Biology subjects

Tran, F.

Publications and source records attributed to Tran, F..

13 recordsLinked to original sources

bioRxiv2025

Long-Term Intestinal Epithelial Remodeling Induced by Acute Protein-Energy Malnutrition

Protein-energy malnutrition (PEM) is a global health burden with lasting effects that extend well beyond the initial nutrient deficiency. To systematically investigate the long-term effects of a single episode of PEM on the structure and function of the intestinal epithelium and its associated microbiota, we employed a comprehensive multi-omics approach, including (spatial) transcriptomics, DNA methylation analysis, fecal metagenomics, and metabolomics. Our findings show that PEM persistently alters the intestinal epithelium by depleting Paneth cells and suppressing antimicrobial gene expression - changes linked to DNA methylation that persist despite dietary recovery. In germ-free mice, the sustained epithelial phenotype after was absent. We identified the microbial lipid metabolite 9-HODE and epigenetically deregulated PPAR-driven GDF15 expression as key molecular drivers of the persistent PEM-induced Paneth cell dysfunction. Targeting microbial lipid production and its link to the host GDF15 pathway could offer novel therapeutic strategies for long-term consequences of malnutrition and other Paneth cell-associated diseases.

immunology↗

bioRxiv2025

Quantifying The Impact of Bulk TCR-Seq Methodological Choices on The Profiled T Cell Repertoire

Bulk T cell repertoire profiling using sequencing (TCR-Seq) is a powerful method to investigate T cell responses to natural infections, vaccines, cancers, and autoimmune diseases. This assay can be conducted using various techniques, such as multiplex PCR or 5-RACE. However, each methods introduces systematic biases that can result in different pictures of the underlying T cell repertoire. Furthermore, the impact of technical variables on the accuracy of these methods remains understudied. Thus, in this study, we systematically characterized different multiplex PCR-based protocols, focusing on the quality and quantity of the utilized RNA/DNA, extraction methods, amplification programs, variations between production batches, and technical handling of samples. Our findings highlight the important role of RNA/DNA quality in shaping the profiling results of T cell repertoires. Whereas low RNA/DNA quantities can be partially compensated for by increasing the number of PCR cycles, this is partially not possible with lower quality. In conclusion, our results highlight the influence of different technical choices on the biological conclusions drawn from TCR-Seq data and provide practical guidelines to finetune these variables to ensure consistent and reliable results under diverse experimental constraints.

immunology↗

bioRxiv2025

Association of ulcerative colitis with atopic dermatitis: identification of shared and unique mechanisms by construction and computational analysis of disease maps

Background and AimsUlcerative colitis (UC) and atopic dermatitis (AD) are immune-mediated inflammatory diseases with limited treatment options. They are known to be related which may explain higher risk of development of UC in patients with AD. The goal of this work is to review and analyse molecular mechanisms of UC in comparison to AD towards insights into UC complexity, potential comorbidities and novel therapies. MethodsWe developed graphical computational models of UC and AD molecular mechanisms (disease maps) by integrating information from over 800 manually curated articles. The maps are available online at https://imi-immuniverse.elixir-luxembourg.org. Disease-specific risk variants and gene expression profiles are visualised to identify signatures specific to UC, and shared with AD. Computational analysis shows key proteins, their interactions and pathways shared between UC and AD. ResultsUC and AD maps include more than 2000 molecular interactions. Systematic computational comparison shows that both disorders exhibit epithelial barrier dysfunction, immune dysregulation involving abnormal Th2, Th1 and ILC response, common inflammatory pathways and biomarkers such as IL-13, IL-4R, IFNG, and IL-18. Visualisation and analysis of omics data demonstrates UC map usability. ConclusionsWe developed the first computational graphic model of UC molecular mechanisms. Its content focuses on mechanisms of epithelial barrier disruption and downstream immune dysregulation through cytokines and other mediators. The comparison of UC to AD mechanisms demonstrates common signalling pathways and biomarkers, and supports potential drug repurposing and treatment options. The workflow can be reused and new findings can be dynamically integrated into the maps. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=113 SRC="FIGDIR/small/650149v1_ufig1.gif" ALT="Figure 1"> View larger version (59K): org.highwire.dtl.DTLVardef@1c4c80eorg.highwire.dtl.DTLVardef@2a1e66org.highwire.dtl.DTLVardef@131ece3org.highwire.dtl.DTLVardef@b74971_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOGRAPHICAL ABSTRACTC_FLOATNO C_FIG

bioinformatics↗

bioRxiv2024

Simultaneous Profiling of the Blood and Gut T and B Cell Repertoires in Crohn's Disease and Symptomatic Controls Illustrates Tissue-specific Alterations in the Immune Repertoire of Crohn's Disease Patients

Crohns disease (CD) is a clinical subset of inflammatory bowel disease that is characterized by patchy transmural inflammation across the gastrointestinal tract. Although the exact etiology remains unknown, recent findings suggest that it is a complex multifactorial disease with contributions from the host genetics and environmental factors such as the microbiome. We have shown that the T cell repertoire of CD patients harbors a group of highly expanded T cells which hints toward an antigen-mediated pathology. To profile the immunological signature of CD at a high-resolution we simultaneously profiled the {beta} and {gamma}{delta} T cell repertoire in addition to the B cell repertoire of both the blood and the colonic mucosa for 27 treatment-naive CD patients and 27 age-matched symptomatic controls. Regardless of disease, we observed multiple physiological differences between the immune repertoire of blood and colonic mucosa. Additionally, by comparing the repertoire of CD patients relative to controls, we observed different alterations that were only detected in the blood or colonic mucosa. These include a depletion of mucosal-associated invariant T (MAIT) cells in the blood repertoire, an expansion of TRAV29/DV5-TRAJ5+ clonotypes and a significant depletion of multiple IGHV3-33-IGHJ4+and IGHV3-33-IGHJ6+ clonotypes in the blood and gut IGH repertoire of CD patients. In conclusion, our findings highlight the importance of studying the immune repertoire in a tissue-specific manner and the need to profile the T and B cell immune repertoire of gut tissues.

immunology↗

bioRxiv2024

Metabolic modeling reveals a multi-level deregulation of host-microbiome metabolic networks in IBD

Inflammatory bowel diseases (IBDs) are chronic disorders involving dysregulated immune responses. Despite the role of disrupted host-microbial interaction in the pathophysiology of IBD, the underlying metabolic principles are not fully understood. We densely profiled microbiome, transcriptome and metabolome signatures from longitudinal IBD cohorts before and after advanced drug therapy initiation and reconstructed metabolic models of the gut microbiome and the host intestine to study host-microbiome metabolic cross-talk in the context of inflammation. We identified concomitant changes in metabolic activity across data layers involving NAD, amino acid, one-carbon and phospholipid metabolism. In particular on the host level, elevated tryptophan catabolism depleted circulating tryptophan, thereby impairing NAD biosynthesis. Reduced host transamination reactions disrupted nitrogen homeostasis and polyamine/glutathione metabolism. The suppressed one-carbon cycle in patient tissues altered phospholipid profiles due to limited choline availability. Simultaneously, microbiome metabolic shifts in NAD, amino acid and polyamine metabolism exacerbated these host metabolic imbalances. Leveraging host and microbe metabolic models, we predicted dietary interventions remodeling the microbiome to restore metabolic homeostasis, suggesting novel therapeutic strategies for IBD.

systems biology↗

bioRxiv2023

Tryptophan wasting and disease activity as a systems phenomenon in inflammation - an analysis across 13 chronic inflammatory diseases.

Chronic inflammatory diseases (CID) are systems disorders affecting various organs including the intestine, joint and skin. The essential amino acid tryptophan (Trp) is not only used for protein synthesis but can also be catabolized to various bioactive derivatives that are important for cellular energy metabolism and immune regulation. Increased Trp catabolism via the kynurenine pathway is seen across individual CID entities1-5. Here, we assessed the levels of Trp and tryptophan derivatives across 13 CID to investigate the extent and nature of Trp wasting as a systems phenomenon in CID. We found reduced serum Trp levels across the majority of CID and a prevailing negative relationship between Trp and systemic inflammatory marker C-reactive protein (CRP). Increases in the kynurenine-to-Trp ratio (Kyn:Trp) indicate that the kynurenine pathway is a major route for CID-related Trp wasting. However, the extent of Trp depletion and its relationship with disease activity varies by disease, indicating potential differences in Trp metabolism. In addition, we find that amino acid catabolism in chronic inflammation is specific to tryptophan wasting, whereas other proteinogenic amino acids are not affected. Hence, our results suggest that increased Trp catabolism is a common metabolic occurrence in CID that may directly affect systemic immunity. Grant supportThis work was supported by the DFG Cluster of Excellence 1261 "Precision medicine in chronic inflammation" (KA, SSchr, PR, BH, SWa), the BMBF (e:Med Juniorverbund "Try-IBD" 01ZX1915A and 01ZX2215, the e:Med Network iTREAT 01ZX2202A, and GUIDE-IBD 031L0188A), DFG RU5042 (PR, KA), and Innovative Medicines Initiative 2 Joint Undertakings ("Taxonomy, Treatments, Targets and Remission", No. 831434, "ImmUniverse", grant agreement No. 853995, "BIOMAP", grant agreement No. 821511).

immunology↗

bioRxiv2023

Evolution of E. coli in a mouse model of inflammatory bowel disease leads to a disease-specific bacterial genotype and trade-offs with clinical relevance

Inflammatory bowel disease (IBD) is a persistent inflammatory condition that affects the gastrointestinal tract and presents significant challenges in its management and treatment. Despite the knowledge that within-host bacterial evolution occurs in the intestine, the disease has rarely been studied from an evolutionary perspective. In this study, we aimed to investigate the evolution of resident bacteria during intestinal inflammation and whether- and how disease-related bacterial genetic changes may present trade-offs with potential therapeutic importance. Here, we perform an in vivo evolution experiment of E. coli in a gnotobiotic mouse model of IBD, followed by multiomic analyses to identify disease-specific genetic and phenotypic changes in bacteria that evolved in an inflamed versus a non-inflamed control environment. Our results demonstrate distinct evolutionary changes in E. coli specific to inflammation, including a single nucleotide variant that independently reached high frequency in all inflamed mice. Using ex vivo fitness assays, we find that these changes are associated with a higher fitness in an inflamed environment compared to isolates derived from non-inflamed mice. Further, using large-scale phenotypic assays, we show that bacterial adaptation to inflammation results in clinically relevant phenotypes, which intriguingly include collateral sensitivity to antibiotics. Bacterial evolution in an inflamed gut yields specific genetic and phenotypic signatures. These results may serve as a basis for developing novel evolution-informed treatment approaches for patients with intestinal inflammation.

evolutionary biology↗

bioRxiv2023

FixNCut: Single-cell genomics through reversible tissue fixation and dissociation

The use of single-cell technologies for clinical applications requires disconnecting sampling from downstream processing steps. Early sample preservation can further increase robustness and reproducibility by avoiding artifacts introduced during specimen handling. We present FixNCut, a methodology for the reversible fixation of tissue followed by dissociation that overcomes current limitations. We applied FixNCut to human and mouse tissues to demonstrate the preservation of RNA integrity, sequencing library complexity, and cellular composition, while diminishing stress-related artifacts. Besides single-cell RNA sequencing, FixNCut is compatible with multiple single-cell and spatial technologies, making it a versatile tool for robust and flexible study designs.

bioinformatics↗

bioRxiv2022

The potent Toxoplasma gondii growth inhibitor QQ-437 does not bind to its predicted target, parasite adaptin3β, in yeast three-hybrid assays

New drugs are needed to treat infections with Toxoplasma gondii, a ubiquitous protozoan parasite that can cause miscarriage, blindness, and life-threatening encephalitis in its human hosts. A novel N-benzoyl-2-hydroxybenzamide named QQ-437 was recently shown to be a potent inhibitor of T. gondii growth in vitro (EC50 = 16nM), and to reduce parasite load in a mouse model of infection. Intriguingly, mutations in the parasite protein TgAP3{beta}, which is thought to play an important role in intracellular protein trafficking, confer resistance to QQ-437. In this report, we use yeast three-hybrid analysis to test the hypothesis that QQ-437 inhibits parasite growth via a direct effect on TgAP3{beta}. We see no evidence for the ability of QQ-437 to bind directly to TgAP3{beta}, suggesting that the mutation in TgAP3{beta} that confers resistance does so through an indirect mechanism. Further studies are needed to identify the direct molecular target(s) of this promising class of compounds.

microbiology↗

bioRxiv2022

Adaptation to ER-stress via serine glycine metabolism licences STING signalling and CMV control in intestinal epithelial cells

Inflammatory bowel diseases (IBD) are characterized by chronic relapsing inflammation of the gastrointestinal tract. While the molecular causality between endoplasmic reticulum (ER) stress and intestinal inflammation is widely accepted, the metabolic consequences of chronic ER-stress on the pathophysiology of IBD remain unclear. By using in vitro, ex vivo, in vivo mouse models and patient datasets, we identified a distinct polarisation of the mitochondrial one-carbon (1C) metabolism and a fine-tuning of the amino acid uptake in intestinal epithelial cells tailored to support GSH and NADPH metabolism upon chronic ER-stress. This metabolic phenotype strongly correlates with IBD severity and therapy-response. Mechanistically, we uncover that both chronic ER-stress and serine limitation disrupt cGAS/STING-signalling, impairing the epithelial response against viral and bacterial infection, fuelling experimental enteritis. Consequently, antioxidant treatment restores STING function and virus control. Collectively, our data highlight the importance of the plasticity of serine metabolism to allow proper cGAS/STING-signalling and innate immune responses upon chronic inflammation in the gut.

cell biology↗

bioRxiv2022

Bacterial produce membrane-binding small molecules to regulate horizontal gene transfer in vesicles

The exchange of bacterial extracellular vesicles facilitates molecular exchange between cells, including the horizontal transfer of genetic material. Given the implications of such transfer events on cell physiology and adaptation, some bacterial cells have likely evolved mechanisms to regulate vesicle exchange. Past work has identified mechanisms that regulate the formation of extracellular vesicles, including the production of small molecules that modulate membrane structure, however whether these mechanisms also regulate vesicle uptake and have an overall impact on the rate of vesicle exchange is unknown. Here we show that membrane-binding molecules produced by microbes regulate both the formation and uptake of extracellular vesicles and have the overall impact of increasing the vesicle exchange rate within a bacterial coculture. In effect, production of compounds that influence vesicle exchange rates enable cells to steal genes from neighboring cells. The ability of several membrane-binding compounds to regulate vesicle exchange was demonstrated. Three of these compounds, nisin, colistin, and polymyxin B, are antimicrobial peptides added at sub-inhibitory concentrations. These results suggest that a key function of exogenous compounds that bind to membranes may be the regulation of vesicle exchange between cells. ImportanceThe exchange of bacterial extracellular vesicles is one route of gene transfer between bacteria, although it was unclear if bacteria developed strategies to regulate the rate of gene transfer within vesicles. In eukaryotes, there are many examples of specialized molecules that have evolved to facilitate the production, loading, and uptake of vesicles. Recent work with bacteria has shown that some small molecules influence membrane curvature and induce vesicle formation. Here we show that similar compounds facilitate vesicle uptake, thereby regulating the overall rate of vesicle exchange within bacterial populations. The addition of membrane-binding compounds, several of them antibiotics at sub-inhibitory concentrations, to a bacterial co-culture increased the rate of horizontal gene transfer via vesicle exchange.

microbiology↗

bioRxiv2021

Biofilm-forming capacity of Escherichia coli isolated from cattle and beef packing plants: relation to virulence attributes, stage of processing, antimicrobial interventions, and heat tolerance

Despite the importance of biofilm formation in contamination of meat by pathogenic Escherichia coli at slaughter plants, drivers for biofilm have been unclear. To identify selection pressures for biofilm, we evaluated 745 Top 7 from cattle and 700 generic E. coli from two beef slaughter plants for motility, expression of curli and cellulose, and biofilm-forming potential. Top 7 were also screened for serogroup, stx1, stx2, eae and rpoS. Generic E. coli were compared by source (hide of carcass, hide-off carcass, processing equipment) before and after implementation of antimicrobial hurdles. The proportion of E. coli capable of forming biofilms was lowest (7.1%; P < 0.05) for cattle isolates and highest (87.3%; P < 0.05) from equipment. Only one enterohemorrhagic E. coli (EHEC) was an extremely-strong biofilm-former, in contrast to 73.4% of E. coli from equipment. Isolates from equipment after sanitation had a greater biofilm-forming capacity (P < 0.001) than those before sanitation. Most Top 7 were motile and expressed curli, although these traits along with expression of cellulose and presence of rpoS were not necessary for biofilm formation. In contrast, isolates capable of forming biofilms on equipment were almost exclusively motile and able to express curli. Results of the present study indicate that cattle would rarely carry EHEC capable of making strong biofilms to slaughter plants. However, if biofilm-forming EHEC contaminated equipment, current antimicrobial hurdles would inadvertently perpetuate the most robust biofilm-forming strains. Accordingly, new and effective anti-biofilm hurdles are required for meat-processing equipment, to reduce future instances of food-borne disease. ImportanceAs the majority of enterohemorrhagic E. coli (EHEC) are not capable of forming biofilms, sources were undetermined of the biofilm-forming EHEC isolated from high-event periods in beef slaughter plants. This study demonstrated that sanitation procedures used on beef-processing equipment inadvertently select for survival of the most robust biofilm-forming strains of E. coli. Cattle only rarely carry EHEC capable of forming strong biofilms (1/745 isolates evaluated), but sanitation of equipment markedly increased (P < 0.001) biofilm-forming capacity of E. coli. In contrast, chilling carcasses for 3 days at 0{degrees}C reduced (P < 0.05) biofilm-forming capacity of E. coli. Consequently, an additional anti-biofilm hurdle for meat-processing equipment, perhaps involving cold exposure, is necessary to further reduce the risk of food-borne disease.

microbiology↗

bioRxiv2018

Engineering bacteria for biogenic synthesis of chalcogenide nanomaterials

Microbes naturally build nanoscale structures, including structures assembled from inorganic materials. Here we combine the natural capabilities of microbes with engineered genetic control circuits to demonstrate the ability to control biological synthesis of chalcogenide nanomaterials in a heterologous host. We transferred reductase genes from both Shewanella sp. ANA-3 and Salmonella enterica serovar Typhimurium into an heterologous host (Escherichia coli) and examined the mechanisms that regulate the properties of biogenic nanomaterials. Expression of arsenic reductase genes and thiosulfate reductase genes in E. coli resulted in the synthesis of arsenic sulfide nanomaterials. In addition to processing the starting materials via redox enzymes, cellular components also nucleated the formation of arsenic sulfide nanomaterials. The shape of the nanomaterial was influenced by the bacterial culture, with the synthetic E. coli strain producing nanospheres and conditioned media or cultures of wild type Shewanella sp. producing nanofibers. The diameter of these nanofibers also depended on the biological context of synthesis. These results demonstrate the potential for biogenic synthesis of nanomaterials with controlled properties by combining the natural capabilities of wild microbes with the tools from synthetic biology.

bioengineering↗