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Biology subjects

Bonnet, M.

Publications and source records attributed to Bonnet, M..

11 recordsLinked to original sources

Generative Chemistry Platform for Small Molecules Targeting RNA: A Case Study for Chemical Optimization

We introduce the Serna Bio GenAI platform, a generative chemistry and multiparametric optimization platform for the design of RNA-targeting small molecules. Targeting RNA with small molecules has proven historically challenging but offers notable potential upsides, including access to unique mechanisms of action and the ability to target otherwise untargetable genes. We consider a major challenge here to be designing chemistry specific to RNA-targeting. Molecular design is a valuable application of AI in drug discovery, but many publicly available models use training data focused on protein-targeting - the modality best historically explored in drug discovery. We showcase the difference and value in building a specifically RNA-targeting platform, comparing its performance to state-of-the-art public chemical generators and experimentally validating its chemical designs in comparison to chemistry designed by a human expert.

bioinformatics↗

Environmental reservoir of resistance genes for the last resort antibiotic Cefiderocol.

Antibiotic resistance poses a global public health threat. Cefiderocol, a recently introduced siderophore cephalosporin, employs a "Trojan Horse" mechanism by exploiting bacterial iron uptake systems for cell entry. Yet, resistant clinical isolates are already observed in clinics and resistance mechanisms are difficult to characterize. Here, we applied functional metagenomics to identify cefiderocol resistance genes. Functional metagenomic DNA libraries from diverse environmental samples collected across several countries were expressed in a cefiderocol-sensitive Escherichia coli host. This yielded four resistant clones with DNA originating from wastewater or freshwater DNA libraries. The identified antibiotic resistance genes (ARGs) causing an increase in cefiderocol minimum inhibitory concentrations encoded for beta-lactamases (VEB-3, OXA-372 homolog and YbxI homolog) and a partial penicillin binding protein homolog. Three of four shared closest homologs in pathogenic bacteria. One ARG was associated with a mobile genetic element and was broadly distributed across all wastewater samples from every country surveyed. This study underscores the critical importance of environmental surveillance for ARGs, particularly for novel agents like cefiderocol with limited understanding of resistance mechanisms.

microbiology↗

A pre-loaded and assembled human Ago2-miRISC orchestrates Shigella-induced vacuolar rupture through the targeting of RhoGDIα

The enteroinvasive bacterium Shigella flexneri causes bacillary dysentery. It invades intestinal epithelial cells and forms a bacterium-containing vacuole, which it rapidly ruptures to reach the cytosol. Here, we found that human Argonaute 2 (Ago2), the central component of miRNA-induced silencing complex (miRISC), positively regulates early steps of Shigella infection, including vacuolar rupture. This is consistent with the rapid recruitment of Ago2 at Shigella entry foci. The ability of Ago2 to form an assembled miRISC was found required for vacuolar maturation, while its slicer activity is dispensable for this process. Furthermore, we found that the RhoGTPase inhibitor RhoGDI is targeted by specific miRNAs, pre-loaded in Ago2, which, collectively, accelerate vacuolar rupture. Therefore, a pre-loaded and assembled Ago2-miRISC orchestrates vacuolar maturation by targeting RhoGDI. These findings may have wider implications in the understanding of how stored Ago2-loaded miRNAs control immediate steps of infection, prior to the differential expression of microbe-responsive miRNAs.

molecular biology↗

Human nasal olfactory stem cell-derived extracellular vesicles improve the repair of rat nerves

Damage to the peripheral nerve impairs quality of life. Despite the advances in surgery to facilitate nerve regeneration, complete recovery remains elusive. Human olfactory ecto-mesenchymal stem cells (OEMSC) have potential for the treatment of peripheral nerve injury through the release of extracellular vesicles (EV). The current research investigates the therapeutic effects of a venous bridge, filled with freshly purified or cryoconserved OEMSC-derived EVs after a peroneal nerve loss of substance. Injured peroneal nerve was bridged with a vein into which freshly purified or cryoconserved EVs were injected or not. Nerve repair was analyzed by measuring locomotor function, muscle mechanical properties, muscle mass, axon number, and myelination. The EVs significantly increased locomotor recovery, maintained the contractile phenotype of the target muscle, and augmented the number of growing axons. These results demonstrate that EVs display a positive effect on peripheral nerve regeneration, representing an alternative to cellular therapies for peripheral nerve repair.

neuroscience↗

Harnessing ALDH1A2 vulnerability in T-cell acute lymphoblastic leukemia

T-cell acute lymphoblastic leukemia (T-ALL) is an aggressive hematologic malignancy with limited therapeutic options, particularly in the relapsed/refractory (R/R) setting. Unlike other hematological malignancies, which benefit from targeted immunotherapies, T-ALL remains reliant on chemotherapy, leading to poor outcomes in R/R cases. Identifying novel therapeutic vulnerabilities is crucial to improving the outcomes of patients. Herein, we identify aldehyde dehydrogenase 1A2 (ALDH1A2) as a T-ALL-specific enzyme essential for leukemic cell survival. Transcriptomic and epigenetic analyses reveal its selective expression, regulated by the TAL1 oncogene. Pharmacological inhibition of ALDH1A2 using Dimate demonstrates potent anti-leukemic activity across diverse T-ALL subtypes, including primary samples of relapsed disease. These findings establish ALDH1A2 as a therapeutic target in T-ALL and support ALDH inhibition as a promising strategy to overcome drug resistance and improve treatment outcomes in R/R T-ALL.

cancer biology↗

A Mimicry-Based Strategy Between Human and Commensal Antigens for the Development of a New Family of Immune Therapies for Cancer

Peptide vaccines have emerged as a promising strategy for cancer immunotherapy, yet often lack of strong, specific and sustained immune responses against tumor antigens. To achieve a robust immune response, the effective selection of tumour antigens is crucial. While neoantigens trigger potent immune responses, their use suffers from patient specificity and their rarity in low-mutational tumors. Alternatively, the immunogenic potential of tumor-associated antigens (TAAs) is limited by central immune tolerance. Molecular mimicry and T cell cross-reactivity is a proposed mechanism to trigger a robust T cell-mediated antitumor response. Although molecular mimicry between pathogens and tumor antigens has been described, the potential benefits of exploiting this molecular mimicry with commensal bacterial antigens in antitumor immunity have not been thoroughly investigated despite strong evidence that the composition of the human microbiota significantly influences immune competency. Our new approach called OncoMimics, which uses molecular mimicry between commensal bacterial and tumoral antigens to induce cross-reactive cytotoxic T cells against tumor cells. In preclinical studies, vaccination with OncoMimic peptides (OMPs) led to the expansion of CD8+ T cells reacting against homologous tumor-associated antigen peptides and elicits cytotoxic activity against tumor cells. OMPs are efficiently recognized by a prevalent T cell population within the peripheral blood mononuclear cells of healthy individuals. An ongoing clinical trial (NCT04116658) using OncoMimics in patients with glioblastoma demonstrates early, durable, and cross-reactive tumor antigen CD8+ T cell responses with pronounced memory persistence. By overcoming the current vaccine limitations, OncoMimics constitutes a promising strategy for enhancing cancer immunity and improving patient outcomes. Statement of SignificanceThis study introduces OncoMimics, a peptide-based immunotherapy leveraging molecular mimicry to induce robust, cross-reactive T cell responses against tumor antigens, showing promising early results in an ongoing glioblastoma clinical trial (NCT04116658)

immunology↗

Culture of human nasal olfactory stem cells and their extracellular vesicles as advanced therapy medicinal products

The olfactory ecto-mesenchymal stem cell (OE-MSC) are mesenchymal stem cells originating from the lamina propria of the nasal mucosa. They have neurogenic and immune-modulatory properties and showed therapeutic potential in animal models of spinal cord trauma, hearing loss, Parkinsonss disease, amnesia, and peripheral nerve injury. In this paper we designed a protocol that meet the requirements set by human health agencies to manufacture these stem cells for clinical applications. Once purified, OE-MSCs can be used per se or expanded in order to get the extracellular vesicles (EV) they secrete. A protocol for the extraction of these vesicles was validated and the EV from the OE-MSC were functionally tested on an in vitro model. Nasal mucosa biopsies from three donors were used to validate the manufacturing process of clinical grade OE-MSC. All stages were performed by expert staff of the cell therapy laboratory according to aseptic handling manipulations, requiring grade A laminar airflow. Enzymatic digestion provides more rapidly a high number of cells and is less likely to be contaminated. Foetal calf serum was replaced with human platelet lysate and allowed stronger cell proliferation, with the optimal percentage of platelet lysate being 10%. Cultivated OE-MSCs are sterile, highly proliferative (percentage of CFU-F progenitors was 15,5%) and their maintenance does not induce chromosomal rearrangement (karyotyping and chromosomal microarray analysis were normal). These cells express the usual phenotypic markers of OE-MSC. Purification of the EVs was performed with ultracentrifugation and size exclusion chromatography. Purified vesicles expressed the recognized markers of EVs (Minimal Information for Studies of Extracellular Vesicles ("MISEV") guidelines) and promoted cell differentiation and neurite elongation in a model of neuroblastoma Neuro2a cell line. We developed a safer and more efficient manufacturing process for clinical-grade olfactory stem cells, these cells can now be used in humans. A phase I clinical trial will begin soon.An efficient protocol for the purification of the OE-MSC EVs have been validated. These EVs exert neurogenic properties in vitro. More studies are needed to understand the exact mechanisms of action of these EVs and prove their efficacy and safety in animal models.

neuroscience↗

The Jak/Stat pathway mediates disease tolerance during systemic bacterial infection in Drosophila

Disease tolerance describes an infected hosts ability to maintain health independently of the ability to clear microbe loads. The Jak/Stat pathway plays a pivotal role in humoral innate immunity by detecting tissue damage and triggering cellular renewal, making it a candidate tolerance mechanism. Here, we find that in Drosophila melanogaster infected with Pseudomonas entomophila disrupting ROS-producing dual oxidase (duox) or the negative regulator of Jak/Stat Socs36E, render male flies less tolerant. Another negative regulator of Jak/Stat, G9a - which has previously been associated with variable tolerance of viral infections - did not affect the rate of mortality with increasing microbe loads compared to flies with functional G9a, suggesting it does not affect tolerance of bacterial infection as in viral infection. Our findings highlight that ROS production and Jak/Stat signalling influence the ability of flies to tolerate bacterial infection sex-specifically and may therefore contribute to sexually dimorphic infection outcomes in Drosophila.

evolutionary biology↗

Lactobacillus rhamnosus Lcr35(R) as an effective treatment for preventing Candida albicans infection in preclinical models: first mechanistical insights

The increased recurrence of Candida albicans infections is associated with greater resistance to antifungal drugs. This involves the establishment of alternative therapeutic protocols such as the probiotic microorganisms whose antifungal potential has already been demonstrated using preclinical models (cell cultures, laboratory animals). Understanding the mechanisms of action of probiotic microorganisms has become a strategic need for the development of new therapeutics for humans. In this study, we investigated the prophylactic anti-Candida albicans properties of Lactobacillus rhamnosus Lcr35(R) using the in vitro Caco-2 cells model and the in vivo Caenorhabditis elegans model. On Caco-2 cells, we showed that the strain Lcr35(R) significantly inhibited the growth of the pathogen (~2 log CFU.mL-1) and its adhesion (150 to 6,300 times less). Moreover, on the top of having a prolongevity activity in the nematode, Lcr35(R) protects the animal from the fungal infection even if the yeast is still detectable in its intestine. At the mechanistic level, we noticed the repression of genes of the p38 MAPK signaling pathway and genes involved in the antifungal response induced by Lcr35(R) suggesting that the pathogen no longer appears to be detected by the worm immune system. However, the DAF-16 / FOXO transcription factor, implicated in the longevity and antipathogenic response of C. elegans, is activated by Lcr35(R). These results suggest that the probiotic strain acts by stimulating its host via DAF-16, but also by suppressing the virulence of the pathogen.

microbiology↗

A Gender-Dependent Molecular Switch of Inflammation via MyD88/Estrogen Receptor-alpha Interaction

Most Toll-like receptors and IL-1/IL-18 receptors activate a signaling cascade via the adaptor molecule MyD88, resulting in NF-{kappa}B activation and inflammatory cytokine and chemokine production. Females are less susceptible than males to inflammatory conditions, presumably due to protection by estrogen. Here we show that MyD88 interacts with a methylated, cytoplasmic form of estrogen receptor-alpha (methER-). This interaction is required for NF-{kappa}B transcriptional activity and pro-inflammatory cytokine production, and is dissociated by estrogen. Importantly, we show a strong gender segregation in gametogenic reproductive organs, with MyD88/methER- interactions found in testicular tissues and in ovarian tissues from menopausal women, but not in ovaries from women age 49 and less -suggesting a role for estrogen in disrupting this complex in situ. Collectively, our results indicate that the formation of MyD88/methER- complexes during inflammatory signaling and their disruption by estrogen may represent a mechanism that contributes to gender bias in inflammatory responses.

immunology↗

A dynamical model of TCRβ gene recombination: Coupling the initiation of Dβ-Jβ rearrangement to TCRβ allelic exclusion

One paradigm of random monoallelic gene expression is that of T-cell receptor (TCR){beta} allelic exclusion in T lymphocytes. However, the dynamics that sustain asymmetric choice in TCR{beta} dual allele usage and the production of TCR{beta} monoallelic expressing T-cells remain poorly understood. Here, we develop a computational model to explore a scheme of TCR{beta} allelic exclusion based on the stochastic initiation of DNA rearrangement [V(D)J recombination] at homologous alleles in T-cell progenitors, and thus account for the genotypic profiles typically associated with allelic exclusion in differentiated T-cells. Disturbances in these dynamics at the level of an individual allele have limited consequences on these pro1les, robust feature of the system that is underscored by our simulations. Our study predicts a biological system in which locus-specific, prime epigenetic allelic activation effects set the stage to both optimize the production of TCR{beta} allelically excluded T-cells and curtail the emergence of their allelically included counterparts.

immunology↗