Cell Metabolism

The release of glucagon from pancreatic alpha cells is a core component of hypoglycaemic counter regulation. Several mechanisms regulate glucagon release including paracrine control by neighbouring cell types, and changes in extracellular glucose. While the inhibitory effect of glucose on glucagon secretion is well established, the exact way in which glucose metabolism contributes to alpha cell function remains unclear. Here, we use live-cell imaging of the redox potential in alpha cells within intact islets to investigate whether non-mitochondrial glucose metabolism contributes to the potentiation of glucagon secretion at low glucose. Our findings show that increased glucose metabolism through the pentose phosphate pathway elevates the cytosolic redox potential in alpha cells. Using a combination of antioxidant treatment and pre-incubation in 5 mM glucose, we find that the cytosolic redox potential affects PKA activity in alpha cells and that changes in whole body redox state affects the counterregulatory response in mice. These findings indicate that prior glucose-driven redox potential charging is essential for maintaining glucagon secretion at low glucose.

Insulin production is a cardinal feature of pancreatic {beta} cells. Studies in rodents show that {beta} cells can switch between low and high insulin gene activity states and that elevated insulin production makes {beta} cells more vulnerable to stresses associated with diabetes. In people, genetically elevated insulin production increases the risk of type 1 diabetes. Via effects on obesity, hyperinsulinemia contributes to the pathogenesis of type 2 diabetes. Here, we characterize {beta} cells in low and high INS gene activity states sorted from primary human islets transduced with INS-GFP adenovirus and differentiated INS-EGFP knock-in embryonic stem cells (SC{beta} cells). We profile {beta} cell function, protein synthesis, resilience to diabetes associated stress, single {beta} cell transcriptomes and their co-activity networks, and purified {beta} cell proteomes. We show that human {beta} cells transition between distinct states. High INS cells have elevated maturity marker mRNAs and proteins, increased protein translation, are larger, but also more susceptible to cell death when exposed to diabetes-relevant stresses. We also catalogue thousands of differences in proteins in high INS stem cell-derived {beta} cells compared directly with high INS primary {beta} cells. Our study improves our understanding of the delicate balance between insulin production and {beta} cell resilience and guides the engineering of better {beta} cells. Blurbtranscriptional, proteomic, and functional analyses of insulin gene expression states in human {beta} cells from donor islets and stem cells Key findingsO_LIWe identify high and low INS gene activity states in human insulin-producing cells from donor islets and embryonic stem cell differentiations. C_LIO_LIWe characterize the relationship between insulin production and fragility, demonstrating that increased insulin production comes at a cost of reduced resilience to multiple stresses. C_LIO_LIFunctional, transcriptomic, and proteomic analyses identify similarities and differences between how primary and stem cell-derived {beta} cells manage stress and insulin production. C_LIO_LIWe report a comprehensive side-by-side proteomic analysis of purified primary and stem cell- derived {beta} cells in the high INS state and identify differences in protein production and secretion machinery, providing a roadmap for making better {beta} cells. C_LI

Alzheimer's disease (AD) unfolds over decades preceding cognitive symptoms, and measuring the full scope of its molecular complexity remains difficult. Blood-based biomarkers of amyloid, phosphorylated tau, astrocytic reactivity and neuroaxonal injury including A{beta}42/40, p-tau181, p-tau217, GFAP and NfL enable scalable assessment of AD-related pathology and associated processes but capture only a narrow slice of the systemic biology ultimately shaping disease progression. Here we link these increasingly routine clinical assays to the plasma proteome using multi-omic linear modeling to resolve functional heterogeneity in AD progression. In 484 older adults spanning normal cognition, mild cognitive impairment (MCI) and AD, we derived proteomic signatures for each key biomarker across more than 6,000 proteins, uncovering overlapping and distinct biological processes and cell types implicated in AD with robust signal across proteomic modalities. From these we built continuous progression-focused functional modules that were consistently preserved across 12 independent cohorts comprising 11,042 participants from the Global Neurodegeneration Proteomics Consortium and that associated with cognitive decline, diagnosis and AD-relevant biology. A synaptic vesicle module marked apparent neuronal resilience as much as 5 years before estimated symptom onset. We show routine and accessible plasma measures can be leveraged to recover reproducible, biologically distinct progression modules that improve characterization of heterogeneous AD and have practical value for risk stratification, trial enrichment, or treatment monitoring.

Macrophages clear excess host and microbial debris to restore homeostasis in inflamed tissues, yet the regulation and molecular fate of phagocytosed lipids during innate immune training remains largely unexplored. Leveraging stable isotope tracing of 13C-labeled bacteria, we establish an experimental framework to track microbe-to-host lipid transfer and define the fates of microbial lipids in macrophages in vitro and in vivo. While naive macrophages scavenge phagocytosed bacterial fatty acids into the host lipidome, TLR4-trained macrophages direct flux to mitochondria for {beta}-oxidation or lipid droplets in the context of mitochondrial dysfunction. While TLR4 signaling increases ACOD1 expression to produce itaconate that throttles TCA flux, trained macrophages produce IL-10 that reduces ACOD1 to sustain bacterial lipid disposal and promote resolution. These findings reveal an IL-10/ACOD1 regulatory axis in trained macrophages that reprograms lipid metabolism to optimally reestablish tissue homeostasis post-inflammation.

Brown adipose tissue (BAT) is a mitochondria-rich thermogenic organ whose function depends on high oxidative capacity, yet how primary mitochondrial dysfunction remodels BAT identity and metabolism remains poorly defined. Using the Deletor mouse model of progressive mtDNA deletion disease, we identify a pseudohypoxiairon-NAD+ axis as a central organiser of BAT pathology. Deletor BAT underwent profound structural, transcriptional and metabolic remodelling, characterised by mitochondrial ultrastructural damage, loss of thermogenic identity, PHD3/HIF associated pseudohypoxic signalling, iron dysregulation and NAD+/NADH redox imbalance. Indirect calorimetry confirmed that this molecular disease program translates to functional thermogenic failure under physiological demand. Deletor mice showed significantly reduced heat production under acute cold challenge and failed to switch to fatty acid oxidation Metabolomic profiling revealed altered TCA cycle intermediates, glycolytic rewiring and selective amino acid accumulation. Pharmacological perturbation showed that the PHD inhibitor roxadustat worsened disease-associated features, whereas HIF-1 suppression with PX-478 attenuated the integrated stress response, indicating that pseudohypoxic signalling is maladaptive in this setting. Nicotinamide riboside broadly attenuated the disease metabolome and transcriptome, restoring NAD+/NADH balance, suppressing ISRmt, iron-stress and pseudohypoxic gene programs, and correcting selective carnitine and acylcarnitine abnormalities consistent with impaired fatty-acid handling. These findings define a therapeutically tractable pseudohypoxia-iron-NAD+ axis as a core determinant of BAT dysfunction in mitochondrial disease.

Immune cells rely on exogenous fatty acids (FA) for membrane synthesis, bioenergetics and signalling, yet current approaches cannot accurately quantify physiological FA uptake in vivo. Here, we use cyclopropene-tagged fatty acids (cpFA) that, unlike existing FA-uptake tools, are taken up by physiologically relevant mechanisms. We measure FA uptake at single-cell resolution in vivo and uncover a previously unappreciated distinction between nutrient uptake capacity and nutrient accessibility. Although arachidonic acid exhibits the highest uptake capacity ex vivo across immune populations, it displays limited tissue accessibility in vivo, whereas palmitate is broadly accessible. In vivo nutrient-uptake measurements reveal that tissue architecture shapes nutrient accessibility, with spatial constraints in the spleen and exclusion of circulating FA, but not amino acids, from the thymus. Together, these findings identify nutrient accessibility as a distinct layer of metabolic regulation and reveal that immune-cell metabolism is shaped by spatial and systemic constraints on nutrient access HighlightsO_LINutrient accessibility is a distinct layer of metabolic regulation C_LIO_LIPhysiological FA uptake differs from ex vivo uptake capacity C_LIO_LISpatial and systemic factors govern fatty-acid accessibility C_LIO_LITissue context shapes immune-cell metabolism in vivo C_LI In briefUsing bioorthogonal FA to quantify physiological nutrient uptake in vivo, Wang et al. show that nutrient accessibility is distinct from nutrient uptake capacity. Tissue architecture and systemic FA distribution create spatial constraints on nutrient access, revealing an underappreciated layer of metabolic regulation in immune cells.

Loss of skeletal muscle mass and strength with age drives sarcopenia, a syndrome affecting >100 million people worldwide that leads to loss of mobility, independence, and increased mortality. Mechanical overload induces hypertrophy in young muscle, but this response is markedly attenuated with age--a poorly understood phenomenon termed "anabolic resistance." Here we test whether impaired paracrine communication between myofibers and their niche underlies this loss of plasticity in geriatric mice. In aged muscle, pharmacological inhibition of 15-PGDH restores prostaglandin E2 (PGE2) bioavailability and rescues the anabolic response, increasing muscle growth and contractile strength. Single-nuclei RNA-seq revealed a paracrine circuit: PGE2 drives IGF1 synthesis in type IIb myonuclei, which signals to stromal, myogenic, myonuclear, and immune cells. Blocking IGF1 receptor signaling abolished these gains, placing PGE2 upstream of an IGF1-mediated circuit that coordinates multicellular hypertrophy. Thus, 15-PGDH inhibition is a pharmacological strategy to overcome the anabolic resistance and rebuild muscle in aging.

Pancreatic ductal adenocarcinoma (PDAC) is commonly associated with obesity, diabetes, and cachexia. The pancreatic anabolic hormone, insulin, is implicated in each of these metabolic diseases, but how insulin levels affect tumor growth and relevant host physiological factors, was unclear. To address this, we transplanted orthotopic PDAC patient-derived organoids into mice consuming a hyperinsulinemia-inducing high-fat diet (HFD). We found that insulin concentrations were higher in tumors compared to circulation. Genetically reducing insulin levels reduced PDAC growth, particularly in HFD-fed mature male mice. In turn, we found the presence of pancreatic tumors increased glucose clearance and limited the expected dietary-induced gains in insulin, weight and fat mass. Interestingly, tumor growth in normal-chow-fed mice, but not HFD-fed mice, was associated with declining circulating insulin levels, as well as declines in fat and muscle mass. Together, these data provide new insights into the complex, insulin-centred interplay between PDAC and the hosts systemic metabolism that underlie cancer-associated metabolic dysfunction.

To address the long-standing question of the respective physiological contributions of classical brown versus beige adipocytes to adaptive nonshivering thermogenesis, we generated mice with lineage-specific ablation of UCP1 in thermogenic adipocytes of myogenic origin. This selectively targeted the major classical brown adipocyte lineage while preserving UCP1 expression in the remaining thermogenic adipocytes, reducing total UCP1 content by approximately 80 %. Unexpectedly, despite this profound reduction in UCP1 abundance, cold acclimation-recruited thermogenic capacity, assessed by adrenergic stimulation, remained largely preserved. In contrast, complete UCP1 deficiency abolished the adrenergically induced thermogenic response, demonstrating that UCP1 is indispensable for adaptive nonshivering thermogenesis. These findings indicate that in cold-acclimated mice only a fraction of the UCP1 normally present is required to sustain maximal thermogenic capacity. We further establish that the capacity to support UCP1-dependent oxidative metabolism, rather than UCP1 abundance, is the principal constraint on maximal thermogenic output under these conditions.

Dysregulated hormone secretion and erosion of endocrine cell identity are features of type 1 and type 2 diabetes, but the transcriptional programs maintaining adult human islet identity and function remain poorly defined. The large MAF transcription factor MAFB is expressed in human - and {beta}-cells, marks their most functionally mature subpopulations, and is downregulated in diabetes, but its role in adult human islets has not been tested directly. Using shRNA-mediated MAFB knockdown (KD) in whole and CD26+ -cell-enriched human pseudoislets, we found that whole pseudoislet MAFB KD impaired glucagon synthesis and secretion while only modestly reducing insulin content and cAMP-potentiated insulin release. Single-cell profiling detected no {beta}-cell transcriptional response beyond MAFB KD itself, consistent with buffering by the related {beta}-cell-enriched MAFA transcription factor. In contrast, -cell-restricted MAFB KD unmasked a cell-autonomous requirement for MAFB in stimulus-secretion coupling. MAFB deficiency also destabilized -cell identity, downregulating canonical -cell and neuroendocrine secretory genes while ectopically inducing mesenchymal and extracellular matrix remodeling programs. In addition, MAFB-dependent downregulation of electron transport chain genes was confined to a large -cell subcluster, manifesting as impaired islet-wide mitochondrial respiration within the broader -cell population. Together, these findings identify MAFB as an essential adult human -cell maintenance factor that links diabetes-associated downregulation to impaired glucagon secretion, -cell identity erosion, and mitochondrial dysfunction. RESEARCH IN CONTEXTO_LIWhat is already known about this subject? O_LIMAFB is expressed in adult human - and {beta}-cells, marks their most functionally mature subpopulations, and is downregulated in type 1 and type 2 diabetes C_LIO_LIIn human stem cell models, MAFB is essential for generating insulin-producing {beta}-like cells, whereas glucagon-producing -like cells are reduced but still formed C_LIO_LINeither model addresses adult human islets: rodent MafB becomes -cell restricted after birth, and stem cell models capture differentiation, not maintenance C_LI C_LIO_LIWhat is the key question? O_LIIs MAFB required to maintain identity and secretory function in adult human islet cells? C_LI C_LIO_LIWhat are the new findings? O_LIMAFB knockdown in primary human pseudoislets impaired glucagon synthesis and secretion but minimally affected {beta}-cells, consistent with buffering by MAFA C_LIO_LIKnockdown in CD26+ -cell-enriched pseudoislets revealed a cell-autonomous requirement for MAFB in stimulus-secretion coupling, and destabilized -cell identity by inducing mesenchymal and extracellular matrix programs C_LIO_LIMAFB loss downregulated electron transport chain genes in the largest -cell subcluster and reduced mitochondrial respiration C_LI C_LIO_LIHow might this impact on clinical practice in the foreseeable future? O_LIPreserving MAFB activity in adult human -cells may represent a strategy to limit -cell dysfunction in diabetes C_LI C_LI

Mitochondria are central metabolic organelles with functions extending beyond energy production to anabolic and folate-mediated one-carbon (1C) metabolism. One-carbon metabolism supports methylation reactions that modify diverse targets including metabolites, nucleic acids, and chromatin, and has emerged as a contributor to mitochondrial disease-related stress responses. Here, we report tissue-specific remodeling of methylation events in response to mtDNA replication defect, using the deletor mice carrying a dominant mutation in Twinkle, the replicative helicase of mtDNA, causing adult-onset mitochondrial myopathy (MM) in humans and mice. In affected skeletal muscle, deletors show a distinct methylation signature, with increased creatine synthesis and reduced phosphatidylcholine production, two major consumers of S-adenosylmethionine-derived methyl groups. We further observed tissue-specific upregulation of selected RNA methylation marks and redistribution of the repressive histone mark H3K9me3, indicating coordinated remodeling of metabolic and epigenetic methylation pathways. Our evidence shows that a mtDNA replication defect remodels muscle-specific methylation signature of phospholipids, histones and RNA, identifying methylation remodeling as a key component of MM pathogenesis.

Clonal hematopoiesis (CH), an aging-related expansion of hematopoietic stem cell (HSC) clones, is associated with hematologic malignancy, cardiovascular disease, and mortality. Most clonal expansions, however, occur in the absence of known driver mutations. Passenger mutations reveal positive selection in HSCs and provide a quantitative, driver-agnostic phenotype that increases statistical power over dichotomized driver-based definitions. We used somatic passenger mutation burden as a quantitative phenotype to map the genetic, phenotypic, and geographic correlates of CH across 791,067 blood whole-genome sequences from UK Biobank (UKB) and the All of Us Research Program (AoU). Multi-ancestry meta-analysis of genome-wide association studies in both cohorts identified 81 loci associated with passenger mutation burden, including 42 novel loci. Rare-variant analyses additionally implicated MBD2, PRKACB, PUF60, and related epigenetic and transcriptional regulators of clonal fitness. Together, common and rare germline associations converged with canonical CH drivers on shared pathways regulating DNA methylation, chromatin, RNA splicing, and genome maintenance. Sex and ancestry stratified analyses revealed the shared and population-specific determinants of CH, including loci undetected in the pooled analysis. Associated variants were concentrated in regulatory elements active in hematopoietic stem and progenitor cells, linking germline associations to relevant cell states and lineages. Phenome-wide analyses revealed distinct consequences of inherited CH liability and observed passenger burden, with passenger burden strongly associated with incident hematologic malignancy and mortality and germline risk showing additional nonhematologic associations. Finally, spatial modelling of passenger mutation burden across U.S. regions revealed persistent geographic heterogeneity incompletely explained by income, air quality, or chemotherapy prevalence, pointing to additional unmeasured environmental exposures. Overall, through parallel analyses of two population-scale biobanks, we characterize the multi-ancestry genetic architecture of CH and reveal convergence of germline and somatic variation on shared pathways governing clonal expansion in aging blood.

Aging is a heterogeneous biological process in which different cellular systems undergo molecular remodeling at distinct rates, yet whether human cellular aging follows an organized architecture across organs remains unclear. Here, we integrate a multi-organ human single-cell transcriptomic atlas with plasma proteomic profiles from approximately 50,000 participants to reconstruct cellular aging states at population scale. By projecting cell-type-enriched molecular signatures onto circulating proteins, we characterize aging patterns across 128 organ-cell type pairs and identify 14 cellular aging modules comprising conserved cross-organ programs and organ-specific aging states. These modules reveal cellular identity as a dominant organizing axis of human aging that transcends anatomical boundaries. Module-level aging states uncover substantial inter-individual heterogeneity, with 34% of individuals exhibiting extreme aging deviation in at least one cellular module. Cellular aging modules exhibit distinct temporal trajectories, with structural and tissue-resident modules showing earlier remodeling than immune lineages. The modular organization of cellular aging is reflected in disease susceptibility, with accelerated aging of specific modules, particularly epithelial aging, showing broad associations with disease burden and mortality. Longitudinal analyses further demonstrate the stability and clinical relevance of cellular aging states, whereas lifestyle, metabolic and pharmacological factors show selective relationships with individual aging programs. Together, our study establishes a modular framework for understanding human cellular aging and reveals an organization of biological aging that may help explain individual differences in healthspan.

Lipid metabolism is dynamically rewired across tissues in response to developmental, environmental and therapeutic cues. This adaptation drives treatment resistance in a range of human pathologies, but current lipidomic techniques fail to capture the underlying mechanisms, relying on steady-state measurements from homogenised samples that obscure spatial heterogeneity and pathway flux. Here we introduce spatial tracing of isotopically labelled lipids (STILL-13C), a workflow that uses stable isotope tracing and high-resolution mass spectrometry imaging (MSI) to map lipid metabolic flux directly in intact human tissues with unprecedented pathway coverage. STILL-13C overcomes longstanding limitations of bulk and MSI-based analyses by spatially resolving isotopologue labelling of simple and complex lipids, enabling simultaneous tracing of fatty acid synthesis, remodelling and multiple convergent pathways required for phospholipid assembly, while preserving tissue architecture and regional metabolic context. Applied to patient-derived prostate cancer explants cultured ex vivo, STILL-13C revealed heterogeneity in lipid pathway activity between neighbouring epithelial regions and spatially resolved responses to pathway inhibition. This work establishes a broadly applicable platform for investigating spatial heterogeneity in lipid metabolic flux and its perturbation in intact tissues.

Hematopoietic stem cell (HSC) aging is associated with epigenetic remodeling, yet the molecular mechanisms driving these changes, their overlap with stress-induced alterations, and whether this course can be durably reset remain incompletely understood. Here, we show that transient induction of the Yamanaka factors OCT4, SOX2, KLF4, and MYC in young mice durably delays and partially reverses physiological and LPS-driven HSC aging in mice. Transient reprogramming improved hematopoietic reconstitution, reduced myeloid bias, and limited DNA damage. Multi-omic analyses revealed reduced chromatin accessibility at AP-1-enriched regulatory regions, attenuated age-associated AP-1 transcriptional programs, and repression of transposable elements (TEs). Pharmacological AP-1 inhibition prevented LPS-induced TE activation and loss of HSC clonogenicity. Reverse transcriptase inhibition in aged mice reduced DNA damage and improved HSC function, demonstrating a functional contribution of TE activity to HSC decline. Together, these findings identify AP-1-associated chromatin remodeling as a candidate mechanism linking inflammatory stress, TE activation and HSC aging.

The role of 2-hydroxyglutarate in lipid metabolism is currently unknown. Here we show that 2HG redistributes the partitioning of fatty acids into triglyceride storage and away from membrane phospholipid synthesis, mitochondrial oxidation, and lipotoxic intermediates. In primary human cardiac and vascular cells, both enantiomers, D2HG and L2HG, expanded triglyceride stores and lipid droplets while selectively depleting phosphatidylethanolamine, with L2HG acting more potently than D2HG despite lower intracellular accumulation. Mechanistically, L2HG increases DGAT-dependent triglyceride synthesis, slows triglyceride turnover, and constrains the ethanolamine branch of the Kennedy pathway. This response limits fatty acid oxidation, long-chain acylcarnitine accumulation, and lipid peroxidation independently of pseudohypoxic transcription or canonical lipid storage regulators, while also remodeling the phosphoproteome and redox proteome. L2HG accumulation induces hypertriglyceridemia in mice, redistributes the acyl chain composition of cardiac triglycerides, and limits ischemia-induced acylcarnitine accumulation in the heart, mirroring a positive association between circulating 2HG and triglycerides in humans. Thus, 2HG expands metabolic flexibility from whether fatty acids are used as fuel to how that fuel is allocated among storage, membrane synthesis, and oxidation.

Stable nitrogen isotopes of amino acids are widely used to reconstruct trophic position. Most applications rely on only two amino acids despite routinely measuring many others. Here, comparative amino acid {delta}15N values from 88 mammal species reveal that threonine records a physiological dimension beyond trophic position. Adding threonine to the canonical glutamate-phenylalanine framework reveals ecological differentiation obscured by broad dietary categories and opposite isotopic relationships between herbivores and secondary consumers. A mechanistic model links this variation to preferential intestinal utilization of threonine for mucin synthesis and predicts experimentally testable patterns of isotope partitioning. These findings show that amino acid {delta}15N values encode complementary dimensions of organismal ecology, expanding amino acid isotope analysis beyond trophic reconstruction to reveal physiological and ecological variation associated with dietary specialization.

Clonal hematopoiesis (CH) increases with age, but whether different somatic clones represent an ageing phenotype or exert distinct systemic effects is unclear. In 450,587 UK Biobank participants, including 46,324 with plasma proteomics, we compared clonal hematopoiesis of indeterminate potential (CHIP) and mosaic loss of chromosome Y (mLOY) or X (mLOX) across biological ageing, incident disease, and circulating proteins. Despite shared age dependence, these alterations showed distinct disease spectra: non-DNMT3A CHIP was associated with broad multisystem disease burden, mLOY with a more focused respiratory, musculoskeletal and cardiovascular profile, whereas mLOX lacked broad age-related disease associations. Clone burden mapped to distinct proteomic programs: mLOY to neutrophil degranulation and extracellular-matrix remodeling, non-DNMT3A CHIP to myeloid immune regulation, and mLOX unexpectedly to cytotoxic lymphocyte/NK-cell responses. Mendelian randomization supported selected protein-disease relationships. Thus, age-related hematopoietic clones are not interchangeable markers of ageing but define alteration-specific systemic programs associated with distinct disease vulnerabilities.

The gut microbiome and its bacterially derived metabolites are known to affect many aspects of the host organisms health, including metabolism, immune response, intestinal inflammation, oxidative stress, and even lifespan. Because pathological changes in the gut microbiome and these functions are associated with aging, many have hypothesized that we could protect against aging by generating beneficial changes to the gut microbiome. Here, we directed evolution outside of the host (ex vivo) and generated a Drosophila gut microbiome resistant to paraquat, a toxin that causes oxidative stress. Compared to a control microbiome, this paraquat-resistant (PQR) microbiome transplanted back into the Drosophila gut endowed the host with multiple health benefits: increased resistance to dietary paraquat, reduced age-related pathologies in the gut, and extended lifespan. We identified the beneficial species of the PQR microbiome as Lactiplantibacillus plantarum and further identified mutations specific to lifespan-extending isolates linked to greater production of acetate. Directly feeding this short-chain fatty acid, acetate, to Drosophila was sufficient to recapitulate an extended lifespan, similar to that induced by gut colonization of PQR bacteria in the gut. These results serve as a proof of principle that increasing the resistance of the microbiome to oxidative stress via directed ex vivo evolution could serve as a therapeutic strategy to protect against aging.

Lipid droplets (LDs) are protein-coated organelles that store neutral lipids and regulate diverse cellular processes beyond energy metabolism. In neural stem/progenitor cells (NSPCs), LD abundance and morphology vary across cellular states, yet whether LD molecular composition is similarly state-dependent remains unknown. Here, we define the first endogenous LD proteome and lipidome atlas of NSPCs and their progeny. State-resolved analyses reveal extensive differences in both LD-associated proteins and stored lipids, allowing for identification of LD signatures that distinguish quiescent and proliferative states, and uncovering selective enrichment of numerous proteins on quiescent NSPC LDs. Functional interrogation of one such protein, CIDEB, showed that its knockdown alters LD morphology and induces senescence-associated transcriptional programs, implicating CIDEB in the maintenance of NSPC quiescence. These findings establish LDs as dynamically specialized organelles in NSPCs and their progeny and provide a resource for investigating LD-mediated regulation of stem cell state and lineage progression.