Search bioRxiv⌕ Search

Biology subjects

Arnaud, M.

Publications and source records attributed to Arnaud, M..

14 recordsLinked to original sources

Mechanical Tension Actively Triggers RhoA-Mediated Cell Extrusion

Cell extrusion is a fundamental process in tissue homeostasis, morphogenesis, and cancer progression, facilitating the removal of cells either alive or through apoptosis. While biochemical signaling pathways are known to regulate extrusion, recent advances have underscored the importance of mechanical forces in this process. Here, using optogenetic control of RhoA activation in epithelial monolayers combined with Bayesian Inversion Stress Microscopy (BISM) and three-dimensional cell-based modeling, we uncover a counterintuitive mechanism whereby elevated tension, instead of stabilizing the monolayer, actively drives extrusion in highly contractile cells. We show that local RhoA activation enhances myosin II-dependent contractility and F-actin reorganization, which promotes cell stiffening, resulting in localized tension buildup. The ensuing tensile stress amplifies vertical mechanical fluctuations, which in turn trigger cell extrusion. Remarkably, these tension-induced extrusions occur both apically and basally. Furthermore, our findings show that RhoA-mediated contractility is not merely an effector of extrusion but also an active promoter of basal extrusion, independently of caspase activation. Our study demonstrates that tensile stress can directly initiate extrusion events and bias their outcome toward apical or basal fates. By identifying tension as a driver rather than a suppressor of extrusion, this work revises current models of epithelial homeostasis and highlights mechanical control as a targetable axis in disease and regeneration.

cell biology↗

From diminishing returns to entrenchment: a unifying theory of epistasis along adaptive walks revealed by Fisher's geometric model

Epistasis makes the fitness effect of a mutation depend on the genetic background in which it occurs, thereby shaping the accessibility and reversibility of evolutionary trajectories. Along adaptive walks, this path-dependent epistasis can take distinct forms: contingency, when a mutation requires prior substitutions to be beneficial; entrenchment, when later substitutions make its reversion increasingly deleterious; and diminishing returns, when successive beneficial mutations reduce one anothers effects. Although these regimes have been documented experimentally, the conditions under which each predominates remain poorly understood. Here we use Fishers geometric model to derive a general framework for path-dependent epistasis under stabilizing selection on a multidimensional phenotype. We show that epistasis between substitutions has a simple geometric interpretation: contingency and entrenchment arise when the collateral effects of mutations, orthogonal to the direction of the optimum, are compensated by the preceding or subsequent adaptive path, whereas diminishing returns arise when successive substitutions remain strongly aligned with the same direction of selection. Analytical results and simulations reveal a transition controlled by a single composite parameter combining phenotypic complexity, mutation size, and distance to the optimum. Far from the optimum, adaptive walks are dominated by diminishing returns epistasis. As populations approach the optimum, or as phenotypic complexity increases, antagonistic pleiotropy generates systematic contingency and entrenchment. At mutation-selection-drift equilibrium, these effects become strong, rapidly established, and increase with phenotypic complexity. These results show that contingency and entrenchment do not require specific molecular interactions between residues: they emerge generically from nonspecific epistasis produced by stabilizing selection on pleiotropic traits. Fishers geometric model thus unifies diminishing returns, contingency, and entrenchment as distinct regimes of the same underlying geometry of adaptation.

evolutionary biology↗

Vimentin bridges scales to convert polarized cell locomotion into coordinated collective migration

Collective cell migration is central in development and disease. Vimentin is an intermediate filament protein expressed by epithelial cells at the edge of wounds where collective cell migration is most efficient. Yet, its functional role in this context remains underexplored. Here, we show that vimentin, over-expressed in cells undergoing partial epithelial to mesenchymal transition at the edge of epithelial monolayers, has a multiscale impact on the whole monolayer mechano-dynamics. Vimentin knock-down delays wound closure, reduces cell coordination, while increasing traction forces exerted by cells on the substratum. It also disrupts the directionality of leader cells migration, as well as the cohesion and coordinated motion of cells deep in the monolayer. We further show that vimentin promotes the conversion of polarized cell locomotion into coordinate collective migration by polarizing actin, focal adhesions and traction forces, sustaining leader cells lamellipodium protrusive activity and directionality, while allowing mechanical coupling of leader with follower cells. Altogether, we show that vimentin is essential for bridging polarized single cell locomotion and coordinated collective migration to allow efficient collective migration. Significant statementEpithelial cells migrate coordinately to repair tissue. Vimentin, transiently enriched at the wound edge plays a key role in guiding this process by converting polarized cell locomotion into coordinate collective migration, enabling leader cells to polarize, form stable protrusions, and maintain directed migration, while allowing mechanical coupling of front cells with followers, necessary for efficient coordinated collective migration. These findings reveal vimentin, a known EMT marker, as a novel positive regulator of efficient wound healing.

cell biology↗

Astrocytes control the Neuroinflammation and ILC2 response through IL-33/ST2 signaling, during protection against Cerebral Malaria in Toxoplasma-P. berghei coinfected Mice

Cerebral malaria (CM) is a complex multi-systemic disorder defined as a diffuse encephalopathy with acute neurological manifestations characterized by alterations in the level of consciousness, deep coma and seizure preceding death. During infection, astrocytes undergo significant morphological and molecular changes, adopting a reactive state that impacts on their functions. This reactivity is characterized by a shift in from a neuroprotective (A2) to a neurotoxic (A1) phenotype, influencing the outcome of the immune response. These phenotypes may vary depending on the chronicity of the infection or multiples infections of the same host. In this study, we investigated how Toxoplasma gondii (Tg) brain infection impacts on the outcome of experimental cerebral malaria (ECM) in mice infected with Plasmodium berghei ANKA (PbA). Our results highlighted an immunomodulatory role of GFAP+ astrocytes underweening significant morphological and molecular alterations and adopting a unique intermediate reactivity state (A1/A2). This state was correlated with production of CXCL-10 and TGF-{beta}, which control inflammation without exacerbating infection. Our study also revealed a key role of the IL-33/ST2 pathway induced by Tg brain infection in protecting against ECM. Astrocyte-derived IL-33 was crucial to promote brain recruitment and activation of innate lymphoid cells (ILC2), which contribute to the hosts antiparasitic response. Additionally, we identified a distinctive intermediate M1/M2 phenotype in CD86+CD206+CD16/32+MHCIIhi microglia and noted an enhanced recruitment of inflammatory monocytes, both contributing to inflammation and control of PbA infection. This study reveals, for the first time, how latent brain infection with T. gondii confers protection against a severe cerebral form of malaria, positioning astrocytes at the core of the neuroinflammatory response that controls PbA infection severity. This expands our understanding of host-pathogen interactions and the potential for targeting astrocytic pathways in preventing CM. Author SummaryCerebral malaria (CM) is one of the most severe complications of Plasmodium infection, often leading to coma and death. The mechanisms that determine why some individuals develop this life-threatening condition remain poorly understood. In this study, we explored how a chronic brain infection with the parasite Toxoplasma gondii influences the development of CM in mice. We found that Tg infection reshapes the brains immune environment, particularly through the actions of astrocytes, cells that normally support and protect neurons. During coinfection, astrocytes adopted a balanced reactive state that limited inflammation without worsening the infection. This response involved the IL-33/ST2 signalling pathway and led to the recruitment of protective immune cells, helping to control Plasmodium infection in the brain. Our findings uncover an unexpected protective role of latent T. gondii infection and identify astrocytes as central regulators of neuroinflammation. This work highlights potential new strategies for preventing or mitigating cerebral malaria by targeting astrocyte-mediated immune responses.

immunology↗

IFNAR1. Neutrophils Orchestrate Chronic Inflammatory Damage Through Mitochondrial Remodeling

Neutrophils are abundant innate effector cells that drive mucosal inflammation, yet the mechanisms by which they contribute to chronic inflammatory diseases across distinct tissues remain incompletely understood. Here, by reanalyzing single-cell RNA-seq datasets from patients with inflammatory bowel disease (IBD) and chronic obstructive pulmonary disease (COPD), we identify a shared neutrophil activation program enriched for type I interferon (IFN) signaling, nuclear factor-{kappa}B (NF-{kappa}B) and AP-1 transcriptional regulators, and effector pathways including NETosis, degranulation, and leukocyte trafficking. To interrogate these signatures, we established a CRISPR-compatible neutrophil differentiation platform from adult CD34 progenitors, which yielded cells closely resembling primary neutrophils at transcriptomic, proteomic, and functional levels. A targeted CRISPR-Cas9 screen revealed a central role for the mitochondrial iron transporter mitoferrin-1 (SLC25A37) in coordinating neutrophil oxidative phosphorylation, NET formation, and type I IFN production downstream of TLR9. Mechanistically, we show that NET-derived citrullinated histones activate an autocrine IFN-IFNAR1 loop, amplifying neutrophil inflammatory functions without impairing phagocytosis. Disruption of this loop, through IFNAR1 depletion or blockade, dampened neutrophil-driven tissue damage in human intestinal and alveolar organoid co-cultures as well as in murine models of colitis and cigarette smoke-induced lung inflammation. These findings uncover a conserved IFN-driven metabolic circuit in neutrophils that underpins pathology across chronic mucosal diseases and identify IFNAR1 as a therapeutic node to selectively disarm neutrophil-mediated tissue injury.

immunology↗

Unique belowground ecological strategies of subtropical and tropical plant species expand the root trait space

Root trait variation may reflect the ecological and evolutionary processes shaping biodiversity, but remains poorly quantified in the (sub)tropics. Here, we aim to further complete our knowledge of belowground functional strategies by assessing the contributions of subtropical and tropical species to global root trait diversity. We gathered root data for 1618 temperate, 341 subtropical, and 775 tropical species. We compared functional diversity among biomes and calculated the unique contribution of each biome to the global root economics space. Further, we determined if the within-variation of subtropical and tropical biomes is shaped by species niches and/or differences in evolutionary history. Root trait expressions differed among biomes, but root functional diversity did not. Furthermore, subtropical and tropical biomes accounted for 40% of the unique root functional space within the global traits space. Species climate niches and phylogenetic turnover explained variation in root traits (e.g., denser root tissue was associated with drier sites) among subtropical but not tropical species. Through their unique root traits, sub(tropical) species strongly expand the current global root trait space. This work underwrites their importance in conceptual models for more complete insights into how various belowground strategies drive plant functional biogeography and biodiversity globally.

ecology↗

CytoBatchNorm: an R package with graphical interface for batch effects correction of cytometry data

Innovation in cytometry propelled it to an almost "omic" dimension technique during the last decade. The application fields concomitantly enlarged, resulting in generation of high-dimensional high-content data sets which have to be adequately designed, handled and analyzed. Experimental solutions and detailed data processing pipelines were developed to reduce both the staining conditions variability between samples and the number of tubes to handle. However, an unavoidable variability appears between samples, barcodes, series and instruments (in multicenter studies) contributing to "batch effects" that must be properly controlled. Computer aid to this aim is necessary, and several methods have been published so far, but configuring and carrying out batch normalization remains unintuitive for scientists with "pure" academic backgrounds in biology. To address this challenge, we developed an R package called CytoBatchNorm that offers an intuitive and user-friendly graphical interface. Although the processing is based on the script by Schuyler et al., the graphical interface revolutionizes its use. CytoBatchNorm enables users to define a specific correction for each marker in a single run. It provides a graph that guides you through quickly setting the correction for each marker. It allows corrections to be previewed and inter-marker effects to be checked as the settings are made. CytoBatchNorm will help the cytometry community to adequately scale data between batches, reliably reducing batch effects and improving subsequent dimension reduction and clustering. VISUAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=129 SRC="FIGDIR/small/596492v1_ufig1.gif" ALT="Figure 1"> View larger version (46K): org.highwire.dtl.DTLVardef@600a1eorg.highwire.dtl.DTLVardef@13860cborg.highwire.dtl.DTLVardef@5ad915org.highwire.dtl.DTLVardef@6218dc_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioinformatics↗

Tumor-reactive clonotype dynamics underlying clinical response to TIL therapy in melanoma

The profiles, specificity and dynamics of tumor-specific clonotypes that are associated with clinical response to adoptive cell therapy (ACT) using tumor-infiltrating lymphocytes (TILs) remain unclear. Using single-cell RNA/TCR-sequencing, we tracked TIL clonotypes from baseline tumors to ACT products and post-ACT blood and tumor samples in melanoma patients treated with TIL-ACT. Patients with clinical responses had baseline tumors enriched in tumor-reactive TILs, which were more effectively mobilized upon in vitro expansion, yielding products with higher numbers of tumor-specific CD8+ cells, which also preferentially infiltrated tumors post-ACT. Conversely, lack of clinical responses was associated with tumors devoid of tumor-reactive resident clonotypes, and with cell products mostly composed of blood-borne clonotypes mainly persisting in blood but not in tumors post-ACT. Upon expansion, tumor-specific TILs lost the specific signatures of states originally exhibited in tumors, including exhaustion, and in responders acquired an intermediate exhausted effector state after tumor engraftment, revealing important functional cell reinvigoration.

cancer biology↗

TCRpcDist: Estimating TCR physico-chemical similarity to analyze repertoires and predict specificities

Approaches to analyse and cluster TCR repertoires to reflect antigen specificity are critical for the diagnosis and prognosis of immune-related diseases and the development of personalized therapies. Sequence-based approaches showed success but remain restrictive, especially when the amount of experimental data used for the training is scarce. Structure-based approaches which represent powerful alternatives, notably to optimize TCRs affinity towards specific epitopes, show limitations for large scale predictions. To handle these challenges, we present TCRpcDist, a 3D-based approach that calculates similarities between TCRs using a metric related to the physico-chemical properties of the loop residues predicted to interact with the epitope. By exploiting private and public datasets and comparing TCRpcDist with competing approaches, we demonstrate that TCRpcDist can accurately identify groups of TCRs that are likely to bind the same or similar epitopes. Additionally, we experimentally validated the ability of TCRpcDist to predict antigen-specificities of tumor-infiltrating lymphocytes orphan TCRs obtained from four cancer patients. TCRpcDist is a promising approach to support TCR repertoire analysis and cancer immunotherapies. One Sentence SummaryWe present a new approach for TCR clustering which allows TCR deorphanization for the first time.

immunology↗

Integrated Proteogenomic Deep Sequencing and Analytics Accurately Identify Non-Canonical Peptides in Tumor Immunopeptidomes

Efforts to precisely identify tumor human leukocyte antigen (HLA) bound peptides capable of mediating T cell-based tumor rejection still face important challenges. Recent studies suggest that non-canonical tumor-specific HLA peptides that derive from annotated non-coding regions could elicit anti-tumor immune responses. However, sensitive and accurate mass-spectrometry (MS)-based proteogenomics approaches are required to robustly identify these non-canonical peptides. We present an MS-based analytical approach that characterizes the non-canonical tumor HLA peptide repertoire, by incorporating whole exome sequencing, bulk and single cell transcriptomics, ribosome profiling, and a combination of two MS/MS search tools. This approach results in the accurate identification of hundreds of shared and tumor-specific non-canonical HLA peptides and of an immunogenic peptide from a downstream reading frame in the melanoma stem cell marker gene ABCB5. It holds great promise for the discovery of novel cancer antigens for cancer immunotherapy.

cancer biology↗

Prevalence of sleep-disordered breathing and associations with malocclusion in children

ObjectiveThis study aimed to determine the prevalence of sleep-disordered breathing (SDB) and its association with malocclusion among children in Recife, Brazil. Methods390 children aged seven to eight years took part in the study, comprised by the body mass measurement, orthodontic examination and parents information required by the Sleep Disturbance Scale for Children. Statistics tools were Pearsons chi-square and Lemeshow test. ResultsSDB was found in 33.3% of the children and associated with overjet (p= 0.007), anterior open bite (p=0.008) and posterior crossbite (p= 0.001). There was no association between BMI and SDB. The multivariate logistic regression model indicated that the anterior open bite (p= 0.002) and posterior crossbite (p = 0.014) have an association with SDB. ConclusionsResults of this study indicated that the prevalence of SDB was high and highly associated with malocclusion; anterior open bite and posterior crossbite are risk factors for SDB.

epidemiology↗

Deep motif deconvolution of HLA-II peptidomes for robust class II epitope predictions

CD4 T cells are key for priming and regulating immune recognition of infected and cancer cells, but predictions of class II epitopes have limited accuracy. We combined unbiased Mass Spectrometry-based HLA-II peptidomics with a novel motif deconvolution algorithm to profile and analyze a total of 99265 unique HLA-II ligands. Our work demonstrates substantial improvement in the definition of HLA-II binding motifs and enhanced accuracy in class II epitope predictions.

immunology↗

Prevalence of TMD and level of chronic pain in a group of Brazilian adolescents

ObjectivesTo determine the prevalence of temporomandibular disorder and associated factors in an adolescent sample from Recife, Brazil.\n\nMaterials and MethodsA cross-sectional study was conducted with 1342 adolescents aged 10-17 years. The Research Diagnostic Criteria for Temporomandibular Disorder (RDC/TMD) was used by calibrated examiners to evaluate the presence and levels of chronic pain. To evaluate the socioeconomic conditions, the Brazilian Economic Classification Criteria (CCEB) questionnaire was answered by the subjects. Data were analyzed by means of binary logistic regression in SPSS.\n\nResultsThe results showed that 33.2% of the subjects had TMD irrespective of age (p= 0.137) or economic class (p=0.507). Statistically significant associations were found between TMD and gender (p= 0.020), headache/migraine in the past six months (p=0,000) and the presence of chronic pain (p=0,000). In final model, logistic regression showed that chronic pain contributes to the presence of TMD.\n\nConclusionsThe prevalence of TMD was considered high (33.2%) and adolescents with chronic pain were more likely to have TMD.\n\nClinical RelevanceThe data contribute to the understanding of TMD among adolescents and to the development of preventive measures and polices to identify the dysfunction promptly.

epidemiology↗

Rapid sensing of L-leucine by human and murine hypothalamic neurons: neurochemical and mechanistic insights

ObjectiveDietary proteins are sensed by hypothalamic neurons and strongly influence multiple aspects of metabolic health, including appetite, weight gain and adiposity. However, little is known about the mechanisms by which hypothalamic neural circuits controlling behavior and metabolism sense protein availability. The aim of this study is to characterize how neurons from the mediobasal hypothalamus respond to a signal of protein availability: the amino acid L-leucine.\n\nMethodsWe used primary cultures of post-weaning murine mediobasal hypothalamic neurons, hypothalamic neurons derived from human induced pluripotent stem cells, and calcium imaging to characterize rapid neuronal responses to physiological changes in extracellular L-Leucine concentration.\n\nResultsA neurochemically diverse subset of both mouse and human hypothalamic neurons responded rapidly to L-leucine. Consistent with L-leucines anorexigenic role, we found that 25% of mouse MBH POMC neurons were activated by L-leucine. 10% MBH NPY neurons were inhibited by L-leucine, and leucine rapidly reduced AGRP secretion, providing a mechanism for the rapid leucine-induced inhibition of foraging behaviour in rodents. Surprisingly, none of the candidate mechanisms previously implicated in hypothalamic leucine sensing (KATP channels, mTORC1 signaling, amino-acid decarboxylation) were involved in the acute activity changes produced by L-leucine. Instead, our data indicate that leucine-induced neuronal activation involves a plasma membrane Ca2+ channel, whereas leucine-induced neuronal inhibition is mediated by inhibition of a store-operated Ca2+ current.\n\nConclusionsA subset of neurons in the mediobasal hypothalamus rapidly respond to physiological changes in extracellular leucine concentration. Leucine can produce both increases and decreases in neuronal Ca2+ concentrations in a neurochemically-diverse group of neurons, including some POMC and NPY/AGRP neurons. Our data reveal that leucine can signal through novel mechanisms to rapidly affect neuronal activity.\n\nHighlights- A neurochemically diverse group of mouse and human hypothalamic neurons rapidly sense and respond to L-leucine\n- Leucine can produce neuronal activation or neuronal inhibition via distinct and novel Ca2+ signaling mechanisms.\n- Leucine activates 25% ARH POMC neurons\n- Leucine inhibits 10% ARH NPY/AGRP neurons and reduces AGRP secretion from fasted mediobasal hypothalamic slices

neuroscience↗