Biology subjects

Vialaret, J.

Publications and source records attributed to Vialaret, J..

9 recordsLinked to original sources

bioRxiv2026

SPEAR: Spatial Epitranscriptomic Analysis by Mass Spectrometry Reveals Localized RNA Modification Remodeling During Glioma Progression

RNA modifications shape cell identity and disease, yet their spatial organization within tissues has remained largely inaccessible to existing technologies. NGS-based methods can map a limited number of individual modifications with spatial resolution, while liquid chromatography-tandem mass spectrometry (LC-MS/MS) provides comprehensive and quantitative coverage of the epitranscriptome from bulk, homogenized tissue. No current approach combines histological resolution, broad modification coverage, quantitative accuracy, and the sensitivity required for microscale clinical specimens. We present SPEAR (SPatial Epitranscriptomic Analysis by mass spectrometRy), a workflow coupling laser microdissection with a redesigned LC-MS/MS pipeline to enable quantitative epitranscriptomic profiling directly from formalin-fixed, paraffin-embedded (FFPE) tissue. This combination enables reproducible detection of dozens of RNA modifications from regions as small as 0.1 mm2, establishing a spatial scale previously inaccessible to mass spectrometry-based approaches. Applied to serial mouse brain sections, SPEAR resolved anatomically defined epitranscriptomic signatures across white and gray matter, establishing its spatial resolution and reproducibility in a controlled system. We then applied SPEAR to human diffuse gliomas containing, within individual specimens, both primary low-grade tumor regions and discrete foci undergoing transformation toward higher-grade malignancy. SPEAR resolved this transition directly, revealing a coordinated decrease in multiple methylated RNA modifications specifically within higher-grade regions, a spatially restricted signal that was masked by bulk analysis and reproducibly observed across patients despite underlying genetic heterogeneity. SPEAR establishes spatial epitranscriptomics as a tractable approach for molecular profiling of clinical tissue, providing a platform for biomarker discovery and molecular stratification based on the spatial organization of RNA modifications.

cancer biology↗

bioRxiv2025

Reversible multiscale corneal sexual dimorphism orchestrates neuro-epithelial coupling and tear proteome composition

Donor-recipient sex mismatch is an under-recognized risk factor for corneal graft rejection, yet the biological underpinnings at the ocular surface remain undefined. We hypothesized that sex hormones coordinately tune the tear-nerve-epithelium axis and that androgen exposure could normalize sex-linked differences relevant to alloimmune risk. We profiled 12-week-old mice in three hormonal contexts, i.e. male, female, and testosterone-treated female, combining tear biochemistry and label-free proteomics with epithelial lineage dynamics, in vivo sensory function, and corneal/trigeminal transcriptional readouts. Tear collection rate was comparable across groups, but total tear protein was reduced in females. Proteomics revealed extensive sex differences in extracellular composition, spanning lipid transport, protease-antiprotease balance, complement activity, and secretory/mucin pathways. Epithelial analyses showed sex-linked differences in progenitor output and spatial deployment, and sensory metrics indicated divergent innervation architecture and function. Across modalities, androgen supplementation in females shifted molecular and physiological profiles toward the male state, attenuating nearly all dimorphic signals, demonstrating that close to all sexual dimorphism observed here is reversible by testosterone and reflects an actively maintained endocrine state rather than a fixed developmental program. Complementary metabolite profiling provides a sex-stratified atlas of free modified nucleosides in tears, positioning extracellular epitranscriptomic markers as accessible indicators of hormonal context. Together, these results establish a multiscale, hormone-responsive sexual dimorphism at the ocular surface and offer a mechanistic framework linking sex and endocrine status to parameters that influence graft integration. They motivate sex-aware biomarkers, stratification by hormonal context in diagnostics and trials, and therapeutic strategies, including androgenic modulation, to mitigate the elevated rejection risk associated with sex mismatch in corneal transplantation.

physiology↗

bioRxiv2025

Loss of tRNA uridine thiolation affects mRNA translation, protein production, and sulfur-compound metabolism in Arabidopsis

The uridine at position 34 of tRNA anticodon loops is always modified at variable levels depending on environmental conditions, but a function for this highly conserved modification has not been firmly established. Using Arabidopsis thaliana, we show that the thiolation of U34 is a prerequisite for the subsequent modifications at position 32 and 37 of the tRNALys(UUU) anticodon loop, revealing a novel modification network. Surprisingly, the level of tRNALys(UUU) is strongly increased rather than reduced in the ctu1 or ctu2 mutant backgrounds that prevent these modifications. This suggests the existence of a regulatory feedback loop that drives the transcription of this specific tRNA gene family. Furthermore, we observed that the ability of the ribosome to decode AAA, GAA and CAA codons is impaired when the thiol group is lost, leading to a reduction in protein production, especially for genes enriched in these codons. Finally, we show that loss of tRNA thiolation results in variations in levels of many proteins involved in sulfur-compound metabolism and several sulfur-containing metabolites, suggesting that the level of tRNA thiolation may act as a sensor that regulates these processes.

molecular biology↗

bioRxiv2025

Integrated tear proteomics define the molecular blueprint of corneal epithelial repair

The tear film plays an essential role in corneal protection and regeneration following injury. Although the cornea is a structurally conserved organ across terrestrial vertebrates, the extent to which tear film mediated wound healing responses are evolutionarily conserved remains unclear. This study aimed to identify core and species-specific molecular pathways activated in the tear film during corneal wound healing in humans and mice. We conducted a meta analysis of tear proteomic datasets from human subjects undergoing photorefractive keratectomy (PRK) and mice subjected to mechanical corneal abrasion. Differentially expressed proteins were identified and subjected to Reactome and Gene Ontology (GO) enrichment analyses to determine conserved and divergent biological responses. Approximately one third of the tear film proteomic response to corneal injury was conserved across species. Shared upregulated pathways included complement activation, actin cytoskeletal remodeling, protein synthesis, and acute inflammatory responses. Simultaneously, pathways related to adaptive immunity, proteolysis, and general metabolism were consistently downregulated. Human specific responses were enriched in secretory pathways, vesicle trafficking, and immune surveillance, whereas murine specific responses highlighted mitochondrial activation, oxidative metabolism, and stress adaptation. These distinctions reflect species dependent physiological strategies in managing epithelial repair. Our findings reveal a conserved molecular framework that governs corneal wound healing across species, with notable species specific adaptations. This cross species comparison underscores the translational relevance of tear film analysis and supports the development of targeted therapies tailored to human specific wound healing mechanisms in ocular surface disease.

physiology↗

bioRxiv2025

Temporal analysis of tear fluid proteome reveals critical corneal repair events after photorefractive surgery

Corneal epithelial wound healing is a complex and finely orchestrated process critical for restoring visual acuity following injury or surgery. Photorefractive keratectomy (PRK), a common refractive surgical procedure, provides an ideal clinical model to study this process. Here, we employed advanced proteomic analysis to comprehensively map the dynamic changes in the tear fluid proteome at distinct phases following PRK. Our findings revealed significant alterations in nearly 45% of the tear proteome, highlighting temporally distinct molecular signatures. Immediately post-injury, a robust but controlled anti-inflammatory response coincided with pronounced upregulation of protein synthesis and cellular stress-management pathways. Subsequently, at day three, the molecular landscape shifted toward sustained epithelial regeneration, extracellular matrix remodeling, and controlled inflammation resolution. By delineating these critical and temporally compartmentalized molecular events, this study identifies novel tear-based biomarkers indicative of corneal healing efficacy and provides essential insights into potential therapeutic targets for improving clinical outcomes in corneal wound healing and ocular surface disorders.

physiology↗

bioRxiv2024

Inherited mitochondrial dysfunction triggered by OPA1 mutation impacts the sensory innervation fibre identity, functionality and regenerative potential in the cornea

Mitochondrial dysfunctions are detrimental to organ metabolism. The cornea, transparent outmost layer of the eye, is prone to environmental aggressions, such as UV light, and therefore dependent on adequate mitochondrial function. While several reports have linked corneal defects to mitochondrial dysfunction, the impact of OPA1 mutation, known to induce such dysfunction, has never been studied in this context. We used the mouse line carrying OPA1delTTAG mutation to investigate its impact on corneal biology. To our surprise, neither the tear film composition nor the corneal epithelial transcriptomic signature were altered upon OPA1 mutation. However, when analyzing the corneal innervation, we discovered an undersensitivity of the cornea upon the mutation, but an increased innervation volume at 3 months. Furthermore, the fibre identity changed with a decrease of the SP+ axons. Finally, we demonstrated that the innervation regeneration was less efficient and less functional in OPA1+/- corneas. Altogether, our study describes the resilience of the corneal epithelial biology, reflecting the mitohormesis induced by the OPA1 mutation, and the adaptation of the corneal innervation to maintain its functionality despite its morphogenesis defects. These findings will participate to a better understanding of the mitochondrial dysfunction on peripheral innervation.

pathology↗

bioRxiv2023

Modeling the simultaneous dynamics of proteins in blood plasma and the cerebrospinal fluid in human in vivo

The analysis of protein dynamics or turnover in patients has the potential to reveal altered protein recycling such as in Alzheimer disease, and to provide informative data regarding drug efficacy, or certain biological processes. The observed protein dynamics in a solid tissue or a fluid is the net result of protein synthesis and degradation, but also transport across biological compartments. We report an accurate 3-biological compartment model able simultaneously account for the protein dynamics observed in blood plasma and the cerebrospinal fluid (CSF) including a hidden central nervous system (CNS) compartment. We successfully applied this model to 69 proteins of a single individual displaying similar or very different dynamics in plasma and CSF. This study put a strong emphasis on the methods and tools needed develop this type of model. We believe it will be useful to any researcher dealing with protein dynamics data modeling.

systems biology↗

bioRxiv2023

Enabling population protein dynamics through Bayesian modeling

The knowledge of protein dynamics or turnover in patients provides invaluable information related to certain diseases, drug efficacy, or biological processes. A great corpus of experimental and computational methods has been developed, including by us, in the case of human patients followed in vivo. Moving one step further, we propose here a new modeling approach to capture the highly relevant notion of population protein dynamics. Using two data sets, we show that models inspired by population pharmacokinetics can accurately capture protein turnover within a cohort of individuals, even in presence of substantial inter-individual variability. Such models pave the way for comparative studies searching for altered dynamics or biomarkers in diseases.

systems biology↗

bioRxiv2019

In Vivo Large Scale Mapping Of Protein Turnover In The Human Cerebrospinal Fluid

The extraction of accurate physiological parameters from clinical samples provides a unique perspective to understand disease etiology and evolution, including under therapy. We introduce a new proteomics framework to map patient proteome dynamics in vivo, either proteome wide or in large targeted panels. We applied it to ventricular cerebrospinal fluid (CSF) and could determine the turnover parameters of almost 200 proteins, whereas a handful were known previously. We covered a large number of neuron biology- and immune system-related proteins including many biomarkers and drug targets. This first large data set unraveled a significant relationship between turnover and protein origin that relates to our ability to investigate the central nervous system physiology precisely in future studies. Our data constitute a reference in CSF biology as well as a repertoire of peptides for the community to design new proteome dynamics analyses. The disclosed methods apply to other fluids or tissues provided sequential sample collection can be performed.

systems biology↗