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Biology subjects

Bernard, M.

Publications and source records attributed to Bernard, M..

At least 19 recordsLinked to original sources

Global structure of new relational knowledge networks is represented in retrosplenial complex, and node-distance in hippocampus

Much of our knowledge is structured in networks, but how the brain represents such networks remains unclear. In most nested knowledge structures a subset of the nodes will be highly connected to other nodes in the network. High levels of connection can exist either locally (high degree centrality) or at a global level (high closeness/betweenness centrality). Here, we explored how the human brain represents network structure using functional magnetic resonance imaging (fMRI) and a novel learning paradigm. During training, participants learned the transition structure for travel between a set of fictious partially connected alien planets. Despite encountering only individual connections, participants choices indicated they could infer the broader network structure. Next day, they viewed each stimulus during a cover task while undergoing fMRI. Representational-similarity analysis showed that shortest-path distances within the learned graph were encoded in the posterior hippocampus and right retrosplenial complex, whereas global connectivity (closeness/ betweenness centrality) was represented in the left retrosplenial complex. These findings extend the view that brain networks associated with spatial navigation also process abstract relational knowledge using principles akin to mapping physical space. The results are also consistent with proposals that the hippocampus represents distance information and that the retrosplenial cortex acts as hub for integrating recently acquired knowledge.

neuroscience↗

Spatiotemporal dynamics of hydrogen peroxide during neutrophil swarming in 3D

Neutrophil swarming enables the coordinated recruitment of large numbers of cells to sites of infection. Although reactive oxygen species (ROS) are key mediators of neutrophil function, their dynamics during collective behavior remain poorly defined. Here, we developed a 3D ex vivo swarming system combined with HyPer7-expressing dHL-60 cells to visualize intracellular hydrogen peroxide (H2O2) dynamics in real time at single-cell resolution. This approach enabled us to reliably measure NADPH oxidase 2 (NOX2) activity during neutrophil swarming, revealing dynamic H2O2 production. We show that H2O2 production is spatially confined to cells at the stimulation site and temporally coupled to swarming initiation and distal cell recruitment. ROS production depends on NOX2 activity and calcium signaling but is not required for swarm formation or amplification. Notably, H2O2 accumulation was detected throughout activated cells rather than being restricted to phagosomes, suggesting a broader intracellular oxidative response. Together, these findings reveal a coordinated oxidative program associated with neutrophil swarm initiation and raise the possibility that ROS contribute to signaling functions beyond their established role in phagocytosis.

Cell Biology↗

Gonadal PIP-seq reveals genes involved in germ cell development and sexual differentiation in sea lamprey ( Petromyzon marinus )

Vertebrate sex determination is highly diverse, with distinct mechanisms that have evolved repeatedly and independently across phylogeny. The sea lamprey (Petromyzon marinus) is an extant jawless vertebrate that remains sexually labile during its larval stage that lasts around 3-20 years. Their gonad contains bipotential, female, and male germ cells before metamorphosis. To examine the genetic programs in germ cells at different developmental stages, we profiled transcriptomes of dissociated gonadal cells from larvae and recently metamorphosed juvenile (transformers, sex-determined) using fluorescence-activated cell sorting (BD FACS Aria IIu) and PIPseqTM (Fluent BioSciences/Illumina). 66,676 cells were sequenced and classified into 19 cell clusters according to their gene expression profiles. Primordial germ cells differentially expressed genes encoding various heat-shock proteins, hormones, growth factors, and their receptors, and proteins sensitive to iron, nitrogen starvation, sugar and lipid metabolisms, and oxidative stress, providing possible links between environmental factors, cellular functions, and cell fate determinants. Germ cells in larvae had enriched expression of genes involved in DNA replication, transcription, translation, apoptosis, autophagy, cell cycle, cell differentiation, cell adhesion and migration, cell survival, chromatin remodeling, and proliferation. Specifically, female germ cells differentially expressed various transcript isoforms of AEP1, CUZD1, S100A1, and ZP genes, whereas male germ cells differentially expressed BOLL and PIWIL1. Pseudotime trajectory and Gene Ontology (GO) analysis revealed that genes with changing expressions along the female differentiation pathway were involved in binding of sperm to zona pellucida, egg coat formation, prevention of polyspermy and positive regulation of acrosome reaction. On the other hand, genes with changing expressions along the male differentiation pathway were involved in ribosome assembly and translation. Several WNT5 transcripts were differentially expressed in germ cells or somatic cells. Our results suggest that sea lamprey sex determination and sexual differentiation likely involve the coordinated action of numerous genes that interact with various environmental factors and regulate germ cell specification and development.

Developmental Biology↗

A novel genetically distinct Amdoparvovirus in Sorex araneus in the United Kingdom highlights an unexplored ancestral link

Amdoparvoviruses have historically been documented almost exclusively in carnivores, with recent detections in bats. However, endogenous viral elements in rodent genomes suggest a more ancient and taxonomically broader evolutionary history. Despite this, small mammals have never been systematically surveyed for extant amdoparvovirus infections. In this study, we used whole genome sequencing to screen four different shrew species and wild American mink in the UK, which may act as a reservoir host for amdoparvoviruses. We identified a highly divergent amdoparvovirus in native common shrews (Sorex araneus) from northern England, tentatively named Shrew parvovirus 1(SP 1). Classical amdoparvovirus sequences were also detected in wild American mink (Neogale vison), confirming the presence of known amdoparvovirus strains in UK mustelids. Phylogenetic analysis revealed that the shrew virus, SP 1, forms a distinct clade, suggesting ancient divergence or long-term cryptic circulation in small mammal reservoirs. These findings fundamentally challenge the hypothesis that amdoparvoviruses are carnivore-restricted pathogens and underscore the importance of systematic wildlife surveillance for understanding viral host range evolution and assessing spillover risks.

evolutionary biology↗

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

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

neuroscience↗

Torque-based immune cell chemotaxis in complex environments

Directed migration in chemical gradients is crucial to the immune response, yet how immune cells navigate complex tissues remains incompletely understood. Using in vitro migration assays and theoretical modeling, we uncover distinct chemotactic strategies in two key immune cell types: neutrophils and dendritic cells (DCs). DCs actively steer toward chemokine gradients via a deterministic torque-like reorientation, while neutrophils bias movement by modulating angular noise and speed. A quantitative Fokker-Planck framework decomposes these behaviors into deterministic and stochastic components. Cytoskeletal perturbations show that microtubules enable torque-based navigation in DCs in collagen gels, whereas actomyosin contractility is required for noise modulation employed by neutrophils and DCs in 2D confined migration assays. Despite both achieving directed migration, the two strategies result in opposing macroscopic outcomes: torque-driven cells minimize dispersion, while noise-biased migration enhances population spread. These results reveal distinct navigation aligned with immune function and demonstrate that immune cell chemotaxis is tuned by cytoskeletal architecture and environmental context.

biophysics↗

MECP2 Mutations Rewire Human ESC Fate and Bias Cortical Lineage Commitment

Rett syndrome arises from loss-of-function mutations in the X-linked chromatin regulator MECP2, yet the earliest molecular derailments in human development remain poorly defined. Using isogenic hESC models carrying three patient-derived MECP2 mutations, we followed the transcriptome from pluripotency through neuro-ectoderm, neural stem, and neural progenitor stages and into three-month cerebral organoids. Stage dominated transcriptional variance, but mutants shared a secondary program enriched for synaptic-membrane and extracellular-matrix genes. Single-cell profiling revealed a naive-like, hyper-proliferative state marked by up-regulation of ZFP42 at ESC stage. Strikingly, EMX1, a cortical radial-glia determinant, was consistently suppressed from the earliest stage onward, and cerebral organoids subsequently generated fewer excitatory neurons in favour of inhibitory and glial lineages. These data chart a continuous developmental trajectory for MECP2-mutant human cells and nominate ZFP42 and EMX1 dysregulation as tractable entry points for dissecting Rett pathogenesis.

neuroscience↗

Super-resolved live imaging of thick biological samples with 3D Random Illumination Microscopy (3D-RIM)

Super-resolved volume imaging of thick, live specimens is greatly hampered by sample induced aberrations and out-of-focus fluorescence. In this work, using a combination of speckled illuminations, remote focusing, three-dimensional photon reassignement and variance processing, we obtained volume images with super-resolution (110 nm transverse, 270 nm axial) on thin samples and maintained a high contrast and high resolution level throughout tens of microns of highly aberrant tissues and up to hundreds of microns in collagen scaffolds.

bioengineering↗

OGDHL regulates nucleotide metabolism, tumor growth, and neuroendocrine marker expression in prostate cancer

As cancer cells evade therapeutic pressure and adopt alternate lineage identities not commonly observed in the tissue of origin, they likely adopt alternate metabolic programs to support their evolving demands. Targeting these alternative metabolic programs in distinct molecular subtypes of aggressive prostate cancer may lead to new therapeutic approaches to combat treatment-resistance. We identify the poorly studied metabolic enzyme Oxoglutarate Dehydrogenase-Like (OGDHL), named for its structural similarity to the tricarboxylic acid (TCA) cycle enzyme Oxoglutarate Dehydrogenase (OGDH), as an unexpected regulator of tumor growth, treatment-induced lineage plasticity, and DNA Damage in prostate cancer. While OGDHL has been described as a tumor-suppressor in various cancers, we find that its loss impairs prostate cancer cell proliferation and tumor formation. Loss of OGDHL profoundly alters Androgen Receptor inhibition-induced plasticity, including suppressing the neuroendocrine markers DLL3 and HES6, induces accumulation of the DNA damage response marker {gamma}H2AX, and reduces nucleotide synthesis. Our data suggest that OGDHL has minimal impact on TCA cycle activity, and that mitochondrial localization is not required for its regulation of prostate cancer plasticity and nucleotide metabolism. Finally, we demonstrate that OGDHL expression is tightly correlated with neuroendocrine differentiation in clinical prostate cancer. These findings underscore the importance of investigating poorly characterized metabolic genes as potential regulators of distinct molecular subtypes of aggressive cancer.

cancer biology↗

Dissecting Oxidative Stress and Organismic Response to various Temperature Regimes in the midge C. riparius

Oxidative stress, driven by reactive oxygen species (ROS), poses a major challenge for organisms facing temperature fluctuations. This study provides the first direct in vivo measurements of ROS production in an insect, Chironomus riparius, across a broad range of ecologically relevant temperatures. We observed a U-shaped pattern of oxidative stress, with minimal ROS levels within an optimal thermal window (12-18{degrees}C) and significantly elevated stress at both cold and warm extremes. Crucially, our findings reveal distinct underlying molecular mechanisms for ROS generation at these extremes: at low temperatures, ROS production is predominantly of the superoxide group, linked to hypoxia-induced hemoglobin autoxidation. Conversely, at high temperatures, the hydrogen peroxide group dominates, associated with increased metabolic rate and heat stress signaling pathways. Transcriptomic analysis shows that C. ripariuss antioxidant defense system adapts accordingly, selectively upregulating mechanisms to counteract the specific dominant ROS type at different temperatures. This mechanistically differentiated oxidative stress and the modulated organismic response profoundly impacts the overall ecological success and evolution of C. riparius as a model for thermal stress in ectotherms. Summary StatementThis study shows that cold and heat stress activate different oxidative damage pathways in midge larvae, explaining how organisms face unique physiological limits in thermal extremes.

ecology↗

Nuclear Speckle Dynamics are Controlled by Polyphosphate Inhibition of CLK Proteins

Nuclear speckles (NS) are membrane-less nuclear organelles that act as critical hubs for pre-mRNA splicing. Defects in splicing are linked to several human diseases, including cancer, Alzheimers disease, and dystrophies. While CLK kinases regulate the mobilization of splicing factors from NS, the molecular mechanisms underlying NS assembly and dissolution remain unclear. Using an adaptation of the Biotinylation by Antibody Recognition (BAR) technique, we identify polyphosphate (polyP) as a novel and essential regulator of NS dynamics. Polyphosphate, a highly conserved polyanion composed of a chain of phosphate molecules, is involved in several functions in mammalian cells. Here, we show that polyP interacts with the NS core component SRRM2, and polyP depletion disrupts NS organization releasing splicing factors into the nucleoplasm. RNA-seq analysis reveals that polyP depletion increases exon inclusion, particularly in long genes with multiple exons, highlighting its role in splicing regulation. Mechanistically, we demonstrate that polyP acts as a physiological inhibitor of CLK3 kinase, preventing the phosphorylation of SR proteins and thereby maintaining NS stability. Our findings not only expand our understanding of NS biology but also provide new insights into the polyP involvement in splicing-related diseases. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=90 SRC="FIGDIR/small/633116v1_ufig1.gif" ALT="Figure 1"> View larger version (22K): org.highwire.dtl.DTLVardef@1dc44b6org.highwire.dtl.DTLVardef@2339e4org.highwire.dtl.DTLVardef@ade454org.highwire.dtl.DTLVardef@69482b_HPS_FORMAT_FIGEXP M_FIG C_FIG

cell biology↗

Fast adaptation of Myosin II activity to confinement sustains neutrophil migration in capillaries

As the first responders of the immune system, neutrophils rapidly and abundantly reach inflamed tissues through blood capillaries. The diameter of capillaries can be as narrow as two microns, imposing considerable deformations on neutrophils. Notably, capillary obstruction due to neutrophil retention causes vascular dysfunction and contributes to the pathogenesis of several diseases. However, the cellular mechanisms that allow neutrophils to migrate into small capillaries and to avoid retention remain unknown. In this study, we demonstrate, both in vivo and in vitro, that capillary size does not influence neutrophil migration velocity. During migration into capillaries of different sizes, neutrophils maintain high speed, a phenomenon associated with a global actomyosin cytoskeleton rearrangement in response to confinement strength. In irregular capillaries, neutrophils rapidly adapt their cell contractility via the ROCK-MyoII pathway, which allows them to sustain their migration speed along the vessels despite changes in confinement. At the single cell level, inhibition of ROCK impairs actomyosin cytoskeleton rearrangement and reduces neutrophil migration speed within confined capillaries. At the collective level, ROCK inhibition hampers efficient neutrophil trafficking in a network of small capillaries, resulting in vessel obstruction. These findings reveal a unique capacity of neutrophils to rapidly and dynamically adapt their migration to the confinement strength of capillaries, an ability that might limit vascular dysfunction during inflammation.

cell biology↗

DMD Human iPSC-derived skeletal muscle cells recapitulate selective calcium dysregulation pathways.

This study investigates the functional characteristics of induced pluripotent stem cell-derived muscle cells (hiPSC-skMCs) from Duchenne muscular dystrophy (DMD) patients, focusing on their regulation of intracellular calcium concentration. DMD, a progressive muscle degenerative disease, arises from mutations in the dystrophin gene and is characterized by elevated intracellular calcium levels, exacerbating disease progression. This work highlights that DMD hiPSC-skMCs demonstrate unique calcium signatures with increased intracellular calcium compared to healthy counterparts. These cells also exhibit both heightened calcium response when stimulated by electrical fields or acetylcholine and more pronounced constitutive calcium entries. While RNAseq data from these cells reaffirmed known dysregulation mechanisms seen in other dystrophin-deficient models, certain pathways like purinergic or store-operated calcium entries did not show disruption in this DMD model. This discrepancy suggests that not all mechanisms observed in animal models may be equally relevant in human cases, pointing towards specific molecular targets that could be more effective for DMD treatment strategies.

cell biology↗

Interleukin-10-producing monocytes contribute to sex differences in pain resolution in mice and humans.

Pain is closely associated with the immune system, which exhibits sexual dimorphism. For these reasons, neuro-immune interactions are suggested to drive sex differences in pain pathophysiology. However, our understanding of peripheral neuro-immune interactions on sex differences in pain resolution remains limited. Here, we have shown, in both a mouse model of inflammatory pain and in humans following traumatic pain, that males had higher levels of interleukin (IL)-10 than females, which were correlated with faster pain resolution. Following injury, we identified monocytes (CD11b+ Ly6C+ Ly6G-F4/80mid) as the primary source of IL-10, with IL-10-producing monocytes being more abundant in males than females. In a mouse model, neutralizing IL-10 signaling through antibodies, genetically ablating IL-10R1 in sensory neurons, or depleting monocytes with clodronate all impaired the resolution of pain hypersensitivity in both sexes. Furthermore, manipulating androgen levels in mice reversed the sexual dimorphism of pain resolution and the levels of IL-10-producing monocytes. These results highlight a novel role for androgen-driven peripheral IL-10-producing monocytes in the sexual dimorphism of pain resolution. These findings add to the growing concept that immune cells play a critical role in resolving pain and preventing the transition into chronic pain. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=135 SRC="FIGDIR/small/565129v1_ufig1.gif" ALT="Figure 1"> View larger version (46K): org.highwire.dtl.DTLVardef@6e158corg.highwire.dtl.DTLVardef@148c8b5org.highwire.dtl.DTLVardef@1711d2dorg.highwire.dtl.DTLVardef@132a755_HPS_FORMAT_FIGEXP M_FIG C_FIG

immunology↗

Tonic Meningeal Interleukin-10 Upregulates Delta Opioid Receptor to Prevent Relapse to Pain

Chronic pain often alternates between transient remission and relapse of severe pain. While most research on chronic pain has focused on mechanisms maintaining pain, there is a critical unmet need to understand what prevents pain from re-emerging in those who recover from acute pain. We found that interleukin (IL)-10, a pain resolving cytokine, is persistently produced by resident macrophages in the spinal meninges during remission from pain. IL-10 upregulated expression and analgesic activity of {delta}-opioid receptor ({delta}OR) in the dorsal root ganglion. Genetic or pharmacological inhibition of IL-10 signaling or {delta}OR triggered relapse to pain in both sexes. These data challenge the widespread assumption that remission of pain is simply a return to the naive state before pain was induced. Instead, our findings strongly suggest a novel concept that: remission is a state of lasting pain vulnerability that results from a long-lasting neuroimmune interactions in the nociceptive system.

neuroscience↗

Cyclosporin A delays the terminal disease stage in Tfam KO mice without improving mitochondrial energy production

AO_SCPLOWBSTRACTC_SCPLOWMitochondrial myopathies are rare genetic disorders characterized by muscle weakness and exercise intolerance. Currently, no effective treatment exists for these myopathies. Interestingly, the pharmacological cyclophilin inhibitor cyclosporine A (CsA) extended lifespan and prevented loss of force and mitochondrial Ca2+ overload in muscle fibers in the skeletal muscle-specific Tfam knockout mouse model of lethal mitochondrial myopathy (Tfam KO). The unaffected expression of proteins involved in mitochondrial energy metabolism suggests that these improvements occurred without improvement in metabolism. In this study, we aimed at investigating the effects of four weeks of CsA administration on in vivo contractile function and mitochondrial energy production in Tfam KO mice. The treatment started before the terminal phase with severe muscle weakness and weight loss. Our results show that CsA treatment delayed progression into the terminal disease phase. This occurred without any obvious positive effects on mitochondrial energy production at rest or during fatigue induced by repeated contractions. In conclusion, cyclophilin inhibitors may have the potential of counteracting devastating muscle weakness in patients with mitochondrial myopathies most probably by preventing deleterious effects triggered by excessive mitochondrial Ca2+ uptake rather than by improving mitochondrial energy production.

pathology↗

Identification of conserved skeletal enhancers associated with craniosynostosis risk genes

Craniosynostosis (CS) is a common congenital defect affecting more than 1/2000 infants. Infants with CS have a premature fusion of one or multiple cranial sutures resulting in restricted brain expansion. Single gene mutations account for 15-20% of cases, largely as part of a syndrome, but the majority are nonsyndromic with complex underlying genetics. Two noncoding genomic regions contributing to CS risk were previously identified by GWAS, one near BMP2 and one within BBS9. We hypothesized that the region within BBS9 contains distal regulatory elements controlling the neighboring gene encoding BMPER, a secreted modulator of BMP signaling. To identify regulatory sequences that might underlie disease risk, we surveyed conserved noncoding sequences from both risk loci identified from the GWAS for enhancer activity in transgenic Danio rerio. We identified enhancers from both regions that direct expression to skeletal tissues, consistent with the endogenous gene expression. Importantly, for each locus, we found a skeletal enhancer that also contains a sequence variant associated with CS risk. We examined the activity of each enhancer during craniofacial development and found that the BMPER-associated enhancer is active in the restricted region of cartilage closely associated with frontal bone initiation. We used an enhanced yeast one-hybrid assay to identify transcription factor interactions with several identified enhancers, implicating multiple signaling pathways in their regulation. In a targeted screen focused on risk-associated SNPs, we further identified differential binding to alternate and reference alleles. Additionally, we found that the risk allele of the BMPER enhancer directs significantly broader expression than the reference allele in transgenic zebrafish. Our findings support a specific genetic mechanism to explain the contribution of two risk loci to CS. More broadly, our combined in vivo approach is applicable to many complex genetic diseases to build a link between association studies and specific genetic mechanisms. Author SummaryGenome-wide association studies (GWASs) provide a wealth of information implicating regions of the genome in disease risk. The great challenge is linking those regions to specific genetic mechanisms. We used complementary approaches in zebrafish and yeast to evaluate the genetic risk of craniosynostosis (CS), a craniofacial birth defect affecting 1/2000 infants where two or more skull bones are fused prematurely. Using transgenic zebrafish, we identified sequences regulating expression of two genes in the BMP signaling pathway that had been previously implicated by GWAS. These included one from each region containing a sequence variant linked to disease risk. We used an assay in cultured yeast to detect proteins binding to identified DNA sequences that could alter expression of the target genes, including changes in protein binding caused by the sequence variants. Finally, we found that transgenic fish carrying one of the variant sequences showed broader and more sustained activity throughout the skeleton. Taken together, our results support a model where variant sequences lead to increased gene expression and BMP pathway activity, contributing to aberrant skull growth in CS. Importantly, our paradigm is broadly applicable to other complex genetic diseases, potentially illuminating many connections between genome variation and disease risk.

genetics↗

Androgen receptor inhibition induces metabolic reprogramming and increased reliance on oxidative mitochondrial metabolism in prostate cancer

Prostate cancer cells that survive clinical androgen receptor (AR) blockade mediate disease progression and lethality. Reprogrammed metabolic signaling is one mechanism by which tumor cells can survive treatment. However, how AR inhibition reprograms metabolism, and whether altered metabolism can be exploited to eradicate cells that survive AR blockade, remains unclear. Here, we comprehensively characterized the effect of AR blockade on prostate cancer metabolism using transcriptomics, metabolomics, and bioenergetics approaches. AR inhibition maintains oxidative mitochondrial metabolism and reduces glycolytic signaling, through hexokinase II downregulation and decreased MYC activity. Robust elongation of mitochondria via reduced DRP1 activity supports cell fitness after AR blockade. In addition, AR inhibition enhances sensitivity to complex I inhibitors in several models, suggesting that AR blockade increases reliance on oxidative mitochondrial metabolism. Our study provides an enhanced understanding of how AR inhibition alters metabolic signaling and highlights the potential of therapies that target metabolic vulnerabilities in AR-inhibited cells.

cancer biology↗