Biology subjects

Carpentier, M.

Publications and source records attributed to Carpentier, M..

10 recordsLinked to original sources

bioRxiv2026

FlavoTyper: a genome-based in-silico serotyping tool for the fish pathogen Flavobacterium psychrophilum

Flavobacterium psychrophilum is a devastating pathogen of fish reared in freshwater worldwide. Serotyping is a relevant method for epidemiological surveillance and outbreak detection, as well as for a better understanding of host-pathogen interactions. Serological diversity may also have important consequences for the selection of appropriate strains for vaccine development and for selective breeding for increased disease resistance. F. psychrophilum serotyping relies on structural variations in the O-polysaccharide (O-PS) moiety of the cell surface lipopolysaccharide (LPS). However, conventional serotyping is costly, labor-intensive and requires significant technical expertise. Moreover, divergent scheme proposals highlighted the absence of harmonization among laboratories. In this context, the development of an mPCR-based serotyping scheme targeting wzy genes greatly improved the reliability and standardization of serotyping. Nevertheless, the proposed mPCR scheme did not capture the entire diversity of genomic variability. The aim of this study was to establish a robust and publicly available tool for F. psychrophilum genome-based serotyping. Extensive genome analysis of the O-antigen biosynthesis locus allowed the identification of biomarkers enabling the development of FlavoTyper, an in-silico-based serotyping tool. The FlavoTyper tool was evaluated on all F. psychrophilum genome assemblies publicly available, providing sound and sensitive predictions and easily interpretable results. When applied to a curated collection of publicly available genomes, the in-silico O-types assigned by the tool were statistically significantly associated with host fish species, confirming previous studies (coho salmon with O:0, rainbow trout with O:1 and O:2, and ayu with O:3) and their distribution across MLST clonal complexes revealed that the O-antigen locus is frequently rearranged independently of the core-genome lineage, consistent with the extensive recombination that shapes the evolution and genomic diversity of this species.

microbiology↗

bioRxiv2026

Lung cancer-fueled emergency myelopoiesis is characterized by an increase of S100A9+ and LCN2+ hematopoietic stem and progenitor cells

The pivotal role of tumor infiltrating myeloid cells in lung cancer composition and response to therapy is universally recognized. Nevertheless, their main cradle being the bone marrow (BM), remains vastly understudied owing to the spatiotemporal complexity of hematopoiesis and its hard to access anatomical location. Therefore, the BM niche of lung cancer subjects remains understudied which is why we integrated transcriptional and translational single-cell profiling, ELISA and two-photon microscopy to characterize the medullary hematopoietic compartment in orthotopic lung cancer-bearing mice with validation in human non-small cell lung cancer (NSCLC) samples. In brief we found that lung cancer remotely alters the entire hematopoietic process resulting in higher levels of hematopoietic stem cells (HSCs), myeloid and lymphoid multipotent progenitors (MPPs) and downstream predominance of Granulocyte Monocyte Progenitors (GMP), early Granulocyte Progenitors (GP) and Common Monocyte Progenitors (cMoP) at the expense of mature neutrophils and B cells. Furthermore, a significant increase in the expression and secretion of S100A9 and Lipocalin-2 (LCN2), was characteristic across the entire hematopoietic trajectory in lung cancer-bearing mice and patients. In vivo inhibition of S100A9 with Tasquinimod reduced tumor growth, irrespective of its combination with immunotherapy. In addition, it altered the secretion profile of S100A9 but also LCN2 in the BM, suggesting that S100A9 serves as an upstream regulator of LCN2 and holds therapeutic premise to treat immunotherapy refractory lung cancer.

immunology↗

bioRxiv2025

Three biophysical constraints determine the variation of structural divergence among residues in enzyme evolution

AO_SCPLOWBSTRACTC_SCPLOWIn enzyme evolution, structural divergence varies among residues, forming residue-dependent structural divergence profiles. The evolutionary constraints that determine these profiles remain unclear. We build on the Mutation-Stability-Activity (MSA) model, a mechanistic mutation-selection model previously developed for sequence evolution. In the MSA model, mutations become fixed or are lost depending on their effects on stability and activity, with parameters aS and aA controlling selection on stability and activity, respectively. The Linearly Forced Elastic Network Model (LFENM) is used to calculate mutational effects on structure, stability, and activity. As substitutions accumulate, structural changes build up unevenly across residues, producing a structural divergence profile that depends on how each residue responds to mutation and on how strongly selection acts on stability and activity. Applied to 34 enzyme families, the MSA model recapitulates observed structural divergence profiles, and nested model comparisons show that mutation, stability, and activity constraints each contribute. However, the balance among these constraints varies widely across families: mutation always contributes substantially, but stability and activity contributions range from negligible to dominant, so any of the three can prevail in a given family. These variations have distinct origins: the mutation contribution depends on how unevenly the proteins flexibility is distributed across residues, while the stability and activity contributions depend on how strongly selection acts, as quantified by aS and aA. The MSA model thus recovers family-specific selection strengths from structural divergence profiles, suggesting these profiles encode information not only about enzyme architecture but also about the selective regime under which enzymes evolve.

biophysics↗

bioRxiv2025

Tripartite ER-Mitochondria-Lipid Droplets contact sites control adipocyte metabolic flexibility

Obesity is a major risk factor for cardiometabolic diseases, with adipocyte dysfunction playing a central role. Understanding how lipid storage and mobilization are regulated--and disrupted--in adipocytes is key to addressing obesity-associated complications. The ER-anchored protein Seipin controls lipid droplet (LD) biogenesis and maintenance, and its loss disrupts ER-LD contact sites. In humans, Seipin deficiency causes generalized lipodystrophy, a severe form of adipocyte dysfunction. We previously showed that Seipin also localizes at ER-mitochondria contact sites (MAM), where it regulates calcium exchange and mitochondrial function. Here, we examined whether Seipin targeting to MAM and ER-LD sites overlaps functionally. We analyzed subcutaneous adipose tissue (AT) from inducible Seipin-knockout mice using transmission electron microscopy (TEM) and proximity ligation assays (PLA) to quantify membrane contact sites (MCS) involving the ER, LDs, and mitochondria. In control mice, feeding reduced MAMs while increasing ER-LD and mitochondria-LD contacts, whereas Seipin deficiency abolished this remodeling. Specifically, under lipid loading, MAMs located in proximity to LDs--tripartite contact sites known as MAM-LD--were increased in control but not in Seipin-deficient adipocytes. Fluorescence recovery after photobleaching assays revealed that Seipin depletion impairs triglyceride transfer to LDs, an effect rescued by the MAM-LD-reinforcing synthetic peptide Linker-ER-Mi. Importantly, this rescue was abolished by silencing the mitochondrial calcium uniporter, demonstrating that calcium exchange is critical for triglyceride storage in LDs. We further investigated how MAM-LD remodeling influences adipocyte metabolic flexibility. Using TEM and PLA, we monitored two MAM subtypes: those forming MAM-LD and those engaging cytosolic mitochondria (MAM-CM). During adipogenesis, MAM-LD frequency increased while MAM-CM decreased. Similarly, in mouse AT and 3T3-L1 adipocytes, lipid loading selectively promoted MAM-LD. Notably, this adaptive remodeling of membrane contact sites was blunted in the adipose tissue of diet-induced obese mice. Genetic disruption of MCS in 3T3-L1 adipocytes altered lipid flux, impaired lipolysis, and reduced insulin signaling. Together, our findings identify MAM-LD contacts as key regulators of adipocyte lipid handling and metabolic flexibility, whose disruption may underlie the metabolic inflexibility of obesity.

cell biology↗

bioRxiv2025

Extracellular vesicles carrying surface-anchored adiponectin prevent obesity-related metabolic complications by enhancing insulin sensitivity

Adiponectin (Adpn) is a potent insulin-sensitizing adipokine with therapeutic promise for type 2 diabetes (T2D) and metabolic dysfunction-associated steatohepatitis (MASH). Its clinical use is limited by challenges in producing stable, bioactive high-molecular weight forms. Adipocyte-derived extracellular vesicles (EVs) naturally carry oligomeric Adpn on their surface, enhancing hormone stability and activity. Here, we engineered EVs displaying membrane-anchored Adpn (EVPP-Adpn) and control EVs lacking Adpn (EVCTL), and evaluated their metabolic effects in high fat diet (HFD)-induced obesity mice. EVPP-Adpn were purified from HEK293T cells stably transfected with a chimeric Adpn fused to a transmembrane domain and a pilot peptide (PP) directing it to EVs; EVCTL were produced from non-transfected cells. HFD-fed male and female mice received intraperitoneal EV injections for six weeks. EVPP-Adpn improved glucose tolerance and insulin sensitivity, promoted adipocyte lipid storage through insulin-regulated lipogenesis and alleviated MASH features (liver steatosis, inflammation and fibrosis). EVPP-Adpn lowered circulating ceramides and reduced FGF21, indicating improved hepatic metabolism, and activated AKT and AMPK pathways in liver and skeletal muscle, consistent with increased adiponectin signaling. These results demonstrate that surface-anchored Adpn EVs restore tissue-specific insulin signaling and improve obesity-related metabolic dysfunctions, highlighting their potential as a novel biotherapeutic strategy for T2D and MASH.

bioengineering↗

bioRxiv2024

On the variation of structural divergence among residues in enzyme evolution

AO_SCPLOWBSTRACTC_SCPLOWStructural divergence varies among protein residues, yet this variation has been largely overlooked compared with the well-studied case of sequence rate variation. Here we show that, in families of functionally conserved homologous enzymes, structural divergence increases with both residue flexibility and distance from the active site. Although these properties are correlated, modelling reveals that the pattern arises from two independent types of evolutionary constraints: non-functional and functional. The balance between these constraints varies widely across enzyme families, from non-functional to functional dominance. As functional constraints strengthen, structural divergence patterns are reshaped, becoming increasingly distinct from flexibility patterns and breaking the commonly assumed correspondence between evolutionary and dynamical structural ensembles. Active sites are more structurally conserved than average, but this conservation stems not only from functional constraints. Because active sites typically lie in rigid regions where non-functional constraints are high, both constraint types contribute comparably on average, with dominance shifting from one to the other depending on active-site rigidity. Together, these findings revise two long-standing assumptions: that evolutionary structural variation universally mirrors protein dynamics, and that active-site conservation reflects functional requirements alone. Both depend on the balance between non-functional and functional constraints that shape enzyme structural evolution.

evolutionary biology↗

bioRxiv2024

Steric Repulsion Counteracts ER-to-Lipid Droplet Protein Movement

Lipid droplets (LDs) are uniquely shaped organelles consisting of a neutral lipid core surrounded by a phospholipid monolayer, continuous with the cytosolic leaflet of the endoplasmic reticulum (ER). The dynamics and function of LDs are closely tied to their proteome composition, which is subject to dynamic remodeling. Key proteins essential for LD biology relocate from the ER to LDs, yet the mechanisms governing their movement and accumulation in LDs remain poorly understood. Here, we developed an innovative ex vivo tool to quantify and classify ER proteins based on their affinity for LDs. We found a broad spectrum of ER-to-LD partitioning affinities. We identified steric hindrance as a key factor in regulating ER-to-LD protein transfer, where proteins with only slightly higher LD affinity can effectively displace those with lower affinity from the LD surface. Consistent with this model, we observed that differentiation of 3T3 pre-adipocytes into adipocytes involves extensive remodeling of ER proteins targeting LDs, with Plin1--a high-affinity LD protein--becoming predominantly recruited and excluding other ER proteins. These findings highlight lateral protein-protein exclusion as a fundamental mechanism in shaping the LD proteome, providing new insights into LD biogenesis and function.

biophysics↗

bioRxiv2024

Seipin Regulates Caveolin-1 Trafficking and Organelle Crosstalk

Caveolin-1 (CAV1), the main structural component of caveolae, is essential in various biological processes, including mechanotransduction, lipid metabolism, and endocytosis1-4. Deregulation of CAV1 dynamics is linked to various pathologies, including cellular senescence, cancer, insulin resistance, and lipodystrophy5-9. However, mechanisms regulating CAV1 trafficking and function remain poorly understood. Here, we show that seipin, a crucial lipid droplet (LD) biogenesis factor10, modulates CAV1 trafficking. Deletion of seipin resulted in the accumulation of saturated lipids, leading to ceramide and sphingomyelin overproduction, which disrupted the membrane order of the trans-Golgi network (TGN). In seipin deficiency, CAV1 location to the plasma membrane (PM) was impaired, reducing caveolae. Instead, CAV1 accumulated in TGN and late endosome compartments, which fused with LDs and delivered the protein. In wild-type (WT) cells, this process was minimal but significantly enhanced by treatment with palmitate, ceramide, or Stearoyl-CoA desaturase-1 (SCD1) inhibition. Conversely, in seipin-deficient cells, inhibiting Fatty Acid Synthase (FASN) or overexpressing SCD1 restored CAV1 localization to the PM and reduced its accumulation in LDs. Our findings reveal that seipin controls the funneling of palmitate toward glycerolipids synthesis and storage in LDs versus conversion to ceramides in the ER. This balance is crucial to cellular protein trafficking by controlling the TGN membrane order. Therefore, our study identifies seipin as a critical regulator of cellular lipid metabolism, protein trafficking, and organelle homeostasis. These findings shed light on the processes regulating CAV1 trafficking and show that convergent pathophysiological mechanisms associated with defects in CAV1 and seipin contribute to metabolic disorders, including insulin resistance and lipodystrophies11-14.

cell biology↗

bioRxiv2022

Triglyceride lipolysis driven by glucose restriction triggers liquid-crystalline phase transitions and proteome remodeling of lipid droplets

Lipid droplets (LDs) are reservoirs for triglycerides (TGs) and sterol-esters (SEs), but how these lipids are organized within LDs and influence its proteome remains unclear. Using in situ cryoelectron tomography, we show that glucose restriction triggers lipid phase transitions within LDs generating liquid-crystalline lattices inside them. Mechanistically this requires TG lipolysis, which decreases the LD TG:SE ratio, promoting SE transition to a liquid-crystalline phase. Molecular dynamics simulations reveal TG depletion promotes spontaneous TG and SE de-mixing in LDs, additionally altering the lipid packing of the phospholipid monolayer surface. Fluorescence imaging and proteomics further reveal that liquid-crystalline phases are associated with selective remodeling of the LD proteome. Some canonical LD proteins including Erg6 re-localize to the ER network, whereas others remain LD-associated. Model peptide LiveDrop also redistributes from LDs to the ER, suggesting liquid-crystalline-phases influence ER-LD inter organelle transport. Our data suggests glucose restriction drives TG mobilization, which alters the phase properties of LD lipids and selectively remodels the LD proteome.

cell biology↗

bioRxiv2018

Protein Multiple Alignments: Sequence-based vs Structure-based Programs

Facing the huge increase of information about proteins, classification has reached the level of a compulsory task, essential for assigning a function to a given sequence, by means of comparison to existing data. Multiple sequence alignment programs have been proven to be very useful and they have already been evaluated. In this paper we wished to evaluate the added value provided by taking into account structures. We compared the multiple alignments resulting from 24 programs, either based on sequence, structure, or both, to reference alignments deposited in five databases. Reference databases, on their side, can be split in two: more automatic ones, and more manually ones. Scores have been attributed to each program. As a global rule of thumb, five groups of methods emerge, with the lead to two of the structure-based programs. This advantage is increased at low levels of sequence identity among aligned proteins, or for residues in regular secondary structures or buried. Concerning gap management, sequence-based programs place less gaps than structure-based programs. Concerning the databases, the alignments from the manually built databases are the more challenging for the programs.

bioinformatics↗