine production. Our observations support the existence of a shared set of TFs that define monoaminergic identity across in bilaterians.

bioinformatics↗

bioRxiv2025

AURKB-driven dissolution of CIZ1-RNA assemblies from the inactive X chromosome in mitosis

Cip1-interacting zinc-finger protein 1 (CIZ1) interacts with Xist lncRNA to form large RNA-protein assemblies at the inactive X-chromosome (Xi) in female mammalian nuclei, plus smaller assemblies in both sexes. CIZ1 assemblies influence underlying chromatin, and their disruption alters the expression of autosomal and X-linked gene clusters. Here, we explore the regulated dissolution of CIZ1-Xi assemblies during mitosis and show that, like Xist, CIZ1 is released in prometaphase under the regulation of Aurora Kinase B (AURKB). The part of human/mouse CIZ1 comprising 179/181 C-terminal amino-acids encodes a matrin-3 domain that facilitates dimerization to form a compact folded core with disordered C-terminal extensions. Mass spectrometry revealed 56 high-confidence interacting partners of the C-terminal fragment, predominantly chromatin, nuclear matrix and RNA-binding proteins. Phosphomimetic mutation of three conserved AURKB sites in the C-terminal extensions released CIZ1 from its nuclear anchor points, but did not affect its interaction with chromatin or nuclear matrix proteins. In contrast, the same mutations, or deletion of the C-terminal extensions, abolished interaction with RNAs including Xist. Together, the data suggest CIZ1 is a regulatable component of the protein-RNA assemblies that preserve epigenetic stability across the nucleus, and that AURKB drives their dissolution in mitosis via dissociation of CIZ1 from RNA. BulletsThe data show regulated dissolution of RNA-protein assemblies involved in protection of epigenetic state. RNA spatially constrains CIZ1 assemblies via multivalent interactions at sub-nuclear sites. CIZ1 dimerizes to present dual extensions whose phosphorylation by AURKB dissolves RNA interaction in mitosis. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=181 SRC="FIGDIR/small/676856v1_ufig1.gif" ALT="Figure 1"> View larger version (56K): org.highwire.dtl.DTLVardef@107bec2org.highwire.dtl.DTLVardef@17cbb4aorg.highwire.dtl.DTLVardef@1ec0144org.highwire.dtl.DTLVardef@1474995_HPS_FORMAT_FIGEXP M_FIG C_FIG

cell biology↗

bioRxiv2025

Clonal dynamics shaped by diverse drug-tolerant persister states in melanoma resistance

Most advanced melanomas initially respond to targeted therapy but eventually relapse. Rather than acquiring new mutations, resistance is driven by drug-tolerant persister cells that enter a reversible drug-refractory state. We developed MeRLin, a high-resolution lineage tracing platform integrating cellular barcoding, single-cell transcriptomics, RNA fluorescence in situ hybridization (FISH), and computational analyses to track clonal and transcriptional dynamics in patient-derived melanoma models during prolonged therapy. Clonal dynamics revealed that persister subpopulations first responded to treatment but persisted and expanded during minimal residual disease, ultimately leading to tumor recurrence. Pre-treatment melanoma populations diversified into four conserved persister states characterized by stress-like, lipid metabolism, PI3K signaling, and extracellular matrix remodeling programs associated with adaptive resistance. Spatial transcriptomics showed the organization of these adaptive programs and a complex signaling network of autocrine and paracrine interactions among persister subpopulations. Barcoded RNA-FISH enabled spatial mapping of clonal identity and gene expression, revealing in situ co-localization of a dominant resistant clone with SLC2A1 expression. MeRLin provides a robust framework for dissecting cancer heterogeneity and identifying vulnerabilities in persister populations.

cancer biology↗

bioRxiv2025

A Toolkit for In Vivo Mapping and Modulating Neurotransmission at Single-Cell Resolution

Understanding the organization and regulation of neurotransmission at the level of individual neurons and synapses requires tools that can track and manipulate transmitter-specific vesicles in vivo. Here, we present SynaptoTagMe, a suite of genetic tools in Caenorhabditis elegans to fluorescently label and conditionally ablate the vesicular transporters for glutamate, GABA, acetylcholine, and monoamines. Using a structure-guided approach informed by protein topology and evolutionary conservation, we engineered endogenously tagged versions for each transporter that maintain their physiological function while allowing for cell-specific, bright, and stable visualization. We also developed conditional knockout strains that enable targeted disruption of neurotransmitter synthesis or packaging in single neurons. We applied this toolkit to map co-expression of vesicular transporters across the C. elegans nervous system, revealing that over 10% of neurons exhibit co-transmission. Using the ADF sensory neuron as a case study, we demonstrate that serotonin and acetylcholine are trafficked in partially distinct vesicle pools. Our approach provides a powerful platform for mapping, monitoring, and manipulating neurotransmitter identity and use in vivo. The molecular strategies described here are likely applicable across species, offering a generalizable approach to dissect synaptic communication in vivo.

neuroscience↗

bioRxiv2025

groovDB in 2026: A community-editable database of small molecule biosensors

The groovDB database (https://groov.bio) was launched in 2022 with the goal of organizing information on prokaryotic ligand-inducible transcription factors (TFs). This class of proteins is important in fundamental areas of microbiology research and for biotechnological applications that develop biosensors for diagnostics, enzyme screening, and real-time metabolite tracking. Uniquely, groovDB contains stringently curated, literature-referenced data on both TF:DNA and TF:ligand interactions. Here, we describe a major technical update to groovDB, making the database community-editable and adding several advanced features. Users can now add new TF entries and update existing entries using a simple online form. New user interface elements display interactive protein structures and DNA-binding motifs. Updated query methods enable database searches via text, chemical similarity, and attribute-filtering. A new data architecture reduces page load time by five-fold. Finally, the number of TF entries has more than doubled and all source code is now open-access. Graphic abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=80 SRC="FIGDIR/small/670880v3_ufig1.gif" ALT="Figure 1"> View larger version (18K): org.highwire.dtl.DTLVardef@17842beorg.highwire.dtl.DTLVardef@65d608org.highwire.dtl.DTLVardef@1c6e2eborg.highwire.dtl.DTLVardef@5bd824_HPS_FORMAT_FIGEXP M_FIG C_FIG

synthetic biology↗

bioRxiv2025

Decoding efficacy and resistance space at a drug binding site

Interactions between drugs and their targets impact efficacy and, when altered by mutation, can result in resistance 1-3. Assessing and understanding the impacts of all possible mutations at a drug binding site remain challenging, however 4-6. Here, we used Multiplex Oligo Targeting (MOT) for mutational profiling, and computational modelling, to decode efficacy and resistance space at the otherwise native binding site for a low nanomolar potency, anti-trypanosomal, proteasome inhibitor 7. We saturation-edited twenty codons in the Trypanosoma brucei proteasome {beta}5 subunit and subjected the resulting MOT libraries to stepwise drug selection. Amplicon sequencing, and codon variant scoring, yielding dose-response profiles for >100 resistance-conferring mutants, among 1,280 possible codon variants. Codon variant scores were predictive of relative resistance observed using a bespoke set of mutants, while fitness profiling revealed otherwise extensive constraints on mutational fitness and resistance space. The resistance profile that emerged allowed us to readily predict routes to spontaneous drug resistance observed within accessible, single nucleotide mutational space. In silico analysis of {beta}5 subunit mutations predicted impacts on ligand affinity via steric effects, hydrogen-bonding and lipophilicity, which when combined with predictions of proteasome function perturbing mutations, were closely aligned with observed impacts on drug resistance. We conclude that MOT-library profiling facilitates assessment of all possible mutations at a drug binding site. Further decoding of drug target structure-activity relationships and drug resistance space will facilitate the design of more effective and durable drugs.

molecular biology↗

bioRxiv2025

Tumor Cells Enriched for Interferon and Inflammatory Programs Pre-Exist in High Grade Serous Ovarian Cancer and are Proportionately Significantly Increased Post Chemotherapy

Drug-tolerant, high-grade serous ovarian cancer (HGSOC) cells that persist after first-line chemotherapy and subsequently relapse often retain sensitivity to secondary treatment, suggesting a therapeutic window before stable chemoresistance emerges. We performed single-cell RNA sequencing (scRNA-seq) on seven matched pairs of tumors, collected pre- and post-chemotherapy, to define vulnerabilities in these reversibly-resistant cells. Treatment induced a marked enrichment of tumor and stromal cell populations expressing correlated interferon (IFN) and inflammatory (IFM) gene signatures, with a concurrent depletion of proliferation-related and MYC-associated states in the tumor cells. Cross-cohort single cell sequencing analysis of >130 treatment-naive tumors revealed heterogeneity in the abundance of IFN/IFM-expressing cells. Multiplex immunofluorescence imaging of IFN-stimulated gene (ISG) products confirmed the presence of spatially clustered ISG-positive tumor cells in all cases, as well as in serous tubal intraepithelial carcinomas (STIC lesions), the presumptive HGSOC precursors. ISG expression correlated strongly with ORF1P, a protein encoded by the endogenous retrotransposon LINE1. These data suggest that early oncogenic events drive LINE1 derepression and innate immune activation, establishing an IFN-rich transcriptional state that persists in tumor subpopulations and is strongly enhanced by chemotherapy.

cancer biology↗

bioRxiv2025

Motor-driven modulation of actin network mechanics across linear and nonlinear regimes

Cytoskeletal networks enable cells to dynamically regulate their mechanical properties in response to internal forces and external cues. Here, we investigate how motor activity influences the structure and mechanics of actomyosin networks reconstituted in vitro from filamentous actin, myosin II minifilaments, and transient -actinin cross-linkers. By varying the myosin-to-actin molar ratio (RMA), we observe a transition from isotropic actin meshes to contractile, coarsened architectures marked by bundled filaments and increasing spatial correlation lengths ({xi}z,{xi} t). Optical tweezers microrheology reveals a nonmonotonic mechanical response: at low RMA, networks fluidize, with reductions in the plateau modulus (G0), zero-shear viscosity (0), and fast relaxation timescales ([Formula],{tau} 1). At higher motor levels, the networks stiffen and retain internal stress, reflecting contractile reinforcement. Notably,{tau} 1 exhibits a minimum when plotted against{xi} z, suggesting that intermediate levels of coarsening facilitate efficient local stress dissipation. These results identify distinct mechanical regimes governed by motor-induced remodeling and highlight a structural basis for the dual roles of myosin in fluidization and reinforcement.

biophysics↗

bioRxiv2025

Identification and optimization of trans-species reactive TfR1-binding VHH as tools for drug delivery across the blood brain barrier

The blood-brain barrier (BBB) is a major obstacle for delivering therapeutic agents to the central nervous system (CNS), posing significant challenges for treating neurological disorders. Among current strategies to improve brain drug exposure, hijacking physiological pathways involved in receptor-mediated transcytosis (RMT) has emerged as a promising strategy. While targeting transferrin receptor 1 (TfR1) is widely explored, many TfR1-antibodies lack cross-species reactivity, limiting translational development. In the present study, we identified and characterized camelid-derived single-domain antibodies (VHHs) with robust cross-reactivity to rodent, rhesus monkey, and human TfR1. Epitope mapping of the VHH revealed a novel binding site at the interface of the TfR1 dimer. When fused to a human IgG1 Fc domain, these VHHs, as monomers or homodimers, were efficiently internalized by engineered CHO cells and brain endothelial cells expressing TfR1 from different species. Systemic administration of VHH-Fc constructs in mice demonstrated significantly improved brain uptake compared to irrelevant controls. Functional delivery was confirmed using neurotensin (NT)-induced hypothermia, and we established correlations between in vivo effects and TfR1 VHH binding properties determined by surface plasmon resonance. Notably, efficient BBB transcytosis was associated with intermediate affinity and rapid dissociation rates. Engineered variants maintained favorable cross-species binding, including similar affinities to human and non-human primate TfR1, facilitating translational studies. The cross-reactive anti-TfR1 VHHs we developed offer a versatile and modular platform for CNS drug delivery and hold promise as molecular shuttles for transporting therapeutic agents across the BBB. Our work establishes a robust foundation for developing next-generation brain-targeted biotherapeutics, including peptides, enzyme replacement therapies, antibody-based treatments for neurodegenerative diseases, and oligonucleotide delivery for CNS disorders, enabling seamless translation from preclinical to clinical applications.

neuroscience↗

bioRxiv2025

Lamin A/C Deficiency Drives Genomic Instability and Poor Survival in Small-Cell Lung Cancer through Increased R-loop Accumulation

Lamin A/C (LMNA), a key component of the nuclear envelope, is essential for maintaining nuclear integrity and genome organization [1]. While LMNA dysregulation has been implicated in genomic instability across cancer and aging, the underlying mechanisms remain poorly understood [2]. Here, we investigate LMNAs role in small-cell lung cancer (SCLC), a highly aggressive malignancy characterized by extreme genomic instability [3, 4]. We demonstrate that LMNA depletion promotes R-loop accumulation, transcription-replication conflicts, replication stress, DNA breaks, and micronuclei formation. Mechanistically, LMNA loss disrupts nuclear pore complex distribution, reducing phenylalanine-glycine (FG)-nucleoporin incorporation and impairing RNA export efficiency. Furthermore, we show that LMNA expression is epigenetically repressed by EZH2 during SCLC differentiation from neuroendocrine (NE) to non-NE states. Clinically, low LMNA levels correlate with significantly worse survival in SCLC patients. These findings uncover a novel role for LMNA in safeguarding genome integrity and shaping tumor heterogeneity, with broad implications for cancer and aging. Significance StatementLamin A/C, a key structural component of the nuclear envelope, is frequently lost or mutated in cancer, laminopathies, and aging-related disorders. Lamin A/C loss is associated with genomic instability, but the underlying mechanisms remain incompletely understood. We demonstrate that LMNA loss drives genomic instability by promoting R-loop accumulation through disrupted nuclear pore dynamics and impaired RNA export. These findings reveal a previously unrecognized link between LMNA loss, nuclear envelope dysfunction, and genome instability. Targeting this pathway could help mitigate genomic instability in aging and laminopathies, while leveraging R-loop accumulation may enhance the efficacy of DNA-damaging therapies in cancer.

cancer biology↗

bioRxiv2025

Targeting Modulated Vascular Smooth Muscle Cells in Atherosclerosis via FAP-Directed Immunotherapy

Vascular smooth muscle cell (VSMC) and immune cell diversification play a central role in driving atherosclerotic coronary artery disease (CAD)1-3. However, the molecular mechanisms governing cell state transitions within the neo-intima in human CAD remain poorly understood, and no lipid-independent therapies are currently approved for its treatment. Here, we performed multi-omic single-cell gene expression profiling, epitope mapping, and spatial transcriptomics from 27 human coronary arteries. Our analysis identified fibroblast activation protein (FAP) as a marker of modulated VSMCs within the neo-intima. Genetic lineage tracing in mice confirmed that FAP cells in the plaque originate from medial VSMCs. Additionally, non-invasive positron emission tomography (PET) imaging in patients with CAD revealed focal FAP uptake in atherosclerotic lesions. Spatial transcriptomics further delineated the distinct localization of VSMC and immune cell subsets within plaques, with FAP states enriched in the neo-intima. To explore the therapeutic potential of targeting de-differentiated VSMCs, we developed an anti-FAP bispecific T-cell engager (BiTE) and demonstrated that it significantly reduced the plaque burden in multiple mouse models of atherosclerosis. Collectively, our study provides the first single-cell and spatially resolved map of human CAD, establishes FAP as a marker of modulated smooth muscle cells, and demonstrates the broader potential of immunotherapeutics for lipid independent targets in atherosclerotic CAD.

genomics↗

bioRxiv2025

Stable Actin As Synaptic Tag

According to the tagging and capture hypothesis, long-lasting long-term potentiation (LTP) requires protein synthesis and a synaptic tag, which is a synapse specific memory of the synapse with a so far unclear molecular or biophysical identity. Here we use an interdisciplinary approach to explore the hypothesis that interaction between the dynamics of actin and the spine geometry can provide such a memory. Using a mathematical model, we demonstrate that this implementation of the tag requires an increase in the stable, cross-linked pool of actin filaments, and is not possible without this stable pool. Using FRAP experiments, we show that such an increase in stable actin can indeed be observed after cLTP in vitro. Thus, the interaction between actin dynamics and spine geometry could indeed serve as a synaptic tag for LTP.

neuroscience↗

bioRxiv2025

Aerobic exercise decreases the number and transcript expression of inflammatory M1 macrophages and CD8+ T cells in the epicardial adipose tissue of female pigs

BackgroundEpicardial adipose tissue (EAT) regulates coronary artery function via lipid metabolism and immune cell recruitment. Increased EAT is a risk factor for coronary artery disease (CAD), but aerobic exercise mitigates CAD. The effect of aerobic exercise on immune cells in EAT is unknown. We hypothesized that aerobic exercise creates an anti-inflammatory environment characterized by increased M2 macrophages and up-regulation of anti-inflammatory cytokine transcripts in EAT. MethodsFemale Yucatan pigs (n=7) were allocated to sedentary or exercised groups. To mimic CAD, a coronary artery was chronically occluded or remained non-occluded. EAT samples were processed for bulk and single nuclei transcriptomic sequencing. ResultsSub-clustering identified immune, endothelial, smooth muscle, adipocytes, adipocyte progenitor cells (APSCs), and neuronal cells, with adipocytes and APSCs being dominant. Non-occluded sedentary EAT had the largest percentage of M1 macrophages and CD8+ T cells. Irrespective of occlusion, sedentary EAT had the largest fraction of cells expressing genes in the tumor necrosis factor (TNF) superfamily. Irrespective of occlusion, exercise upregulated peroxisome proliferator-activated receptor (PPAR) gamma (G) expression and enriched PPAR signaling pathways in adipocytes, macrophages, and T cells. However, PPARG expression was lowest in CD8+ T cells from non-occluded exercised EAT. The greatest number of significant cell-cell communications between adipocytes and immune cells via growth factors and adhesion molecules occurred in occluded sedentary EAT. ConclusionAerobic exercise mitigates the proinflammatory nature of EAT in CAD via modulation of immune cell subpopulations, decreased TNF superfamily and increased PPARG gene expression, and decreased growth factor communication between adipocytes and immune cells.

cell biology↗

bioRxiv2025

A Single-Graph Visualization to Reveal Hidden Explainability Patterns of SHAP Feature Interactions in Machine Learning for Biomedical Issues

BackgroundIn the last decades, the utility of Machine Learning (ML) in the biomedical domain has been demonstrated repeatedly. Their inherent opacity need augmenting ML with explainability techniques. A common practice in model explainability however, is to focus solely on the explanatory values themselves without accounting for both the main and interaction effects. While this approach simplifies interpretation, it potentially overlooks critical medical information since the nature of the interactions may provide clues to the underlying biological mechanisms. ResultsThis article introduces a novel method for analyzing explanatory values of machine learning (ML) models, in the form of a comprehensive graphical visualization. The method not only emphasises the individual contributions of the features but also gives insights about the interactions they share with one another. Designed for local additive explanation methods, the proposed tool effectively translates the complex and multidimensional nature of these values into an intuitive single-graph format. It offers a clear window into how feature interactions contribute to the overall prediction of the ML model while aiding in the identification of various interaction types, such as mutual attenuation, positive/negative synergies or dominance of one feature over another. ConclusionsThis approach provides insights for generating hypotheses, improving the transparency of ML models, particularly in the context of biology and medicine since living organisms are characterised by a multitude of parameters in complex interactions, a complexity that ensures the "stability" and robustness of structures and functions.

systems biology↗