Biology subjects

Riezman, H.

Publications and source records attributed to Riezman, H..

16 recordsLinked to original sources

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

Lysosome-Dependent Sphingolipid Regulation as a potential therapeutic Target for Cohen Syndrome

Cohen Syndrome (CS) is a rare autosomal recessive disorder caused by biallelic mutations in the VPS13B gene, affecting approximately 50,000 individuals worldwide. Clinical features include postnatal microcephaly, developmental delay, intellectual disability, neutropenia, and retinal dystrophy. VPS13B belongs to the bridge-like lipid transfer protein (BLTP) family, which also includes VPS13A, VPS13C, and VPS13D in mammals. Although its precise function remains unclear, VPS13B localizes to the Golgi complex, and its loss leads to Golgi fragmentation, a consistent cellular phenotype observed in VPS13B-deficient models. We used the rescue of this cell-autonomous phenotype as the basis for a microscopy-based high-throughput screening assay, through which we identified several small molecules capable of restoring Golgi morphology. Most of these compounds shared a common mechanism of action, relying on lipid accumulation in acidic organelles due to their cationic amphiphilic properties (CADs). Lipidomic profiling revealed a reduction in C18-N-acyl sphingolipids as a characteristic feature of VPS13B knockout (KO) cells, a defect that was reversed by the majority of the identified compounds. To evaluate the physiological relevance of these findings, we tested two compounds, azelastine and raloxifene, in cortical organoids (COs) derived from VPS13B KO human pluripotent stem cells. These organoids exhibited smaller size and reduced neurite outgrowth, reminiscent of the secondary microcephaly observed in CS patients. Treatment with either compound significantly recovered the neurite outgrowth phenotype, reinforcing physiological relevance of the compound effect. Taken together, our findings highlight a potential effect of the CAD on lysosome-dependent sphingolipid regulation, allowing the recovery of Golgi integrity and partial rescue in the cortical organoid CS model. Although additional studies are required to delineate the exact molecular targets, this work uncovers a potential mechanism that could be leveraged for the treatment of CS.

cell biology↗

bioRxiv2024

ER sensing of lipid metabolism drives PRA family-dependent regulation of COPII vesicle transport

Newly synthesized secretory proteins and many lipids are transported from the endoplasmic reticulum (ER) to the Golgi prior to their ultimate destinations. The ER-to-Golgi transport must be tightly regulated during adaptation to environmental stress. However, the sensing mechanism and regulatory pathways governing the consecutive formation, budding and transportation of COPII vesicles from the ER remain insufficiently explored. Here, we present evidence indicating that COPII-mediated vesicle transport is transcriptionally controlled through the phosphatidic acid-dependent Opi1-Ino2/Ino4 regulatory circuit. Our analysis indicates that YIP3, a target gene of Ino2/Ino4, exerts a negative regulatory impact on COPII-mediated vesicle transport. Furthermore, we demonstrated that Ino2/Ino4 but not Yip3 modulates Sar1 activation, the initial step in COPII vesicle formation, whereas Yip3 hinders Sec16 assembly on the ER membrane, thereby implying that Ino2/Ino4 governs COPII-mediated trafficking at multiple steps. Thus, this study provides the first evidence for an ER sensing system that transcriptionally fine-tunes multiple steps of anterograde vesicular transport in response to alterations in lipid composition of the ER membrane.

cell biology↗

bioRxiv2023

Development of novel genetically-encoded fluorescent probes to track ceramides during phagocytosis

Ceramides regulate phagocytosis, however their exact function remains poorly understood. Here we sought 1) to develop genetically encoded fluorescent tools for imaging ceramide, and 2) to use them to examine ceramide dynamics during phagocytosis. Fourteen EGFP fusion constructs based on four known ceramide-binding domains were generated and screened. While most constructs localized to the nucleus or cytosol, three based on the CA3 ceramide-binding domain of KSR1 localized to plasma membrane or endolysosomes. C-terminally-tagged CA3 with a vector-based (C-KSR) or glycine-serine linker (C-KSR-GS) responded sensitively and similarly to ceramide depletion and accumulation using a panel of ceramide modifying drugs, whereas N-terminally tagged CA3 (N-KSR) responded differently to a subset of treatments. Lipidomic and liposome microarray analysis suggested that, instead, N-KSR preferentially binds to glucosyl-ceramide. Additionally, the three probes showed distinct dynamics during phagocytosis. Despite partial lysosomal degradation, C-KSR robustly accumulated at the plasma membrane during phagocytosis, whereas N-KSR becomes cytoplasmic at later timepoints. Moreover, weak recruitment of C-KSR-GS to endoplasmic reticulum and phagosomes was enhanced by overexpression of the endoplasmic reticulum proteins STIM1 and Sec22b, and was more salient in dendritic cells. The data suggest these novel probes can be used to analyze sphingolipid dynamics and function in living cells.

cell biology↗

bioRxiv2022

Cell type-specific assessment of cholesterol distribution in models of neurodevelopmental disorders

Most nervous system disorders manifest through alterations in neuronal signaling based on abnormalities in neuronal excitability, synaptic transmission, and cell survival. However, such neuronal phenotypes are frequently accompanied - or even caused - by metabolic dysfunctions in neuronal or non-neuronal cells. The tight packing and highly heterogenous properties of neural, glial and vascular cell types pose significant challenges to dissecting metabolic aspects of brain disorders. Perturbed cholesterol homeostasis has recently emerged as key parameter associated with sub-sets of neurodevelopmental disorders. However, approaches for tracking and visualizing endogenous cholesterol distribution in the brain have limited capability of resolving cell type-specific differences. We here develop tools for genetically-encoded sensors that report on cholesterol distribution in the mouse brain with cellular resolution. We apply these probes to examine sub-cellular cholesterol accumulation in two genetic mouse models of neurodevelopmental disorders, Npc1 and Ptchd1 knock-out mice. While both genes encode proteins with sterol-sensing domains that have been implicated in cholesterol transport, we uncover highly selective and cell type-specific phenotypes in cholesterol homeostasis. The tools established in this work should facilitate probing sub-cellular cholesterol distribution in complex tissues like the mammalian brain and enable capturing cell type-specific alterations in cholesterol flow between cells in models of brain disorders.

neuroscience↗

bioRxiv2022

Organelle-specific photoactivation and dual-isotope labeling strategy reveals phosphatidylethanolamine metabolic flux

Phosphatidylethanolamine metabolism plays essential roles in eukaryotic cells but has not been completely resolved due to its complexity. This is because lipid species, unlike proteins or nucleic acids, cannot be easily manipulated at the single molecule level or controlled with subcellular resolution, two of the key factors toward understanding their functions. Here, we use the organelle-targeting photoactivation method to study PE metabolism in living cells with a high spatiotemporal resolution. Containing predefined PE structures, we designed probes which can be selectively introduced to the ER or mitochondria to compare their metabolic products according to their subcellular localization. We combined photo-uncaging method with dual stable isotopic labeling to track PE metabolism in living cells by mass spectrometry analysis. Our results reveal that both mitochondrial- and ER-released PE participate in phospholipid remodeling, and that PE methylation can be detectable only under particular conditions. Thus, our method provides a framework to study phospholipid metabolism at subcellular resolution.

cell biology↗

bioRxiv2022

Optical Control of Membrane Fluidity Modulates Protein Secretion

The lipid composition of cellular membranes is dynamic and undergoes remodelling affecting biophysical properties, such as membrane fluidity, which are critical to biological function. Here, we introduce an optical approach to manipulate membrane fluidity based on exogenous synthetic fatty acid with an azobenzene photoswitch, termed FAAzo4. Cells rapidly incorporate FAAzo4 into phosphatidylcholine (PC), the major phospholipid in mammalian cells, in a concentration- and cell type-dependent manner. This generates photoswitchable PC analogs (AzoPC), which are predominantly located in the endoplasmic reticulum (ER). Irradiation causes a rapid photoisomerization that increases membrane fluidity with high spatiotemporal precision. We use these PhotoCells to study the impact of membrane mechanics on protein export from the ER and demonstrate that this two-step process has distinct membrane fluidity requirements. Our approach represents an unprecedented way of manipulating membrane fluidity in cellulo and opens novel avenues to probe roles of fluidity in a wide variety of biological processes.

cell biology↗

bioRxiv2022

The small GTPase Arf1 regulates ATP synthesis and mitochondria homeostasis by modulating fatty acid metabolism

Lipid mobilization through fatty acid {beta}-oxidation is a central process essential for energy production during nutrient shortage. In yeast, this catabolic process starts in the peroxisome from where {beta}-oxidation products enter mitochondria and fuel the TCA cycle. Little is known about the physical and metabolic cooperation between these organelles. We found that expression of fatty acid transporters and of the rate-limiting enzyme involved in {beta}-oxidation are decreased in cells expressing a hyperactive mutant of the small GTPase Arf1, leading to an accumulation of fatty acids in lipid droplets. As a consequence, mitochondria became fragmented and ATP synthesis decreased. Genetic and pharmacological depletion of fatty acids phenocopied the arf1 mutant mitochondrial phenotype. Although {beta}-oxidation occurs mainly in mitochondria in mammals, Arf1s role in fatty acid metabolism is conserved. Together, our results indicate that Arf1 integrates metabolism into energy production by regulating fatty acid storage and utilization, and presumably organelle contact-sites.

cell biology↗

bioRxiv2021

Vacuole-specific lipid release for tracking intracellular lipid metabolism and transport in Saccharomyces cerevisiae

Lipid metabolism is spatiotemporally regulated within cells, yet intervention into lipid functions at subcellular resolution remains difficult. Here we report a method that enables site-specific release of sphingolipids and cholesterol inside the vacuole in Saccharomyces cerevisiae. Using this approach, we monitored real-time sphingolipid metabolic flux out of the vacuole by mass spectrometry and found that the ER-vacuole tethering protein Mdm1 facilitated the metabolism of sphingoid bases into ceramides. In addition, we showed that cholesterol, once delivered into yeast using our method, could restore cell proliferation induced by ergosterol deprivation, overcoming the previously described sterol-uptake barrier under aerobic conditions. Together, these data define a new way to study intracellular lipid metabolism and transport from the vacuole in yeast.

cell biology↗

bioRxiv2020

Receptor-linked environment-sensitive probe monitors the local membrane environment surrounding the insulin receptor

Functional membrane proteins in the plasma membrane are suggested to have specific membrane environments that play important roles to maintain and regulate the function of proteins. However, the local membrane environments of membrane proteins remain largely unexplored due to the lack of techniques allowing to monitor them in living cells. We have developed a method to probe the local membrane environment surrounding a membrane protein in the plasma membrane by covalently tethering a solvatochromic, environment-sensitive dye, Nile red, to a membrane protein via a flexible linker. Our direct imaging reported on the spatio-temporal properties of membrane fluidity of the local environment surrounding the insulin receptor. The local environment was distinct from the average plasma membrane fluidity and was quite dynamic and heterogeneous. Upon addition of insulin, the local membrane environment surrounding the receptor increased in fluidity in an insulin receptor-kinase dependent manner. This new technology should allow researchers to examine changes in membrane properties caused by receptor activation and devise ways to address the role of these changes in physiological processes.

cell biology↗

bioRxiv2020

Establishment of a highly efficient gene disruption strategy to analyze and manipulate lipid co-regulatory networks

Gene disruption has been dramatically facilitated by genome editing tools. Despite improvements in gene disruption rates in cultured cells, clone isolation remains routinely performed to obtain mutants, potentially leading to artifacts due to clonal variation in cellular phenotypes. Here we report GENF, a highly efficient strategy to disrupt genes without isolating clones, which can be multiplexed. Using it, we obtained reliable lipidomics datasets from mutant cells without being affected by variances related to clone isolation. Through this, we found that an enzyme involved in congenital generalized lipodystrophy regulates glycerophospholipids with specific acyl-chains. We also demonstrate the possibility to dissect complex lipid co-regulatory mechanisms, explaining cell adaptations to altered lipid metabolism. With its simplicity and the avoidance of cloning-related artifacts, GENF is likely to contribute to many cell biology studies, especially those involving -omics approaches.

genetics↗

bioRxiv2020

CHO/LY-B cell growth under limiting sphingolipid supply: correlation between lipid composition and biophysical properties of sphingolipid-restricted cell membranes

ABSTRACTSphingolipids (SL) are ubiquitous in mammalian cell membranes, yet there is little data on the behavior of cells under SL-restriction conditions. LY-B cells derive from a CHO line in which serine palmitoyl transferase (SPT), thus de novo SL synthesis, is suppressed, while maintaining the capacity of taking up and metabolizing exogenous sphingoid bases from the culture medium. In the present study LY-B cells were adapted to grow in a fetal bovine serum (FBS)-deficient medium to avoid external uptake of lipids. The lowest FBS concentration that allowed LY-B cell growth, though at a slow rate, under our conditions was 0.04%, i.e. 250-fold less than the standard (10%) concentration. Cells grown under limiting SL concentrations remained viable for at least 72 h. Enriching with sphingomyelin the SL-deficient medium allowed the recovery of control LY-B cell growth rates. Studies including whole cells, plasma membrane preparations, and derived lipid vesicles were carried out. Laurdan fluorescence was recorded to measure membrane molecular order, showing a significant decrease in the rigidity of LY-B cells, not only in plasma membrane but also in whole cell lipid extract, as a result of SL limitation in the growth medium. Plasma membrane preparations and whole cell lipid extracts were also studied using atomic force microscopy in the force spectroscopy mode. Force measurements demonstrated that lower breakthrough forces were required to penetrate samples obtained from SL-poor LY-B cells than those obtained from control cells. Mass-spectroscopic analysis was also a helpful tool to understand the rearrangement undergone by the LY-B cell lipid metabolism. The most abundant SL in LY-B cells, sphingomyelin, decreased by about 85% as a result of SL limitation in the medium, the bioactive lipid ceramide and the ganglioside precursor hexosylceramide decreased similarly, together with cholesterol. Quantitative SL analysis showed that a 250-fold reduction in sphingolipid supply to LY-B cells led to a 6-fold decrease in membrane sphingolipids, underlining the resistance to changes in composition of these cells. Plasma membrane compositions exhibited similar changes, at least qualitatively, as the whole cells with SL restriction. A linear correlation was observed between the sphingomyelin concentration in the membranes, the degree of lipid order as measured by laurdan fluorescence, and membrane breakthrough forces assessed by atomic force microscopy. Concomitant changes were detected in glycerophospholipids under SL-restriction conditions.Competing Interest StatementThe authors have declared no competing interest.View Full Text

biophysics↗

bioRxiv2019

Conserved function of ether lipids and sphingolipids in the early secretory pathway

Sphingolipids have been shown to play important roles in physiology and cell biology, but a systematic examination of their functions is lacking. We performed a genome-wide CRISPRi screen in sphingolipid-depleted cells and identified hypersensitive mutants in genes of membrane trafficking and lipid biosynthesis, including ether lipid synthesis. Systematic lipidomic analysis showed a coordinate regulation of ether lipids with sphingolipids, where depletion of one of these lipid types resulted in increases in the other, suggesting an adaptation and functional compensation. Biophysical experiments on model membranes show common properties of these structurally diverse lipids that also share a known function as GPI anchors in different kingdoms of life. Molecular dynamics simulations show a selective enrichment of ether phosphatidylcholine around p24 proteins, which are receptors for the export of GPI-anchored proteins and have been shown to bind a specific sphingomyelin species. Our results support a model of convergent evolution of proteins and lipids, based on their physico-chemical properties, to regulate GPI-anchored protein transport and maintain homeostasis in the early secretory pathway.

biochemistry↗

bioRxiv2019

Patched regulates lipid homeostasis by controlling cellular cholesterol levels

AbstractHedgehog (Hh) signaling is essential during development and in organ physiology. In the canonical pathway, Hh binding to Patched (PTCH) relieves the inhibition of Smoothened (SMO). Yet, PTCH may also perform SMO-independent functions. While the PTCH homolog PTC-3 is essential in C. elegans, worms lack SMO, providing an excellent model to probe non-canonical PTCH function. Here, we show that PTC-3 is a cholesterol transporter. ptc-3(RNAi) leads to accumulation of intracellular cholesterol and defects in ER structure and lipid droplet formation. These phenotypes were accompanied by a reduction in acyl chain (FA) length and desaturation. ptc-3(RNAi)-induced lethality, fat storage and ER morphology defects were rescued by reducing dietary cholesterol. We provide evidence that cholesterol accumulation modulates the function of nuclear hormone receptors such as of the PPAR homolog NHR-49 and NHR-181, and affects FA composition. Our data uncover a novel role for PTCH in organelle structure maintenance and fat metabolism.

cell biology↗

bioRxiv2019

Cytotoxicity of 1-deoxysphingolipid Unraveled by Genome-wide Genetic Screens and Lipidomics

Hereditary Sensory and Autonomic Neuropathy (HSAN) type IA and IC are caused by elevated levels of an atypical class of lipid named 1-deoxysphingolipid (DoxSL). How elevated levels of DoxSL perturb the physiology of the cell and how the perturbations lead to HSAN IA/C are largely unknown. In this study, we show that C26-1-deoxydihydroceramide (C26-DoxDHCer) is highly toxic to the cell, while C16- and C18-DoxDHCer are less toxic. Genome-wide genetic screens and lipidomics revealed the dynamics of DoxSL accumulation and DoxSL species responsible for the toxicity over the course of DoxSL accumulation. Furthermore, we show that disruption of F-actin organization, alteration of mitochondrial shape, and accumulation of hydrophobic bodies by DoxSL are not sufficient to cause complete cellular failure. However, combined with collapsed ER membrane, these perturbations cause cell death. Thus, we have unraveled key principles of DoxSL cytotoxicity that help to explain the clinical features of HSAN IA/C.

cell biology↗

bioRxiv2018

A chemogenetic approach for optical monitoring of voltage in neurons

Optical monitoring of neuronal voltage using fluorescent indicators is a powerful approach for interrogation of the cellular and molecular logic of the nervous system. Here we describe a Semisynthetic Tethered Voltage Indicator (STeVI1) based upon Nile Red that displays voltage sensitivity when genetically targeted to neuronal membranes. This environmentally sensitive probe allows for wash-free imaging and faithfully detects supra- and subthreshold activity in neurons.

neuroscience↗