Biology subjects

Nicolas, A.

Publications and source records attributed to Nicolas, A..

At least 19 recordsLinked to original sources

bioRxiv2026

Exploring dog-owner microbiota and bacterial pathogens in Southeast Asia

Domestic dogs may influence human microbiota and act as reservoirs or sentinels for zoonotic bacteria, yet little is known about these dynamics in Southeast Asia. Using full-length 16S rRNA gene sequencing from rectal swabs, we analyzed microbiota from dog-owner pairs from four villages of rural Thailand (Nan province) to assess microbial diversity, shared taxa, and zoonotic potential. Dogs exhibited higher microbial and putative pathogen diversity than humans, particularly during the rainy season. While dog-owner pairs shared more bacteria than unrelated individuals, overall overlap remained limited - likely driven by their dogs free-roaming lifestyles and broader environmental exposures. However, co-occurrence of putative zoonotic pathogens such as Shigella spp. and Klebsiella pneumoniae suggests dogs could serve as useful indicators for specific public health risks, with further targeted pathogen screening needed to validate these results. Our findings highlight the value of integrating dogs into zoonotic surveillance programs, particularly in regions with free-ranging dog populations and close human-animal contact.

microbiology↗

bioRxiv2026

Space partitioning by self-organized epithelial networks

Branching epithelia build supracellular networks that must simultaneously ensure connectivity, mechanical integrity, and efficient space partitioning, yet a general framework for how such networks form beyond the endothelial lineage has been lacking. Here we show that epithelial cells from multiple branching organs spontaneously self-organize into extended reticulate networks in simplified environments, revealing a conserved network-forming capacity. Combining wide-field lensless holographic imaging, deep-learning segmentation (EpiNet), and graph-theoretic analysis, we resolve a reproducible assembly sequence - contact initiation, clustering, percolation, and post-percolation relaxation - and quantify its geometry across scales. Actomyosin contractility controls both the growth of connectivity and the relaxation dynamics that set network geometry, tuning the effective cost of forming connections and thereby selecting between tree-like and reticulate topologies. After percolation, epithelial networks behave as active tension networks that progressively refine space partitioning toward centroidal, near-optimal configurations while maintaining a characteristic mesh size through continuous edge nucleation. These findings establish epithelial network formation as a generic, physically regulated mode of tissue self-organization and provide a quantitative framework linking single-cell mechanics, network topology, and space-partitioning dynamics, with implications for branching morphogenesis, organoid models, and tissue engineering.

biophysics↗

bioRxiv2026

Isolation and characterization of novel filamentous phages from Swiss-type cheeses infecting the Gram-positive bacterium Propionibacterium freudenreichii

Filamentous phages infecting Gram-positive bacteria remain largely unexplored. Notably, only two filamentous phages, B5 and Philemon infecting Propionibacterium freudenreichii, have been described to date in the phage-rich dairy ecosystem. Although both were genomically characterized, only B5 was confirmed to be an infective filamentous single-stranded DNA phage. The aim of this study was to isolate and characterize new filamentous phages from Swiss-type cheese to investigate their diversity, structural features, host specificity, and potential adaptation to the dairy environment. Thirty raw and pasteurized milk cheeses from France were screened for phages infecting P. freudenreichii strains. Eleven phages were isolated, nine of which displayed a filamentous morphology. Named MINOG1 to MINOG9, these filamentous phages exhibited genomic features typical of this morphotype, including small single-stranded DNA genomes with collinear genes organized into functional modules. Comparison with B5 and Philemon revealed sequence divergence ranging from 0.1% to 7%. These phages also exhibited a diverse host range. To further explore phage-P. freudenreichii interactions, we screened the genomes of the strains used in this study, as well as additional genomes retrieved from the NCBI database, for CRISPR spacers predicted to target these filamentous phages. Numerous strains contained CRISPR spacers showing 79 to 100% identity to genomic regions of these phages. Two P. freudenreichii strains displayed markedly different phage resistance levels despite exact spacer-protospacer matches with phages B5, MINOG1, MINOG2, and MINOG8. Conversely, several strains were resistant to nearly all tested phages despite lacking CRISPR spacers targeting them suggesting the presence of additional defense systems in P. freudenreichii. IMPORTANCEFilamentous phages can play important roles in bacterial ecology by modulating host physiology, population dynamics, and bacterial adaptation to specific environments. However, filamentous phages infecting Gram-positive bacteria remain among the least explored bacterial viruses, and their diversity, ecology, and interactions with their hosts are still poorly understood. This knowledge gap is particularly relevant in dairy ecosystems, where phages are abundant and can influence microbial communities and fermentation processes. In characterizing nine new filamentous phages infecting Propionibacterium freudenreichii from Swiss-type cheeses, this study expands the known diversity of filamentous phages associated with Gram-positive bacteria and provides new insights into phage-host interactions and bacterial defense strategies in dairy-associated bacteria.

microbiology↗

bioRxiv2025

Analysis of intratumoral immune heterogeneity reveals spatial organisation of immunosuppression in breast cancer

Recent advances in single-cell transcriptomics have illuminated intratumoral heterogeneity (ITH) in breast cancer, yet the spatial organization and functional states of immune populations within luminal tumors remain poorly understood. Here, we generated a spatially and clonally resolved single-cell immune atlas of early-stage luminal breast cancer by integrating paired single-cell RNA/TCR sequencing with multiplex immunohistochemistry across three spatially distinct tumor regions: central (core-proximal), intermediate and peripheral (invasive margin-proximal), in five patients. Peripheral regions are enriched in naive CD4 T cells, monocytes, dendritic cells, and memory CD8 T cells with bystander properties, alongside TCF1+ exhausted progenitors (Tpex), and displayed elevated antigen presentation and tertiary lymphoid structures (TLS) signatures. In contrast, central regions harbor macrophages, clonally expanded regulatory T cells (Tregs), and two subsets of terminally exhausted CD8 T cells (Tex), one tissue-resident and one circulating, both expressing tumor-reactive features. Clonal overlap was observed between peripheral Tpex and central, tissue-resident Tex cells, revealing a spatially confined differentiation trajectory toward exhaustion within the tumor microenvironment. Central T cells also upregulate TGF-{beta} signaling and metabolic pathways including fatty acid oxidation and oxidative phosphorylation, consistent with adaptation to an immunosuppressive microenvironment. Together, these findings reveal a spatially structured immune landscape in luminal breast cancer, marked by progressive immunosuppression from the tumor margin to the core, providing a framework for future region-specific immunotherapeutic strategies.

immunology↗

bioRxiv2025

Sleep after Motor Sequence Learning Enhances Post-Movement Parietal Beta Synchronization

The neural substrates supporting the beneficial effect of sleep on motor memory consolidation are well described. However, less is known about the brain oscillatory dynamics underlying these processes. We characterized the oscillatory dynamics associated with motor sequence learning and their modulation by post-learning sleep using magnetoencephalography (MEG) in young healthy adults. After learning a motor sequence task while their brain activity was recorded with MEG, participants were distributed in two groups according to whether they slept or were totally sleep deprived during the first post-training night. Consolidation was assessed with a retest in the MEG three days after training. Behaviorally, performance improved over the consolidation interval irrespective of whether sleep was afforded during the first night. MEG results showed that initial motor sequence learning was characterized by a progressive decrease in beta Event Related Desynchronization (ERD, 18-25Hz) over bilateral motor areas. Interestingly, while these practice-related modulations of beta ERD were not influenced by the sleep status, post-learned-movement beta Event Related Synchronization (ERS) over bilateral parietal areas increased over the consolidation interval in the sleep, compared to the sleep deprived, group. These results extend current models of motor memory consolidation by identifying ERS as an oscillatory marker of sleep-dependent consolidation.

neuroscience↗

bioRxiv2025

Reducing Glioblastoma Cell Aggressiveness via Static and Dynamic Magneto-Mechanical Stimulation with Vortex Microdiscs on Substrates of Physiological Stiffness

External mechanical stresses acting on cellular compartments critically regulate cell behaviour and can induce cell death. Magnetically actuated particles present a promising strategy to apply such forces in a controlled manner, with potential applications in cancer therapy. In this study, we investigate the effects of actuating vortex magnetic microdiscs on a glioblastoma cell line cultured on soft, biomimetic substrates that mimic in vivo stiffness. Using a Halbach array, we applied either static mechanical compression or a combination of compressive and low-frequency vibrational stresses (2-20 Hz). Our results demonstrate that both compressive and vibrational stresses impair important cellular functions associated with glioblastoma persistence in a dose-dependent and stiffness-dependent manner. In particular on soft 2D substrates, sufficiently strong compressive loads limit proliferation, while the addition of vibrations alter cell motility, cell morphology and the acto-myosin machinery. Our findings demonstrate that magnetic particles-mediated mechanical stimulation can disrupt glioblastoma cell aggressiveness in physiologically relevant 2D substrates, supporting its potential as an adjunct to conventional chemo-and radiotherapies by both inducing cell death and limiting resistant populations.

biophysics↗

bioRxiv2024

Developmental rewiring of the NGAL/CUC/KLU network associated with pleiotropic roles of NGAL genes

Gene Regulatory Networks (GRNs) play prominent roles in regulating developmental processes, and their modulation across species is a major source for evolutionary innovation. However, it remains poorly understood how GRNs are rewired between different organs within a single species. This question is particularly relevant for pleiotropic genes, which may exhibit organ-specific GRN modulations potentially reflecting their diverse functions. To address this, we investigated the NGATHA-like (NGAL) genes, as a model for pleiotropic genes that regulate growth or patterning in multiple Arabidopsis organs via two distinct pathways involving the CUP-SHAPED COTYLEDON (CUC) and KLUH (KLU) genes. By combining genetic analysis with gene expression characterization, we uncovered significant organ-specific rewiring of the NGAL/CUC/KLU regulatory module. Our findings highlight that changes in gene expression patterns, potentially arising from developmental constraints, play a pivotal role in the organ-specific modulation of GRNs. Furthermore, GRNs at the molecular and functional levels do not always align perfectly, potentially due to the influence of additional regulatory mechanisms. Altogether, our findings reveal significant modulation of the GRNs associated with pleiotropic genes. We propose that this flexibility in GRNs facilitates gene pleiotropy.

plant biology↗

bioRxiv2024

Dynamic valuation bias explains social influence on cheating behavior

Observing immoral behavior increases ones dishonesty by social influence and learning processes. The neurocomputational mechanisms underlying such moral contagion remain unclear. We tested different mechanistic hypotheses to account for moral contagion. We used model-based fMRI and a new cheating game in which participants were sequentially placed in honest and dishonest social norm contexts. Participants cheating behavior increased in the dishonest norm context but was unchanged in the honest. The best model to account for behavior indicated that participants valuation was dynamically biased by learning that others had cheated. At the time of choice, the internalization of social norms was implemented in the lateral prefrontal cortex and biased valuations of cheating. During learning, simulation of others cheating behavior was encoded in the posterior superior temporal sulcus. Together, these findings provide a mechanistic understanding of how learning about others dishonesty biases individuals valuation of cheating but does not alter ones established preferences. Significance statementSocial influence is at the root of human behavior. For example, we tend to follow others bad moral behavior such as cheating. Here, we explore the neuro-computational mechanisms of social influence on cheating behavior. We validated a new model capturing both how we learn about others (dis)honesty and how this bias our choice. We show that if we observe dishonest others we tend to be more dishonest ourselves. This behavioral change is driven by a bias dynamically changing with our knowledge about the others cheating behavior. Neurally, we found that the lateral prefrontal cortex implements this bias into the decision process while the posterior superior temporal sulcus and the temporo-parietal junction encode our learned representation of others cheating.

neuroscience↗

bioRxiv2024

M2WISH: an easy and efficient protocol for whole-mount mRNA in situ hybridization that allows 3D cell resolution of gene expression in Arabidopsis thaliana.

Gene expression analysis is essential for understanding the mechanisms involved in plant development. Here, we developed M2WISH, a protocol based on MicroWave treatment for Wholemount mRNA In Situ Hybridization in Arabidopsis. By permeabilizing tissues without damaging cellular organisation this protocol results in high and homogeneous hybridization yields that enables systematic analysis of gene expression dynamics. Moreover, when combined with cellular histochemical staining, M2WISH provides a cellular resolution of gene expression on roots, aerial meristems, leaves and embryos in the seed. We applied M2WISH to study the spatial dynamics of WUSCHEL (WUS) and CLAVATA3 (CLV3) expression during in vitro meristematic conversion of roots into shoot apical meristems. Thus, we showed that shoot apical meristems could arise from two different types of root structures that differed by their CLV3 gene expression patterns. We constructed 3D cellular representations of WUS and CLV3 gene co-expression pattern, and stressed the variability inherent to meristem conversion. Thus, this protocol generates a large amount of data on the localization of gene expression, which can be used to model complex systems.

plant biology↗

bioRxiv2023

2D cell culture on soft hydrogel drives an endoplasmic reticulum stress-dependent S quiescence underlying molecular traits of pulmonary basal cells

Cell culture on soft matrix, either in 2D and 3D, preserves the characteristics of progenitors. However, the mechanism by which the mechanical microenvironment determines progenitor phenotype, and its relevance to human biology, remains poorly described. Here we designed multi-well hydrogel plates with a high degree of physico-chemical uniformity to reliably address the molecular mechanism underlying cell state modification driven by physiological stiffness. Cell cycle, differentiation and metabolic activity could be studied in parallel assays, showing that the soft environment promotes an atypical S-phase quiescence and prevents cell drift, while preserving the differentiation capacities of human bronchoepithelial cells. These softness-sensitive responses are driven by defects in proteostasis and enhanced basal endoplasmic reticulum stress. The analysis of available single cell data of the human lung also showed that this non-conventional state coming from the soft extracellular environment is indeed consistent with molecular feature of pulmonary basal cells. Overall, this study demonstrates that mechanical mimicry in 2D culture supports allows to maintain progenitor cells in a state of high physiological relevance for characterizing novel molecular events that govern progenitor biology in human tissues.

cell biology↗

bioRxiv2023

Targeting the cell and non-cell autonomous regulation of 47S synthesis by GCN2 in colon cancer.

Nutrient availability is a key determinant of tumor cell behavior. While nutrient-rich conditions favor proliferation and tumor growth, scarcity, and particularly glutamine starvation, promotes cell dedifferentiation and chemoresistance. Here, linking ribosome biogenesis plasticity with tumor cell fate, we uncover that the amino acid sensor GCN2 represses the expression of the precursor of ribosomal RNA, 47S, under metabolic stress. We show that blockade of GCN2 triggers cell death by an irremediable nucleolar stress and subsequent TP53-mediated apoptosis in patient-derived models of colon adenocarcinoma (COAD). In nutrient-rich conditions, GCN2 activity supports cell proliferation through the transcription stimulation of 47S rRNA, independently of the canonical ISR axis. However, impairment of GCN2 activity prevents nuclear translocation of the methionyl tRNA synthetase (MetRS) underlying the generation of a nucleolar stress, mTORC1 inhibition and autophagy induction. Inhibition of the GCN2-MetRS axis drastically improves the cytotoxicity of RNA pol I inhibitors, including the first-line chemotherapy oxaliplatin, on patient-derived COAD tumoroids. Our data thus reveal that GCN2 differentially controls the ribosome biogenesis according the nutritional context. Furthermore, pharmacological co-inhibition of the two GCN2 branches and the RNA pol I activity may represent a valuable strategy for elimination of proliferative and metabolically-stressed COAD cell.

cancer biology↗

bioRxiv2022

A third SARS-CoV-2 mRNA vaccine dose in people receiving hemodialysis overcomes B cell defects but elicits a skewed CD4+ T cell profile

Cellular immune defects associated with suboptimal responses to SARS-CoV-2 mRNA vaccination in people receiving hemodialysis (HD) are poorly understood. We longitudinally analyzed antibody, B cell, CD4+ and CD8+ T cell vaccine responses in 27 HD patients and 26 low-risk control individuals (CI). The first two doses elicit weaker B cell and CD8+ T cell responses in HD than in CI, while CD4+ T cell responses are quantitatively similar. In HD, a third dose robustly boosts B cell responses, leads to convergent CD8+ T cell responses and enhances comparatively more Thelper (TH) immunity. Unsupervised clustering of single-cell features reveals phenotypic and functional shifts over time and between cohorts. The third dose attenuates some features of TH cells in HD (TNF/IL-2 skewing), while others (CCR6, CXCR6, PD-1 and HLA-DR overexpression) persist. Therefore, a third vaccine dose is critical to achieve robust multifaceted immunity in hemodialysis patients, although some distinct TH characteristics endure.

immunology↗

bioRxiv2022

A long interval between priming and boosting SARS-CoV-2 mRNA vaccine doses enhances B cell responses with limited impact on T cell immunity

Spacing the first two doses of SARS-CoV-2 mRNA vaccines beyond 3-4 weeks raised initial concerns about vaccine efficacy. While studies have since shown that long-interval regimens induce robust antibody responses, their impact on B and T cell immunity is poorly known. Here, we compare in SARS-CoV-2 naive donors B and T cell responses to two mRNA vaccine doses administered 3-4 versus 16 weeks apart. After boost, the longer interval results in higher magnitude and a more mature phenotype of RBD-specific B cells. While the two geographically distinct cohorts present quantitative and qualitative differences in T cell responses at baseline and after priming, the second dose led to convergent features with overall similar magnitude, phenotype and function of CD4+ and CD8+ T cell responses at post-boost memory timepoints. Therefore, compared to standard regimens, a 16-week interval has a favorable impact on the B cell compartment but minimally affects T cell immunity.

immunology↗

bioRxiv2022

Multi-omics comparison of malignant and normal uveal melanocytes reveals novel molecular features of uveal melanoma.

Uveal Melanoma (UM) is a rare cancer resulting from transformation of melanocytes residing in the uveal tract. Integrative analysis has identified four molecular and clinical subsets in UM. To improve our molecular understanding of UM we performed extensive multi-omics characterization comparing two aggressive UM patient-derived xenograft models with normal choroidal melanocytes, including DNA optical mapping, specific histone modifications, and DNA topology analysis by Hi-C. Our gene expression and cytogenetic analyses suggest that genomic instability is a hallmark of UM. We also identified a recurrent deletion in the BAP1 promoter resulting in loss of expression and associated with high risk of metastases in UM patients. Hi-C revealed chromatin topology changes associated with up-regulation of PRAME, an independent prognostic biomarker in UM and potential therapeutic target. Our findings illustrate how multi-omics approaches can improve the understanding of tumorigenesis and reveals two novel mechanisms of gene expression dysregulation in UM.

genomics↗

bioRxiv2022

Tissue-wide Effects Overrule Cell-intrinsic Gene Function in Cortical Projection Neuron Migration

The mammalian neocortex is composed of diverse neuronal and glial cell classes that broadly arrange in six distinct laminae. Cortical layers emerge during development and defects in the developmental programs that orchestrate cortical lamination are associated with neurodevelopmental diseases. The developmental principle of cortical layer formation is based on concerted radial projection neuron migration, from their birthplace to their final target position. Radial migration occurs in defined sequential steps that are regulated by a large array of signaling pathways. However, based on genetic loss-of-function experiments, most studies have thus far focused on the role of cell-autonomous gene function. Yet, cortical neuron migration in situ is a complex process and migrating neurons traverse along diverse cellular compartments and environments. The role of tissue-wide properties and genetic state in radial neuron migration is however not well understood. Here, we utilized Mosaic Analysis with Double Markers (MADM) technology to either sparsely or globally delete gene function followed by quantitative single cell phenotyping. The MADM-based gene ablation paradigms in combination with computational modeling demonstrated that global tissue-wide effects predominate cell-autonomous gene function albeit in a gene-specific manner. Our results thus suggest that the genetic landscape in a tissue critically impacts the overall migration phenotype of individual cortical projection neurons. In a broader context our findings imply that global tissue-wide effects represent an essential component of the underlying etiology associated with focal malformations of cortical development (FMCD) in particular, and neurological diseases in general. LAY SUMMARYThe assembly of the mammalian brain is a complex process and depends on tightly regulated developmental and genetic programs. The coordinated process of nerve cell (neuron) migration is essential to home neurons into their correct position which is vital for normal brain development. Disturbance of the neuron migration process at any point of development leads to severe brain malformations which result in devastating disease. To date, studies have mainly focused on cell-intrinsic gene functions controlling neuronal migration. Therefore, very little is known about the possible contribution of the cellular surrounding and tissue-wide effects. The scale and nature of such global tissue-wide effects remain completely unclear. We thus established genetic platforms based on Mosaic Analysis with Double Markers (MADM) to visualize and quantify tissue-wide effects in a defined genetic context and at single cell resolution. We found a critical predominant role of the genetic landscape and state of cellular environment affecting overall neuron migration properties. In a broader context our results suggest that global tissue-wide effects are a major component of the underlying etiology of neurological diseases such as focal malformations of cortical development (FMCD).

neuroscience↗

bioRxiv2022

De novo stem cell establishment in meristems requires repression of organ boundary cell fate

Stem cells play important roles in animal and plant biology as they sustain morphogenesis and tissue replenishment following aging or injuries. In plants, stem cells are embedded in multicellular structures called meristems and the formation of new meristems is essential for the plastic expansion of the highly branched shoot and root systems. In particular, axillary meristems that produce lateral shoots arise from the division of boundary domain cells at the leaf base. The CUP-SHAPED COTYLEDON (CUC) genes are major determinants of the boundary domain and are required for axillary meristem initiation. However, how axillary meristems get structured and how stem cells become established de novo remains elusive. Here, we show that two NGATHA-LIKE transcription factors, DPA4 and SOD7, redundantly repress CUC expression in the initiating axillary meristem. Ectopic boundary fate leads to abnormal growth and organisation of the axillary meristem and prevents de novo stem cell establishment. Floral meristems of the dpa4 sod7 double mutant show a similar delay in stem cell de novo establishment. Altogether, while boundary fate is required for the initiation of axillary meristems, our work reveals how it is later repressed to allow proper meristem establishment and de novo stem cell niche formation.

plant biology↗

bioRxiv2021

Temporal associations of B and T cell immunity with robust vaccine responsiveness in a 16-week interval BNT162b2 regimen

Spacing of the BNT162b2 mRNA doses beyond 3 weeks raised concerns about vaccine efficacy. We longitudinally analyzed B cell, T cell and humoral responses to two BNT162b2 mRNA doses administered 16 weeks apart in 53 SARS-CoV-2 naive and previously-infected donors. This regimen elicited robust RBD-specific B cell responses whose kinetics differed between cohorts, the second dose leading to increased magnitude in naive participants only. While boosting did not increase magnitude of CD4+ T cell responses further compared to the first dose, unsupervised clustering analyses of single-cell features revealed phenotypic and functional shifts over time and between cohorts. Integrated analysis showed longitudinal immune component-specific associations, with early Thelper responses post-first dose correlating with B cell responses after the second dose, and memory Thelper generated between doses correlating with CD8 T cell responses after boosting. Therefore, boosting elicits a robust cellular recall response after the 16-week interval, indicating functional immune memory.

immunology↗

bioRxiv2021

Cancer/Testis genes are predictive of breast tumor subtypes

Breast cancer is the most prevalent type of cancer in women worldwide. Within breast tumors, the basal-like subtype has the worst prognosis and no dedicated therapy, therefore new tools to understand, detect, and treat these tumors are needed. Certain germline genes are re-expressed in tumors, and constitute the Cancer/Testis genes; their misexpression has diagnostic and therapeutic applications. Here, we designed a new approach to examine Cancer/ Testis gene misexpression in breast tumors. We identify several new markers in Luminal and HER-2 positive tumors, some of which predict response to chemotherapy. We then use machine learning to identify the 2 Cancer/Testis genes most associated with basal-like breast tumors: HORMAD1 and CT83. We show that these genes are expressed by tumor cells but not the microenvironment, and that they are not expressed by normal breast progenitors, in other words their activation occurs de novo. We find these genes are epigenetically repressed by DNA methylation, and that their activation upon DNA demethylation is irreversible, providing a memory of past epigenetic disturbances. Basal-like tumors expressing both genes have a poorer outcome than tumors expressing either gene alone or neither gene. Therefore, these findings suggest a potential synergistic effect between Cancer/Testis genes in basal breast tumors; these findings have consequences for the understanding, diagnosis, and therapy of the breast tumors with the worse outcomes.

cancer biology↗