Lipid rafts as a membrane-organizing principle

Interaction of major facilitator superfamily domain containing 2A with the blood-brain barrier

The functional and structural integrity of the blood-brain barrier is crucial in maintaining homeostasis in the brain microenvironment; however, the molecular mechanisms underlying the formation and function of the blood-brain barrier remain poorly understood. The major facilitator superfamily domain containing 2A has been identified as a key regulator of blood-brain barrier function. It plays a critical role in promoting and maintaining the formation and functional stability of the blood-brain barrier, in addition to the transport of lipids, such as docosahexaenoic acid, across the blood-brain barrier. Furthermore, an increasing number of studies have suggested that major facilitator superfamily domain containing 2A is involved in the molecular mechanisms of blood-brain barrier dysfunction in a variety of neurological diseases; however, little is known regarding the mechanisms by which major facilitator superfamily domain containing 2A affects the blood-brain barrier. This paper provides a comprehensive and systematic review of the close relationship between major facilitator superfamily domain containing 2A proteins and the blood-brain barrier, including their basic structures and functions, cross-linking between major facilitator superfamily domain containing 2A and the blood-brain barrier, and the in-depth studies on lipid transport and the regulation of blood-brain barrier permeability. This comprehensive systematic review contributes to an in-depth understanding of the important role of major facilitator superfamily domain containing 2A proteins in maintaining the structure and function of the blood-brain barrier and the research progress to date. This will not only help to elucidate the pathogenesis of neurological diseases, improve the accuracy of laboratory diagnosis, and optimize clinical treatment strategies, but it may also play an important role in prognostic monitoring. In addition, the effects of major facilitator superfamily domain containing 2A on blood-brain barrier leakage in various diseases and the research progress on cross-blood-brain barrier drug delivery are summarized. This review may contribute to the development of new approaches for the treatment of neurological diseases.

Interactions of Micro- and Nanoplastics with Biomolecules: From Public Health to Protein Corona Effect and Beyond

Micro- and nanoplastics (M/NPs), as ubiquitous global environmental pollutants, have garnered increasing attention due to their pervasive presence. These particles can interact with biological molecules through various mechanisms, subsequently inducing potential toxic effects on living organisms. This review investigates the hazards of M/NPs and their interactions with biological membranes and proteins, focusing on their interaction mechanisms and potential effects on biomolecular structure and function. Specifically, we summarize the exposure pathways and potential harms of M/NPs, which can enter the human body through ingestion, inhalation, and skin contact, potentially causing toxicity, inflammation responses, oxidative stress, and endocrine disruption. Additionally, we highlight the interaction between M/NPs and biological membranes, which can induce structural changes, including membrane thickening, increased fluidity, and pore formation, thereby compromising membrane integrity and affecting cellular health. Besides, we emphasize the interaction between M/NPs and proteins, suggesting that protein structural changes and corona formation can influence oxidative stress responses and cytotoxicity, thereby impacting cellular functions and viability. Ultimately, suggestions and outlooks for further research are proposed. Overall, this review systematically summarizes current research on the interactions between M/NPs and biomolecules, including their mechanisms and biological effects, providing researchers with a comprehensive understanding of the field.

Mapping in situ the assembly and dynamics in aqueous supramolecular polymers

Supramolecular polymers, bonded through directional non-covalent interactions, closely mimic dynamic behaviors of biological nanofibers. However, the complexity of assembly pathways makes it highly challenging to unravel the nature of supramolecular dynamics in aqueous environments. Here we introduce a precise combinatorial titration methodology to probe in situ the assembly of peptide amphiphiles (PAs). This approach reveals a binary assembly mechanism governed by equilibrium between spheroidal micelles and β-sheet polymers. Weakening hydrogen bonding shifts the equilibrium towards micelles and decreases the internal structural order of filamentous polymers, promoting supramolecular dynamics. Extending this methodology to two-component copolymerization systems, we find a surprising tendency to form blocky nanostructures with reduced internal phase separation as the mismatch in peptide sequence decreases. Interestingly, while well-mixed copolymers acquire different dynamics, mismatched ones retain the characteristic supramolecular motion of their homopolymer counterparts. These critical insights into supramolecular dynamics offer strategies to tailor the dynamic functions of supramolecular nanomaterials.

Modeling the role of supramolecular clustering in multivalent assembly

In self-assembled systems, a combination of multiple weak supramolecular interactions is often utilized to enable strong yet reversible binding. When modeling the behavior of these multivalent interfaces, it is commonly assumed that binding pairs are independent, i.e., the probability of a pair being bound is unaffected by the bound state of neighboring pairs. Inspired by recent experimental work, we report that for a variety of systems this assumption may not hold, leading to the formation of clusters at the binding interface. Through a series of analytical and numerical models of end-functionalized brushes, we reveal the role of cluster size on binding thermodynamics, detail how entropic contributions from polymer chains provide tunable control of cluster size, and provide predictions for cluster size as a function of system architecture. Investigation of these models yields surprising results: within the melting window, the enthalpy of binding of multivalent interfaces is predicted to depend only on cluster size and not on the overall valency of the multivalent system. Moreover, clustering is predicted to be significant even in systems with only weak dipole and dispersion interactions between neighboring groups. Combined, this work brings to light the potential impacts of clustering on multivalent self-assembly, providing theoretical justification for previous experimental observations and paving the way for future work in this area.

A Minimalist Model Lipid System Mimicking the Biophysical Properties of Escherichia coli's Inner Membrane

Biological membranes are essential for the development and survival of organisms. They can be highly complex, usually comprising a variety of lipids, proteins, and other biomolecules organized around a lipid bilayer structure. This complexity makes studying specific features of biological membranes difficult, with many research studies relying on simplified models, such as artificial vesicles or supported lipid bilayers. Here, we search for a minimal, lipid-only model system of the Escherichia coli inner membrane. We aim to retain the main lipidomic components in their native ratio while mimicking the membrane's thermal and mechanical properties. Based on previous studies, we identify 18 potential model systems reflecting key aspects of the known lipidomic composition and progressively narrow down our selection based on the systems' phase transition temperature and mechanical properties. We identify three ternary model systems able to form stable bilayers that can be made of the commercially available synthetic lipids 16:0-18:1 phosphatidylethanolamine (POPE), 16:0-18:1 phosphatidylglycerol (POPG), and 16:0-18:1 cardiolipin (CL). We anticipate our results to be of interest for future studies making use of E. coli models, for example, investigating membrane proteins' function or macromolecule-membrane interactions.

Invadopodia in cancer metastasis: dynamics, regulation, and targeted therapies

Pseudopodia and invadopodia are dynamic, actin-rich membrane structures extending from the cell surface. While pseudopodia are found in various cell types, invadopodia are exclusive to tumor cells and play a key role in cancer progression. These specialized structures enable tumor cells to degrade the extracellular matrix, breach tissue barriers, and invade surrounding tissues and blood vessels, thus facilitating metastasis. Extensive research has elucidated the distinct structure of invadopodia, the signaling pathways driving their formation, and their interaction with the tumor microenvironment. Integrin- and Src kinase-mediated signaling pathways regulate invadopodia dynamics. This review explores the mechanisms underlying invadopodia stabilization and highlights recent insights into their regulation by the tumor microenvironment. Particular emphasis is placed on the role of cell surface signaling in modulating invadopodia activity and the intracellular targeting of matrix metalloproteinases (MMPs) in enhancing invasive potential. A deeper understanding of invadopodia-driven cancer cell migration and metastasis provides valuable implications for therapeutic development. These findings support the potential for receptor-mediated and molecularly targeted therapies to inhibit tumor metastasis, improve clinical outcomes, and enhance the efficacy of existing cancer treatments.

Reprogramming and targeting of cholesterol metabolism in tumor-associated macrophages

Cholesterol, as a major component of cell membranes, is closely related to the metabolic regulation of cells and organisms; tumor-associated macrophages play an important push role in tumor progression. We know that tumor-associated macrophages are polarized from macrophages, and the abnormalities of cholesterol metabolism that may be induced during their polarization are worth discussing. This manuscript focuses on metabolic abnormalities in tumor-associated macrophages, and first provides a basic summary of the regulatory mechanisms of abnormal macrophage polarization. Subsequently, it comprehensively describes the features of abnormal glucose, lipid and cholesterol metabolism in TAMs as well as the different regulatory pathways. Then, the paper also discusses the link between abnormal cholesterol metabolism in TAMs and tumors, chronic diseases and aging. Finally, the paper summarizes cancer therapeutic strategies targeting cholesterol metabolism that are already in clinical trials, as well as nanomaterials capable of targeting cholesterol metabolism that are in the research stage, in the hope of providing value for the design of targeting materials. Overall, elucidating metabolic abnormalities in tumor-associated macrophages, particularly cholesterol metabolism, could provide assistance in tumor therapy and the design of targeted drugs.

Deactivating Symmetry Breaking of a Soft Frank-Kasper Phase via Water-Induced Conformational Ordering of a Shapeshifting Dendritic Amphiphile

Water guides biomolecules to their native conformations in a high-dimensional conformational space. To explore a similar role in synthetic self-assembly, a wedge-shaped, shape-shifting dendron (SD) was studied. Cooling from the isotropic melt trapped SD in a metastable Frank-Kasper σ phase with symmetry breaking due to high conformational freedom. In situ SAXS, microbeam SAXS, and ATR-FTIR confirmed that water vapor disrupts supramolecular micelles in the σ phase and unfolds some cone-shaped SD molecules, facilitating improved chain-chain packing and inducing the low-symmetry σ phase to transition into a more symmetric hydrated lamellar (Lw) phase. The water-induced conformational ordering of the SD thus enables a rare σ → Lw phase transition, initially blocked by the SD's hydrophilic volume fraction. Spectroscopy results also illustrated that during the conformational ordering, water molecules are encapsulated into the hydrophilic domains of the ordered phases, enhancing the phase stability of the Lw phase and the hydrated quasicrystalline DDQC and σ phases that evolved from the Lw phase. These findings reveal a novel self-assembly pathway for the wedge-shaped amphiphile that deactivates the symmetry breaking in the Frank-Kasper σ phase and emphasize the role of water in guiding synthetic molecules to their optimal supramolecular structures, echoing the self-assembly principles in nature.

Cholesterol metabolism: A strategy for overcoming drug resistance in tumors

Despite significant advancements in targeted tumor therapies, the emergence of drug resistance remains a complex challenge. Cholesterol accumulation within tumor cells plays a crucial role in mediating drug resistance through various mechanisms, including altered membrane dynamics, enhanced drug efflux, and activation of survival signaling pathways. Targeting cholesterol metabolism presents an innovative strategy to enhance therapeutic sensitivity, particularly in breast cancer. Consequently, ongoing preclinical studies and clinical trials involving cholesterol-lowering agents indicate a promising direction for improving treatment outcomes in tumors. The combination of these agents with existing therapeutic regimens may lead to enhanced efficacy, highlighting the necessity for continued research in this vital area. This review examines the impact of cholesterol metabolism on drug resistance in tumors, particularly solid tumors, identifies therapeutic targets in this metabolic pathway (with a special focus on breast cancer), and discusses recent advances in cholesterol-lowering drugs in preclinical, as well as those that have entered clinical trials.

Nonequilibrium asymmetry in the living cell membrane

We will discuss how sustained nonequilibrium processes operating at the plasma membrane (PM) determine the dynamical organisation (both lateral and transverse) of lipids, their maintenance and control, under physiological conditions. These nonequilibrium processes include active contractile stresses arising from the inevitable interaction of the inner leaflet of the PM with the adjoining actomyosin cortex, and active flipping of specific lipids. Recently, we showed that the inner leaflet phosphatidylserine (PS) interacts with the actomyosin cortex and engages in a strong transbilayer coupling across the leaflets. Here we develop an active Flory-Huggins theory for the mesoscale segregation of liquid-ordered (lo)-liquid-disordered (ld) domains in an asymmetric membrane bilayer, that incorporates both active contractile stresses at the inner leaflet and transbilayer coupling across the leaflets. The interplay between chemical potential gradients, transbilayer coupling and active stresses drives a rich pattern of mesoscale lo domains - static, strongly fluctuating and moving active emulsions - even at temperatures beyond the equilibrium phase transition temperature. We study conditions under which domain registry and slippage could be observed. We end with a discussion on the role of active flippases on PS in maintaining the active mesoscale organisation.

Pilocarpine inhibits Candida albicans SC5314 biofilm maturation by altering lipid, sphingolipid, and protein content

Candida albicans filamentation and biofilm formation are key virulence factors tied to tissue invasion and antifungal tolerance. Pilocarpine hydrochloride (PHCl), a muscarinic receptor agonist, inhibits biofilm maturation, although its mechanism remains unclear. We explored PHCl effects by analyzing sphingolipid and lipid composition and proteomics in treated C. albicans SC5314 biofilms. PHCl significantly decreased polar lipid and ergosterol levels in biofilms while inducing phytoceramide and glucosylceramide accumulation. PHCl also induced reactive oxygen species and early apoptosis. Proteomic analysis revealed that PHCl treatment downregulated proteins associated with metabolism, cell wall remodeling, and DNA repair in biofilms to levels comparable to those observed in planktonic cells. Consistent with ergosterol reduction, Erg2 was found to be reduced. Overall, PHCl disrupts key pathways essential for biofilm integrity, decreasing its stability and promoting surface detachment, underscoring its potential as a versatile antifungal compound.

IMPORTANCE

Candida albicans filamentation and biofilm formation represent crucial virulence factors promoting fungus persistence and drug tolerance. The common eukaryotic nature of mammalian cells poses significant limitations to the development of new active nontoxic compounds. Understanding the mechanism underlying PHCl inhibitory activity on yeast-hypha transition, biofilm adhesion, and maturation can pave the way to efficient drug repurposing in a field where pharmaceutical investment is lacking.

Asymmetric membrane properties through a protein lens

Plasma membranes are asymmetric, with each monolayer presenting specific lipid compositions and biophysical properties. Transmembrane domains (TMDs) of single-pass transmembrane proteins (spTMPs) have adapted their physico-chemical properties to these asymmetric constraints. In this study, we analysed the structural features of such TMDs across the tree of life to obtain information about their interaction with asymmetric membrane bilayers and predict species-specific membrane properties. We observed that TMDs in the plasma membranes of all eukaryotic species possess asymmetries in lipid accessible surface area (ASA), hydrophobicity, aromaticity and charge. Bacteria deviate from this trend, with strong differences between bacterial clades. Notably, TMDs in the Golgi and the endoplasmic reticulum of eukaryotic species display inverted profiles for accessible surface area, hydrophobicity and aromaticity compared to their plasma-membrane counterparts. To determine how well TMD profiles reflect average membrane properties, we performed molecular dynamics simulations of a spTMP in an asymmetric lipid bilayer whose composition approximates the human plasma membrane. The simulated spTMP was chosen to represent the average TMD properties of the human proteome. We compared the electron density profiles of the simulated asymmetric membrane to the average TMD profiles derived from the human proteome and observed that phospholipid acyl-chain density overlapped very well with TMD hydrophobicity, and phosphate group density with TMD charge. The profiles of phospholipid unsaturation in the acyl chains overlapped well with the average location of TMD phenylalanines in the cytoplasmic leaflet, while there was additional accumulation of large hydrophobic and aromatic residues in the membrane midplane, which had low acyl-chain density. This study reveals the complementarity of membrane and TMD properties in asymmetric membranes, suggesting that the properties of TMDs can be used to make predictions about the properties of their solvating membranes.

Mechanosensitive Conjugated Oligoelectrolytes for Visualizing Temporal Changes in Live Cells

Membrane-intercalating conjugated oligoelectrolytes (COEs) are lipid-bilayer-spanning molecules that serve as fluorescent dyes for bioimaging. However, COE emission has thus far only been capable of visualizing dye location and their preferential accumulation in different membrane-bound intracellular compartments. Herein, we report the first example of environmentally sensitive COEs for visualizing temporal changes in live cells, providing information on the physical properties of intracellular lipid bilayer membranes. The new COE-BY series is designed around a BODIPY central unit with a membrane-spanning topology and six cationic pendant groups ensuring solubility in aqueous media. These reporters feature high two-photon absorption cross section, NIR-II excitation capabilities under multiphoton excitation, and high dye brightness; all highly desirable photophysical features for bioimaging. The emission lifetime of the probes was sensitive to changes to both the lipid composition of model vesicle systems and membrane tension within cells, induced by either mechanical or osmotic stress. Using two-photon fluorescence lifetime imaging microscopy, it is possible to use the most efficient emitter, namely, COE-BYPhOC4, to image changes in the mechanical properties of intracellular membranes. We show that these COEs remain stably vesicle-bound within the endolysosomal pathway over extended periods, allowing for long-term monitoring of the associated biophysical changes of these vesicles over time.

Using phase-resolved vibrational sum-frequency imaging to probe the impact of head-group functionality on hierarchical domain structure in lipid membranes

The substantial diversity in phospholipids within a plasma membrane, varying in tail length, degree of saturation, and head-group functionality, generates widespread structural heterogeneity. This exists both laterally across the membrane through the spontaneous formation of condensed domains that differ from their surrounding expanded phase in density, composition, and molecular packing order, as well as between its two leaflets, which normally maintain significant compositional asymmetry. Of particular importance is the exposure of phosphatidylserine (PS) lipids which is a marker for important physiological processes e.g. apoptosis. Despite this, the molecular-level alterations to the phase-structure of the membrane that result from PS exposure remain generally unknown. In this work, we utilise recently developed phase-resolved azimuthal-scanned sum-frequency generation (SFG) microscopy to investigate structural changes that occur heterogeneously across model membranes as a result of PS-lipid exposure. Specifically, by probing mixed monolayers of 1,2-dipalmitoylphosphatidylcholine (DPPC) and deuterated 1-palmitoyl-2-oleoylphosphatidylcholine (dPOPC) in both the C-H and C-D stretching regions as well as equivalent films with DPPC exchanged with DPPS, we analyse the variations in the apparent phase distributions and domain morphologies, and quantitatively extract the density, composition, and relative out-of-plane packing order for both mixtures. We find that, in these mixtures, DPPS shows vast differences in the domain growth and coalescence behaviour compared to DPPC, as well as in the relative compositions and molecular ordering within each phase. This demonstrates the critical role the head-group plays in the heterogeneous phase structure of the membrane and may give insights into their impact on important physiological processes.

The role of alpha-synuclein in synucleinopathy: Impact on lipid regulation at mitochondria-ER membranes

The protein alpha-synuclein (αSyn) plays a pivotal role in the pathogenesis of synucleinopathies, including Parkinson's disease and multiple system atrophy, with growing evidence indicating that lipid dyshomeostasis is a key phenotype in these neurodegenerative disorders. Previously, we identified that αSyn localizes, at least in part, to mitochondria-associated endoplasmic reticulum membranes (MAMs), which are transient functional domains containing proteins that regulate lipid metabolism, including the de novo synthesis of phosphatidylserine. In the present study, we analyzed the lipid composition of postmortem human samples, focusing on the substantia nigra pars compacta of Parkinson's disease and controls, as well as three less affected brain regions of Parkinson's donors. To further assess synucleinopathy-related lipidome alterations, similar analyses were performed on the striatum of multiple system atrophy cases. Our data reveal region- and disease-specific changes in the levels of lipid species. Specifically, our data revealed alterations in the levels of specific phosphatidylserine species in brain areas most affected in Parkinson's disease. Some of these alterations, albeit to a lesser degree, are also observed in multiple system atrophy. Using induced pluripotent stem cell-derived neurons, we show that αSyn regulates phosphatidylserine metabolism at MAM domains, and that αSyn dosage parallels the perturbation in phosphatidylserine levels. These findings support the notion that αSyn pathophysiology is linked to the dysregulation of lipid homeostasis, which may contribute to the vulnerability of specific brain regions in synucleinopathy. These findings have significant therapeutic implications.

Comprehensive Identification of Lipid-Membrane Protein Interactions via Advanced Proteomics and Extended Lipid-Immobilized Bead Technology

In biological membranes, lipids interact with membrane proteins (MPs) and play important roles in allosterically regulating their structure and function. Analyzing lipid-MP interactions is necessary for understanding these regulatory mechanisms; however, there have been few comprehensive and systematic studies to date. To address this, we developed a high-sensitivity, high-throughput platform that integrates lipid-immobilized beads with advanced proteomics to analyze lipid-MP interactions in detail. We prepared six types of lipid-immobilized beads, including sphingomyelin (SM), ceramide (Cer), dihydrosphingomyelin (DHSM), dihydroceramide (DHCer), phosphatidylcholine (PC), and cholesterol (Chol). In addition, we introduced a novel type of beads that immobilized SM and Chol (SM/Chol beads) to mimic lipid rafts. We first demonstrated that SM/Chol beads coprecipitated with Nakanori, a protein that specifically recognizes and binds to SM/Chol complexes, whereas beads immobilized with SM or Chol alone did not coprecipitate. This indicates the effectiveness of SM/Chol beads for the identification of raft-associated proteins. Next, the cell lysates were incubated with the seven types of lipid-immobilized beads and the recovered proteins were analyzed using shotgun proteomics. This approach successfully identified over 7000 lipid-binding proteins. Filtering based on fold-change values and subsequent enrichment analysis revealed distinct binding protein profiles for each lipid, highlighting the functional diversity of lipid-MP interactions and their roles in cellular processes. In summary, our methodology enables an unprecedented large-scale exploration of lipid-MP interactions. This platform provides a versatile tool for examining the lipid-mediated regulation of MPs and offers new insights into the physiological significance of the lipidome and its implications for health and disease.

Elucidating metabolites and biosynthetic pathways during musk maturation: insights from forest musk deer

Background

Musk is a blackish-brown solid used in traditional Chinese medicine with a unique and intense scent. Limited evidence on its function and pathways is available from databases due to the complexity, variability, and derivativity of chemical composition.

Results

In this study, musk samples from three different stages during maturation: the end of June (group A), August (group B), and October (group C) were harvested from six male forest musk deer. A gas chromatography and mass spectrometry (GC-MS) approach was used to explore the chemical composition. Results indicated the presence of 66 known and 14 unknown chemicals, including 29 aromatic compounds. Lipids (51.52%), organic oxygen compounds (28.79%), and organoheterocyclic compounds (12.12%) were the most abundant substances. A total of 13 differential metabolites were found, including four macrocyclic ketones and six androgens and derivatives that increased as musk matured. Biosynthesis of unsaturated fatty acids was enriched in differential metabolites across stages. Tetracosanoic acid, methyl ester, and TES1 [EC: 3.1.2.2] participated in the biosynthesis of muscone. A total of nine chemicals and six steroidogenic enzymes participated in steroid hormone biosynthesis.

Conclusion

This study annotates and defines metabolites in musk systematically, macrocyclic ketones (9.09%) and lipids (51.52%) were categorized unambiguously, suggesting that previous studies have underestimated the lipid content in musk, and critical role for lipid metabolism in musk gland development and odor profile formation. The high lipid content may reflect energy storage for glandular activity or serve as precursors for volatile compound synthesis, offering new mechanistic insights into musk maturation. Therefore, we preliminarily decipher the biosynthetic pathways of muscone and steroids through providing involved enzymes and metabolites. These results will deepen the understanding of the composition of natural musk and offer new theoretical insights to promote the comprehensive use of this resource.

Local mapping of the nanoscale viscoelastic properties of fluid membranes by AFM nanorheology

Biological membranes are intrinsically dynamic entities that continually adapt their biophysical properties and molecular organisation to support cellular function. Current microscopy techniques can derive high-resolution structural information of labelled molecules but quantifying the associated viscoelastic behaviour with nanometre precision remains challenging. Here, we develop an approach based on atomic force microscopy in conjunction with fast nano-actuators to map the viscoelastic response of unlabelled supported membranes with nanometre spatial resolution. On fluid membranes, we show that the method can quantify local variations in the molecular mobility of the lipids and derive a diffusion coefficient. We confirm our experimental approach with molecular dynamics simulations, also highlighting the role played by the water at the interface with the membrane on the measurement. Probing ternary model bilayers reveals spatial correlations in the local diffusion over distances of ≈20 nm within liquid disordered domains. This lateral correlation is enhanced in native bovine lens membranes, where the inclusion of protein-rich domains induces four-fold variations in the diffusion coefficient across < 100 nm of the fluid regions, consistent with biological function. Our findings suggest that diffusion is highly localised in fluid biomembranes.

Anionic Cyanine Membrane Probes for Live Cells and In Vivo Fluorescence Imaging

Molecular probes for cell plasma membranes are indispensable for fluorescence imaging. Herein, we present an array of five anionic cyanine-based turn-on plasma membrane probes with emission spanning from green to near infrared. They are analogous to the commonly used MemBright probe family, where two zwitterionic anchor groups are replaced with anionic sulfonates with dodecyl chains. The developed probes provide selective wash-free staining of plasma membranes of live cells in vitro, featuring improved brightness and slower internalization inside the cells. In comparison to protein-based (wheat germ agglutinin) membrane markers, new membrane probes provide better staining in poorly accessible cell-cell contacts. A key challenge is to stain cell plasma membranes directly in vivo. During in vivo brain tissue imaging in living mice by two-photon microscopy, the anionic cyanine probes allowed us to visualize in detail the pyramidal neurons with high image quality, clearly resolving neuron soma, dendrites with dendritic spines, and axons with axonal boutons. The developed anionic cyanine-based plasma membrane probes constitute an important extension of the toolbox for plasma membrane research.

Lipid rafts: novel therapeutic targets for metabolic, neurodegenerative, oncological, and cardiovascular diseases

Lipid rafts are specialized microdomains within cellular membranes enriched with cholesterol and sphingolipids that play key roles in cellular organization, signaling, and homeostasis. This review highlights their involvement in protein clustering, energy metabolism, oxidative stress responses, inflammation, autophagy, and apoptosis. These findings clarify their influence on signaling, trafficking, and adhesion while interacting with the extracellular matrix, cytoskeleton, and ion channels, making them pivotal in the progression of various diseases. This review further addresses their contributions to immune responses, including autoimmune diseases, chronic inflammation, and cytokine storms. Additionally, their role as entry points for pathogens has been demonstrated, with raft-associated receptors being exploited by viruses and bacteria to increase infectivity and evade immune defenses. Disruptions in lipid raft dynamics are linked to oxidative stress and cellular signaling defects, which contribute to metabolic, neurodegenerative, and cardiovascular diseases. This review underscores their potential as therapeutic targets, discussing innovations such as engineered lipid raft transplantation. Advances in analytical techniques such as mass spectrometry have expanded our understanding of lipid raft composition and dynamics, opening new directions for research. By consolidating the current insights, we highlight the therapeutic potential of lipid rafts and highlight the need for further exploration of their molecular mechanisms.

Modular Design of Membrane-Impermeable Versatile Probe for Specific Imaging of Cell Walls and Real-Time Detection of Cell Membrane Damage

The versatile fluorescent dyes are essential for specifically labeling plant cell walls in vivo, monitoring plasma membrane damage, and assessing cell viability. However, such dyes are rare and often discovered accidentally due to a lack of design principles. Propidium iodide, a well-known example, has limitations like low brightness, high toxicity, and poor bacterial differentiation. To address these challenges, we developed VersaDye, a modular probe designed for specific imaging of live plant cell walls and monitoring plasma membrane damage in plant cells, human cells, and certain bacteria. The design integrates impermeability principles and environment-dependent fluorophore scaffolds. VersaDye enables bright, wash-free labeling of plant cell walls and can stain various plant organs for constructing 3D tissue organization. Notably, it can selectively distinguish live Gram-positive from Gram-negative bacteria, a feature absent in other dyes. Its impermeability and targeting ability also allow it to probe membrane damage caused by physical, chemical, and biological stimuli. This study marks the first use of VersaDye in analyzing cell damage in live plants under salt stress. VersaDye offers a robust platform for wash-free, in vivo membrane damage monitoring and simultaneous cell wall labeling. Additionally, its design suggests adaptability for regulating permeability to meet specific diagnostic needs, such as identifying membrane-compromised cells in diseases or enabling high-throughput antibiotic screening targeting specific bacteria.

T cells in ARAP-deficient mice present defective T cell receptor signaling and reduced severity in an experimentally-induced autoimmune disease

We previously reported a novel adaptor protein, ARAP, required for T cell receptor signaling and integrin-mediated adhesion. The present study investigates further the role of ARAP in T cell biology using mice with an ARAP gene deficiency. Similar to wild-type mice, ARAP-deficient mice participate in normal breeding and immune cell development. Similar defects were observed in the T cell receptor signaling and adhesion of ARAP-deficient mice, as shown in previous studies investigating ARAP-suppressed Jurkat T cells. ARAP deficiencies analyzed in vivo presented a less severe clinical course of experimental autoimmune encephalomyelitis (EAE) following immunization of mice with the myelin oligodendrocyte glycoprotein (MOG). Serum levels of MOG-specific antibodies and IFN-γ were also reduced in ARAP-deficient EAE mice compared to wild-type EAE mice. Moreover, adoptive transfer of ARAP-deficient T cells induced less severe EAE in recombination-activating gene 1-deficient mice than wild-type T cell transfer. These results strongly suggest that ARAP positively regulates T cell function, while ARAP deficiency in T cells reduces the severity and incidence of EAE.

Emerging roles of mechanically activated ion channels in autoimmune disease

Mechanically activated (MA) ion channels have rapidly gained prominence as vital conduits bridging aberrant mechanical cues in tissues with the dysregulated immune responses at the core of autoimmune diseases. Once regarded as peripheral players in inflammation, these channels, exemplified by PIEZO1, TRPV4, and specific K2P family members, now play a central role in modulating T-cell effector functions, B- cell activation and the activity of macrophages and dendritic cells. Their gating is intimately tied to physical distortions such as increased tissue stiffness, osmotic imbalances, or fluid shear, triggering a cascade of ionic fluxes that elevate proinflammatory signaling and drive tissue-destructive loops. Recognition of these channels as central mediators of mechanical stress-induced inflammation responses in autoimmune pathogenesis is rapidly expanding. In parallel, the emerging therapeutic strategies aim to restrain overactive mechanosensors or selectively harness them in affected tissues. Small molecules, peptide blockers, and gene-targeting approaches show preclinical promise, although off-target effects and the broader homeostatic roles of these channels warrant caution. This review explores how integrating mechanobiological concepts with established immunological paradigms enables a more detailed understanding of autoimmune pathogenesis. By elucidating how mechanical forces potentiate or dampen pathological immunity, we propose innovative strategies that exploit mechanosensitivity to recalibrate immune responses across a spectrum of autoimmune conditions.

Nanotechnology-Driven Strategy Against SARS-CoV-2: Pluronic F127-Based Nanomicelles with or Without Atazanavir Reduce Viral Replication in Calu-3 Cells

Despite extensive efforts, no highly effective antiviral molecule exists for treating moderate and severe COVID-19. Nanotechnology has emerged as a promising approach for developing novel drug delivery systems to enhance antiviral efficacy. Among these, polymeric nanomicelles improve the solubility, bioavailability, and cellular uptake of therapeutic agents. In this study, Pluronic F127-based nanomicelles were developed and evaluated for their antiviral activity against SARS-CoV-2. The nanomicelles, formulated using the direct dissolution method, exhibited an average size of 37.4 ± 8.01 nm and a polydispersity index (PDI) of 0.427 ± 0.01. Their antiviral efficacy was assessed in SARS-CoV-2-infected Vero E6 and Calu-3 cell models, where treatment with a 1:2 dilution inhibited viral replication by more than 90%. Cytotoxicity assays confirmed the nanomicelles were non-toxic to both cell lines after 72 h. In SARS-CoV-2-infected Calu-3 cells (human type II pneumocyte model), treatment with Pluronic F127-based nanomicelles containing atazanavir (ATV) significantly reduced viral replication, even under high MOI (2) and after 48 h, while also preventing IL-6 upregulation. To investigate their mechanism, viral pretreatment with nanomicelles showed no inhibitory effect. However, pre-exposure of Calu-3 cells led to significant viral replication reduction (>85% and >75% for 1:2 and 1:4 dilutions, respectively), as confirmed by transmission electron microscopy. These findings highlight Pluronic F127-based nanomicelles as a promising nanotechnology-driven strategy against SARS-CoV-2, reinforcing their potential for future antiviral therapies.

Glycosphingolipids in neurodegeneration - Molecular mechanisms, cellular roles, and therapeutic perspectives

Neurodegenerative diseases, including Alzheimer's (AD), Parkinson's (PD), Huntington's (HD), and amyotrophic lateral sclerosis (ALS), are characterized by progressive neuronal loss and pose significant global health challenges. Glycosphingolipids (GSLs), critical components of neuronal membranes, regulate signal transduction, membrane organization, neuroinflammation, and lipid raft functionality. This review explores GSL roles in neural development, differentiation, and neurogenesis, along with their dysregulation in neurodegenerative diseases. Aberrations in GSL metabolism drive key pathological features such as protein aggregation, neuroinflammation, and impaired signaling. Specific GSLs, such as GM1, GD3, and GM3, influence amyloid-beta aggregation in AD, α-synuclein stability in PD, and mutant huntingtin toxicity in HD. Therapeutic strategies targeting GSL metabolism, such as GM1 supplementation and enzyme modulation, have demonstrated potential to mitigate disease progression. Further studies using advanced lipidomics and glycomics may support biomarker identification and therapeutic advancements. This work aims to highlight the translational potential of GSL research for diagnosing and managing devastating neurodegenerative conditions.

Metabolome and RNA-seq reveal discrepant metabolism and secretory metabolism profile in skeletal muscle between obese and lean pigs at different ages

Metabolites and metabolism-related gene expression profiles in skeletal muscle change dramatically under obesity, aging and metabolic disease. Since obese and lean pigs are ideal models for metabolic research. Here, we compared metabolome and transcriptome of Longissimus dorsi (LD) muscle between Taoyuan black (TB, obese) and Duroc (lean) pigs at different ages. We defined the "window phase" of intramuscular fat (IMF) deposition in TB pig, which has significantly higher IMF than Duroc pig. Our results displayed discrepant lipid composition and different expression genes (DEGs) enriched in lipid metabolism, and both metabolome and transcriptome analyses revealed stronger energy expenditure and more active amino acid and protein metabolism in Duroc pig. 10 up- and 51 down-regulated biomarker metabolites with age- and breed-specificity were identified. Potential secretory metabolites, including organic acid (fumaric acid, succinate, malic acid, and gamma-aminobutyric acid), amino acid (L-lysine, and L-glutamic acid), lipid (2-hydroxyisovaleric acid, and L-carnitine) were demonstrated a significant correlation with IMF deposition. Our research highlights the huge difference of metabolic spectrum in skeletal muscle between obese and lean model and muscle-derived secretory metabolites might act as an ambassador of intercellular communication to regulate systematic metabolism.

Regulation of osteoclast-mediated bone resorption by lipids

Hyperactivation of osteoclasts has been identified as a significant etiological factor in several bone resorption-related disorders, including osteoporosis, periodontitis, arthritis, and bone metastasis of tumors. It has been demonstrated that the severity of these diseases is influenced by lipids that regulate osteoclast differentiation and activity through specific signaling pathways and cytokine levels. The regulatory mechanisms of different types of lipids on osteoclastogenesis vary across diverse disease contexts in bone resorption regulated by osteoclasts. This review presents an overview of the mechanisms underlying osteoclast formation and summarizes the pathways through which various lipids regulate osteoclastogenesis in different pathological contexts. We also discuss effective therapeutic strategies for osteolytic diseases based on modulation of lipid metabolism.

Stromal Stiffness-Regulated IGF2BP2 in Pancreatic Cancer Drives Immune Evasion via Sphingomyelin Metabolism

BACKGROUND AND AIMS

Immunotherapy has shown promising results in cancer treatment; however, it remains largely ineffective for pancreatic ductal adenocarcinoma (PDAC). N6-methyladenosine (m6A), known for its crucial role in cancer biology, is not yet fully understood regarding immune evasion. This study aims to elucidate the associations and mechanisms linking m6A modification with immune evasion in PDAC and propose strategies for clinical intervention.

METHODS

A multimodal PDAC cohort of 122 patients was developed, integrating transcriptomic profiling, imaging mass cytometry, and m6A quantification to identify m6A regulators associated with immunosuppressive tumor microenvironment (TME) and clinical outcomes. Findings were validated across 6 independent PDAC cohorts. Assays including MeRIP, RIP, and RNA pull-down confirmed that IGF2BP2 binds to targets, whereas scRNA-seq, flow cytometry, and mIHC profiled the TME. Preclinical interventions were tested in PDAC organoids, patient-derived tissue fragments, and humanized mouse models.

RESULTS

Our comprehensive analysis identified the m6A reader protein IGF2BP2 as a critical factor associated with poor prognosis in PDAC, linked to reduced effector cell infiltration and a fibrotic TME. High matrix stiffness in PDAC stabilized IGF2BP2, which subsequently promoted sphingomyelin synthesis via SGMS2 up-regulation. This pathway facilitates PD-L1 localization on membrane lipid rafts, enhancing immune evasion. The elastographic properties of PDAC enabled noninvasive screening of patients with overexpressed IGF2BP2/SGMS2. Disrupting sphingomyelin synthesis improved antitumor immunity and suppressed PDAC growth in humanized mice, highlighting immunotherapeutic opportunities for PDAC.

CONCLUSIONS

These findings emphasize the critical interplay between extrinsic matrix stiffness and intrinsic IGF2BP2-regulated sphingomyelin synthesis, identifying a promising target for immunotherapeutic strategies in PDAC.

Cholesterol´s role in membrane organization and nicotinic acetylcholine receptor function: Implications for aging and Alzheimer's disease

Biological membranes are complex entities composed of various molecules exhibiting lateral and transbilayer lipid asymmetries, along with a selective spatial distribution of different membrane proteins. This dynamic orchestration is crucial for proper physiological functions, undergoes changes with aging, and is disturbed in several neurological disorders. In this review, we analyze the impact of disruption in this equilibrium on physiological aging and the onset of pathological conditions. Alzheimer´s disease (AD) is a multifactorial neurodegenerative disorder in the elderly, characterized by the increased presence of the Aβ peptide, which supports the amyloid hypothesis of the disease. However, AD also involves a progressive loss of cholinergic innervation, leading to the cholinergic hypothesis of the disease. Nicotinic acetylcholine receptors (nAChRs) are transmembrane proteins, and Aβ peptides, their oligomeric and fibrillar species, which increase in hydrophobicity as they develop, interact with membranes. Therefore, a membrane hypothesis of the disease emerges as a bridge between the other two. Here, we discuss the impact of the membrane environment, through direct or indirect mechanisms, on cholinergic signaling and Aβ formation and subsequent incorporation into the membrane, with a special focus on the crucial role of cholesterol in these processes.

Dynamic Lipidome Reorganization in Response to Heat Shock Stress

The heat shock response (HSR) is a conserved cellular mechanism critical for adaptation to environmental and physiological stressors, with broad implications for cell survival, immune responses, and cancer biology. While the HSR has been extensively studied at the proteomic and transcriptomic levels, the role of lipid metabolism and membrane reorganization remains underexplored. Here, we integrate mass spectrometry-based lipidomics with RNA sequencing to characterize global lipidomic and transcriptomic changes in HeLa cells exposed to three conditions: control, heat shock (HS), and HS with eight hours of recovery. Heat shock-induced extensive lipid remodeling, including significant increases in fatty acids, glycerophospholipids, and sphingolipids, with partial normalization during recovery. Transcriptomic analysis identified over 2700 upregulated and 2300 downregulated genes under heat shock, with GO enrichment suggesting potential transcriptional contributions to lipid metabolism. However, transcriptional changes alone did not fully explain the observed lipidomic shifts, suggesting additional layers of regulation. Joint pathway analysis revealed enrichment in glycerophospholipid and sphingolipid metabolism, while network analysis identified lipid transport regulators (STAB2, APOB), stress-linked metabolic nodes (KNG1), and persistent sphingolipid enrichment during recovery. These findings provide a comprehensive framework for understanding lipid-mediated mechanisms of the HSR and highlight the importance of multi-omics integration in stress adaptation and disease biology.

Malabaricone C isolated from edible plants as a potential inhibitor of SARS-CoV-2 infection

Although the SARS-CoV-2 epidemic worldwide has gradually decreased, in some areas, the situation has not yet been stamped and has become a global health emergency. It is quite possible that we could again be threatened by a new coronavirus. Therefore, new nucleotide analog drugs and vaccines or using drug repositioning for SARS-CoV-2 still has been developed, yet their safety and efficacy against COVID-19 remains underexplored. Malabaricone C is 2,6-dihydroxyphenyl acylphenol found in edible plants such as the mace spice of nutmeg derived from the seeds of Myristica fragrans. In this study, we identified malabaricone C as the first inhibitor of SARS-CoV-2 from natural food with a safe alternative for drugs. Malabaricone C and its chemical derivatives showed EC50 values of 1-1.5 μM against SARS-CoV-2 (WK-521, ancestral strain) and its variant strains in mammalian cells (HEK293T and Vero E6). In addition, we have successfully established novel evaluation system for the inhibition of SARS virus cell fusion by visualization for providing a versatile tool for study SARS-CoV-2 mediated fusion. Furthermore, our experiments suggested that malabaricone C could affect the distribution of sphingomyelin on the plasma membrane, which involves in viral infections. Thus, in light of the beneficial effect of malabaricone C on viral infection, the nontoxic malabaricone C is a suitable candidate as a drug that can be employed in the treatment and prevention of COVID-19. Moreover, it may potentially be used to treat acute infections of other enveloped viruses.

Temperature dependence of membrane viscosity of ternary lipid GUV with Lo domains

In the cell membrane, it is considered that saturated lipids and cholesterol organize liquid-ordered (Lo) domains in a sea of liquid-disordered (Ld) phases and proteins relevant to cellular functions are localized in the Lo domains. Since the diffusion of transmembrane proteins is regulated by the membrane viscosity, we investigate the temperature dependence of the membrane viscosity of the ternary giant unilamellar vesicles (GUVs) composed of the saturated lipid 1,2-dipalmitoyl-sn-glycero-3-phosphocholine, the unsaturated lipid 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC), and cholesterol to understand the effect of the phase separation on the membrane viscosity using a microinjection technique. In the microinjection method, membrane viscosity is estimated by comparing the flow pattern induced on a spherical membrane with a hydrodynamic model. For phase-separated GUVs, the flow pattern is visualized by the motion of the domains. In this study, we developed a method to visualize the flow patterns of homogeneous GUVs above the phase separation temperature by using beads attached to the GUVs. We succeeded in measuring the membrane viscosity of ternary GUVs both above phase separation temperature and in the phase-separated region and found that the membrane viscosity decreases dramatically by phase separation. In the phase-separated region, i.e., GUVs with Lo domains, the membrane viscosity is determined by that of the Ld phase, ηLd, and shows weak temperature dependence compared to that of the DOPC single-component GUV, which is a main component of the Ld phase. We revealed that the Moelwyn-Hughest model, which takes into account the effects of the membrane composition, viscosity of the pure component, and interaction between components, well describes the obtained membrane viscosity of the ternary GUV both above the phase separation temperature and in the phase-separated region. The drastic decrease of the membrane viscosity by the phase separation plays an important role in regulating the mobility of constituents in multi-component membranes.

Identification of AXL as a novel positive regulator of lipid raft in gastric cancer

Lipid rafts are highly heterogeneous and dynamic microdomains involved in molecule trafficking and signaling transduction. This study investigates the role of lipid rafts in gastric cancer and their key regulators. Analyzing FFPE samples from 111 gastric cancer patients, we found that high lipid raft levels predict poor prognosis. Modulating these levels in gastric cancer cell lines significantly impacted cell proliferation, migration, and invasion. Weighted Gene Co-expression Network Analysis identified AXL as a hub gene associated with lipid rafts. AXL knockdown experiments revealed its interaction with Caveolin-1, a caveolae lipid raft protein, which regulates lipid raft levels and promotes AKT and ERK signaling, enhancing cancer development and metastasis. In vivo tumorigenesis assays and survival analyses further supported these findings. This study underscores the significance of lipid rafts in gastric cancer and identifies AXL as a novel regulator, offering new insights into the molecular mechanisms of cancer progression and suggesting potential therapeutic targets.

Machine learning in molecular biophysics: Protein allostery, multi-level free energy simulations, and lipid phase transitions

Machine learning (ML) techniques have been making major impacts on all areas of science and engineering, including biophysics. In this review, we discuss several applications of ML to biophysical problems based on our recent research. The topics include the use of ML techniques to identify hotspot residues in allosteric proteins using deep mutational scanning data and to analyze how mutations of these hotspots perturb co-operativity in the framework of a statistical thermodynamic model, to improve the accuracy of free energy simulations by integrating data from different levels of potential energy functions, and to determine the phase transition temperature of lipid membranes. Through these examples, we illustrate the unique value of ML in extracting patterns or parameters from complex data sets, as well as the remaining limitations. By implementing the ML approaches in the context of physically motivated models or computational frameworks, we are able to gain a deeper mechanistic understanding or better convergence in numerical simulations. We conclude by briefly discussing how the introduced models can be further expanded to tackle more complex problems.

Large, recursive membrane platforms are associated to Trop-1, Trop-2, and protein kinase signaling for cell growth

The transmembrane glycoproteins Trop-1/EpCAM and Trop-2 independently trigger Ca2+ and kinase signals for cell growth and tumor progression. Our findings indicated that Trop-1 and Trop-2 tightly colocalize at macroscopic, ruffle-like protrusions (RLP), that elevate from the cell perimeter, and locally recur over hundreds of seconds. These previously unrecognized elevated membrane regions ≥20-µm-long, up to 1.5 µm high were revealed by Z-stack analysis and three-dimensional reconstruction of signal transducer-hosting plasma membrane regions. Trop-2 stimulates cell growth through a membrane supercomplex that comprises CD9, PKCα, ion pumps, and cytoskeletal components. Our findings indicated that the growth-driving Trop-2 supercomplex assembles at RLP. RLP behaved as sites of clustering of signal transducers, of phosphorylation/activation of growth-driving kinases, as recruitment sites of PKCα and as origin of Ca2+ signaling waves, suggesting RLP to be novel signaling platforms in living cells. RLP were induced by growth factors and disappeared upon growth factor deprivation and β-actin depolymerization, candidating RLP to be functional platforms for high-dimensional signaling for cell growth.

Green fluorescent FM dyes with prolonged retention for 4D tracking of plasma membrane dynamics in live plants under environmental stress

Macroscopic phenotypic changes in plants are frequently employed as a means of evaluating the biological response of plants to external environmental stresses. However, the lack of effective observational tools at the microscopic cellular level hinders the ability to fully comprehend the intricacies of this response. Herein, we developed a plasma membrane fluorescent dye with target-activated green emission complemented with conventional FM dyes, and established a four-dimensional (4D) imaging approach based on this dye for spatio-temporal monitoring of plasma membrane dynamics during cellular responses to external environmental stress. A green fluorescent dye, designated FMG-DBO, was constructed by modifying the bridged unit between the aniline donor and the pyridinium acceptor. Its green emission can be combined with that of conventional FM dyes, enabling high-resolution imaging of plant leaf cells containing chlorophyll. The anchoring ability of the dyes was enhanced by incorporating a rigid diaza[2.2.2]octane unit as an anti-permeability group. The long retention time of the FMG-DBO dye in the plasma membrane enables the tracking of three-dimensional dynamics of the plasma membrane of plant cells. Consequently, an FMG-DBO-based four-dimensional imaging approach was established to monitor dynamic changes of plant cells under external environmental stress at the cellular level. The biological responses of two different drought-tolerant rice root cells to drought stress were examined by this four-dimensional imaging approach. It was observed that the two types of rice root cells exhibited disparate responses to the drought environmen. This approach offers alternative cell-level visualization tools for evaluating the biological responses of plant cells under environmental stress.

The Bacterium P. aeruginosa Disperses Ordered Membrane Domains by Targeting Phase Boundaries

Various pathogens use receptors on the host's plasma membrane for their cellular uptake. For the bacterium Pseudomonas aeruginosa, interactions between its lectin LecA and the host cell glycosphingolipid globotriaosylceramide (also known as Gb3) are crucial for its internalization via the so-called lipid zipper mechanism. In this study, we investigated the interactions of the P. aeruginosa strain PAO1 with phase-separated lipid bilayers containing Gb3. Surprisingly, bacteria are mostly bound to the interphase of liquid-ordered (Lo) and liquid-disordered (Ld) membrane domains. Simultaneously with the formation of bacterial aggregates and the accumulation of membrane lipids, the lipid bilayers were drastically reorganized and Lo domains were dissolved. Surprisingly, Gb3 was found to play a role in the localization of the bacterium at the interface, less so LecA. When microspheres were used as a minimal mimic of the bacterium, these beads also localized preferentially at the Lo-Ld phase boundaries, but in contrast to living bacteria, beads were unable to cause membrane reorganization and dissolution of the Lo domain, even when coated with LecA. Targeting phase boundaries as "weak points" in membranes and thereby reorganizing and destabilizing the host cell plasma membrane could be an attractive entry strategy for P. aeruginosa and many other bacteria and viruses.

Role of Protein Regulators of Cholesterol Homeostasis in Immune Modulation and Cancer Pathophysiology

Cholesterol metabolism and homeostasis have emerged as important factors governing various aspects of cancer biology. Clinical associations between circulating cholesterol and poor prognosis or use of cholesterol-lowering medication and improved prognosis have been noted for several different solid tumors. Mechanistically, cholesterol has many different direct and indirect effects on cancer cells themselves but is also critically involved in shaping the function of other cells of the tumor microenvironment, especially immune cells. There are 2 major feedback loops regulating cholesterol homeostasis. Here we highlight the major proteins involved in the so-called oxysterol-bile acid feedback loop and discuss how each has been implicated in cancer biology. We focus on roles within the immune system with implications for cancer. Given that many of these proteins are enzymes or nuclear receptors, both of which are amenable to small molecule intervention, we posit that this axis may represent a promising area for therapeutic intervention.

Sorting of complex sphingolipids within the cellular endomembrane systems

Cells contain a plethora of structurally diverse lipid species, which are unevenly distributed across the different cellular membrane compartments. Some of these lipid species require vesicular trafficking to reach their subcellular destinations. Here, we review recent advances made in the field that contribute to understanding lipid sorting during endomembrane trafficking.

Lipid-Directed Covalent Labeling of Plasma Membranes for Long-Term Imaging, Barcoding and Manipulation of Cells

Fluorescent probes for cell plasma membranes (PM) generally exploit a noncovalent labeling mechanism, which constitutes a fundamental limitation in multiple bioimaging applications. Here, we report a concept of lipid-directed covalent labeling of PM, which exploits transient binding to the lipid membrane surface generating a high local dye concentration, thus favoring covalent ligation to random proximal membrane proteins. This concept yielded fluorescent probes for PM called MemGraft, which are built of a dye (cyanine Cy3 or Cy5) bearing a low-affinity membrane anchor and a reactive group: an activated ester or a maleimide. In contrast to specially designed control dyes and commercial Cy3-based labels of amino or thiol groups, MemGraft probes stain efficiently PM, revealing the crucial role of the membrane anchor combined with optimal reactivity of the activated ester or the maleimide. MemGraft probes overcome existing limitations of noncovalent probes, which makes them compatible with cell fixation, permeabilization, trypsinization, and the presence of serum. The latter allows long-term cell tracking and video imaging of cell PM dynamics without the signs of phototoxicity. The covalent strategy also enables staining and long-term tracking of cocultured cells labeled in different colors without exchange of probes. Moreover, the combination of MemGraft-Cy3 and MemGraft-Cy5 probes at different ratios enabled long-term cell barcoding in at least 5 color codes, important for tracking and visualizing multiple populations of cells. Ultimately, we found that the MemGraft strategy enables efficient biotinylation of the cell surface, opening the path to cell surface engineering and cell manipulation.

Dynamic Lipidome Reorganization in Response to Heat Shock Stress

The heat shock response (HSR) is a conserved cellular mechanism critical for adaptation to environmental and physiological stressors, with broad implications for cell survival, immune responses, and cancer biology. While the HSR has been extensively studied at the proteomic and transcriptomic levels, the role of lipid metabolism and membrane reorganization remains underexplored. Here, we integrate mass spectrometry-based lipidomics with RNA sequencing to characterize global lipidomic and transcriptomic changes in HeLa cells exposed to three conditions: control, heat shock (HS), and HS with eight hours of recovery. Heat shock-induced extensive lipid remodeling, including significant increases in fatty acids, glycerophospholipids, and sphingolipids, with partial normalization during recovery. Transcriptomic analysis identified over 2,700 upregulated and 2,300 downregulated genes under heat shock, with GO enrichment suggesting potential transcriptional contributions to lipid metabolism. However, transcriptional changes alone did not fully explain the observed lipidomic shifts, suggesting additional layers of regulation. Joint pathway analysis revealed enrichment in glycerophospholipid and sphingolipid metabolism, while network analysis identified lipid transport regulators (STAB2, APOB), stress-linked metabolic nodes (KNG1), and persistent sphingolipid enrichment during recovery. These findings provide a comprehensive framework for understanding lipid-mediated mechanisms of the HSR and highlight the importance of multi-omics integration in stress adaptation and disease biology.

Spectrally Resolved Single-Molecule Orientation Imaging Reveals a Direct Correspondence between the Polarity and Microviscosity Experienced by Nile Red in Supported Lipid Bilayer Membranes

Molecular-level interactions among lipids, cholesterol, and water dictate the nanoscale membrane organization of lipid bilayers into liquid-ordered (Lo) and liquid-disordered (Ld) phases, characterized by different polarities and orders. Generally, solvatochromic dyes easily discriminate polarity difference between Lo and Ld phases, whereas molecular flippers and rotors show distinct photophysics depending on the membrane order. Despite progress in single-molecule spectral imaging and single-molecule orientation mapping, direct experimental proof linking polarity with microviscosity sensed by the same probe eludes us. Here, we demonstrate spectrally resolved single-molecule orientation localization microscopy to connect nanoscopic localization of a probe on a bilayer membrane with its emission spectra, three-dimensional dipole orientation, and rotational constraint offered by the local microenvironment and highlight the excellent correspondence between the polarity and order experienced by the same probe. This technique has the potential to address nanoscale heterogeneity and dynamics, especially in biology and material sciences.

Phosphorylated glycosphingolipids are commonly detected in Caenorhabditis elegans lipidomes

INTRODUCTION

The identification of lipids is a cornerstone of lipidomics, and due to the specific characteristics of lipids, it requires dedicated analysis workflows. Identifying novel lipids and lipid species for which no reference spectra are available is tedious and often involves a lot of manual work. Integrating high-resolution mass spectrometry with enhancements from chromatographic and ion mobility separation enables the in-depth investigation of intact lipids.

OBJECTIVES

We investigated phosphorylated glycosphingolipids from the nematode Caenorhabditis elegans, a biomedical model organism, and aimed to identify different species from this class of lipids, which have been described in one particular publication only. We checked if these lipids can be detected in lipid extracts of C. elegans.

METHODS

We used UHPLC-UHR-TOF-MS and UHPLC-TIMS-TOF-MS in combination with dedicated data analysis to check for the presence of phosphorylated glycosphingolipids. Specifically, candidate features were identified in two datasets using Mass Spec Query Language (MassQL) to search fragmentation data. The additional use of retention time (RT) and collisional cross section (CCS) information allowed to filter false positive annotations.

RESULTS

As a result, we detected all previously described phosphorylated glycosphingolipids and novel species as well as their biosynthetic precursors in two different lipidomics datasets. MassQL significantly speeds up the process by saving time that would otherwise be spent on manual data investigations. In total over 20 sphingolipids could be described.

CONCLUSION

MassQL allowed us to search for phosphorylated glycosphingolipids and their potential biosynthetic precursors systematically. Using orthogonal information such as RT and CCS helped filter false positive results. With the detection in two different datasets, we demonstrate that these sphingolipids are a general part of the C. elegans lipidome.

BBSome deficiency in Lotmaria passim reveals divergent functions in trypanosomatid parasites

BACKGROUND

The BBSome is an octameric protein complex crucial for ciliary transport, though it also participates in multiple other cellular processes. These diverse functions may result from the co-option of its ancestral roles. Studying the BBSome in flagellated protists can provide insights into these ancestral functions and their subsequent adaptations.

METHODS

We examined the functions of the BBSome (LpBBS1 and LpBBS2) in Lotmaria passim, a monoxenous trypanosomatid parasite infecting honey bees. The phenotypes resulting from depletion of LpBBS1 using the auxin-inducible degron system and disruption of LpBBS2 were characterized.

RESULTS

Parasites deficient in LpBBS2 are smaller and less motile compared with wild-type. Although intraflagellar transport of a marker membrane protein is only mildly impaired, its association with lipid rafts is significantly disrupted in the mutants. This suggests that the BBSome is essential for maintaining lipid raft integrity in L. passim. Transcriptomic comparisons between wild-type and LpBBS2-deficient parasites reveal that the BBSome may also influence processes related to metabolism, membrane localization of specific proteins, DNA repair, microtubules, and mitochondria.

CONCLUSIONS

In contrast to Leishmania mexicana, the BBSome in L. passim is crucial for efficient infection of the honey bee gut, demonstrating that its cellular functions vary between related trypanosomatid species. The BBSome is likely an adaptor that links multiple proteins in a species-specific manner under various cellular contexts.

Cholesterol modulates the interaction of sodium salt with negatively charged phospholipid membrane

We present a systematic study on how alkali metal salts, like NaCl and NaI, affect negatively charged phospholipid vesicles using a range of experimental methods. Our goal was to find out how chain saturation and cholesterol affect the interaction between the ions and the membrane. An isothermal titration calorimetry study on large unilamellar vesicles made from dimyristoyl phosphatidylcholine (DMPC) revealed that Na+ shows higher binding affinity to the gel phase at 15 °C compared to the fluid phase at 30 °C. Further, cations also show stronger affinity to the membrane in the fluid composed of saturated lipids than that of unsaturated lipids. The binding affinity of Na + with anionic vesicles prepared from a mixture of DMPC and DMPG was found to decrease significantly with increasing cholesterol as well as salt concentrations, as revealed by the zeta potential study. Besides the binding constant, the Gouy Chapman theory based on the electrostatic double layer shows that cholesterol reduces the surface charge density without altering the significant area per molecule. Further, the effect of counterions was investigated using fluorescence spectroscopy of an environment-sensitive lipophilic dye, nile red. Although cholesterol alters the emission properties of nile red significantly, there is no significant change in the presence of ions. This result suggests that anions do not bind significantly to anionic vesicles. The main striking feature of the ion-membrane interaction in the presence of cholesterol is that membranes with saturated lipids exhibit a completely opposite trend from membranes with unsaturated lipids.

Specific iron binding to natural sphingomyelin membrane induced by non-specific co-solutes

HYPOTHESIS

Sphingomyelin (SPM), a crucial phospholipid in the myelin sheath, plays a vital role in insulating nerve fibers. We hypothesize that iron ions selectively bind to the phosphatidylcholine (PC) template within the SPM membrane under near-physiological conditions, resulting in disruptions to membrane organization. These interactions could potentially contribute to the degradation of the myelin sheath, thereby playing a role in the development of neurodegenerative diseases.

EXPERIMENTS

We utilized synchrotron-based X-ray spectroscopy and diffraction techniques to study the interaction of iron ions with a bovine spinal-cord SPM monolayer (ML) at the liquid-vapor interface under physiological conditions. The SPM ML serves as a model system, representing localized patches of lipids within a more complex membrane structure. The experiments assessed iron binding to the SPM membrane both in the presence of salts and with additional evaluation of the effects of various ion species on membrane behavior. Grazing incidence X-ray diffraction was employed to analyze the impact of iron binding on the structural integrity of the SPM membrane.

FINDINGS

Our results demonstrate that iron ions in dilute solution selectively bind to the PC template of the SPM membrane exclusively at near-physiological salt concentrations (e.g., NaCl, KCl, KI, or CaCl2) and are pH-dependent. In-significant binding was detected in the absence of these salts or at near-neutral pH with salts. The surface adsorption of iron ions is correlated with salt concentration, reaching saturation at physiological levels. In contrast, multivalent ions such as La3+ and Ca2+ do not bind to SPM under similar conditions. Notably, iron binding to the SPM membrane disrupts its in-plane organization, suggesting that these interactions may compromise membrane integrity and contribute to myelin sheath damage associated with neurological disorders.

Integrated Microbiome and Metabolomic to Explore the Mechanism of Coptisine in Alleviating Ulcerative Colitis

Coptisine (COP), a naturally occurring alkaloid, is known for its diverse pharmacological effects and its supportive role in intestinal health. Despite this, the detailed mechanisms behind its therapeutic benefits are not yet fully understood. The objective of this study is to investigate the therapeutic potential of COP for the treatment of Ulcerative Colitis (UC) and to delineate the critical pathways by which it exerts its therapeutic effects. To assess COP's therapeutic effectiveness, mice were administered COP and monitored for clinical symptoms, activity, and disease activity index (DAI) changes. Intestinal histopathology, mucosal barrier function, and gut microbiota structure were evaluated, along with metabolic profiling, focusing on Prenol lipids in the colon to identify COP-induced metabolic shifts. Mice treated with COP exhibited significant relief from diarrhea and bleeding, along with increased activity and a marked reduction in DAI scores. Histopathological evaluation revealed a reduction in intestinal inflammation, and the intestinal mucosal barrier function was notably enhanced. The gut microbiota composition in COP-treated mice showed improvements. Additionally, the levels of Prenol lipids in the colon were elevated by COP treatment, which is crucial for the recovery of intestinal function. Our study demonstrates that COP effectively ameliorates colitis symptoms by modulating colon Prenol lipids metabolism, particularly under the influence of key bacterial species. The findings of this study provide novel insights into the therapeutic mechanisms of COP in the treatment of UC.

Sphingoid Base Diversity

Sphingolipids (SL) are crucial components of cellular membranes and play pivotal roles in various biological processes, including cell growth, differentiation, apoptosis, and stress responses. All SL contain a sphingoid base (SPB) backbone which is the shared and class-defining element. SPBs are heterogeneous in length and structure. This review summarizes our current understanding on minor SPBs and the role of the serine palmitoyltransferase (SPT) in particular of its subunits SPTLC3 and SPTSSA/B in forming a spectrum of structurally and metabolically distinct SPBs. Some minor SPBs, such as 1-deoxysphingolipids (1-deoxySL) are neurotoxic and associated with neurological disorders such as hereditary sensory neuropathy type 1 (HSAN1) and diabetic neuropathy. Furthermore, the review discusses the pathological implications of atypical SPBs in cardiometabolic conditions such as obesity, type 2 diabetes or cardiomyopathy, where the induction of the SPTLC3 subunit alters the SPB profile and contributes to disease progression. Understanding these, often neglected aspects of the sphingolipid metabolism provides potential therapeutic targets for metabolic and neurodegenerative diseases, emphasizing the need for continued research in this area.

Lipids and chromatin: a tale of intriguing connections shaping genomic landscapes

Recent studies in yeast reveal an intricate interplay between nuclear envelope (NE) architecture and lipid metabolism, and between lipid signaling and both epigenome and genome integrity. In this review, we highlight the reciprocal connection between lipids and histone modifications, which enable metabolic reprogramming in response to nutrients. The endoplasmic reticulum (ER)-NE regulates the compartmentalization and temporal availability of epigenetic metabolites and its lipid composition also impacts nuclear processes, such as transcriptional silencing and the DNA damage response (DDR). We also discuss recent work providing mechanistic insight into lipid droplet (LD) formation and sterols in the nucleus, and the collective data showing Opi1 as a central factor in both membrane sensing and transcriptional regulation of lipid-chromatin interrelated processes.

Implications of Raftlin in different diseases: from molecular biology to diagnostic value

Raftlin (raft-linking) protein is an essential component of the lipid raft structure and plays a crucial role in B and T cell signaling pathways. It facilitates B cell receptor (BCR) signaling by promoting calcium mobilization and tyrosine phosphorylation in the cells while colocalizing with BCR on the cell membrane. Interestingly, Raftlin is internalized in lipopolysaccharide-stimulated T cells by colocalization with Toll-like receptor 4 (TLR4), wherein it exerts a similar role as in B cells. The protein also effectuates poly(I:C) internalization into TLR3-positive endosomes in dendritic and epithelial cells through clathrin binding, thereby affecting interferon-β production. In addition, Raftlin controls the vascular endothelial cells and participates in cell growth and proliferation. Recent studies have indicated Raftlin to be a novel biomarker for the diagnosis due to its upregulated expression in malignant diseases. In this integrated study, we present the biological functions of Raftlin and its expression to provide a theoretical basis for the prevention, diagnosis, and treatment of various diseases.