Biology subjects

Debayle, D.

Publications and source records attributed to Debayle, D..

16 recordsLinked to original sources

bioRxiv2026

Sfh3 is a sterol-modulated PI/PI4P transfer protein that confers azole resistance in yeast by specifically mediating lanosterol/PI exchange

Lipid transfer proteins precisely distribute lipids within eukaryotic cells, supporting functions such as vesicular trafficking and cellular signaling. Here, we analyzed whether Sfh3 (Sec14 homolog 3) functions as a sterol/phosphatidylinositol (PI) exchanger to clarify its role in neutral lipid mobilization from lipid droplets and in azole resistance in yeast. Using real-time assays, we found that its ergosterol transfer capacity is not activated by PI and is inhibited by ergosterol biosynthesis intermediates, such as lanosterol. Next, we found that Sfh3 exhibits both PI and PI4P transfer activities, which sterols can modulate. Through kinetic, structure-function, and thermal stability analyses, we identified remarkable Sfh3 mutants and ranked Sfh3's relative affinity for its lipid ligands. This allowed us to show that Sfh3 performs selective lanosterol/PI exchange, provided it recognizes PI, in the presence of ergosterol, and that this activity is necessary for yeast resistance to miconazole. Collectively, our data show that Sfh3 is a sterol-regulated PI/PI4P transfer protein, potentially linking sterol metabolism and PI4P signaling during lipid droplet utilization. In azole-treated yeast, elevated lanosterol levels may shift Sfh3 into an exclusive PI/lanosterol exchange mode, promoting cellular detoxification and conferring drug resistance. By revealing unanticipated Sfh-mediated lipid transfer mechanisms, our study provides new insights into the Sec14 family.

biochemistry↗

bioRxiv2026

Deletion of Ferritin Heavy Chain Limits Tumor Growth and Promotes Iron-Dependent Stress in Medulloblastoma

Iron is essential for tumor proliferation and metabolic adaptation but becomes cytotoxic when unbuffered, creating a potential metabolic vulnerability. Ferritin, a conserved iron-storage complex, limits labile iron and establishes the upper threshold of iron tolerance in cancer cells. Here, we report the first ferritin heavy chain (FTH) knockout in a brain tumor model system. Although FTH loss was tolerated under basal conditions through adaptive remodeling of iron metabolism, it exposed profound vulnerabilities under iron stress. FTH deficiency lowered the threshold for iron toxicity, sensitizing medulloblastoma (MB) cells to both canonical ferroptosis and a mechanistically distinct iron-dependent cell death pathway. Oxidative iron stress impaired tumor growth and prolonged survival in orthotopic xenografts, whereas vitamin C-induced iron reduction triggered a selective, iron-dependent, but non-ferroptotic elimination of MB-like cells in tumor organoids. Notably, sensitivity to iron toxicity correlated strongly with cellular phenotype, with mesenchymal-like cells displaying greater susceptibility than epithelial-like counterparts. Collectively, these findings identify ferritin as a central regulator of iron tolerance in MB and establish iron toxicity, not via iron deprivation, as a therapeutically exploitable vulnerability. More broadly, this work provides a mechanistic framework for targeting iron metabolism through modulation of ferritin-dependent iron buffering and iron redox homeostasis in cancers. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=170 SRC="FIGDIR/small/739635v1_ufig1.gif" ALT="Figure 1000"> View larger version (53K): org.highwire.dtl.DTLVardef@1c499a4org.highwire.dtl.DTLVardef@431c70org.highwire.dtl.DTLVardef@2b5borg.highwire.dtl.DTLVardef@11e9ac1_HPS_FORMAT_FIGEXP M_FIG C_FIG

cancer biology↗

bioRxiv2026

Ether lipid remodeling during neuronal differentiation prevents ferroptosis

Ferroptosis is a form of cell death driven by iron-dependent lipid peroxidation, with specific lipid species playing key roles in modulating susceptibility. Among these, ether lipids have shown conflicting effects, being linked to both protection and sensitization. Here, we dissect the relationship between lipid structure and ferroptosis sensitivity and explain how ether lipids exert context-dependent effects. Ether lipids can promote ferroptosis through a metabolic bias towards the accumulation of polyunsaturated acyl chains and ethanolamine head groups, whereas this pro-ferroptotic tendency is counterbalanced by the anti-ferroptotic vinyl ether moiety introduced by plasmanylethanolamine desaturase 1. We show that this protective effect is critical for preventing ferroptosis in hiPSC-derived neurons, which accumulate otherwise pro-ferroptotic ether lipids during differentiation. This effect is not solely due to its antioxidant properties but also stems from the reprogramming of mitochondrial respiration. The lack of vinyl ether bonds leads to multiple mitochondrial defects, including increased mitochondrial reactive oxygen species (ROS), lower membrane potential, and abnormal cristae structures. These findings indicate that vinyl ether bonds in ether lipids offer dual ferroptosis resistance by scavenging ROS and minimizing its production at the mitochondrial level. The disruption of this system in Caenorhabditis elegans leads to iron-induced death and impaired motility. Thus, our study reveals ether lipid structural remodeling as a key regulator of ferroptosis sensitivity in neurons.

cell biology↗

bioRxiv2025

Chain length defines the spatial segregation and metabolic fate of fatty acids in adipocytes

Adipocytes primarily store fatty acids (FAs) as triacylglycerols (TGs) within lipid droplets, releasing them through lipolysis to meet systemic energy demands. While the metabolism of long-chain fatty acids (LCFAs) in adipocytes has been extensively characterized, it remains ill-defined how adipocytes utilize fatty acids depending on chain length and structure. Our work demonstrates that short- and medium-chain fatty acids (SMCFAs) are esterified into TGs within lipid droplets, rather than being incorporated into other FA-containing lipid species. During lipolytic activation, TGs enriched in SMCFAs are hydrolysed more rapidly than those containing LCFAs. This accelerated mobilization is facilitated by the preferential localization of SMCFA-containing TGs at the lipid droplet surface, which enhances accessibility to adipose triglyceride lipase. Unlike LCFAs, which are efficiently released for utilization by peripheral tissues, SMCFAs are predominantly oxidized within adipocytes. These findings reveal a unique metabolic routing of SMCFAs, indicating their preferential intracellular oxidation to support adipocyte energy requirements.

biochemistry↗

bioRxiv2025

Human mammary 3D spheroid models uncover the role of filopodia in breaching the basement membrane to facilitate invasion

Basement membranes (BM) are thin, nanoporous sheets of specialized extracellular matrix (ECM) that line epithelial tissues. They are dynamic structures that serve multiple key functions, as evidenced by numerous diseases, including cancer progression, that are associated with their alterations. Our understanding of the BM and its communication with adjoining epithelial cells remains highly fragmented due to the BMs complex molecular architecture, the lack of molecular tools, limitations in utilizing high-resolution imaging techniques to BMs assembled on tissues, and the difficulty of assessing their functional contributions in vivo. Here, by combining multiple -omics analyses and advanced microscopy methodologies, we characterized the BM from two normal human mammary epithelial cell lines, MCF10 and HMLE, grown as spheroids in 3D matrices. Our findings indicate that the spheroids autonomously assemble a BM exhibiting all the molecular, structural, and biophysical characteristics of physiological BM. Using these minimalist model systems, we show for the first time that the laminins, perlecan, and the hemidesmosomes are all arranged along a shared porous lattice defined by the collagen IV molecular network. Next, we demonstrate that the invasion-promoting PSD4/EFA6B knockout, found in patients with breast cancer, decreases the expression of BM components and their assembly on the spheroid surface. We then show that invasive spheroids develop enlarged pores in the BM via filopodia-like plasma membrane extensions, which further expand in a protease-dependent manner, thereby facilitating the passage of invasive cells. Significance StatementThe basement membrane (BM) directs epithelial tissue architecture and behavior. How tumor cells breach this barrier during invasion remains poorly understood. Using minimalist 3D spheroid models mimicking physiological BM assembly, we reveal a novel infiltration mechanism. Filopodia-like protrusions perforate and widen BM pores. This facilitates cell dissemination through sequential protease-independent and -dependent steps.

cell biology↗

bioRxiv2025

Large extracellular vesicles containing mitochondria (EVMs) derived from Alzheimer disease cells harbor pathologic functional and molecular profiles and spread mitochondrial dysfunctions

In addition to small extracellular vesicles known as exosomes, cells release large extracellular vesicles containing mitochondria (EVMs). However, the molecular and functional characteristics of EVMs, as well as the impact of EVM secretion on the spreading of mitochondrial dysfunction between cells, remain unknown in the context of Alzheimers Disease (AD). Here, we provide an ultrastructural, biochemical, and functional characterization of EVMs isolated from cells expressing the amyloid precursor protein (APP) with the familial Swedish mutation (APPswe). We identified differential proteomic and lipidomic signatures in APPswe-derived EVMs compared to control EVMs and revealed a specific proteomic profile in EVMs isolated from conditioned media of fibroblasts from AD patients at the prodromal stage of the disease. Our findings show that APP-C terminal fragments (APP-CTFs) pathogenic accumulation in cells potentiates EVM secretion through the budding of the plasma membrane. We lastly demonstrated that APP-CTFs loaded EVMs are active carriers of dysfunctional mitochondria that transfer mitochondrial pathology to naive control recipient cells.

neuroscience↗

bioRxiv2024

Acyltransferases in the first step of glycerophospholipid synthesis have redundant and non-redundant roles in sn-1 acyl chain regulation, ether lipid levels, and cell survival

The increased use of lipidomics analyses in biomedical research made it crucial to understand correctly how lipid compositions are regulated. Lipid acyl chains are important regulators of membrane physicochemical properties, and are incorporated by various acyltransferases. The acyltransferases implicated in the first step of glycerophospholipid synthesis, the GPATs and GNPAT, have distinct localizations and substrate preferences. This suggests that they have distinct roles on lipid regulation, but a complete understanding of their redundant and non-redundant functions is missing. We report here a comprehensive analysis of cells having mutations in GPATs and GNPAT, either alone or in combinations. Our results suggest that the balance between GPATs and GNPAT affect the levels of ether lipids, together with glycerophospholipid acyl chain length and unsaturation. In addition, we found that lipid synthesis initiated at peroxisomes, but not mitochondria, is sufficient to provide the lipid synthesis flux required for normal cell growth. Our study unveils the multifaceted roles of the first step of de novo glycerophospholipid synthesis, thus leading to a better understanding of how lipidomes are shaped.

cell biology↗

bioRxiv2023

FAO-supported OxPhos leukemic stem cells are sensitive to cold.

Targeting mitochondrial oxidative phosphorylation (OxPhos) metabolism has revealed a potential weakness for leukemic stem cells (LSCs) that can be exploited for therapeutic purposes. Fatty acids oxidation (FAO) is a crucial OxPhos-fueling catabolic pathway for some AML and for chemotherapy-resistant AML cells. Here, we identified cold sensitivity at 4{degrees}C (cold killing challenge: CKC4), as a novel vulnerability that selectively kills FAO-supported OxPhos LSCs in Acute Myeloid Leukemia while sparing normal hematopoietic stem cells (HSCs). Cell death of OxPhos leukemic cells was induced by membrane permeabilization at 4{degrees}C while by sharp contrast, leukemic cells relying on glycolysis were resistant. Forcing glycolytic cells into OxPhos metabolism sensitized them to CKC4. We show using lipidomic and proteomic analyzes that OxPhos shapes the composition of the plasma membrane and introduce variation of 22 lipid subfamilies between cold-sensitive and cold-resistant cells. Cold sensitivity is a potential OxPhos biomarker. SignificanceThis study reveals that mitochondrial energetics fueled by FAO metabolism introduces membrane fragility upon cold exposure in OxPhos-driven AMLs and in LSCs. This novel physical property of Leukemic cells and LSCs opens new avenues for biomarker and diagnostics as well as for anti-OxPhos drug screening and LSCs targeting. One Sentence SummaryOxPhos leukemic cells die at 4{degrees}C

cancer biology↗

bioRxiv2023

Multiomics study of CHCHD10S59L-related disease reveals energy metabolism downregulation: OXPHOS and beta-oxidation deficiencies associated with lipids alterations

Mutations in the coiled-coil-helix-coiled-coil-helix domain containing 10 (CHCHD10) gene have been associated with a large clinical spectrum including myopathy, cardiomyopathy and amyotrophic lateral sclerosis (ALS). Herein, we analyzed the metabolic changes induced by the p.S59L CHCHD10 mutation to identify new therapeutic opportunities. Using metabolomic, lipidomic and proteomic analysis we observed a strong alteration of metabolism in plasma and heart of Chchd10S59L/+ mice compared to their wild type littermates at pre-symptomatic and symptomatic stages. In plasma, levels of phospholipids were decreased while those of carnitine derivatives and most of amino acids were increased. The cardiac tissue from Chchd10S59L/+ mice showed a decreased Oxidative Phosphorylation (OXPHOS) and {beta}-oxidation proteins levels as well as tricarboxylic acid cycle (TCA) intermediates and carnitine pathway metabolism. In parallel, lipidomics analysis reveals a drastic change in the lipidome, including triglycerides, cardiolipin and phospholipids. Consistent with this energetic deficiency in cardiac tissue, we show that L-acetylcarnitine supplementation improves the mitochondrial network length in IPS-derived cardiomyocytes from a patient carrying the CHCHD10S59L/+ mutation. These data indicate that a bioenergetic intermediate such as L-acetylcarnitine may restore mitochondrial function in CHCHD10-related disease, due to the reduction in energy deficit that could be compensated by carnitine metabolic pathways.

cell biology↗

bioRxiv2022

VAP-A intrinsically disordered regions enable versatile tethering at membrane contact sites

Membrane contact sites (MCSs) between organelles are heterogeneous in shape, composition and dynamics. Despite this diversity, VAP proteins act as receptors for multiple FFAT motif-containing proteins and drive the formation of most MCSs involving the endoplasmic reticulum (ER). Although the VAP-FFAT interaction is well characterized, no model explains how VAP adapts to its partners in various MCSs. We report here that VAP-A localization to different MCSs depends on its intrinsically disordered regions (IDRs). We show that VAP-A interaction with PTPIP51 and VPS13A at ER-mitochondria MCS conditions mitochondria fusion by promoting lipid transfer and cardiolipin buildup. VAP-A also enables lipid exchange at ER-Golgi MCS by interacting with OSBP and CERT. However, removing IDRs from VAP-A restricts its distribution and function to ER- mitochondria MCS, at the expense of ER-Golgi MCS. Our data suggest that IDRs of VAP-A do not modulate its preference towards specific partners, but adjust its geometry to the constraints linked to different MCS organization and lifetime. Thus, VAP-A conformational flexibility mediated by its IDRs ensures membrane tethering plasticity and efficiency.

cell biology↗

bioRxiv2021

OSBP-mediated cholesterol transfer determines epithelial polarity and associated cargo secretion

Golgi lipid environment regulates sorting and cargo secretion. However, the mechanisms that spatiotemporally control the lipid composition of the secretory membranes to drive cargo trafficking are poorly understood. Lipid transfer proteins regulate the concentration of specific lipids at membrane contact sites. We hypothesised that by catalysing cholesterol/PI(4)P exchange at ER-trans-Golgi membrane contact sites the lipid transfer protein oxysterol binding protein (OSBP) affects the secretion of a subset of cargoes. Here, we report that OSBP is a major epithelial protein as its inhibition leads to complete loss of apico-basal polarity. By mapping the OSBP proximity proteome with the biotin ligase TurboID, we found that OSBP controls the secretion of multiple membrane associated proteins, including key polarity determinants such as E-cadherin. Mechanistically, we established that OSBP contributes to E-cadherin secretion by supplying cholesterol to post-Golgi membranes. Importantly, when cells downregulate cell-cell junctions upon epithelial-to-mesenchymal transition, they re-wire their lipid homeostasis and downregulate OSBP as well, thus altering the trafficking of the OSBP-dependent secretory cargoes.

cell biology↗

bioRxiv2021

Tumor protein D54 binds intracellular nanovesicles via an amphipathic lipid packing sensor (ALPS) motif

Tumor Protein D54 (TPD54) is an abundant cytosolic protein that belongs to the TPD52 family, a family of four proteins (TPD52, 53, 54 and 55) that are overexpressed in several cancer cells. Even though the functions of these proteins remain elusive, recent investigations indicate that TPD54 binds to very small cytosolic vesicles with a diameter of ca. 30 nm, half the size of classical transport vesicles (e.g. COPI and COPII). Here, we investigated the mechanism of intracellular nanovesicle capture by TPD54. Bioinformatical analysis suggests that TPD54 contains a small coiled-coil followed by several amphipathic helices, which could fold upon binding to lipid membranes. One of these helices has the physicochemical features of an Amphipathic Lipid Packing Sensor (ALPS) motif, which, in other proteins, enables membrane binding in a curvature-dependent manner. Limited proteolysis, CD spectroscopy, tryptophan fluorescence and cysteine mutagenesis coupled to covalent binding of a membrane sensitive probe show that binding of TPD54 to small liposomes is accompanied by large structural changes in the amphipathic helix region. TPD54 binding to artificial liposomes is very sensitive to liposome size and to lipid unsaturation but is poorly dependent on lipid charge. Cellular investigations confirmed the key role of the ALPS motif in vesicle targeting. Surprisingly, the vesicles selected by TPD54 poorly overlap with those captured by the golgin GMAP-210, a long vesicle tether at the Golgi apparatus, which displays a dimeric coiled-coil architecture and an N-terminal ALPS motif. We propose that TPD54 recognizes nanovesicles through a combination of ALPS-dependent and -independent mechanisms.

cell biology↗

bioRxiv2020

UBTD1 regulates ceramide balance and endolysosomal positioning to coordinate EGFRsignaling

To adapt in an ever-changing environment, cells must integrate physical and chemical signals and translate them into biological meaningful information through complex signaling pathways. By combining lipidomic and proteomic approaches with functional analysis, we have shown that UBTD1 (Ubiquitin domain-containing protein 1) plays a crucial role in both the EGFR (Epidermal Growth Factor Receptor) self-phosphorylation and its lysosomal degradation. On the one hand, by modulating the cellular level of ceramides through ASAH1 (N-Acylsphingosine Amidohydrolase 1) ubiquitination, UBTD1 controls the ligand-independent phosphorylation of EGFR. On the other hand, UBTD1, via the ubiquitination of SQSTM1/p62 (Sequestosome 1) and endolysosome positioning, participates in the lysosomal degradation of EGFR. The coordination of these two ubiquitin-dependent processes contributes to the control of the duration of the EGFR signal. Moreover, we showed that UBTD1 depletion exacerbates EGFR signaling and induces cell proliferation emphasizing a hitherto unknown function of UBTD1 in EGF-driven cell proliferation.

cell biology↗

bioRxiv2020

Osh6 requires Ist2 for localization to the ER-PM contacts and efficient phosphatidylserine transport

Osh6 and Osh7 are lipid transfer proteins (LTPs) that move phosphatidylserine (PS) from the endoplasmic reticulum (ER) to the plasma membrane (PM). High PS level at the PM is key for many cellular functions. Intriguingly, Osh6/7 localize to ER-PM contact sites, although they lack membrane-targeting motifs, in contrast to multidomain LTPs that both bridge membranes and convey lipids. We show that Osh6 localization to contact sites depends on its interaction with the cytosolic tail of the ER-PM tether Ist2, a homologue of TMEM16 proteins. We identify a motif in the Ist2 tail, conserved in yeasts, as the Osh6-binding region, and we map an Ist2-binding surface on Osh6. Mutations in the Ist2 tail phenocopy osh6{Delta} osh7{Delta} deletion: they decrease cellular PS levels, and block PS transport to the PM. Our study unveils an unexpected partnership between a TMEM16-like protein and a soluble LTP, which together mediate lipid transport at contact sites.

cell biology↗

bioRxiv2019

Molecular and cellular dissection of the OSBP cycle through a fluorescent inhibitor

ORPphilins, natural molecules that strongly and selectively inhibit the growth of some cancer cell lines, are proposed to target intracellular lipid-transfer proteins of the Oxysterol-binding protein (OSBP) family. These conserved proteins exchange key lipids, such as cholesterol and phopsphatidylinositol-4-phosphate (PI(4)P), between organelle membranes. Among ORPphilins, molecules of the schweinfurthin family interfere with intracellular lipid distribution and metabolism, but their functioning at the molecular level is poorly understood. We report here that cell line sensitivity to schweinfurthin G (SWG) is inversely proportional to cellular level of OSBP. By taking advantage of the intrinsic fluorescence of SWG, we follow its fate in cell cultures and show that its incorporation at the TGN depends on OSBP cellular abundance. We report that SWG inhibits specifically the lipid exchange cycle of OSBP. As a consequence, post-Golgi trafficking, membrane cholesterol levels and PI(4)P turnover are affected. Finally, we demonstrate the direct binding of SWG into OSBP lipid-binding cavity by intermolecular FRET. Collectively these data describe for the first time a specific and intrinsically fluorescent pharmacological tool to dissect OSBP properties at the cellular and molecular levels.

cell biology↗

bioRxiv2019

Fat food exacerbates post-prandial hypothalamic inflammation involving GFAP+ cells and microglia

In humans, obesity was associated with brain inflammation and glial cell proliferation. Studies in rodents showed that glial cell proliferation occurs within 24 hours of high-fat diet (HFD) consumption, before obesity development. This proliferation was mainly observed in the hypothalamus (HT), a crucial brain structure for controlling body weight. Therefore, we sought to characterize the post-prandial HT inflammatory response to 1-3-6 hours exposure to a standard diet and HFD. HFD exposure increased gene expression of astrocyte and microglial marker (GFAP and Iba1) compare to standard treated mice and induced morphological modifications of microglial cells in HT. This remodeling was associated with higher expression of inflammatory genes and differential activation of hypothalamic neuropeptides involved in energy balance regulation. DREADD and PLX5622 technologies, used to modulate GFAP-positive or microglial cells activity respectively, showed that both glial cell types are involved in hypothalamic post-prandial inflammation, but in a different time frame and with a diet specificity Thus, an exacerbated post-prandial inflammation in brain might predispose individuals to obesity and needs to be characterized to address this worldwide crisis.

neuroscience↗