Patrice Codogno

• Université Paris Cité

Blood-borne factors are essential to maintain neuronal synaptic plasticity and cognitive resilience throughout life. One such factor is osteocalcin (OCN), a hormone produced by osteoblasts that influences multiple physiological processes, including hippocampal neuronal homeostasis. However, the mechanism through which this blood-borne factor commun...

Insulin-producing pancreatic β cells play a crucial role in the regulation of glucose homeostasis, and their failure is a key event for diabetes development. Prolonged exposure to palmitate in the presence of elevated glucose levels, termed gluco-lipotoxicity, is known to induce β cell apoptosis. Autophagy has been proposed to be regulated by gluco...

Shear stress induced by urinary flow stimulates macroautophagy (hereafter referred to as autophagy) in kidney proximal tubule epithelial cells. Autophagy and selective degradation of lipid droplets by lipophagy contribute to tubule homeostasis by the production of ATP and control of epithelial cell size. Autophagy/lipophagy is controlled by a signa...

In recent years, primary familial brain calcification (PFBC), a rare neurological disease characterized by a wide spectrum of cognitive disorders, has been associated to mutations in the sodium (Na)-Phosphate (Pi) co-transporter SLC20A2 . However, the functional roles of the Na-Pi co-transporters in the brain remain still largely elusive. Here we s...

Background The ability to respond to mechanical forces is a basic requirement for maintaining endothelial cell (ECs) homeostasis, which is continuously subjected to low shear stress (LSS) and high shear stress (HSS). In arteries, LSS and HSS have a differential impact on EC autophagy processes. However, it is still unclear whether LSS and HSS diffe...

Shear stress generated by urinary fluid flow is an important regulator of renal function. Its dysregulation is observed in various chronic and acute kidney diseases. Previously, we demonstrated that primary cilium-dependent autophagy allows kidney epithelial cells to adapt their metabolism in response to fluid flow. Here, we show that nuclear YAP/T...

Macroautophagy is a lysosomal degradative pathway for intracellular macromolecules, protein aggregates and organelles. The formation of the autophagosome, a double membrane‐bound structure that sequesters cargoes before their delivery to the lysosome, is regulated by several stimuli in multicellular organisms. Pioneering studies in rat liver showed...

In recent years, primary familial brain calcification (PFBC), a rare neurological disease characterized by a wide spectrum of cognitive disorders, has been associated to mutations in the sodium (Na)-Phosphate (Pi) co-transporter SLC20A2. However, the functional roles of the Na-Pi co-transporters in the brain remain still largely elusive. Here we sh...

Shear stress generated by the urinary fluid flow is an important regulator of renal function. Its dysregulation is observed in various chronic and acute kidney diseases. Previously, we demonstrated that primary cilium-dependent autophagy allows kidney epithelial cells to adapt their metabolism in response to fluid flow. Here, we show that nuclear Y...

The ability to adapt the proteolysis rates based on fluctuations in essential amino acid (EAA) availability is essential for life. The GCN2-eIF2α-ATF4 signaling pathway is involved in the adaptive response to EAA deprivations. Our previous results demonstrated that activation of this pathway is involved in upregulating the expression of many autoph...

The maintenance of cellular homeostasis in response to extracellular stimuli, i.e., nutrient and hormone signaling, hypoxia, or mechanical forces by autophagy, is vital for the health of various tissues. The primary cilium (PC) is a microtubule-based sensory organelle that regulates the integration of several extracellular stimuli. Over the past de...

Naked mole-rats (NMR) are subterranean rodents characterized by an unusual longevity coupled with an unexplained resistance to aging. In the present study, we performed extensive in situ analysis and single-cell RNA-sequencing comparing young and older animals. At variance with other species, NMR exhibited a striking stability of skin compartments...

Kidney mass and function are sexually determined, but the cellular events and the molecular mechanisms involved in this dimorphism are poorly characterized. By combining female and male mice with castration/replacement experiments, we showed that male mice exhibited kidney overgrowth from five weeks of age. This effect was organ specific, since liv...

Mechanical forces, such as compression, shear stress and stretching, play major roles during development, tissue homeostasis and immune processes. These forces are translated into a wide panel of biological responses, ranging from changes in cell morphology, membrane transport, metabolism, energy production and gene expression. Recent studies demon...

Physical constraints, such as compression, shear stress, stretching and tension, play major roles during development, tissue homeostasis, immune responses and pathologies. Cells and organelles also face mechanical forces during migration and extravasation, and investigations into how mechanical forces are translated into a wide panel of biological...

Autophagy is a core molecular pathway for the preservation of cellular and organismal homeostasis. Pharmacological and genetic interventions impairing autophagy responses promote or aggravate disease in a plethora of experimental models. Consistently, mutations in autophagy-related processes cause severe human pathologies. Here, we review and discu...

The naked mole-rat, Heterocephalus glaber, is the longest-lived rodent known with a lifespan in captivity >30 years, 10 times longer than mice, a comparable size rodent. In addition to a particularly long life, it exhibits exceptional resistance to many age-related diseases: cancer, cardiovascular, neurodegenerative, and metabolic diseases. It resi...

Autophagy is a versatile degradation system for maintaining cellular homeostasis whereby cytosolic materials are sequestered in a double-membrane autophagosome and subsequently delivered to lysosomes, where they are broken down. In multicellular organisms, newly formed autophagosomes undergo a process called ‘maturation’, in which they fuse with ve...

The primary cilium (PC), a plasma membrane microtubule-based structure, is a sensor of extracellular chemical and mechanical stress stimuli. Upon ciliogenesis, the autophagy protein ATG16L1 and the ciliary protein IFT20 are co-transported to the PC. We demonstrated in a recent study that IFT20 and ATG16L1 interact in a multiprotein complex. This in...

The primary cilium (PC), a plasma membrane microtubule-based structure, is a sensor of extracellular chemical and mechanical stress stimuli. Upon ciliogenesis, the autophagy protein ATG16L1 and the ciliary protein IFT20 are co-transported to the PC. We demonstrated in a recent study that IFT20 and ATG16L1 interact in a multiprotein complex. This in...

Autophagy is a catabolic process that maintains cellular homeostasis and plays crucial roles during development, adaptation to stress, and immune response. Dysfunctional autophagy has been linked to several human pathologies, ranging from cancer to neurodegenerative and inflammatory diseases. During the past two decades, advances have been made in...

The cyclin-dependent kinase inhibitor p27 Kip1 (p27) has been involved in promoting autophagy and survival in conditions of metabolic stress. While the signaling cascade upstream of p27 leading to its cytoplasmic localization and autophagy induction has been extensively studied, how p27 stimulates the autophagic process remains unclear. Here, we in...

Article The autophagy protein ATG16L1 cooperates with IFT20 and INPP5E to regulate the turnover of phosphoinositides at the primary cilium Graphical abstract Highlights d ATG16L1 regulates ciliogenesis independently of macro-autophagy d ATG16L1 interacts with ciliary protein IFT20 via WD40 domain to regulate ciliogenesis d ATG16L1 interacts with th...

The primary cilium (PC), a plasma membrane microtubule-based structure, is a sensor of extracellular chemical and mechanical stress stimuli. Upon ciliogenesis, the autophagy protein ATG16L1 and the ciliary protein IFT20 are co-transported to the PC. We demonstrated in a recent study that IFT20 and ATG16L1 interact in a multiprotein complex. This in...

Despite the great advances in autophagy research in the last years, the specific functions of the four mammalian Atg4 proteases (ATG4A-D) remain unclear. In yeast, Atg4 mediates both Atg8 proteolytic activation, and its delipidation. However, it is not clear how these two roles are distributed along the members of the ATG4 family of proteases. We s...

A Correction to this paper has been published: https://doi.org/10.1038/s41418-021-00783-2

[This corrects the article DOI: 10.1371/journal.ppat.1009340.].

Influenza virus infections are major public health threats due to their high rates of morbidity and mortality. Upon influenza virus entry, host cells experience modifications of endomembranes, including those used for virus trafficking and replication. Here we report that influenza virus infection modifies mitochondrial morphodynamics by promoting...

Mechanical stress has been shown to induce the degradation of lipid droplets in kidney epithelial cells. Here, we illustrate the technical equipment and devices that are currently used in our laboratory to apply shear stress on cells. We provide a detailed protocol to monitor lipophagy in response to shear stress. The aim of this review is to guide...

Several human pathologies including neurological, cardiac, infectious , cancerous, and metabolic diseases have been associated with altered mitochondria morphodynamics. Here, we identify a small organic molecule, which we named Mito-C. Mito-C is targeted to mitochondria and rapidly provokes mitochondrial network fragmentation. Biochemical analyses...

The kidney, similar to many other organs, has to face shear stress induced by biological fluids. How epithelial kidney cells respond to shear stress is poorly understood. Recently we showed in vitro and in vivo that proximal tubule epithelial cells use lipophagy to fuel mitochondria with fatty acids. Lipophagy is stimulated by a primary cilium-depe...

Human Cytomegalovirus (HCMV) is a frequent opportunistic pathogen in immunosuppressed patients, which can be involved in kidney allograft dysfunction and rejection. In order to study the pathophysiology of HCMV renal diseases, we concentrated on the impact of HCMV infection on human renal tubular epithelial HK-2 cells. Our aim was to develop a mode...

Autophagy is a catabolic process whereby cytoplasmic components are degraded within lysosomes, allowing cells to maintain energy homeostasis during nutrient depletion. Several studies reported that the CDK inhibitor p27Kip1 promotes starvation-induced autophagy by an unknown mechanism. Here we find that p27 controls autophagy via an mTORC1-dependen...

Organs and cells must adapt to shear stress induced by biological fluids, but how fluid flow contributes to the execution of specific cell programs is poorly understood. Here we show that shear stress favours mitochondrial biogenesis and metabolic reprogramming to ensure energy production and cellular adaptation in kidney epithelial cells. Shear st...

Control of systemic and hepatic inflammation, in particular originating from monocytes/macrophages, is crucial to prevent liver fibrosis and its progression to end-stage cirrhosis. LC3-associated phagocytosis (LAP) is a non-canonical form of autophagy that shifts the monocyte/macrophage phenotype to an anti-inflammatory phenotype. In a recent study...

Sustained hepatic and systemic inflammation, particularly originating from monocytes/macrophages, is a driving force for fibrosis progression to end-stage cirrhosis and underlies the development of multiorgan failure. Reprogramming monocyte/macrophage phenotype has emerged as a strategy to limit inflammation during chronic liver injury. Here, we re...

SupplementalData_Blood-2016-02-697003-1

Background: Although both circular RNAs (circRNAs) and autophagy are associated with the function of breast cancer (BC), whether circRNAs regulate BC progression via autophagy remains unknown. In this study, we aim to explore the regulatory mechanisms and the clinical significance of autophagy-associated circRNAs in BC. Methods: Autophagy associ...

Primary cilium-dependent macroautophagy/autophagy is induced by the urinary flow in epithelial cells of the kidney proximal tubule. A major physiological outcome of this cascade is the control of cell size. Some components of the ATG machinery are recruited at the primary cilium to generate autophagic structures. Shear stress induced by the liquid...

Primary cilium-dependent macroautophagy/autophagy is induced by the urinary flow in epithelial cells of the kidney proximal tubule. A major physiological outcome of this cascade is the control of cell size. Some components of the ATG machinery are recruited at the primary cilium to generate autophagic structures. Shear stress induced by the liquid...

Cells subjected to stress situations mobilize specific membranes and proteins to initiate autophagy. Phosphatidylinositol-3-phosphate (PI3P), a crucial lipid in membrane dynamics, is known to be essential in this context. In addition to nutriments deprivation, autophagy is also triggered by fluid-flow induced shear stress in epithelial cells, and t...

Autophagy is a catabolic process whereby cytoplasmic components are degraded within lysosomes, allowing cells to maintain energy homeostasis during nutrient depletion. Several studies have shown that the CDK inhibitor p27Kip1 promotes starvation-induced autophagy. However, the underlying mechanism remains unknown. Here, we report that in amino acid...

Background and aims: Previous studies demonstrated that autophagy is protective in hepatocytes and macrophages, but detrimental in hepatic stellate cells in chronic liver diseases. The role of autophagy in liver sinusoidal endothelial cells (LSECs) in nonalcoholic steatohepatitis (NASH) is unknown. Our aim was to analyze the potential implication...

STK38 (also known as NDR1) is a Hippo pathway serine/threonine protein kinase with multifarious functions in normal and cancer cells. Using a context-dependent proximity-labeling assay, we identify more than 250 partners of STK38 and find that STK38 modulates its partnership depending on the cellular context by increasing its association with cytop...

Introduction L’autophagie est un système de dégradation et de recyclage du matériel cytoplasmique indispensable à l’homéostasie cellulaire qui peut être déclenchée par différents stimulis dont le stress mécanique. Elle est impliquée dans de nombreuses pathologies rénales lorsqu’elle est déficiente. Son mécanisme dans l’appareil juxta-glomérulaire e...

Primary cilium (PC) is a microtubule-based structure that regulate different signal transduction cascades related to external stress sensing. Previous works established a functional interplay between PC and autophagic machineries (Pampliega et al 2013 Nature). Under serum starvation, ATG16L1 is transported to the PC with the ciliary protein IFT20....

Introduction: Autophagy plays a critical role in cancer initiation and progression. CircRNAs were recently identified as new molecules in regulation of cancer cell biology. However, it remains unclear whether circRNAs are involved in the process of autophagy and regulate cancer biology via autophagy. Methods: We performed circRNAs microarray to scr...

Introduction: Autophagy plays a critical role in cancer initiation and progression. CircRNAs were recently identified as new molecules in regulation of cancer cell biology. However, it remains unclear whether circRNAs are involved in the process of autophagy and regulate cancer biology via autophagy. Methods: We performed circRNAs microarray to scr...

The NIH-funded center for autophagy research named Autophagy, Inflammation, and Metabolism (AIM) Center of Biomedical Research Excellence, located at the University of New Mexico Health Science Center is now completing its second year as a working center with a mission to promote autophagy research locally, nationally, and internationally. The cent...

Autophagy is a conserved molecular pathway directly involved in the degradation and recycling of intracellular components. Autophagy is associated with a response to stress situations, such as nutrients deficit, chemical toxicity, mechanical stress or microbial host defense. We have recently shown that primary cilium-dependent autophagy is importan...

Autophagy is a conserved molecular pathway directly involved in the degradation and recycling of intracellular components. Autophagy is asso-ciated with a response to stress situations, such as nutrients deficit, chemical toxicity, mechanical stress or microbial host defense. We have recently shown that primary cilium-dependent autophagy is importa...

Autophagy is a conserved molecular pathway directly involved in the degradation and recycling of intracellular components. Autophagy is asso-ciated with a response to stress situations, such as nutrients deficit, chemical toxicity, mechanical stress or microbial host defense. We have recently shown that primary cilium-dependent autophagy is importa...

Autophagy is an essential self-digestion machinery for cell survival and homoeostasis. Membrane elongation is fundamental, as it drives the formation of the double-membrane vesicles that engulf cytosolic material. LC3-lipidation, the signature of autophagosome formation, results from a complex ubiquitin-conjugating cascade orchestrated by the ATG16...

PiT1/SLC20A1 is an inorganic phosphate transporter with additional functions including the regulation of TNFα-induced apoptosis, erythropoiesis, cell proliferation and insulin signaling. Recent data suggest a relationship between PiT1 and NF-κB-dependent inflammation: (i) Pit1 mRNA is up-regulated in the context of NF-κB pathway activation; (ii) NF...

Age-related declines in cognitive fitness are associated with a reduction in autophagy, an intracellular lysosomal catabolic process that regulates protein homeostasis and organelle turnover. However, the functional significance of autophagy in regulating cognitive function and its decline during aging remains largely elusive. Here, we show that st...

Fluidic shear stress applied to epithelial cells inside the kidney tubules affects cell size in an autophagy-related manner. Here, we describe the technical equipment that we routinely use to apply shear stress on cells, as well as immunoblotting, immunofluorescence, and three-dimensional cell volume reconstruction techniques used in analysis of th...

Primary cilium (PC) is a microtubules-based structure that regulate different signal transduction cascades related to external stress sensing. Previous works established a functional interplay between primary cilium and autophagic machineries (Pampliega et al 2013 Nature; Orhon and Dupont et al 2016 Nat Cell Biol). Under serum starvation and in res...

Primary cilia (PC) are microtubules-based structures which regulate different signal transduction cascades related to stress sensing. Previous works established a functional interplay between primary cilium and autophagy pathway (Pampliega et al 2013 Nature; Orhon and Dupont et al 2016 Nat Cell Biol). Under serum starvation and in response to shear...

The European Autophagy consortium Driving next-generation autophagy researchers towards translation (DRIVE) held its kick-off meeting in Groningen on the 14th and 15th of June 2018. This Marie Skłodowska-Curie Early Training Network was approved under the European Union’s Horizon 2020 Research and Innovation Program and is funded for 4 years. Withi...

Autophagosome biogenesis is the key event associated with the stress-responsive autophagic pathway, allowing the capture of specific cargoes and their delivery to the lysosomal degradative compartment. Although the endoplasmatic reticulum (ER) appears to be central for the assembly of autophagosomal membranes, it is also involved in several events...

Recently, NIH has funded a center for autophagy research named the Autophagy, Inflammation, and Metabolism (AIM) Center of Biomedical Research Excellence, located at the University of New Mexico Health Science Center (UNM HSC), with aspirations to promote autophagy research locally, nationally, and internationally. The center has 3 major missions:...

[This corrects the article DOI: 10.18632/oncotarget.9875.].

FOXO3a, a member of the Forkhead transcription factor family, has roles in apoptosis and autophagy. In this issue of Developmental Cell, Fitzwalter et al. (2018) describe how the blockade of FOXO3a turnover, which normally occurs through autophagy, sensitizes cancer cells to apoptosis through FOXO3a-mediated stimulation of pro-apoptotic PUMA/BBC3 e...

Table S2. Raw Data from Metabolomics Analysis Performed on Unlabeled Aspirin versus Control and [13C]-Aspirin versus Aspirin, Related to Figures 5, S5, and S6 Each metabolite is annotated for its mass and retention time. For each metabolite, p values and Fold change for each comparison are depicted.

Table S1. Quantification of Immunoblot Analyses of Autophagic Flux Depicted in Figures 2B, S1B–S1F, S2A, and S2B Data represent averaged Fold Change ± SEM n values refer to the number of independent experiments. p values have been calculated by means of the unpaired t test, as indicated in Supplemental Experimental Procedures.

Autophagy is a catabolic pathway by which cellular components are delivered to the lysosome for degradation and recycling. Autophagy serves as a crucial intracellular quality control and repair mechanism but is also involved in cell remodelling during development and cell differentiation. In addition, mitophagy, the process by which damaged mitocho...

The age-associated deterioration in cellular and organismal functions associates with dysregulation of nutrient-sensing pathways and disabled autophagy. The reactivation of autophagic flux may prevent or ameliorate age-related metabolic dysfunctions. Non-toxic compounds endowed with the capacity to reduce the overall levels of protein acetylation a...

Blood flowing in arteries generates shear forces at the surface of the vascular endothelium that control its anti-atherogenic properties. However, due to the architecture of the vascular tree, these shear forces are heterogeneous and atherosclerotic plaques develop preferentially in areas where shear is low or disturbed. Here we review our recent s...

Endoplasmic Reticulum (ER), spreading in the whole cell cytoplasm, is a central player in eukaryotic cell homeostasis, from plants to mammals. Beside crucial functions, such as membrane lipids and proteins synthesis and outward transport, the ER is able to connect to virtually every endomembrane compartment by specific tethering molecular machineri...

Significance Atherosclerotic plaques tend to develop preferentially in areas of the vasculature exposed to low and disturbed shear stress (SS), but the mechanisms are not fully understood. In this study, we demonstrate that inefficient autophagy contributes to the development of atherosclerotic plaques in low-SS areas. Defective endothelial autopha...

Phosphatidylinositol 3-phosphate (PtdIns3P) is a key player of membrane trafficking regulation, mostly synthesized by the PIK3C3 lipid kinase. The presence of PtdIns3P on endosomes has been demonstrated; however, the role and dynamics of the pool of PtdIns3P dedicated to macroautophagy/autophagy remains elusive. Here we addressed this question by s...

The biogenesis of autophagosome, the double membrane bound organelle related to macro-autophagy, is a complex event requiring numerous key-proteins and membrane remodeling events. Our recent findings identify the extended synaptotagmins, crucial tethers of Endoplasmic Reticulum-plasma membrane contact sites, as key-regulators of this molecular sequ...

The paradigm of cancer stem cells (CSCs) defines the existence of cells exhibiting self-renewal and tumor-seeding capacity. These cells have been associated with tumor relapse and are typically resistant to conventional chemotherapeutic agents. Over the past decade, chemical biology studies have revealed a significant number of small molecules able...

Over the past two decades, the molecular machinery that underlies autophagic responses has been characterized with ever increasing precision in multiple model organisms. Moreover, it has become clear that autophagy and autophagy-related processes have profound implications for human pathophysiology. However, considerable confusion persists about th...

The double-membrane-bound autophagosome is formed by the closure of a structure called the phagophore, origin of which is still unclear. The endoplasmic reticulum (ER) is clearly implicated in autophagosome biogenesis due to the presence of the omegasome subdomain positive for DFCP1, a phosphatidyl-inositol-3-phosphate (PI3P) binding protein. Contr...

Cancer stem cells (CSCs) represent a subset of cells within tumours that exhibit self-renewal properties and the capacity to seed tumours. CSCs are typically refractory to conventional treatments and have been associated to metastasis and relapse. Salinomycin operates as a selective agent against CSCs through mechanisms that remain elusive. Here, w...

Autophagy is an essential mechanism to maintain homeostasis at cellular and organismal levels. Autophagy controls nutrient balance, and purges excessive or damaged organelles, misfolded proteins, and invading microorganisms. Regarding human health, several examples highlight its importance as a therapeutic target since autophagy modulation has reco...

Objective: Preferential development of atherosclerotic lesions in areas of low shear stress is associated with increased endothelial inflammation, apoptosis and senescence. On the contrary, high shear stress areas are protected from plaque development, but the mechanisms remain elusive. Autophagy is a protective mechanism allowing recycling of defe...

Macroautophagy (hereafter called autophagy) is a vacuolar, lysosomal pathway for catabolism of intracellular material that is conserved among eukaryotic cells. Autophagy plays a crucial role in tissue homeostasis, adaptation to stress situations, immune responses, and the regulation of the lammatory response. Blockade or uncontrolled activation of...

The ability of cells to adapt to their microenvironment and to respond to changes in nutrient availability is essential for cell survival. Macroautophagy is one of the key cellular processes induced in response to environmental changes, nutrient starvation in particular. By sequestering and degrading cytoplasmic material (such as obsolete macromole...