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Gil, L.

Publications and source records attributed to Gil, L..

15 recordsLinked to original sources
bioRxiv2026

In vitro-generated murine monocyte-derived dendritic cells habor a unique identity compared to other mononuclear phagocytes, largely conserved with their human and putative in vivo counterparts.

Whether the cells differentiating in vitro from total murine bone marrow (BM) cultures with GM-CSF +/- IL-4 are homologous to the human cells derived in vitro from purified circulating monocytes (Mo) cultured with GM-CSF and IL-4, mostly correspond to monocyte-derived dendritic cells (moDCs) or rather to macrophages (MFs), and have in vivo counterparts, is debated. It has been proposed to define cell types based on their ontogeny, leading to the proposal of excluding from the dendritic cell (DC) family the cells that do not arise from the common DC progenitors (CDP). However, recent discoveries support defining cell types rather by functions, or, as a surrogate, their instructive molecular networks. Indeed, Langerhans cells, Rorgt+ DCs, some cDC2As and human in vitro-derived moDCs do not arise from the CDP but exert hallmark DC functions instructed by specific transcriptomic modules shared with cDCs. Actually, the study of both LCs and moDCs has been key for dissecting DC biology. Yet, the existence of moDCs is put into questions. The functions once attributed to moDCs are now proposed to be exerted by type 2B conventional DCs (cDC2Bs) or type 3 DCs (DC3s) that have been characterized recently, harbor strongly overlapping phenotypes with moDCs and a similar mixed expression of genes from both the cDC and Mo/MF lineages, but a different ontogeny. To clarify these issues, we generated a transcriptomic atlas of in vitro-derived mononuclear phagocytes (MNPs). We show that moDCs are the only DC type arising in BM cultures in the presence of GM-CSF and IL-4. They express a unique transcriptomic and phenotypic signature, different from those of cDC2Bs and DC3s that are produced in FLT3-L cultures and appear to correspond to the same DC type differentiating though two different but converging ontogenetic paths. By harnessing the phenotypic and transcriptomic signatures identified from the analysis of our in vitro MNP atlas, we are able to identify in vivo a population of putative DCs differentiated from monocytes derived from the common monocyte-granulocyte progenitor (GMP), in a respiratory allergy model, specifically in the lungs of mice sensitized to house dust mite (HDM). Using the model of thioglycolate-induced peritonitis, we also characterized the CD226+ Mo-derived cells that have been reported to be moDCs or small cavity MFs (SCM) depending on studies. We showed that these cells are mainly differentiated from monocytes derived from the MDP, and split into two populations, one resembling MFs (SCMs) and the other one closer to lung moDCs but expressing distinct genes suggesting a different functional potential. Collectively, we show that the generation and characterization of specific MNP types in vitro can be harnessed to rigorously define their in vivo counterparts based on phenotypic analysis and gene module assessment, as we demonstrate for moDCs.

immunology↗
bioRxiv2025

Clonal analysis of SepSecS-specific CD4 T cells reveals a new HLA-DPA1*02:01/HLA-DPB1*01:01-restricted immunodominant epitope in autoimmune hepatitis

Autoreactive CD4 T cells, recognizing liver-self-antigens such as SepSecS, are main drivers of the chronic inflammatory response during autoimmune hepatitis (AIH). Previous studies have uncovered immunodominant SepSecS epitopes often associated with HLA-DRB1*03 or HLA-DRB1*04 restriction, two alleles enriched in AIH population. However, HLA restriction of numerous SepSecS epitopes remains incomplete and it is still unclear if immunodominant epitopes could be presented by non-HLA-DR molecules. Here, we investigated epitope recognition of SepSecS-specific TCRs isolated from AIH patients, and their HLA restriction by generating TCR hybridoma cell lines. Seventeen TCRs recognized eight SepSecS epitopes with four distinct HLA restrictions, including a novel HLA-DPA1*02:01/DPB1*01:01-restricted SepSecS epitope. TCR clustering analysis using GLIPH2 algorithm suggested that this epitope is recognized by multiple distinct TCRs in HLA-DPA1*02:01[~]HLA-DPB1*01:01 patients. Our study provides new insights into liver-self-antigen T cell reactivity during AIH, which could offer potential therapeutic strategies by targeting autoreactive CD4 T cells.

immunology↗
bioRxiv2025

Signals from the bone marrow B cell niches shape pre-leukemic fate in murine B cell acute lymphoblastic leukemia

The bone marrow (BM) microenvironment plays a key role in supporting B cell development. In acute lymphoblastic leukemia (B-ALL), the acquisition of oncogenic driver mutations blocks B cell differentiation at specific stages. When these pre-leukemic cells acquire secondary mutations, B-ALL develops. However, the role of the BM microenvironment in pre-leukemic cell fate remains unknown. Here, using a murine model of spontaneous B-ALL development, we show that disrupted pre-BCR signaling in pre-leukemic cells modifies their fate. Blocking expression of the pre-BCR ligand Galectin-1 by the microenvironment impaired pre-leukemic cell proliferation and leukemia-initiating capacity. Consequently, B-ALL development was delayed, and B-ALL had a more mature phenotype, with cells expressing a BCR. Secondary mutations were also altered by changes to Galectin-1 expression, in its absence mutations almost exclusively affected IL-7R signaling rather than both pre-BCR and IL-7R signaling. These results show that signals from BM niches can directly influence pre-leukemic B cell fate.

cancer biology↗
bioRxiv2024

Cross-species transmission of human hepatitis B virus to wild Neotropical primates

Hepatitis B virus (HBV) infects approximately one-third of the worlds human population and kills over one million people each year. HBV is also prevalent in Old World apes but not in New World primates. Human-to-primate transmission of HBV was suspected in zoo-captive monkeys and Mauritius macaques, but empirical data are scarce. Here, we collected blood and liver samples from 88 monkeys of 27 species in two areas of the Amazon, one with pristine forest and the other highly occupied and deforested by humans. A total of 17 (34.7%) out of 49 specimens from the human-occupied region tested positive for HBV. At this site, there was a positive relationship between human population density in the sampling location and the likelihood of primates being infected by HBV. Conversely, all 39 samples from the pristine forest tested negative for HBV. By sequencing a portion of the HBV S gene in five positive samples, each from a distinct primate genus, we found that four samples were closely related to the globally widespread human HBV-A strain, but not to the Americas-native HBV-F strain. The fifth sample aligned with the human HBV-D type, prevalent in the region where these samples were obtained. To our knowledge, this study represents the first reported cases of HBV in multiple wild New World primate species anywhere in the world. Our results suggest that primates were infected by strains brought into this part of Brazil by human immigrants, where HBV transmission may have been facilitated by the close contact between humans and monkeys due to high human occupation. This shows that the impact of human immigration, occupation and population growth in the Amazon extends beyond habitat loss; it also facilitates cross-species infections, potentially leading to the emergence of new, virulent viral strains that threaten both Amazonian biodiversity and human health. Author SummaryJean P. Boubli: Professor in Primate Ecology and Evolution, School of Science, Engineering and the Environment, University of Salford, Uk Hani R. El Bizri: PhD in Wildlife Conservation with a focus on Amazonian sustainable development. Analyst of Center for International Forestry Research (CIFOR), Bogor, Indonesia Luan F. Botelho-Souza: Masters and doctorate in experimental biology at the Universidade Federal de Rondonia/Brazil, Chrysoula Gubili: Researcher at the Fisheries Research Institute Nea Peramos, Kavala, Greece, specializing in population ecology and conservation genetics. Stephen J. Martin: Professor in Social Insects, School of Science, Engineering and the Environment, University of Salford, Uk Maisa da S. Araujo: Masters and doctorate in experimental biology, at the Universidade Federal de Rondonia/Brazil, Mariluce R. Messias: Professor of Zoology and curator of the Mammalogy Museum at the Universidade Federal de Rondonia/Brazil. Alcione de O. dos Santos: Masters and doctorate in experimental biology at the Universidade Federal de Rondonia/Brazil. Luiz S. Ozaki: Masters degree from Universidade de Brasilia and PhD in Physiological Sciences, Molecular Biology in Fukuoka, Kyushu, Japan. Andre V.C. Pereira: Bachelor in Biology the Universidade Federal de Rondonia/Brazil. Tony H. Katsuragawa: Masters and doctorate in experimental biology, at the Universidade Federal de Rondonia/Brazil. Ana Maisa Passos-Silva: Masters degree in experimental biology from the Federal University of Rondonia/Brazil. Luiz H. S. Gil: Masters in experimental biology, at the Universidade Federal de Rondonia/Brazil. Izeni P. Farias: Professor of Genetics, Universidade Federal do Amazonas, Brazil Juan M.V. Salcedo: Master in Tropical Medicine from the University of Brasilia/Brazil and PhD in Sciences from the University of Sao Paulo/Brazil. Tommy C. Burch: Masters in Biological Sciences and PhD candidate from the University of Salford, UK. Deusilene Vieira: Master in Tropical Medicine from the University of Brasilia/Brazil and PhD in Sciences from the University of Sao Paulo/Brazil.

pathology↗
bioRxiv2024

Specific pre-plasma cell states and local proliferation at the dark zone - medulla interface characterize germinal center-derived plasma cell differentiation in lymph node

High affinity antibody-producing plasma cells (PC) generated in germinal centers (GC) are crucial for durable immunity after vaccination or infection. The selection of high affinity B cells in the GC light zone instructs PC differentiation in a subset of cells, but the cellular transitions and spatial organization of GC to PC differentiation remain poorly understood. Here, we have used a mouse model to track GC-derived B cells with integrative single-cell and spatial analyses in draining lymph node after immunization or infection. We first identified putative PrePC cells in scRNA-seq datasets, then enriched those cells through their specific surface phenotype for further analysis of their gene expression trajectories and BCR repertoire. We found a continuum of actively proliferating transitional states bridging selected LZ GC B cells and recently exported PCs, with gradually increasing levels of endoplasmic reticulum stress-associated genes and Ig transcripts. Spatial analyses revealed that recently differentiated PC continued their maturation and affinity-restricted proliferation at a previously uncharacterized interface between the DZ and extensions of the lymph node medulla. Our findings provide insights into the intermediate stages and microenvironmental factors involved in the differentiation of GC B cells into PC, with implications for vaccine development and understanding antibody responses.

immunology↗
bioRxiv2024

Transcriptomic, clonal, and functional analyses reveal Liver tissue-imprinted immuno-profile of circulating autoreactive CD4 T cells in autoimmune liver diseases

Autoimmune liver diseases (AILD) are immune-mediated disorders in which CD4 T cells play a central role. However, the link between circulating self-antigen-specific CD4 T cells and the targeted tissue has not been extensively studied in AILD. We hypothesized that circulating autoreactive CD4 T cells were clonally and functionally related to dominant intra-hepatic pathogenic CD4 T cell clones. Single cell transcriptomic analysis of circulating self-antigen-specific CD4 T cells revealed a specific B-helper and immuno-exhausted transcriptional profile, which was conserved for different autoantigens, but distinct from several other types of foreign antigen specificities. In the blood, the dominant hepatic CD4 T cell clones had a similar transcriptomic signature and were enriched in the PD-1+ TIGIT+ HLA-DR+ CD4 T cell subset. In a mouse model, antigen-specific CD4 T cells acquired the immuno-exhausted transcriptional profile when they accumulated in the liver after local antigen reactivity. Locally, immune checkpoint molecules controlled the response of antigen-specific CD4 T cells responsible for liver damage. Our study reveals the origin and biology of liver-derived autoreactive CD4 T cells in the blood of AILD patients that are imprinted by the liver environment, and suggest a dysregulation of the immune checkpoint molecules pathways. Our study enables tracking and isolating circulating autoreactive CD4 T cells for future diagnostic and therapeutic purposes.

immunology↗
bioRxiv2022

Functional plasticity and recurrent cell states of malignant B cells in follicular lymphoma

Follicular lymphoma (FL) derives from malignant transformation of germinal center (GC) B cells. FL malignant B cells are heterogeneous and diverge from their GC B cell-of-origin, but the diversity, function, and location of malignant B cell states remain to be addressed. Based on integrative single-cell RNA-seq, we identified and studied recurrent FL malignant B cell states and dynamics. Most FL B cells spanned a continuum of states from proliferating GC-like to quiescent memory (Mem)-like cell states. That GC-to-Mem axis was the main source of intra-tumor transcriptional heterogeneity. While FL B cell states were independent from subclonal B cell receptor genetics divergence, T follicular helper (TFH) cell-derived signals controlled the transition from Mem-like to GC-like states. GC-like, TFH-activated and Mem-like FL B cells tended to occupy distinct niches within and around tumor follicles. Our study characterizes novel malignant cell states recurrent in B cell lymphomas, and highlights the functional plasticity of malignant B cells.

cancer biology↗
bioRxiv2022

No priming, just fighting - endophytic yeast attenuates the defense response and the stress induced by Dutch elm disease in Ulmus minor

One century after the first report of Dutch Elm Disease (DED), there is still no practical solution for this problem threatening European and American elms (Ulmus spp.). The long breeding cycles needed to select resistant genotypes and the lack of efficient treatments keep disease incidence at high levels. In the present work, the expression of defense-related genes to the causal agent of DED, Ophiostoma novo-ulmi, were analyzed in in vitro clonal plantlets from two DED-resistant and two DED-susceptible U. minor trees. In addition, the effect of the inoculation of an endophytic pink-pigmented yeast (Cystobasidium sp.) on the plants defense system was tested both individually and in combination with O. novo-ulmi. The multifactorial nature of the resistance to DED was confirmed, as no common molecular response was found in the two resistant genotypes. However, the in vitro experimental system allowed to discriminate the susceptible from the resistant genotypes, showing higher levels of oxidative stress and phenolic compounds in the susceptible genotypes after pathogen inoculation. Inoculation of the endophyte before O. novo-ulmi attenuated the plant molecular response induced by the pathogen and moderated oxidative stress levels. Niche competition, endophyte-pathogen antagonism, and molecular crosstalk between the host and the endophyte are discussed as possible mechanisms of stress reduction. In sum, our results confirm the multifactorial nature of DED resistance mechanisms and highlight the possibility of using certain endophytic yeasts as biological tools to improve tree resilience against biotic stress.

plant biology↗
bioRxiv2022

A novel mouse model based on intersectional genetics enables unambiguous in vivo discrimination between plasmacytoid and other dendritic cells and their comparative characterization

Plasmacytoid dendritic cells (pDC) were identified about 20 years ago, based on their unique ability to rapidly produce copious amounts of all subsets of type I and type III interferon (IFN-I/III) upon virus sensing, while being refractory to infection. Yet, the identity and physiological functions of pDC are still a matter of debate, in a large part due to their lack of specific expression of any single cell surface marker or gene that would allow to track them in tissues and to target them in vivo with high specificity and penetrance. Indeed, recent studies showed that previous methods that were used to identify or deplete pDC also targeted other cell types, including pDC-like cells and transitional DC (tDC) that were proposed to be responsible for all the antigen presentation ability previously attributed to steady state pDC. Hence, improving our understanding of the nature and in vivo choreography of pDC physiological functions requires the development of novel tools to unambiguously identify and track these cells, including in comparison to pDC-like cells and tDC. Here, we report successful generation of a pDC-reporter mouse model, by using an intersectional genetic strategy based on the unique co-expression of Siglech and Pacsin1 in pDC. This pDC-Tomato mouse strain allows specific ex vivo and in situ detection of pDC. Breeding them with Zbtb46GFP mice allowed side-by-side purification and transcriptional profiling by single cell RNA sequencing of bona fide pDC, pDC-like cells and tDC, in comparison to type 1 and 2 conventional DC (cDC1 and cDC2), both at steady state and during a viral infection, revealing diverging activation patterns of pDC-like cells and tDC. Finally, by breeding pDC-Tomato mice with Ifnb1EYFP mice, we determined the choreography of pDC recruitment to the micro-anatomical sites of viral replication in the spleen, with initially similar but later divergent behaviors of the pDC that engaged or not into IFN-I production. Our novel pDC-Tomato mouse model, and newly identified gene modules specific to combinations of DC types and activations states, will constitute valuable resources for a deeper understanding of the functional division of labor between DC types and its molecular regulation at homeostasis and during viral infections.

immunology↗
bioRxiv2021

Viral infection engenders bona fide and bystander lung memory B cell subsets through permissive selection

Lung-resident memory B cells (MBCs) provide localized protection against reinfection in the respiratory airways. Currently, the biology of these cells remains largely unexplored. Here, we combined influenza and SARS-CoV-2 infection with fluorescent-reporter mice to identify MBCs regardless of antigen specificity. scRNA-seq analysis and confocal imaging revealed that two main transcriptionally distinct subsets of MBCs colonize the lung peribronchial niche after infection. These subsets arise from different progenitors and are both class-switched, somatically mutated and intrinsically biased in their differentiation fate towards plasma cells. Combined analysis of antigen-specificity and B cell receptor repertoire unveiled a highly permissive selection process that segregates these subsets into "bona fide" virus-specific MBCs and "bystander" MBCs with no apparent specificity for eliciting viruses. Thus, diverse transcriptional programs in MBCs are not linked to specific effector fates but rather to divergent strategies of the immune system to simultaneously provide rapid protection from reinfection while diversifying the initial B cell repertoire.

immunology↗
bioRxiv2020

Structure of core fungal endobiome in Ulmus minor: patterns within the tree and across genotypes differing in tolerance to Dutch elm disease

Plants harbour a diverse fungal community with complex symbiotic interactions and significant roles in host physiology. However, the cues that steer the composition and structure of this community are poorly understood. Trees are useful models for assessing these factors because their large size and long lifespan give these ecosystems time and space to evolve and mature. Investigation of well-characterised pathosystems such as Dutch elm disease (DED) can reveal links between endomycobiome and pathogens. We examined the endophytic mycobiome across the aerial part of a landmark elm tree to identify structural patterns within plant hosts, highlighting not only commonalities but also the effect of local infections in some branches of the crown. We used a common garden trial of trees with varying levels of genotypic susceptibility to DED to identify associations between susceptibility and endomycobiome. Three families of yeasts were linked to higher DED tolerance: Buckleyzymaceae, Herpotrichiellaceae and Tremellaceae. Surveying a natural population with a gradient of vitality, we found some taxa enriched in declining trees. By combining all surveys and adding a further study in a distant natural population, we found evidence of a U. minor core mycobiome, pervasive within the tree and ubiquitous across locations, genotypes and health status.

microbiology↗
bioRxiv2020

Functional traits of three Ulmus minor fungal endophytes and their role in host resistance to Ophiostoma novo-ulmi

Certain fungal endophytes are known to improve plant resistance to biotic stresses in forest trees. In this study, three stem fungal endophytes belonging to classes Cystobasidiomycetes, Eurotiomycetes and Dothideomycetes were selected from 210 isolates for their potential as enhancers of Ulmus minor resistance to Ophiostoma novo-ulmi. We evaluated phenotypic traits of these endophytes that could be beneficial for inhibiting O. novo-ulmi in the host plant. Under in vitro conditions, the Dothideomycetous isolate YCB36 strongly inhibited O. novo-ulmi growth, released antipathogenic VOCs, chitinases and siderophores, and overlapped with the pathogen in nutrient utilization patterns. These functional traits could explain the 40% reduction in leaf wilting due to O. novo-ulmi in elm trees pre-inoculated with this endophyte. Ulmus minor trees inoculated with this endophyte showed increased leaf stomatal conductance and higher concentrations of flavonoids and total phenolic compounds in xylem tissues, suggesting induction of defence metabolism.

plant biology↗
bioRxiv2020

Integrative molecular profiling of autoreactive CD4 T cells in autoimmune hepatitis

Background & AimsIn most autoimmune disorders, crosstalk of B cells and CD4 T cells results in the accumulation of autoantibodies. In autoimmune hepatitis (AIH), the presence of anti-Soluble Liver Antigen (SLA or SepSecs) autoantibodies is associated with significantly reduced overall survival, but the associated autoreactive CD4 T cells have not been characterized yet. Here we isolated and deeply characterized SLA-specific CD4 T cells in AIH patients. MethodsWe used brief ex vivo restimulation with overlapping SLA-derived peptides to isolate and phenotype circulating SLA-specific CD4 T cells, and integrative single-cell RNA-seq (scRNA-seq) to characterize their transcriptome and TCR repertoire in n=5 AIH patients. SLA-specific CD4 T cells were tracked in peripheral blood through TCR sequencing, to identify their phenotypic niche. We further characterized disease-associated peripheral blood T cells by high content flow cytometry in an additional cohort of n=46 AIH patients and n=18 non-alcoholic steatohepatitis (NASH) controls. ResultsAutoreactive SLA-specific CD4 T cells were only detected in patients with anti-SLA autoantibodies and had a memory PD-1+CXCR5-CCR6-CD27+ phenotype. ScRNA-seq revealed their pro-inflammatory/B-Helper profile (IL21, IFNG, TIGIT, CTLA4, NR3C1, CD109, KLRB1 and CLEC2D). Autoreactive TCR clonotypes were restricted to the memory PD-1+CXCR5- CD4 T cells. This subset was significantly increased in the blood of AIH patients and supported B cell differentiation through IL-21. Finally, we identified a specific phenotype (PD-1+CD38+CD27+CD127-CXCR5-) of CD4 T cells linked to disease activity and IgG response during AIH. ConclusionsThis work provides for the first time a deep characterization of rare circulating autoreactive CD4 T cells and the identification of their peripheral reservoir in AIH. We also propose a generic phenotype of pathogenic CD4 T cells related to AIH disease activity.

immunology↗
bioRxiv2019

FB5P-seq: FACS-based 5-prime end single-cell RNAseq for integrative analysis of transcriptome and antigen receptor repertoire in B and T cells

Single-cell RNA sequencing (scRNA-seq) allows the identification, characterization, and quantification of cell types in a tissue. When focused on B and T cells of the adaptive immune system, scRNA-seq carries the potential to track the clonal lineage of each analyzed cell through the unique rearranged sequence of its antigen receptor (BCR or TCR, respectively), and link it to the functional state inferred from transcriptome analysis. Here we introduce FB5P-seq, a FACS-based 5-end scRNA-seq method for cost-effective integrative analysis of transcriptome and paired BCR or TCR repertoire in phenotypically defined B and T cell subsets. We describe in details the experimental workflow and provide a robust bioinformatics pipeline for computing gene count matrices and reconstructing repertoire sequences from FB5P-seq data. We further present two applications of FB5P-seq for the analysis of human tonsil B cell subsets and peripheral blood antigen-specific CD4 T cells. We believe our novel integrative scRNA-seq method will be a valuable option to study rare adaptive immune cell subsets in immunology research.

immunology↗
bioRxiv2017

Drug repurposing for yellow fever using high content screening

BackgroundYellow fever is an acute febrile illness caused by a mosquito-borne flavivirus. The discovery that mosquitos were responsible for transmission and that the disease was preventable by vector control, as well as the development of an efficacious vaccine (in the 1930s) have reduced its public health impact. However, underutilization of vaccination and discontinuation of vector control measures have led to yellow fever outbreaks, affecting thousands of people in Africa and South America, and is a continued threat to people who travel to endemic regions without vaccination. An additional concern is that the vaccine has important contraindications, and the currently available doses are insufficient to immunize the populations under risk of contracting yellow fever. Specific antiviral chemotherapy would be an alternative to vaccination, however there is none yet available. Drug repurposing is one strategy that can speed up drug discovery and development and has been underexplored for yellow fever.\n\nMethodsA high content screening assay for the discovery of anti-yellow fever compounds was developed and used to screen a library of pharmacologically compounds, which includes approved drugs and covers most signalling pathways and all major drug target classes. The same library was screened against cells infected with a serotype 2 of the dengue virus.\n\nResults and conclusionFrom 1280 compounds screened, 88 compounds (6,9% of the library) were found to reduce yellow fever virus (YFV) infection in 50% or more. Interestingly, the number of compounds that presented similar activity against dengue (DENV) infection was considerably lower (18 compounds, 1,4%). Among these, 12 compounds were active against both viruses, highlighting the potential of finding compounds with broad antiviral activity in diversity libraries. The top 27 anti-YFV compounds were selected for further activity determination in dose-response. Five compounds (Gant61, benztropine mesylate, brequinar sodium salt hydrate, PF-429242 dihydrochloride and U-73343) presented selective activity against YFV infection in a human cell line, but only two of them, brequinar and U-73343, were also active against DENV. These compounds, which represent a broad spectrum of pharmacological functions, have not been previously described as having anti-YFV activity, thus offering a valuable opportunity for the development of specific antiviral chemotherapy for yellow fever.

microbiology↗