Biology subjects

Gregoire, S.

Publications and source records attributed to Gregoire, S..

12 recordsLinked to original sources

bioRxiv2026

Micro-elastography of biopsies

Micro-elastography is an optical technique that studies elastic waves for the mechanical characterisation of micrometric objects, such as cells. We propose to adapt this technique for the characterisation of millimetre-sized samples using a white light microscope. The objective is to perform a rapid, global characterisation of the elasticity of a biopsy. The millimetre-sized samples to be characterized are embedded in an agarose gel. A vibrator generates shear waves in this gel that transmit naturally inside the sample. This technique removes the need for precise manipulation of the wave source. A high-speed camera records the propagation of the waves in the sample. Their velocity is calculated using a noise correlation approach. Due to the lack of millimetric phantoms of calibrated elasticity, we choose to validate this method with a three step process. The experimental setup is first validated on homogeneous gels, then on biological samples of increasing elasticity, biopsies of beef liver hardened by heating, and finally on biological samples of clinical interest: biopsies of mouse endometrium. This method can be applied to all types of biological tissue, paving the way for rapid mechanical characterization of biopsies.

biophysics↗

bioRxiv2025

Contactless micro-elastography of single cells using oscillating microbubbles as shear wave sources

The mechanical properties of cells play key roles in their physiology, function, physiological and pathological transformations. Micro-elastography has recently emerged as a promising tool to estimate cellular viscoelastic properties within a millisecond, without the need for mechanical modeling. Here, we report a fully contactless approach to single-cell micro-elastography, using acoustically oscillating gas microbubbles positioned near individual cells (20 {micro}m diameter megakaryocytes) as localized shear wave sources. Using this approach, we successfully performed micro-elastography on cells up to five times smaller than those studied in previous works, establishing the smallest single-cell elastography measurements to date. Spherical or non-spherical bubble oscillations generated 15 kHz elastic waves, which we detected using a high-speed camera coupled to a standard bright-field microscope. Noise correlation elastography enabled the measurement of average and local shear-wave velocities within single cells. Our results demonstrate that this method is robust and reproducible across multiple cells from the same cell line, paving the way for real-time, label-free mechanical monitoring of single cells during fast biological processes. Significance StatementCell mechanics are central to processes such as differentiation, migration, and disease progression, but current imaging tools are often slow or limited to unusually large cells. By harnessing acoustically oscillating microbubbles as localized wave sources, we achieve contactless micro-elastography of cells five times smaller than previously possible, with acquisition times under one millisecond. This advance enables real-time, label-free monitoring of fast biological processes in diverse cell types, offering powerful opportunities for cell biology, mechanopathology, and drug discovery.

biophysics↗

bioRxiv2025

Prenatal maternal stress is associated with increased sensitivity to neuropathic pain and sex-specific epigenetic and transcriptomic dynamics in the prefrontal cortex

Prenatal maternal stress (PNS) is a common early-life adversity. PNS has been linked to greater vulnerability to chronic pain in the offspring. PNS results in increased hypersensitivity after Chronic Constriction Injury (CCI) of the sciatic nerve, a common rodent model for chronic neuropathic pain. These behavioral effects are accompanied by altered levels of enzymes that regulate DNA methylation in the frontal cortex. DNA methylation, the addition of a methyl group onto cytosine bases of cytosine-guanine (CpG) sites in the genome, is an epigenetic mechanism by which life experiences can reprogram gene expression. The goal of this study was to identify differentially methylated regions that might contribute to the increased pain sensitivity following nerve injury in adulthood. Prior studies indicate widespread, sex-specific transcriptomic changes and numerous differentially methylated regions (DMRs) in the frontal cortex following PNS and nerve injury. Here we performed genome wide DNA methylation and transcriptome-wide RNAseq analysis in the frontal cortex of male and female mice that underwent PNS, CCI or both. Our analysis revealed sex-dependent changes in DNA methylation and mRNA expression, including in pathways related to neuronal and brain development, axonogenesis and synaptic regulation. The effect of DNA methylation on mRNA expression was tested in a subset of target genes. These studies suggest a role for DNA methylation in embedding increased risk for chronic pain in adulthood associated with early-life adversity.

neuroscience↗

bioRxiv2025

Regulation of lipid metabolism is a primordial function of STING

The stimulator of interferon genes (STING) is a pivotal regulator of type I interferon (IFN) responses. Although the IFN system is confined to vertebrates, STING is present across metazoans and in some unicellular eukaryotes, suggesting involvement in distinct functions prior to vertebrate divergence. We here explored the conservation of STING-mediated regulation of polyunsaturated fatty acid (PUFA) metabolism. We found that tested STING homologs from vertebrates, invertebrates, and unicellular eukaryotes interacted with the fatty acid desaturase 2 (FADS2) rate-limiting enzyme in PUFA metabolism and subsequent functional outputs. The ability to regulate lipid metabolism did not correlate with antiviral activity, suggesting that the cooptation of this metabolic pathway by the IFN-based immune system is independent of STING-associated immune responses. Thus, STING-mediated metabolic regulation is an evolutionarily conserved feature and a primordial STING function.

immunology↗

bioRxiv2025

Maternal n-3 PUFA deficiency alters brain fatty acid and oxylipin profiles across perinatal development in offspring

Long-chain polyunsaturated fatty acids (LC-PUFAs), particularly arachidonic acid (AA, 20:4n-6) and docosahexaenoic acid (DHA, 22:6n-3), are essential for optimal neurodevelopment through their effect on neuronal proliferation, neurite outgrowth and synaptogenesis. Emerging evidence highlights that brain PUFAs are metabolized in oxylipins, the bioactive oxidized PUFA metabolites known to regulate inflammatory processes. Recent data highlighted that both PUFA and oxylipin profiles are modulated in the adult male brain by dietary PUFA content. However, little is known on the impact of maternal dietary n-3 PUFA intake during the perinatal period and the neurodevelopmental profile of brain fatty acids and associated oxylipins in offspring, and whether these effects differ between sexes. To address this question, we first measured fatty acid levels in the placenta and embryonic brain of male and female offspring of mothers fed a sufficient or deficient diet in n-3 PUFAs at embryonic day (E)17.5. Then, fatty acids and oxylipins were measured at different post-natal stages, in the brain at P0 and P7, and in the hippocampus at P14 and P21, in both male and female offspring. Our results show that maternal n-3 PUFA dietary deficiency alters fatty acid profiles as early as E17.5 in both the placenta and the brain. Furthermore, dietary intervention affects both fatty acid and oxylipin profiles throughout postnatal brain development, with notable sex-specific differences. These findings underscore the critical importance of adequate maternal n-3 PUFA intake during the perinatal period for maintaining an optimal PUFA and oxylipin profiles, with potential implications for fetal and postnatal brain development.

neuroscience↗

bioRxiv2025

High-resolution HIV-1 m6A epitranscriptome reveals splicing-dependent methylation clusters and unique 2-LTR transcript modifications

The N6-methyladenosine (m6A) modification of HIV-1 has been widely studied but the number and precise positions of the m6A sites remain unclear due to the lack of precision of detection methods. Using the latest Nanopore chemistry and direct m6A base-calling, we identified 18 m6A: 14 at the 3 end and 4 in central regions of the genome. Our data reveal differential methylation of these positions between splicing isoforms. Eleven of these sites are clustered in two short segments with peak-shaped methylation profiles. Single-molecule analysis revealed that a very small number of transcripts were unmethylated in both clusters. We also identified a [~]732 nt RNA species resulting from the transcription of non-integrated viral DNA circles closed by two long terminal repeats. These transcripts started in the first LTR, terminated at the polyA site of the second LTR and harbored six m6A sites. Five of these sites were present in other transcripts and, remarkably, had the highest methylation rates. The sixth site was methylated only in this transcript, suggesting a role for this RNA in HIV-1 infection. These findings reveal a new landscape of HIV m6A transcriptome modifications and pave the way for studies deciphering their role in the viral life cycle.

bioinformatics↗

bioRxiv2024

Unveiling novel conserved HIV-1 open reading frames encoding T cell antigens using ribosome profiling.

The development of ribosomal profiling (Riboseq) revealed the immense coding capacity of human and viral genomes. Here, we used Riboseq to delineate the first translatome of HIV-1 in infected CD4+ T cells. In addition to canonical viral protein coding sequences (CDSs), we identify 98 alternative open reading frames (ARFs), corresponding to small Open Reading Frames (sORFs) that are distributed across the HIV genome including the UTR regions. Using a database of HIV genomes, we observed that most ARF amino-acid sequences are likely conserved among clade B and C of HIV-1, with 8 ARF-encoded amino-acid sequences being more conserved than the overlapping CDSs. Using T cell-based assays and mass spectrometry-based immunopeptidomics, we demonstrate that ARFs encode viral polypeptides. In the blood of HIV-infected individuals, ARF-derived peptides elicit potent poly-functional T cell responses mediated by both CD4+ and CD8+ T cells. Our discovery expands the list of conserved viral polypeptides that are targets for vaccination strategies and might reveal the existence of viral microproteins or pseudogenes.

immunology↗

bioRxiv2022

High sensitivity limited material proteomics empowered by data-independent acquisition on linear ion traps

In recent years, the concept of cell heterogeneity in biology has gained increasing attention, concomitant with a push towards technologies capable of resolving such biological complexity at the molecular level. For single-cell proteomics using Mass Spectrometry (scMS) and low-input proteomics experiments, the sensitivity of an orbitrap mass analyzer can sometimes be limiting. Therefore, low-input proteomics and scMS could benefit from linear ion traps, which provide faster scanning speeds and higher sensitivity than an orbitrap mass analyzer, however at the cost of resolution. We optimized an acquisition method that combines the orbitrap and linear ion trap, as implemented on a tribrid instrument, while taking advantage of the high-field asymmetric waveform ion mobility spectrometry (FAIMS) pro interface, with a prime focus on low-input applications. First, we compared the performance of orbitrap-versus linear ion trap mass analyzers. Subsequently, we optimized critical method parameters for low-input measurement by data-independent acquisition (DIA) on the linear ion trap mass analyzer. We conclude that linear ion traps mass analyzers combined with FAIMS and Whisper flow chromatography are well-tailored for low-input proteomics experiments, and can simultaneously increase the throughput and sensitivity of large-scale proteomics experiments where limited material is available, such as clinical samples and cellular sub-populations.

systems biology↗

bioRxiv2022

Impact of membrane lipid polyunsaturation on dopamine D2 receptor ligand binding and signaling

The heterogenous and dynamic constitution of the membrane fine-tunes signal transduction. In particular, the polyunsaturated fatty acid (PUFA) tails of phospholipids influence the biophysical properties of the membrane, production of second messengers, or membrane partitioning. Few evidence mostly originating from studies of rhodopsin suggest that PUFAs directly modulate the conformational dynamic of transmembrane proteins. However, whether such properties translate to other G protein-coupled receptors remains unclear. We focused on the dopamine D2 receptor (D2R), a main target of antipsychotics. Membrane enrichment in n-3, but not n-6, PUFAs potentiates ligand binding. Molecular dynamics simulations show that the D2R preferentially interacts with n-3 over n-6 PUFAs. Furthermore, even though this mildly affects signalling in heterologous systems, in vivo n-3 PUFA deficiency blunts the effects of D2R ligands. These results suggest that n-3 PUFAs act as allosteric modulators of the D2R and provide a putative mechanism for their potentiating effect on antipsychotic efficacy.

cell biology↗

bioRxiv2021

The Autophagy Receptor TAX1BP1 (T6BP) is a novel player in antigen presentation by MHC-II molecules.

CD4+ T lymphocytes play a major role in the establishment and maintenance of immunity. They are activated by antigenic peptides derived from extracellular or newly synthesized (endogenous) proteins presented on the surface of antigen presenting cells (APCs) by the MHC-II molecules. The pathways leading to endogenous MHC-II presentation remain poorly characterized. We demonstrate here that the autophagy receptor, T6BP, influences both autophagy-dependent and -independent endogenous presentation of HIV- and HCMV-derived peptides. By studying the immunopeptidome of MHC-II molecules, we show that T6BP affects both the quantity and quality of peptides presented. T6BP silencing induces the mislocalization of the MHC-II-loading compartments and a rapid degradation of the invariant chain (CD74) without altering the expression and internalization kinetics of MHC-II molecules. We determined the interactome of T6BP, identified calnexin as a T6BP partner and show that CANX cytosolic tail is required for this interaction. Remarkably, calnexin silencing replicates the functional consequences of T6BP silencing: decreased CD4+ T cell activation and exacerbated CD74 degradation. Altogether, we unravel T6BP as a key player of the MHC-II-restricted endogenous presentation pathway and we propose one potential mechanism of action.

immunology↗

bioRxiv2020

The Transition from Acute to Chronic Pain: Dynamic Epigenetic Reprogramming of the Mouse Prefrontal Cortex up to One Year Following Nerve Injury

Chronic pain is associated with persistent structural and functional changes throughout the neuroaxis, including in the prefrontal cortex (PFC). The PFC is important in the integration of sensory, cognitive and emotional information and in conditioned pain modulation. We previously reported wide-spread epigenetic reprogramming in the PFC many months following nerve injury in rodents. Epigenetic modifications, including DNA methylation, can drive changes in gene expression without modifying DNA sequences. To date, little is known about epigenetic dysregulation at the onset of acute pain or how it progresses as pain transitions from acute to chronic. We hypothesize that acute pain following injury results in rapid and persistent epigenetic remodelling in the PFC that evolves as pain becomes chronic. We further propose that understanding epigenetic remodelling will provide insights into the mechanisms driving pain-related changes in the brain. Epigenome-wide analysis was performed in the mouse PFC 1 day, 2 weeks, 6 months, and 1 year following peripheral injury using the spared nerve injury (SNI) in mice. SNI resulted in rapid and persistent changes in DNA methylation, with robust differential methylation observed between SNI and sham-operated control mice at all time points. Hundreds of differentially methylated genes were identified, including many with known function in pain. Pathway analysis revealed enrichment in genes related to stimulus response at early time points, immune function at later time points and actin and cytoskeletal regulation throughout the time course. Increased attention to pain chronicity as a factor is recommended for both pain research and management.

neuroscience↗

bioRxiv2019

Essential omega-3 fatty acids tune microglial phagocytosis of synaptic elements in the developing brain

Omega-3 fatty acids (n-3 polyunsaturated fatty acids; n-3 PUFAs) are essential for the functional maturation of the brain. Westernization of dietary habits in both developed and developing countries is accompanied by a progressive reduction in dietary intake of n-3 PUFAs. Low maternal intake of n-3 PUFAs has been linked to neurodevelopmental diseases in epidemiological studies, but the mechanisms by which a n-3 PUFA dietary imbalance affects CNS development are poorly understood. Active microglial engulfment of synaptic elements is an important process for normal brain development and altered synapse refinement is a hallmark of several neurodevelopmental disorders. Here, we identify a molecular mechanism for detrimental effects of low maternal n-3 PUFA intake on hippocampal development. Our results show that maternal dietary n-3 PUFA deficiency increases microglial phagocytosis of synaptic elements in the developing hippocampus, through the activation of 12/15- lipoxygenase (LOX)/12-HETE signaling, which alters neuronal morphology and affects cognition in the postnatal offspring. While women of child bearing age are at higher risk of dietary n-3 PUFA deficiency, these findings provide new insights into the mechanisms linking maternal nutrition to neurodevelopmental disorders.\n\nOne Sentence SummaryLow maternal omega-3 fatty acids intake impairs microglia-mediated synaptic refinement via 12-HETE pathway in the developing brain.

neuroscience↗