Biology subjects

Bonne, I.

Publications and source records attributed to Bonne, I..

8 recordsLinked to original sources

bioRxiv2026

Layered phage therapy exploits capsule-loss escape and altered antibiotic susceptibility in CG23 hypervirulent Klebsiella pneumoniae

The rise of drug-resistant Klebsiella pneumoniae infections is prompting a re-evaluation of phage therapy as an alternative treatment. Phage therapy has achieved successful outcomes, yet important limitations persist, including the rapid emergence of phage resistance and the time required to source suitable phages. Combining multiple phages into a phage cocktail based on genetic diversity, morphology or distinct infection mechanisms is a common strategy to mitigate resistance. Phage pairing based on these criteria neither mitigates nor delays the emergence of resistance, using CG23 hypervirulent Klebsiella pneumoniae (hvKp) EC0675 as a model. In CG23 Kp strains, resistance arises through disruption of the capsular biosynthetic pathway, leading to capsule impairment and global cross-resistance to all capsule-active phages. Combining phages active against encapsulated wild-type bacteria with those active against capsule-deficient escape mutants can overcome this constraint, improving bacterial suppression in vitro and reducing bacterial burdens across multiple organs in a mouse systemic infection model. In parallel, phage-driven capsule loss increased susceptibility of hvKp EC0675 to selected antibiotics targeting the bacterial envelope or cell wall in vitro. These findings highlight the contribution of capsule-associated resistance to phage cross-resistance in the CG23 Kp strains examined, and support further evaluation of phage combinations targeting both wild-type bacteria and resistant derivatives, including their use alongside selected antibiotics, informing future clinical translation.

microbiology↗

bioRxiv2026

Ecologically inspired assembly of a Bacillales synthetic community for lignin degradation

Lignin remains a major bottleneck in biomass valorization due to its heterogeneous and recalcitrant structure. Traditionally, lignin degradation has been developed using a single-microorganism or single-enzyme approach, with efforts focused on identifying ligninolytic activities of individual bacteria or fungi. Here, we establish a framework for designing lignin-degrading synthetic microbial communities (SynComs) by integrating top-down ecological filtering with bottom-up trait-based selection. This approach enables the selection of bacteria with ligninolytic capacity while retaining community members that form strong biofilms and contribute indirectly to overall community function. Proteomic profiling uncovered lignin-driven functional reprogramming of the SynCom, highlighting strain-specific enzymatic specializations that collectively enable lignin depolymerization. Our work highlights the potential of SynComs for lignin degradation and shows how rationally designed, functionally partitioned communities can enhance lignin conversion.

microbiology↗

bioRxiv2026

Theca cell mechanosensing and regulation of follicular extracellular matrix during ovarian follicle development

Mammalian folliculogenesis is essential for female hormonal regulation and successful reproduction. While the steroidogenic functions of theca cells (TCs) have been implicated in ovarian diseases and infertility, the physico-structural properties of TCs and their associated extracellular matrix (ECM), or theca matrix, remain poorly understood. Using murine ovaries, we show that a stiff basement membrane (BM) and theca matrix constitute a mechanically instructive niche that modulates TC proliferation and Yes-associated protein (YAP) signalling in secondary follicles. We identify hyaluronic acid (HA) as a key matrix component that is actively secreted by contractile TCs. The HA scaffold, in turn, regulates TC proliferation, YAP signalling and motility, and is required for overall follicle growth. We showed that stiffer substrates enhance YAP nuclear transport in TCs, while mechanical stretch, cell packing, and curvature affect TC proliferation. In addition, TCs exhibit directed migration towards regions of positive curvature. Together, this study reveals a mechanochemical feedback mechanism that establishes TC mechanics and HA as key regulators of theca matrix formation that is essential for mammalian folliculogenesis. SIGNIFICANCEThe structural properties and mechanical functions of the basement membrane and theca cell-matrix encapsulating mammalian ovarian follicles are poorly understood. Our findings reveal that during early stage of follicle development, the basement membrane remains thin and stiff, while the theca cells actively secrete hyaluronic acid in a contractility-dependent manner. The hyaluronic acid scaffold, in turn, regulates theca cell YAP signalling, proliferation and motility that are required for functional growth of follicles. We further showed that the theca cells are mechanosensitive and fine-tune their proliferative capacity and Hippo pathways in response to substrate stiffness, stretch and curvature. Together, our study uncovers mechanoregulatory feedback between theca cells and associated extracellular matrix, offering new insights into environmental control of folliculogenesis in female reproduction.

developmental biology↗

bioRxiv2025

Critical phenomenon underlies de novo luminogenesis during mammalian follicle development

A key process during mammalian folliculogenesis is the formation of a fluid-filled antrum around the oocyte. While it is known that the antrum is critical for oocyte maturation and the eventual ovulation, the detailed process underlying de novo luminogenesis remains poorly understood. In this study, we investigated the spatiotemporal dynamics of lumen growth and the cellular mechanism driving this process, using advanced microscopy, molecular perturbations and computational modelling. We found that in secondary follicles, the interstitial gaps exist in a near-critical regime, characterised by a highly dynamic and interconnected fluid network with gap size obeying a power-law distribution. Above a critical size of 180 m, we observed an onset of cell death and the emergence of a stably growing dominant fluid cavity resembling phase separation. By modelling the granulosa cells and the interstitial fluid as a binary fluid, we reproduced the near-critical and phase-separated regimes and found that a spatial gradient of cell-fluid interfacial tension, as observed experimentally, is sufficient to robustly maintain the secondary follicles in a near-critical state. Reducing cell-fluid interfacial tension globally by weakening the cell-cell adhesion between granulosa cells leads to fragmentation of fluid and growth arrest of the dominant cavity, as predicted by the model. Importantly, perturbing the critical state in secondary follicles leads to impaired follicle growth. Altogether, our study reveals how collective spatiotemporal regulation of cell junction mechanics and cell death can contribute to the effective transition between distinct regimes of fluids, which are indispensable for functional maturation of follicles.

developmental biology↗

bioRxiv2024

Runx3 Acts as Homodimeric Chromatin Binding Factor Regulating Heterochromatin-Mediated Cancerous Phenotype

The recent paradoxical dual citizenships of Runt-related transcription factor 3 (Runx3) in tumorigenesis remains poorly characterized. Here, we report the oncogenic capacity of Runx3 as chromatin modulator in metastatic gastric cancer model. Runx3 exists as homodimer and binds cooperatively to modified nucleosomes. Additionally, we detected a synergistic functional enhancement of octamer transfer, nucleosome sliding and stochiometric integrity of SWI/SNF by Runx3. We found that Runx3 depletion increased nucleosomes occupancy and promoted chromatin silencing by heterochromatin condensation and HP1 oligomerization. ATAC-seq analysis revealed differential accessibility per chromosome due to Runx3 null expression with dysregulation of multiple inflammatory response and DNA repair pathways. Mechanistically, these modulations resulted in aberrant DNA damage repair response, which is rescued by RUNX3 overexpression. These findings reveal a new paradigm in Runx3 biology as dynamic chromatin regulatory element vital for the maintenances of cancerous phenotype. SignificanceTo the best of our knowledge, the present study is the first to explore the role of Runx3 as homodimeic chromatin binding factor and establishes its oncogenic-function as modulator of heterochromatin de-condensation and SWI/SNF chromatin remodeling activities. These emerging features of Runx3 at the epigenetic level imply a promising direction to screen for anti-Runx3 epigenetic drugs "Epi-drugs" in search of novel gastric cancer treatment.

cancer biology↗

bioRxiv2024

Theca cell mechanics and tissue pressure regulate mammalian ovarian folliculogenesis

The maturation of functional eggs within the ovaries is essential for successful reproduction and organismal functions in mammals. Yet, despite its biological and clinical importance, the underlying mechanisms regulating folliculogenesis remain enigmatic. Here, we report a novel role of the surface-anchoring theca cells (TCs) in regulating follicle growth through mechanical signalling. Direct mechanical measurements reveal that these TCs are highly contractile and exert compressive stress to the follicular interior, potentially through active assembly of fibronectin scaffold around the follicles. Abolishing TC contractility disrupts fibronectin assembly, increases follicle size, and decreases intrafollicular pressure and viscosity. We further reveal that the granulosa cells (GCs) within the follicles exhibit spatial patterns of YAP signalling and proliferation, which appear to be decoupled. Transient manipulation of tissue pressure through bulk follicle compression, laser ablation or pharmacological perturbation of TC contractility leads to changes in GC YAP signalling, proliferation, and oocyte-GC communications, while long term abrogation of TC contractility leads to impaired follicle growth. Altogether, our study unveils the unique role of TC-mediated tissue pressure in ensuring robust mammalian ovarian folliculogenesis.

developmental biology↗

bioRxiv2023

MFSD7c functions as a transporter of choline at the blood-brain barrier

Mutations of MFSD7c (also known as Flvcr2), which is an orphan transporter, are linked to Fowler syndrome 1, 2. Here, we use Mfsd7c knockout mice and cell-based assays to reveal that MFSD7c is a choline transporter at the blood-brain barrier (BBB). We performed comprehensive metabolomics and detected differential changes of metabolites in the brains and livers of Mfsd7c knockout (Mfsd7c-/-) embryos. Particularly, we found that choline-related metabolites were altered in the brains but not in the livers of Mfsd7c-/- embryos. Thus, we hypothesized that MFSD7c regulates the levels of choline in the brain. Indeed, expression of human MFSD7c in cells significantly increased choline uptake. Interestingly, we showed that choline uptake by MFSD7c is greatly increased by choline-metabolizing enzymes, leading us to demonstrate that MFSD7c is a facilitative transporter of choline. Furthermore, single-cell patch-clamp showed that the import of choline by MFSD7c is electrogenic. Choline transport function of MFSD7c is conserved in vertebrates, but not in yeasts. We show that human MFSD7c is a functional ortholog of HNM1, the yeast choline importer. Employing our transport assays, we showed that several missense mutations of human MFSD7c from Fowler patients had abolished or reduced choline transport activity. Mice lacking Mfsd7c in the CNS endothelial cells suppressed the import of exogenous choline from blood but unexpectedly had increased choline levels in the brain. Stable-isotope tracing study revealed that MFSD7c is required for exporting choline derived from lysophosphatidylcholine (LPC) in the brain. Collectively, our work identifies MFSD7c as a choline transporter at the BBB. This study suggests that defective export of choline in the brain may be a cause of Fowler syndrome.

biochemistry↗

bioRxiv2021

The novel conserved NAD+ binding micropeptide SGHRT regulates mitochondrial function and metabolism in human cardiomyocytes

AbstractsNicotinamide adenine dinucleotide (NAD) is a critical metabolite and coenzyme for multiple metabolic pathways and cellular processes (1-4). In this study, we identified Singheart, SGHRT as a nuclear genome-encoded NAD+-binding mitochondrial micropeptide. SGHRT, present in both monomeric and dimeric forms, binds directly to NAD, but not NADH or flavin adenine dinucleotide (FAD). Localized to the inner mitochondrial membrane and mitochondrial matrix, SGHRT interacts with the mitochondrial enzymes Succinate-CoA Ligase and Succinate Dehydrogenase. SGHRT deletion in human embryonic stem cell derived cardiomyocytes disrupted mitochondria morphology, decreased total NAD and ATP abundance, and resulted in defective TCA cycle metabolism, the electron transport chain and in Ox-Phos processes. These results comprise the first report of an NAD+-binding micropeptide, SGHRT, required for mitochondrial function and metabolism.

cell biology↗