Biology subjects

Bravo, M.

Publications and source records attributed to Bravo, M..

11 recordsLinked to original sources

bioRxiv2026

DSF signalling integrates c-di-GMP and σ54 pathways with metabolic reprogramming to control Stenotrophomonas maltophilia pathogenicity and antibiotic resistance

Stenotrophomonas maltophilia is an opportunistic, multidrug-resistant pathogen whose pathogenicity is mainly driven by biofilm formation, extracellular enzyme production, surface adhesins and motility. In addition, a diffusible signal factor (DSF)-mediated quorum sensing (QS) system encoded by the rpf gene cluster coordinates collective behaviours and contributes to pathogenicity. While DSF signalling has been extensively studied in plant-pathogenic xanthomonads, its integration with transcriptional and metabolic regulation in human pathogens remains poorly defined. Here, we investigate how the DSF/Rpf system shapes virulence and adaptation in S. maltophilia by modulating downstream regulatory and metabolic pathways. Cell density-dependent activation of the RpfC-RpfG two-component system reduces intracellular c-di-GMP levels, promoting a growth phase-dependent switch between biofilm formation and motile lifestyle. This transition requires the global transcriptional regulator Clp, which functions as a transcriptional activator when unbound to c-di-GMP. Clp controls genes involved in motility, adhesion, and the alternative sigma factor {sigma} RpoN2, which inversely regulates flagellar motility and type IV pilus-mediated adhesion. Transcriptomic profiling uncovered additional DSF-dependent regulatory circuits linking quorum sensing to metabolism and antibiotic resistance. Notably, at the onset of stationary phase, the {sigma} paralog RpoN1 acts together with RpfF and RpfB to fine-tune DSF production through fatty acid and central carbon metabolism, coupling QS output to cellular metabolic state. This metabolic control constrains DSF output and impacts colistin susceptibility, highlighting clinically relevant consequences of DSF homeostasis. Together, these findings define a species-specific DSF regulatory architecture in S. maltophilia that integrates quorum sensing, second-messenger signalling, transcriptional regulation, and metabolic reprogramming to promote survival and pathogenicity. Author SummaryStenotrophomonas maltophilia is a bacterial pathogen that causes infections, particularly in hospitalized and immunocompromised patients. Its clinical impact is driven by intrinsic multidrug resistance and the ability to switch between a free-swimming state and a surface-attached biofilm state. Biofilms protect bacteria from antibiotics and the immune system, making infections persistent, while motility promotes spread and colonization. Understanding how S. maltophilia controls this balance is critical for combating infection. Like many bacteria, S. maltophilia uses chemical communication, known as quorum sensing, to sense population density and coordinate behaviours linked to virulence and survival. This system is based on the autoinducer DSF, allowing bacteria to decide when to move, attach, or alter metabolism. In this work, we show that DSF-based quorum sensing activates a regulatory cascade that modulates levels of the signalling molecule c-di-GMP, triggering a switch between biofilm formation and motility. This switch relies on global regulators that control genes involved in movement, adhesion, metabolism, and antibiotic resistance. We also uncover a metabolic feedback mechanism that fine-tunes DSF concentration, impacting bacteria state and antibiotic susceptibility. These findings reveal how bacterial communication, metabolism, and pathogenic behaviour are linked in S. maltophilia, highlighting opportunities for antimicrobial intervention.

microbiology↗

bioRxiv2025

Beyond One-Size-Fits-All: Tumor Biology Influences Nanoparticle Behaviour in Cancer Models

Nanoparticles (NPs) are a promising tool for cancer therapy, yet few have successfully reached clinical application. Current nanomedicine development pipelines are focused on optimizing physical properties of NPs, overlooking the impact of tumor biology on their behavior. Here, we show that the same NPs exhibit distinct accumulation and penetration patterns in 3D spheroids derived from four tumor models (representative of lung, colon, breast, and cervical cancer). We uncover an inverse relationship between NP uptake and penetration: tumors with slower internalization show deeper NP diffusion. Proteomic analysis revealed that tumor-specific expression of endocytic and extracellular matrix proteins underlies this variability. Our findings challenge the prevailing one-size-fits-all approach and highlight the need to integrate tumor biology into NP design. Tailoring NPs to the unique cellular and extracellular features of each tumor type will be critical for developing more effective and clinically relevant nanotherapies.

cell biology↗

bioRxiv2025

Comparative mortality of dominant Staphylococcus aureus lineages in human bacteremia and animal infection models

Staphylococcus aureus is a major cause of severe infections including infective endocarditis, but lineage-specific virulence determinants remain unclear. We analyzed 77 S. aureus bacteremic isolates from major lineages using phenotypic assays, infection models, and transcriptomics. Our results revealed significant heterogeneity in S. aureus pathogenicity. ST398 isolates exhibited heightened virulence, characterized by increased hemolysin production, whereas CC30 strains showed reduced growth, biofilm formation, and infectivity. Notably, the ST398 agrC mutant Sau7 exhibited unique phenotypic behavior, with high biofilm production and decreased virulence in Galleria mellonella larvae model. Infection studies in the rabbit experimental endocarditis model showed increased vegetation size and bacterial load in Sau7-infected animals, highlighting the role of agr system in S. aureus colonization and biofilm formation. Transcriptomic analysis identified key pathways, including quorum sensing systems and hemolysins, driving virulence in ST398 strains. These findings provide insights into the lineage-specific virulence mechanisms and the multifaceted nature of S. aureus pathogenicity.

microbiology↗

bioRxiv2025

Cellular Responses to Photothermal Therapy: Heat-Induced ERK Signaling and Intercellular Communication in Solid Tumors

Nanoparticle-mediated photothermal therapy (PTT) shows promise as a standalone cancer treatment but faces clinical challenges due to inconsistent efficacy. Its translation is further hindered by a limited understanding of plasmon-induced heat effects, such as stress responses and intercellular signaling. Here, we investigate how plasmon-induced local heating affects cellular behavior and fate within tumor spheroids by focusing on the activity of the extracellular signal-regulated kinase (ERK). Spheroids were prepared from HeLa cells that express a FRET-based ERK sensor, and ERK activity changes under photothermal stimuli were tracked using a deep-learning program, 3DeeCellTracker. Gold nanostars were used as highly efficient photothermal transducers. Our results revealed significant alterations in ERK signaling patterns upon photothermal stimulation compared to spontaneous ERK activity in untreated spheroids, including changes in the activation frequency, timing, and duration. Notably, photothermal-induced ERK activity propagated across neighboring cells within the spheroid, suggesting intercellular communication. Furthermore, analysis of cell death and division further demonstrated that laser power modulates cellular fate during photothermal therapy. This study provides insights for predicting the therapeutic effects of PPT and guides the rational design of next-generation photothermal strategies. Additionally, our approach demonstrates the potential of FRET-based biosensors and deep-learning tools as powerful methods to study the effects of various therapeutic stimuli on solid tumors at the single-cell level.

cancer biology↗

bioRxiv2024

Nanoparticle Accumulation and Penetration in 3D Tumor Models: the Effect of Size, Shape, and Surface Charge

Preclinical studies have demonstrated that nanoparticles (NPs) hold significant potential for advancing cancer therapy by enhancing therapeutic efficacy while reducing side effects. Their effectiveness in solid tumors is, however, often constrained by insufficient accumulation and penetration. Understanding how the physicochemical properties of NPs - such as size, shape, and surface charge - influence their interaction with cells within the tumor is critical for optimizing NP design. In this study, we addressed the challenge of inconsistent NP behavior by systematically evaluating NP uptake in both 2D and 3D tumor models, and NP penetration in spheroids. Our results showed that larger NPs exhibited higher internalization rates in 2D models but limited penetration in 3D spheroids. Furthermore, negatively charged NPs consistently achieved superior accumulation and deeper penetration than neutral and positively charged NPs. Spherical NPs outperformed rod-shaped NPs in tumor accumulation and penetration. These findings underscore the importance of carefully tailoring NP properties to the complex tumor microenvironment for improved therapeutic outcomes in real tumors.

cancer biology↗

bioRxiv2024

Biocompatible Neodymium-Doped Nanocrystals as Probes for Diffraction-limited, in vitro Temperature Sensing

Localized hyperthermia is a promising approach to cancer therapy. However, its clinical potential is limited by heterogeneous heat distribution within tumors, and advanced methods to measure temperature at the sub-micron level are therefore required. To address this challenge, luminescent nanothermometers, such as lanthanide-doped nanocrystals (Ln-NC) operating in the near-infrared (NIR), have been investigated for accurate spatiotemporal thermal monitoring. In this study, the synthesis of neodymium-doped, sodium yttrium fluoride nanocrystals (Nd-NCs) was optimized to achieve high photoluminescence (PL) intensity by adjusting the dopant concentration and by shelling with inert layers. Standard curves for luminescence-based temperature readout were developed using ratiometric analysis of the temperature-dependent PL spectra in the 850-920 nm biological window, showing excellent linearity and high thermal sensitivity. A silica shell was added to the particles and shown to confer excellent aqueous stability and biocompatibility in A549 lung cancer cells. Finally, luminescent thermal readout was demonstrated in vitro in A549 cells by spectrally resolving the diffraction-limited luminescence spots at a single-particle scale over a clinically relevant temperature range from 20-50 {degrees}C. The application of the developed nanothermometer as preclinical tools for NP-HT characterization could provide crucial information on the therapeutic temperature achieved in and around the tumor area. This could be key to optimizing NP properties and therapeutic parameters, for the development of viable hyperthermal cancer treatments. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=84 SRC="FIGDIR/small/579538v2_ufig1.gif" ALT="Figure 1"> View larger version (23K): org.highwire.dtl.DTLVardef@1b06abdorg.highwire.dtl.DTLVardef@12fa23corg.highwire.dtl.DTLVardef@4439c1org.highwire.dtl.DTLVardef@12bcedd_HPS_FORMAT_FIGEXP M_FIG C_FIG

biophysics↗

bioRxiv2023

IL-15 complex-induced IL-10 enhances Plasmodium-specific CD4+ Tfh differentiation and antibody production

Malaria, which results from infection with Plasmodium parasites, remains a major public health problem. While humans do not develop long-lived, sterilizing immunity, protection against symptomatic disease develops after repeated exposure to Plasmodium parasites and correlates with the acquisition of humoral immunity. Despite the established role antibodies play in protection from malaria disease, dysregulated inflammation is thought to contribute to the sub-optimal immune response to Plasmodium infection. Plasmodium berghei ANKA (PbA) infection results in a fatal severe malaria disease in mice. We previously demonstrated that treatment of mice with IL-15 complex (IL-15C; IL-15 bound to an IL-15R-Fc fusion protein) induces IL-10 expression in NK cells, which protects mice from PbA-induced death. Using a novel MHC class II tetramer to identify PbA-specific CD4+ T cells, herein we demonstrate that IL-15C treatment enhances Tfh differentiation. Moreover, genetic deletion of NK cell-derived IL-10 or IL-10R expression on T cells prevents IL-15C-induced Tfh differentiation. Additionally, IL-15C treatment results in increased anti-PbA IgG antibody levels and improves survival following reinfection. Overall, these data demonstrate that IL-15C treatment, via its induction of IL-10 from NK cells, modulates the dysregulated inflammation during Plasmodium infection to promote Tfh differentiation and antibody generation, correlating with improved survival from reinfection. These findings will facilitate improved control of malaria infection and protection from disease by informing therapeutic strategies and vaccine design.

immunology↗

bioRxiv2022

A TetR-like transcriptional regulator in Stenotrophomonas maltophilia involved in fatty acid metabolism is controlled by quorum sensing signals

Stenotrophomonas maltophilia is an environmental bacterium and it is also an emerging opportunistic multidrug-resistant pathogen. It uses the endogenous DSF quorum sensing (QS) system to coordinate population behaviors and to regulate virulence processes but can also respond to exogenous AHL signals produced by neighboring bacteria. Whole-transcriptome sequencing analyses were performed for S. maltophilia K279a in the exponential and stationary phases as well as in exponential cultures after treatment with exogenous DSF or AHLs. The results revealed that at the beginning of the stationary phase 1673 genes are differentially expressed. COG analysis showed that most of these genes were enriched for energetic metabolism processes and regulation of gene expression. After adding DSF or AHLs, 28 or 82 genes were found deregulated, respectively, 22 of which upregulated by both autoinducers. Interestingly, among these later genes, 14 were also upregulated in the stationary phase. Gene functions regulated by all conditions include lipid and amino acid metabolism, stress response and signal transduction, nitrogen and iron metabolism, and adaptation to microoxic conditions. Among the common top upregulated QS core genes, a putative TetR-like regulator (Smlt2053) was selected for functional characterization. This regulator has been shown to control a narrow regulon, including its own operon. It was found to sense long-chain fatty acids, including the QS signal DSF, and regulate a {beta}-oxidation catabolic pathway. Overall, our findings provide clues on the role that the QS could have in S. maltophilia in the transition from the exponential to the stationary phase and bacterial fitness under high-density growth. IMPORTANCEThe quorum sensing system in Stenotrophomonas maltophilia, in addition to coordinating the bacterial population, controls virulence-associated phenotypes, such as biofilm formation, motility, protease production, and antibiotic resistance mechanisms. Biofilm formation is frequently associated with the persistence and chronic nature of nosocomial infections. In addition, biofilms exhibit high resistance to antibiotics, making treatment of these infections extremely difficult. The importance of studying the metabolic and regulatory systems controlled by quorum sensing autoinducers will make it possible to discover new targets to control pathogenicity mechanisms in S. maltophilia.

microbiology↗

bioRxiv2022

ChemPert: mapping between chemical perturbation and transcriptional response for non-cancer cells

Prior knowledge of perturbation data can significantly assist in inferring the relationship between chemical perturbations and their specific transcriptional response. However, current databases mostly contain cancer cell lines, which are unsuitable for the aforementioned inference in non-cancer cells. Here we present ChemPert (https://chempert.uni.lu/), a database consisting of 82270 transcriptional signatures across 167 non-cancer cell types, enabling more accurate predictions of perturbation responses and drugs compared to cancer databases in non-cancer cells. In particular, ChemPert correctly predicted drug effects for treating non-alcoholic steatohepatitis and novel drugs for osteoarthritis. Overall, ChemPert provides a valuable resource for drug discovery in non-cancer diseases.

bioinformatics↗

bioRxiv2021

Versatile and Robust Method for Antibody Conjugation to Nanoparticles with High Targeting Efficiency

The application of antibodies in nanomedicine is now standard practice in research since it represents an innovative approach to deliver chemotherapy agents selectively to tumours. The variety of targets or markers that are overexpressed in different types of cancers results in a high demand for antibody conjugated nanoparticles which are versatile and easily customizable. Considering upscaling, the synthesis of antibody conjugated nanoparticles should be simple and highly reproducible. Here, we developed a facile coating strategy to produce antibody conjugated nanoparticles using click chemistry and further evaluated their selectivity towards cancer cells expressing different markers. Our approach was consistently repeated for the conjugation of antibodies against CD44 and EGFR, which are prominent cancer cell markers. The functionalized particles presented excellent cell specificity towards CD44 and EGFR overexpressing cells, respectively. Our results indicated that the developed coating method is reproducible, versatile, non-toxic, and can be used for particle functionalization with different antibodies. This grafting strategy can be applied to a wide range of nanoparticles and will contribute to the development of future targeted drug delivery systems.

biochemistry↗

bioRxiv2020

Early life adversity decreases fear expression in pre-adolescence by accelerating amygdalar parvalbumin cell development

Resource insecurity (e.g., poverty) can be a significant source of stress. Decreased resources during childhood has been associated with increased risk for developing stress-related disorders, including major depressive disorder and anxiety Although the link between early life adversity and increased risk for psychopathology has been well established, the developmental mechanisms remain unclear. Using a mouse model of poverty-like rearing, limited bedding and nesting materials (LB), we tested the effects of LB on the development of fear learning and of key neuronal structures involved in emotional regulation, the medial prefrontal cortex (mPFC) and basolateral amygdala (BLA). LB delayed the ability of pre-adolescent mice to express, but not form, an auditory conditioned fear memory. LB disrupted typical fear circuit development, accelerating parvalbumin positive (PV+) inhibitory interneuron maturation in the BLA and delaying the maturation of connections between the mPFC and BLA. The decreased fear expression in LB reared mice during early development was rescued through optogenetic inactivation of PV+ cells in the BLA. Together our data demonstrate that LB has profound and deleterious effects on mPFC and BLA development, decreasing threat-associated behavior expression, but not learning, in childhood. The current results provide a model of transiently blunt emotional reactivity in childhood, with fear-associated memories emerging later in adolescence, and possibly contributing to later pathology development.

animal behavior and cognition↗