Biology subjects

Boyer, C.

Publications and source records attributed to Boyer, C..

12 recordsLinked to original sources

bioRxiv2026

Ecology, genomics and biocontrol potential of bacteriophages infecting the bacterial wilt pathogen Ralstonia solanacearum species complex in Reunion Island

The Ralstonia solanacearum species complex (RSSC), the causal agent of bacterial wilt, is among the most destructive soil-borne plant pathogens worldwide, yet effective and sustainable control strategies remain limited. Bacteriophages represent promising biocontrol agents, but their efficacy depends on ecological compatibility with local pathogen populations. Here, we combined ecological sampling, comparative genomics, phenotypic characterization and plant assays to investigate RSSC-infecting phages in Reunion Island and evaluate their biocontrol potential. We isolated 45 phages from diverse agricultural matrices and obtained complete genome sequences for 35 novel isolates. Phylogenomic analyses revealed a locally diversified assemblage comprising multiple known taxa and several putative new genera, forming clusters largely distinct from global reference phages. Phage diversity and antibacterial activity were structured primarily by bacterial phylogeny rather than plant host or geographic origin, indicating that plants act mainly as ecological interfaces while environmental bacterial populations shape phage specialization. The community displayed two contrasting evolutionary strategies: expanding virulent lineages associated with strong antibacterial activity and persistent temperate lineages carrying integration and host-interaction functions. Host-range assays confirmed phylotype-dependent susceptibility, and strictly lytic phages showed consistently higher inhibitory activity. Guided by combined genomic and phenotypic screening, we designed a multi-family phage cocktail targeting dominant local RSSC lineages. The cocktail exhibited strong in vitro suppression of bacterial growth and significantly reduced disease severity in tomato plants. Together, our results demonstrate that effective phage biocontrol depends on evolutionary matching between phages and regional pathogen populations. Integrating ecological, genomic and functional characterization provides a robust framework for selecting locally adapted phages and developing durable phage-based strategies for managing bacterial wilt.

microbiology↗

bioRxiv2026

Genotypic and functional characterization of fibroblasts derived from pressure sores

IntroductionPressure sores are a major health problem in people with spinal cord injury resulting in ischaemic tissue lesions caused by prolonged pressure against a bony surface. Conventional therapies are often defective and fundamental researches on the healing process of pressure sores must be enriched in order to understand any novel therapies that may be applied. We focalize on pressure sores fibroblasts as dermal fibroblasts perform a critic role in wound healing by populating the wound site to produce extracellular matrix. After characterizing morphological and the genetic profile of healthy fibroblasts and fibroblasts from pressure ulcers, we conducted an analysis of fibroblast proliferation, migration and myofibroblastic differentiation capacity. Materials and Methodsafter acquisition of dermal explants and fibroblasts culture, we conducted histological analysis, an evaluation of gene expression by RT-qPCR and an assessment of fibroblasts proliferation and migration capacity through IncuCyte. A study of the differentiation of fibroblasts into myofibroblasts through the detection of Alpha-Smooth Muscle Actin (-SMA) expression by immunofluorescence was also conducted. Resultshistological analysis showed histological analysis showed dermal disorganization in pressure sore compared with health skin, differences in morphological aspects and density of fibroblasts. Pressure sore fibroblasts express less genes coding for ECM proteins, metalloproteases, collagen III, Connective tissue growth factor (CTGF) and ACTA2 coding for -SMA. Pathological fibroblasts appear to proliferate less quickly than healthy fibroblasts but no differences in migration capacity were found. After stimulation under TGF-{beta}, pressure sore fibroblasts lose their ability to differentiate into myofibroblasts compared to healthy fibroblasts and this could be in relation with a less expression of ACTA2. ConclusionAll of our results highlight a morphological, genetic and functional difference between healthy and pathological fibroblasts which have a modified phenotype, less effective for skin repair. This suggests that new therapies for chronic wounds must take into account the environment in which they are applied and that pathological cells do not necessarily respond to treatments in the same way as healthy cells. Our results are not statistically significant, although several trends emerge. This is explained by the heterogeneity of the patients medical history and requires repetition of the experiments.

pathology↗

bioRxiv2025

Reconstructing a physiological state space via chronic jugular microdialysis in freely moving mice

Maintaining physiological homeostasis requires a complex interplay among endocrine organs, peripheral tissues, and distributed neuroendocrine control circuits, all of which are coupled through feedback loops that operate over minutes to hours. Although many physiological needs are broadcast through hormones, metabolites, and other chemical compounds circulating in the bloodstream, we rarely observe more than a few of these messengers together and at high cadence during behavior. To address this, we developed a minimally disruptive workflow to measure the free fraction of hundreds of amines and small peptides at a 7.5-minute cadence for [~]8 hrs in freely moving mice using chronic jugular microdialysis implants and chemical isotope labeling Liquid Chromatography-Mass Spectrometry. Single-compound profiles behave according to known physiology, such as purine turnover correlating with movement, delayed histamine/5-HIAA changes, and coordinated amino-acid dynamics. Our multiplexed measures enable high-dimensional analyses that uncover properties of the underlying dynamics. For example, systems-level analyses show that 10 dimensions explain over 70% of the variance in hormone/metabolite covariation, consistent with a low rank description of the physiological state space, with projections aligned to locomotion state transitions. Our work opens avenues for the discovery of hormonal dynamics, compound interactions, and their effects on behavior.

physiology↗

bioRxiv2025

A Rapid and Scalable Subcutaneously Administered Murine Thymus Micro-organoid for Generating Functional T cells

Thymic function can decline due to age-related involution, congenital disorders, acute infections, or chemo/radiation therapy. Decline in thymic function leads to decreased T cell production and weakened immunity. To address these thymic insufficiencies, we aimed to develop a transplantable and scalable micro-organoid system utilizing fibroblasts and thymic cells. We have developed a reliable and rapid method to generate thymic micro-organoids using selectively screened fibroblasts and murine thymic cells. The thymic micro-organoids are cryo-preservable, injectable, and give rise to T cells both in vitro and in vivo. Thymic organoids expressed key genes required to sustain T cell development and maturation: ccl25, dll-1, dll-4, foxn-1, il-7, scf. When injected into T cell-deficient Prkdcscid mice, the organoids gave rise to functional {beta}, {psi}8, natural killer T (NKT) cells, and FoxP3+ regulatory T cells. Organoid-derived T cells expressed a diverse T cell receptor (TCR) repertoire in vivo and responded to stimulation with anti-CD3/28, Concanavalin-A, or Phytohemagglutinin. Thymic organoids derived from pmel-1 thymocytes gave rise to V{beta}13+ T cells that delayed the growth of B16 melanoma and enhanced activation of T and NK cells. This approach presents a valuable tool for mechanistic studies and addressing current therapeutic gaps in diseases associated with thymic decline and insufficiencies.

immunology↗

bioRxiv2025

Human Dermal Fibroblast-derived Spheroids Demonstrate Efficacious Immune Modulation in a Psoriasis Mouse Model

BackgroundPsoriasis is a chronic inflammatory disease associated with high morbidity and few cases of sustained remission. Innovative immunomodulatory therapies, including fibroblast-based cell therapies, offer promising alternatives. This study investigates the therapeutic potential of human dermal fibroblasts (HDFs) organized into three-dimensional (3D) spheroids in a mouse model of imiquimod (IMQ)-induced psoriasis. MethodsHDF spheroids were cultured using Elplasia(R) microcavity plates, and their size, viability, and phenotype were compared with single cells in 2D monolayer cultures. Cellular responses in whole blood and acute inflammatory responses were evaluated at various time points following intravenous injection of HDFs. The therapeutic efficacy of HDF spheroids was assessed using an IMQ-induced psoriasis mouse model, with disease severity scored using the Psoriasis Area and Severity Index (PASI). Optimized HDF spheroids ([~]150 {micro}m, 1x106 cells/mouse) were administered intravenously in a single dose for mild psoriasis or multiple doses for moderate-to-severe psoriasis. The efficacy of HDF spheroids was compared to a pre-clinical monoclonal antibody targeting interleukin 23 (anti-IL-23). ResultsSpheroid cultures of HDFs showed reduced cell size, enhanced viability, and distinct phenotypic changes compared to monolayer cultures. Intravenous injection of HDF spheroids resulted in less thrombocytopenia and reduced acute inflammatory responses compared to single-cell injection. A single dose of HDF spheroids reduced the severity of mild psoriasis by 35%, while repeated doses resulted in a 36% reduction in moderate-to-severe psoriasis. Single-dose administration normalized blood cell counts, alleviated spleen enlargement, and improved cytokine dysregulation. Although HDF spheroids and anti-IL-23 reduced epidermal thickening and immune cell infiltration, HDF spheroids uniquely inhibited monocyte production and infiltration, a benefit not observed with anti-IL-23. No acute or chronic toxicity was observed. ConclusionsHDF spheroids offer comparable therapeutic efficacy to anti-IL-23 in treating psoriasis, with a distinct mechanism involving inhibiting monocyte production and infiltration. Their safety profile and broader immunomodulatory potential support their development as a novel therapeutic strategy for psoriasis and other inflammatory diseases.

immunology↗

bioRxiv2025

Genomic footprint of a shared Type 5 prophage in 'Candidatus Liberibacter asiaticus' and 'Candidatus Liberibacter africanus', two destructive bacterial pathogens of citrus huanglongbing

Huanglongbing (HLB) is a bacterial disease that affects citrus trees and is considered the most severe citrus disease in the world. The three HLB-associated Ca. Liberibacter species harbor prophage regions which have been described to play critical roles in their evolution and biology. In this study, we assembled and characterized the accessory genome of the first circular de novo Candidatus Liberibacter asiaticus (CLas) assembly (V1R1) from Reunion, one of the sparse areas worldwide hosting CLas and Ca. Liberibacter africanus (CLaf). This 1,272 Mb-long whole-genome harbored 1,129 coding sequences and two complete prophages, including a 37,934 bp-long Type 1 prophage, frequently present in CLas genomes, and a 40,501 bp-long undescribed CLas prophage designated as P-V1R1-5. Comparative genomic approaches suggested that P-V1R1-5 have all the genetic elements to produce new viral particles and revealed that it likely belongs to a new CLas Type 5 prophage. While being reported for the first time in a CLas strain, P-V1R1-5-like prophages were previously identified in CLaf genomes, making it the first evidence of shared prophage-like sequence among HLB-associated Ca, Liberibacter species. Using PCR amplifications targeting P-V1R1-5, we also showed that 85.7% of the tested CLas strains from Reunion and all tested CLaf strains from Madagascar and Reunion harbored a Type 5-like prophage. The identification of CLas Type 5-like prophages not only expanded our knowledge of CLas genomic diversity in Reunion, but also provided new insights into the role of horizontally transferred elements in the evolution of the sympatric HLB-associated bacteria. IMPORTANCEHuanglongbing (HLB) is the most severe citrus disease worldwide. The disease is associated with three Candidatus Liberibacter species harboring prophage regions that have been described to play critical roles in their biology. In this study, we assembled and characterized the accessory genome of the first circular de novo Ca. Liberibacter asiaticus (CLas) assembly from Reunion, one of the very few areas in the world where both of CLas and Ca. Liberibacter africanus (CLaf) coexist. Comparative genomic approaches demonstrated that this genome harbored two complete prophages, including a new CLas Type 5 prophage that was previously identified in CLaf but was reported for the first time in a CLas strain. This first evidence of shared prophage-like sequences among HLB-associated species expands our knowledge of CLas genomic diversity, but also provides new insights into the role of the accessory genome in the evolution of these bacteria.

genomics↗

bioRxiv2024

A phylogenetic host range index reveals contrasted relationships between phage virulence and specialisation

Phages are typically known for having a limited host range, targeting various strains within a specific bacterial species. However, factors like the phylogeny or epidemiology of host bacteria are often disregarded, despite their potential influence on phage specialization and virulence. This research utilizes a new "phylogenetic host range index" that accounts for the genetic diversity of bacterial hosts, to classify phages into specialists and generalists accurately. We provide evidence that the CRISPR-Cas immune system of bacteria more frequently targets generalist phages than specialist phages. We explore the hypothesis that generalist phages might exhibit lower virulence than specialist ones due to potential evolutionary trade-offs between host range breadth and virulence. Importantly, contrasted correlations between phage virulence and host range depend on the epidemiological context. A trade-off was confirmed in a homogeneous bacterial epidemiology situation, but not in more complex epidemiological scenario, where no apparent costs were detected for phages adapted to a wide range of hosts. This study highlights the need for genetic analyses in phage host range and of investigating ecological trade-offs that could improve their applications in biocontrol or therapy.

microbiology↗

bioRxiv2023

Microencapsulation of mesenchymal stromal cells in covalent alginate hydrogels for cell therapy

Osteoarthritis (OA) is the most common inflammatory joint disease and currently lacks an effective curative treatment. Intra-articular injection of mesenchymal stromal cells (MSCs) has gained attention as a relevant therapeutic approach for OA treatment due to the MSCs ability to secrete anti-inflammatory and immunomodulatory factors. Given their limited viability post- intraarticular injection and the potential leakage of cells out of the injection site, encapsulating MSCs in hydrogels is considered a promising strategy to protect them and provide a suitable 3D microenvironment to support their biological activities. Calcium-cross-linked alginate hydrogels are commonly used for MSC encapsulation, but their long-term in vivo stability remains uncertain. On the other hand, alginate cross-linking by the strain-promoted azide- alkyne cycloaddition (SPAAC) reaction would create a network unaffected by an ionic environment. Hence, this study aimed to develop an alginate-based hydrogel cross-linked via stable and cytocompatible covalent bonds for cell encapsulation. We established for the first time the formation of covalent alginate hydrogels between two SPAAC precursors, namely alginate-BCN and alginate-N3. These hydrogels exhibited in vitro stability and enabled the diffusion of molecules of interest. We then generated alginate-based SPAAC microgels of 170 m in mean diameter, suitable for intra-articular injection. We next encapsulated human adipose MSCs (hASCs) in these alginate-based SPAAC microgels and confirmed their cytocompatibility, with over 90 % of cells remaining viable after 14 days in culture. Finally, the microencapsulated hASCs maintained their biological properties and were able to secrete anti-inflammatory factors (IDO, PGE2, and HGF) when exposed to pro-inflammatory cytokines (TNF- and IFN-{gamma}). In the end, human-activated lymphocytes were cultured in contact with microencapsulated hASCs, and CD3+ T cell proliferation was quantified by flow cytometry. We demonstrated that the encapsulation process did not impair the hASC immunomodulatory activity. Overall, our findings show the potential of alginate-based SPAAC hydrogels for microencapsulating hASCs for cell therapy.

bioengineering↗

bioRxiv2023

A synthetic peptide mimic kills Candida albicans and synergistically prevents infection

More than two million people worldwide are affected by life-threatening, invasive fungal infections annually. Candida species are the most common cause of nosocomical, invasive fungal infections and are associated with mortality rates above 40%. Despite the increasing incidence of drug-resistance, the development of novel antifungal formulations has been limited. Here we investigate the antifungal mode of action and therapeutic potential of positively charged, synthetic peptide mimics to combat infections by Candida albicans. These synthetic polymers cause stress to the endoplasmic reticulum and affect protein glycosylation, a distinct mode of action compared to currently approved antifungal drugs. The most promising polymer composition caused damage to the mannan layer of the cell wall, with additional membrane-disrupting activity. The synergistic combination of the polymer with caspofungin prevented infection of human epithelial cells in vitro, improved fungal clearance by human macrophages, and significantly increased host survival in a Galleria mellonella model of systemic candidiasis. Additionally, prolonged exposure of C. albicans to the synergistic combination of polymer and caspofungin did not lead to the evolution of resistant strains in vitro. Together, this work highlights the enormous potential of these synthetic peptide mimics to be used as novel antifungal formulations as well as adjunctive antifungal therapy.

microbiology↗

bioRxiv2022

βIII-Tubulin is a Brake on Extrinsic Cell-Death in Pancreatic Cancer

The microtubule protein, {beta}III-tubulin, has been implicated as a prognostic, pro-survival, and chemoresistance factor in some of the most lethal malignancies including pancreatic ductal adenocarcinoma (PDAC). However, precise survival mechanisms controlled by {beta}III-tubulin in cancer cells are unknown. Here, we report an unexpected role of {beta}III-tubulin as a brake on extrinsic caspase 8-dependent apoptosis in PDAC. We show that {beta}III-tubulin knockdown frees death-receptor DR5 to increase its membrane diffusion, clustering, and activation of cell-death. We demonstrate that {beta}III-ubulin silencing increases sensitivity of PDAC cells to chemotherapeutic and microenvironment-derived extrinsic cell-death signals including TRAIL, TNF, and FasL. Finally, nanoparticle delivery of {beta}III-tubulin siRNA to mouse orthotopic PDAC tumours in vivo and human patient-derived PDAC tumour explants ex vivo increases extrinsic apoptosis and reduces tumour progression. Thus, silencing of {beta}III-tubulin represents an innovative strategy to unleash a suicide signal in PDAC cells and render them sensitive to microenvironment and chemotherapy-derived death signals.

cancer biology↗

bioRxiv2020

Bringing the pancreas patient back to the bench: Ex vivo culture of intact human patient derived pancreatic tumour tissue

The poor prognosis of pancreatic ductal adenocarcinoma (PDAC) is attributed to the highly fibrotic stroma and complex multi-cellular microenvironment that is difficult to fully recapitulate in pre-clinical human models. To fast-track translation of therapies and to inform personalised medicine, we aimed to develop a whole-tissue ex vivo explant model that maintains viability, 3D multicellular architecture, and microenvironmental cues present in human pancreatic tumours. Patient-derived surgically-resected PDAC tissue was cut into 2 mm explants, cultured on gelatin sponges, and grown for 12 days. Immunohistochemistry revealed that human PDAC tissue explants were viable for 12 days and maintained their original tumour, stromal and extracellular matrix architecture. As proof-of-principle, human PDAC tissue explants responded to Abraxane(R) treatment with a 3.7-fold increase in cell-death (p=0.0007). PDAC explants were also transfected with polymeric nanoparticles+Cy5-siRNA and we observed abundant cytoplasmic distribution of nanoparticle+Cy5-siRNA throughout the PDAC explant tissue. Our novel model retains the 3D architecture of human pancreatic tumours and has several advantages over standard organoids: presence of functional multi-cellular stroma and fibrosis and no tissue manipulation, digestion, or artificial propagation of organoids. This provides an unprecedented opportunity to study PDAC biology, tumour-stromal interactions and rapidly assess therapeutic response that could drive personalised treatment for PDAC.

cancer biology↗

bioRxiv2020

Time-calibrated genomic evolution of a monomorphic bacterium during its establishment as an endemic crop pathogen

The reconstruction of the evolutionary histories of pathogen populations in space and time has greatly improved our understanding of their epidemiology. However, analyses are usually restricted to the non-recombining genomic regions and, thus, fail to inform on the dynamics of the accessory genome. Yet, horizontal gene transfer is of striking importance to the evolution of bacteria as it can redistribute phenotypically important genes. For bacterial pathogens, those include resistance to antimicrobial compounds and virulence factors. Understanding the gene turnover in genomes at microevolutionary scales is key to apprehend the pace of this evolutionary process. Here we addressed this question for the epidemic lineage of a major bacterial plant pathogen, relying on a dense geographic sampling spanning 39 years of evolution. Gene turnover rate exceeded SNP mutation rates by three orders of magnitude. Accessory genes were preferentially plasmid-encoded, but we evidenced a highly plastic chromosomal region hosting ecologically important genes such as transcription activator-like effectors. We argue that turnover of accessory genes provides a potent evolutionary force in monomorphic bacteria, and exemplify this statement retracing the history of a mobile element conferring resistance to copper compounds widely used for the management of plant bacterial pathogens.

genomics↗