Biology subjects

Farese, R.

Publications and source records attributed to Farese, R..

10 recordsLinked to original sources

bioRxiv2026

Shared lipidome and proteome signatures of frontotemporal lobar degeneration and Alzheimer's disease

Frontotemporal lobar degeneration (FTLD) and Alzheimers disease (AD) differ in their clinical features and genetic etiologies but share progressive cognitive decline. Emerging evidence implicates lipid dysregulation in neurodegeneration, but its extent across FTLD subtypes and how it compares to AD are unclear. Here, we performed integrated lipidomic and proteomic analyses of matched frontal (disease-vulnerable) and occipital (relatively spared) post-mortem cortices from individuals with genetic and sporadic FTLD-TDP, FTLD-tau (Picks disease, PiD), AD, and controls. FTLD and AD exhibited convergent lipid alterations, including reduced levels of cardiolipins and phosphatidylethanolamines, alongside increased gangliosides, diacylglycerols, cholesterol esters, acylcarnitines, and coenzyme Q, with generally greater changes in FTLD frontal cortex. FTLD displayed additional alterations, including reductions in bis(monoacylglycerol)phosphate, ceramides, phosphatidylserines, phosphatidylinositols, and sulfatides. These lipid changes were accompanied by proteomic alterations involving lysosomal proteins, phospholipases, phospholipid remodeling enzymes, and fatty acid oxidation pathways. Although lipidomic and proteomic signatures were broadly shared across FTLD subtypes, GRN associated FTLD-TDP and PiD showed the most extensive alterations. Triglycerides were selectively reduced in PiD in association with decreased DGAT1 expression, whereas cholesterol esters were elevated across all subtypes except C9orf72 associated FTLD-TDP. These findings identify shared disruptions in lipid homeostasis and lysosomal lipid metabolism across FTLD and AD, highlighting convergent metabolic pathways underlying neurodegeneration.

neuroscience↗

bioRxiv2025

Proteome Landscapes Decode Organelle Vulnerabilities in cortical and dopaminergic-like induced neurons Across Lysosomal Storage Disorders

Lysosomes maintain cellular homeostasis by degrading proteins delivered via endocytosis and autophagy, and by recycling building blocks for organelle biogenesis. Lysosomal Storage Disorders (LSDs) comprise a group of diseases affecting diverse lysosomal functions. To facilitate molecular phenotyping across diverse LSD gene classes, we are developing a library of human embryonic stem cells engineered to lack individual LSD genes as a resource for the field. Here, we report our initial stem cell toolkit lacking one of 23 LSD genes, including the majority of genes associated with sphingolipidoses and neuronal ceroid lipofuscinoses, and its use in the generation of a proteomic resource for induced cortical-like and midbrain dopaminergic-like neurons In-depth abundance and correlation profiling across organelles and sub-organelle components revealed potential vulnerabilities that reflect distinct patterns of proteome alterations across both genotypes and neuronal cell types. We characterize alterations in the mitochondrial proteome associated with GBA1 and ASAH1 deficiency and identify synaptic and mitochondrial defects in ASAH1-/- induced neurons that correlate with defects in neuronal firing rates. Moreover, we developed an informatic pipeline for proteome-wide identification of individual protein interactions and protein complexes that may be disrupted as a result of LSD gene deficiency. Finally, we visualized structural alterations of ASAH1-deficient endolysosomes in situ using cryo-electron tomography, revealing swollen organelles that were largely devoid of dense internal membranes characteristic of wild-type cells, but containing numerous intralumenal vesicle compartments. This toolkit and associated proteomic landscapes provide a resource for defining molecular signatures associated with LSD gene dysfunction and organelle vulnerability.

cell biology↗

bioRxiv2025

Mechanism for oil-phase separation by the lipid droplet assembly complex

Cells store metabolic energy as triglyceride (TG) oils in lipid droplets (LDs). LDs form de novo from the endoplasmic reticulum. How the lipid droplet assembly complex (LDAC), composed of seipin and LDAF11,2, catalyzes the organized formation of an oil phase in a membrane bilayer before spontaneous phase separation is triggered is unknown. Here, we reconstitute LD formation in vitro using purified LDAC and membranes containing physiologic levels of TG, demonstrating that the LDAC is both necessary and sufficient to catalyze oil-phase formation below the threshold of spontaneous phase separation. Structural studies of the LDAC reveal that LDAF1 forms a central ring within a seipin cage, creating a toroidal, membrane-spanning structure. Molecular dynamics simulations and biochemical assays show that this structure forms a selective chamber within the ER bilayer that limits phospholipids but allows TG to access a reaction compartment between the inner and outer rings of the LDAC. Within this compartment, TG interacts with LDAF1 and each other to form an oil phase to initiate LD formation. Thus, the LDAC acts as a protein catalyst for oil-phase separation in cells, revealing a fundamental mechanism for how cells resolve the biophysical challenge of storing oils within a hydrophilic environment in an organized manner.

cell biology↗

bioRxiv2025

LipidCruncher: An open-source web application for processing, visualizing, and analyzing lipidomic data

BackgroundAdvances in mass spectrometry (MS)-based lipidomics have led to a significant surge in data volume, underscoring a need for robust tools to efficiently evaluate and visualize these expansive datasets. While numerous software tools have been developed, current workflows are hindered by manual spreadsheet handling and insufficient data quality assessment prior to analysis. Here, we introduce LipidCruncher, an open-source, web-based platform designed to easily process, visualize, and analyze lipidomic data with high efficiency and rigor. ResultsLipidCruncher consolidates key steps of the lipidomics analysis workflow, including data standardization, normalization, and stringent quality controls. The platform also provides advanced visualization and analysis tools that are tailored to interrogate lipidomic data and enable detailed and holistic data exploration. To illustrate LipidCrunchers utility, we analyzed lipidomic data from adipose tissue of mice lacking the triacylglycerol synthesis enzymes DGAT1 and DGAT2. ConclusionsLipidCruncher fills a specific gap in the lipidomics analysis ecosystem by providing an integrated, quality-focused platform that accepts data from multiple sources and complements existing specialized tools. By bridging the critical divide between data generation and biological interpretation, LipidCruncher facilitates rigorous lipidomics analyses to accelerate the translation of complex lipid profiles into biological insights.

bioinformatics↗

bioRxiv2025

Plasma lipidome dysregulation in frontotemporal dementia reveals shared, genotype-specific, and severity-linked alterations

Developing new treatment strategies for frontotemporal dementia (FTD) and other forms of neurodegeneration requires biomarkers to monitor disease progression. Dysregulated brain lipid metabolism, particularly sphingolipids enriched in the nervous system, is a key feature of neurodegeneration. However, plasma lipids have been investigated less for their potential as biomarkers than brain imaging and serum proteins. Here we examined the plasma lipidomes of a cohort of heterozygous carriers of gene variants associated with autosomal dominant familial FTD (including GRN, C9orf72, and MAPT loci), comparing them with aged-matched controls. In general, FTD subjects exhibited increases in plasma levels of specific species of gangliosides (GM3(d18:1_16:0), GM3(d18:1_18:0), and GM3(d18:1_24:1)) and ceramide (Cer(d18:1_23:0)) and selected polyunsaturated triacylglycerols (TG). Other species of ceramides (Cer(d18:0_22:0)), phosphatidylethanolamine (PE(18:0_24:0)), and sphingomyelin (SM(38:0)) were reduced in plasma of FTD subjects. Levels of glucosylsphingosine (GlcSph(d18:1)) were elevated specifically in GRN carriers, SM(34:1) was reduced in C9orf72 carriers, and TG(16:0_18:1_20:3)) were decreased in MAPT variant carriers. Notably, the ganglioside GM3(d18:1_16:0) was consistently elevated across all FTD genetic subtypes. Furthermore, the levels of these lipids correlated with disease severity in FTD patients. Our findings suggest that specific plasma lipid changes, notably several sphingolipids, may be useful biomarkers for FTD disease or progression.

systems biology↗

bioRxiv2022

Fitm2 is required for ER homeostasis and normal function of murine liver

The ER-resident protein fat-inducing transcript 2 (FIT2) catalyzes acyl-CoA cleavage in vitro and is required for endoplasmic reticulum (ER) homeostasis and normal lipid storage in cells. The gene encoding FIT2 is essential for the viability of mice and worms. Whether FIT2 acts as an acyl-CoA diphosphatase in vivo and how this activity affects liver, where the protein was discovered, are unknown. Here, we report that hepatocyte-specific Fitm2 knockout (FIT2-LKO) mice exhibited elevated acyl-CoA levels, ER stress, and signs of liver injury. FIT2-LKO mice fed a chow diet had more triglycerides in their livers than control littermates due, in part, to impaired secretion of triglyceride-rich lipoproteins and reduced capacity for fatty acid oxidation. Challenging FIT2-LKO mice with a high-fat diet to increase FIT2 acyl-CoA substrates worsened hepatic ER stress and liver injury, but unexpectedly reversed the steatosis phenotype, similar to what is observed in FIT2-deficient cells loaded with fatty acids. Our findings support the model that FIT2 acts as an acyl-CoA diphosphatase in vivo and is crucial for normal hepatocyte function and ER homeostasis in murine liver.

cell biology↗

bioRxiv2022

Lipodystrophy can be uncoupled from detrimental metabolic consequences

Triglycerides (TG) in adipocytes provide the major stores of metabolic energy in the body. Optimal amounts of TG stores are desirable as insufficient capacity to store TG, as in lipodystrophy, or exceeding the capacity for storage, as in obesity, results in metabolic disease. We hypothesized that mice lacking TG storage in adipocytes would result in excess TG storage in cell types other than adipocytes and severe lipotoxicity accompanied by metabolic disease. To test this hypothesis, we selectively deleted both TG-synthesis enzymes, DGAT1 and DGAT2, in adipocytes (ADGAT DKO mice). As expected with depleted energy stores, ADGAT DKO mice did not tolerate fasting well and, with prolonged fasting, entered torpor. However, ADGAT DKO mice were unexpectedly otherwise metabolically healthy and did not accumulate TGs ectopically or develop associated metabolic perturbations, even when fed a high-fat diet. The favorable metabolic phenotype resulted from activation of energy expenditure, in part via BAT activation and beiging of white adipose tissue. Thus, the ADGAT DKO mice provide a fascinating new model to study the coupling of metabolic energy storage to energy expenditure.

physiology↗

bioRxiv2021

Key Factors Governing Initial Stages of Lipid Droplet Formation

Lipid droplets (LDs) are neutral lipid storage organelles surrounded by a phospholipid (PL) monolayer. LD biogenesis from the endoplasmic reticulum (ER) is driven by phase separation of neutral lipids, overcoming surface tension and membrane deformation. However, the core biophysics of the initial steps of LD formation remain relatively poorly understood. Here, we use a tunable, phenomenological coarse-grained (CG) model to study triacylglycerol (TG) nucleation in a bilayer membrane. We show that PL rigidity has a strong influence on TG lensing and membrane remodeling: When membrane rigidity increases, TG clusters remain more planar with high anisotropy but a minor degree of phase nucleation. This finding is confirmed by free energy sampling simulations that calculate the potential of mean force (PMF) as a function of the degree of nucleation and anisotropy. We also show that asymmetric tension, controlled by the number of PLs on each membrane leaflet, determines the budding direction. A TG lens buds in the direction of the monolayer containing excess PLs to allow for better PL coverage of TG, consistent with reported experiments. Finally, two governing mechanisms of the LD growth, Ostwald ripening and merging, are observed. Taken together, this study characterizes the interplay between two thermodynamic quantities during the initial LD phases, the TG bulk free energy and membrane remodeling energy.

biophysics↗

bioRxiv2020

Lipid Droplets in Brown Adipose Tissue Are Dispensable for Cold-Induced Thermogenesis

Brown adipocytes store metabolic energy as triglycerides (TG) in multilocular lipid droplets (LDs). Fatty acids released from brown adipocyte LDs by lipolysis are thought to activate and fuel UCP1-mediated thermogenesis. Here we test this hypothesis by preventing fatty acid storage in murine brown adipocytes through brown adipose tissue (BAT)-specific deletions of the TG synthesis enzymes, DGAT1 and DGAT2 (BA-DGAT KO). Despite the absence of LDs, BA-DGAT KO mice had functional BAT and maintained euthermia during acute or chronic cold exposure. As apparent adaptations to the lack of TG, brown adipocytes of BA-DGAT KO mice appear to utilize circulating glucose and fatty acids, as well as stored glycogen to fuel thermogenesis. Moreover, BA-DGAT KO mice were resistant to diet-induced glucose intolerance, likely due to increased glucose disposal by BAT. Thus, surprisingly, TGs in BAT are dispensable for its function, in part through adaptations to utilize other fuel sources.

physiology↗

bioRxiv2018

Cryo-electron microscopy structure of the lipid droplet-formation protein seipin

Sui et al. report the cryo-EM structure of the conserved luminal domain of the lipid droplet (LD)-formation protein seipin. The structure reveals key features of this domain and suggest a new model for seipins role in LD formation.\n\nMetabolic energy is stored in cells primarily as triacylglycerols in lipid droplets (LDs), and LD dysregulation leads to metabolic diseases. The formation of monolayer-bound LDs from the endoplasmic reticulum (ER) bilayer is poorly understood, but the ER protein seipin is essential to this process. Here, we report a cryo-electron microscopy structure and functional characterization of D. melanogaster seipin. The structure reveals a ring-shaped dodecamer, with the luminal domain of each monomer resolved at [~]4.0 [A]. Each luminal domain monomer exhibits two distinctive features: a hydrophobic helix positioned towards the ER bilayer, and a {beta}-sandwich domain that has structural similarity with lipid-binding proteins. This structure, and our functional testing in cells, suggest a model in which seipin oligomers initially detect forming LDs in the ER via hydrophobic helices and subsequently act as membrane anchors to enable lipid transfer and LD growth.

cell biology↗