Etienne Morel

Macroautophagy (autophagy) is a fundamental catabolic process requiring the biogenesis of the autophagosome to support cell survival during stress. Although the roles of F-actin and microtubule cytoskeleton in autophagy are well established, the contribution of intermediate filaments (IFs) remains poorly understood. Here, we investigated the role of the type III IF vimentin in supporting the early steps of starvation-induced autophagy. We demonstrate that starvation triggers a rapid, perinuclear compaction of vimentin IFs, which showed enhanced overlap with the endoplasmic reticulum (ER) and correlated with transient vimentin phosphorylation at serine 56. We reveal that autophagic proteins accumulate at the vimentin–ER interface, physically connecting the autophagosome biogenesis machinery to the vimentin IF network. Knockout or pharmacological perturbation of vimentin–IFs dynamics using withaferin-A significantly impairs starvation-induced autophagic flux. Mechanistically, we reveal that vimentin IFs are essential coordinators for the mobilization of endosome–ER membrane contact sites (EERCS), a crucial hub for autophagosome nucleation. Together, our findings uncover a novel role for vimentin IFs as a dynamic cytoskeletal coordinator that spatially organizes membrane contact sites to promote the efficient initiation of autophagosome biogenesis in response to nutrient stress.

Autophagosome biogenesis is a highly coordinated membrane remodeling process that relies on the de novo formation and expansion of the phagophore, yet the cellular principles governing its spatial and temporal organization remain incompletely understood. Accumulating evidence now places the endoplasmic reticulum (ER) at the center of this process, not merely as a membrane source, but as a dynamic scaffold that organizes phagophore assembly through extensive membrane contact sites with multiple organelles. ER-mediated contacts with endosomes, mitochondria, the plasma membrane, and ER–Golgi intermediates create specialized microenvironments that integrate signaling, lipid transfer, vesicle formation and trafficking, and biophysical constraints to drive phagophore nucleation and growth. These contact sites enable the coordinated mobilization of diverse membrane carriers and autophagy regulators in a stress- and context-dependent manner. In this review, we discuss how ER-driven membrane contact sites orchestrate autophagosome biogenesis, highlight emerging mechanistic and biophysical concepts, and consider their broader implications for cellular stress adaptation and disease.

Médecine/sciences (M/S), revue internationale dans le domaine de la recherche biologique, médicale et en santé

Kidney epithelial cells play a pivotal role in maintaining body water and electrolyte homeostasis. In this context, the continuous urinary flow imposing shear stress on their apical surface is essential for their proper differentiation and metabolic functions. This process notably relies on mitochondrial biogenesis and ATP production through oxidative phosphorylation. Although autophagy and lipid droplet (LD) catabolism have been implicated in the metabolic shift induced by shear stress, the coordinated remodeling of intracellular membranes that governs mitochondrial dynamics during this adaptation remains poorly understood. Here, we show that physiological shear stress induces rapid mitochondrial remodeling in kidney tubular cells and in zebrafish pronephros, marked by the emergence of a distinct pool of donut-shaped mitochondria. During this process of mitochondrial specialization, endoplasmic reticulum (ER)–mitochondria contact sites become transiently stabilized, underscoring their importance in metabolic adaptation. Using a split-TurboID proximity labelling approach combined with mass spectrometry, we identify the local recruitment of proteins involved in LD metabolism at the ER–mitochondria interface during the early stages of shear stress response. We further demonstrate the formation of triple ER–LD–mitochondria contact sites, required for the localized transfer of free fatty acids from LDs to mitochondria during metabolic adaptation to shear stress. Specifically, we show that vacuolar membrane protein 1 (VMP1), a key component of contact sites, is essential for lipid transfer from LDs to mitochondria and for proper metabolic adaptation to shear stress. Together, our findings uncover a critical role for LD–ER–mitochondria crosstalk in the early stages of cellular adaptation to shear stress and identify membrane contact sites as central hubs coordinating metabolic turnover.

Melanin pigments block genotoxic agents by positioning on the sun-exposed side of the nucleus in human skin keratinocytes. How this positioning is regulated and its role in genome photoprotection remain unknown. Here, by developing a model of human keratinocytes internalizing extracellular melanin into pigment organelles, we show that keratin 5 and keratin 14 intermediate filaments and microtubules control the three-dimensional perinuclear position of pigments, shielding DNA from photodamage. Imaging and microrheology in a human-disease-related model identify structural keratin cages surrounding pigment organelles to stiffen their microenvironment and maintain their three-dimensional position. Optimum supranuclear spatialization of pigment organelles is required for DNA photoprotection and relies on intermediate filaments and microtubules bridged by plectin cytolinkers. Thus, the mechanically driven proximity of pigment organelles to the nucleus is a key photoprotective parameter. Uncovering how human skin counteracts solar radiation by positioning the melanin microparasol next to the genome anticipates that dynamic spatialization of organelles is a physiological response to ultraviolet stress.

Summary: Macroautophagy (autophagy) is a fundamental catabolic process requiring the biogenesis of the autophagosome to support cell survival during stress. While the roles of F-actin and microtubule cytoskeleton in autophagy are well established, the contribution of intermediate filaments (IFs) remains poorly understood. Here, we investigated the role of the type III IF vimentin in supporting the early steps of starvation-induced autophagy. We demonstrate that starvation triggers a rapid, perinuclear compaction of vimentin IFs, correlating with transient phosphorylation at serine 56 and enhanced overlap with the endoplasmic reticulum (ER). We reveal that autophagic proteins accumulate at the vimentin/ER interface, physically connecting the autophagosome biogenesis machinery to the vimentin IF network. Knock-out or pharmacological perturbation of vimentin-IFs dynamics using Withaferin-A significantly impairs starvation-induced autophagic flux. Mechanistically, we reveal that vimentin IFs are essential coordinators for the mobilization of endosome-ER-membrane contact sites (EERCS), a critical hub for autophagosome nucleation. Together, our findings uncover a novel role for vimentin IFs as a dynamic cytoskeletal coordinator that spatially organizes membrane contact sites to promote the efficient initiation of autophagosome biogenesis in response to nutrient stress. Summary statement: This study reveals that vimentin intermediate filaments rapidly reorganize to mobilize ER-endosome contact sites, establishing a critical spatial platform for starvation-induced autophagy initiation.

Phosphoinositides, a versatile class of phosphorylated phosphatidylinositols, are emerging as central orchestrators of cellular stress responses. Beyond defining the organization and identity of endomembranes, these dynamic lipids act as highly adaptable signaling hubs that integrate diverse stress cues, from nutrient deprivation and mechanical strain to osmotic imbalance and DNA damage. Across evolution—from unicellular organisms to mammals—they drive conserved adaptation programs, including vacuolar remodeling, endosomal trafficking, and autophagosome biogenesis, through a finely tuned metabolism governed by an intricate network of kinases, phosphatases, and regulatory partners. Recent advances uncover how compartment‐specific regulation, enzymatic diversity, and organelle crosstalk converge on phosphoinositide signaling, revealing these lipids as not only molecular adaptors but also promising therapeutic entry points in diseases marked by defective stress resolution. This review synthesizes emerging insights into the multifaceted roles of phosphoinositides in mobilizing membranes under stress, with a focus on mechanistic principles and recent research.

The genomic RNAs of influenza A viruses (IAVs) are replicated in the nucleus of infected cells in the form of viral ribonucleoproteins (vRNPs) before being exported to the cytoplasm. The small GTPase RAB11A is involved in the transport of vRNPs to the sites of viral assembly at the plasma membrane, but the molecular mechanisms involved remain largely unknown. Here we show that IAV infection remodels the architecture of the endoplasmic reticulum (ER) sheets, where vRNPs tend to accumulate in the absence of RAB11A. To decipher the interplay between RAB11A, vRNPs, and the ER, we investigated viral-induced perturbations of RAB11A proximity interactome. To this end, we generated cells stably expressing a TurboID-RAB11A fusion protein and performed biotin-based proximity labeling upon viral infection. We found that cellular regulators of phophatidylinositol-4-phosphate (PI4P) homeostasis, including the autophagic and stress response protein ATG16L1, are significantly enriched at the vicinity of RAB11A in infected cells. Infection induces an increase in cellular PI4P levels in an ATG16L1-dependent manner, while ATG16L1 relocalizes to ER membranes upon infection. Depletion of ATG16L1 decreases the co-distribution of vRNPs with PI4P punctae on ER membranes, and reduces the accumulation of vRNPs at the plasma membrane as well as the production of IAV infectious particles. Our data extend to IAVs the notion that viruses can modulate the metabolism and localization of phosphoinositides to control host membrane dynamics and point to the ER as an essential platform for vRNP transport. They provide evidence for a pivotal role of ATG16L1 in regulating the identity of endomembranes and coordinating RAB11A and PI4P-enriched membranes to ensure delivery of vRNPs to the plasma membrane.