Cell Metabolism

The molecular basis of caloric restriction (CR) has been defined primarily at a metabolic steady state, leaving the initiating events that drive the transition from ad libitum feeding to an adapted CR state largely unresolved. Here, we combine continuous indirect calorimetry with longitudinal bulk RNA-seq of liver and inguinal white adipose tissue (iWAT) sampled at six circadian timepoints across four stages of adaptation to 30% CR in male C57BL/6J mice. We show that whole-body metabolic adaptation proceeds through two discrete adaptive phases separated by a threshold at approximately 14 days; during this initial transition, consolidated feeding attenuates ketogenesis, establishing a distinct whole-body metabolic phenotype prior to long-term adaptation. To elucidate the molecular mechanisms underlying these physiological shifts, weighted gene co-expression network analysis (WGCNA) was performed, revealing that hepatic transcriptional remodeling is organized proportionally to fasting duration, whereas iWAT remodeling remains restricted to specific circadian timepoints. Because systemic adaptation requires coordinated inter-tissue communication, we conducted a cartographic analysis to evaluate network topology and inter-modular connectivity. This approach identifies restricted populations of early kinless and connector hub genes, nucleated by Casp3 in the liver and Lpl in iWAT, whose structural integration is established prior to the broader transcriptional remodeling observed at later timepoints. Functional annotation indicates the hepatic hub network is enriched for mitochondrial bioenergetics and FOXO/TP53-mediated transcription, while the iWAT hub network exhibits a bifurcated enrichment spanning ribosomal biosynthesis and immune-regulatory signaling. Although these tissues exhibit distinct transcriptional profiles, projecting both datasets onto a shared phenotypic eigenspace reveals a unified systemic response; as CR is maintained, dynamically regulated transcripts in both liver and iWAT converge on an adiponectin-coupled state. Ultimately, the identification of adiponectin as an integrative signal coordinating chronic adaptation across metabolically distinct tissues delineates the temporal sequence of early CR adaptation; furthermore, it establishes a mechanistic framework defining how early molecular and physiological shifts converge to achieve steady-state metabolic homeostasis.

GLP-1 receptor agonists (GLP-1 RAs) effectively reduce weight in obesity, although significant weight regain typically follows discontinuation. Here, in a randomized clinical trial (ChiCTR2200066014), we found that GLP-1 RA (semaglutide) and a high-fibre diet achieved similar 12-week weight reduction, but semaglutide recipients exhibited significantly higher weight rebound at the 14th week after intervention cessation. Shotgun metagenomic sequencing revealed that semaglutide aggravated the proinflammatory signature in the gut microbiome, which contrasted with high-fibre diet intervention. The microbiota transplanted from semaglutide-treated subjects to germ-free mice induced gut barrier dysfunction, systemic inflammation and an increase in the bacterial antigen load in the liver and adipose tissue, which activated the NF-{kappa}B pathway to drive lipid accumulation. Using a diet-induced obesity mouse model, we found that semaglutide exacerbated gut microbiome dysbiosis by weakening host immune surveillance of the gut microbiota through downregulating IFN-{gamma} to reduce antimicrobial peptides expression and delaying gut transit time to shift microbial metabolism from saccharolysis towards proteolysis. Crucially, combining semaglutide with dietary fibre in mice mitigated microbiome dysbiosis and attenuated weight regain post-cessation. These findings suggest that GLP-1 RA-exacerbated gut microbiome dysbiosis in obesity as a key mediator of post-treatment weight rebound and propose adjunctive fibre supplementation as a strategy to sustain weight loss.

Brown adipose tissue (BAT) regulates systemic metabolism beyond thermogenesis, yet the circulating mediators through which BAT communicates with other organs remain less defined. Here, we performed comprehensive serum metabolomics and lipidomics in BAT-ablated mice and human cohorts with varying BAT activity to delineate how BAT activity shapes the circulating metabolome. By integrating datasets across serum, tissues, extracellular fluids, and conditioned media, we assembled BAT-linked circulating molecular signatures. The analyses support a role for BAT in the clearance of circulating branched-chain amino acids and triglycerides, and also identify a cold-inducible metabolite, 3-hydroxystearic acid (3-OHSA), produced by BAT and released into circulation. 3-OHSA serves as a circulating readout of cold-activated BAT and acts on the liver to reduce mitochondrial membrane potential and reactive oxygen species (ROS) production, thereby limiting oxidative stress. This work provides a framework for identifying BAT-derived mediators and uncovers a BAT-liver axis that coordinates adaptation to metabolic stress. HIGHLIGHTSO_LIComprehensive analyses of BAT-linked circulating metabolome and lipidome in mice and humans. C_LIO_LIMulti-level metabolomics supports the role of BAT in circulating BCAA and triglyceride clearance. C_LIO_LICold-inducible 3-OHSA is secreted by BAT and signals to the liver. C_LIO_LI3-OHSA decreases hepatic oxidative stress by decreasing mitochondrial membrane potential. C_LI

Central carbon metabolism undergoes extensive remodeling in cancers, yet the extent to which the resulting network architectures and operating principles are conserved across species and oncogenic contexts in vivo remains unclear. Here, central carbon metabolism was evaluated in Hippo/Yki-driven Drosophila gut tumors, as Hippo-YAP/TAZ signaling links nutritional cues to metabolic state and contributes to epithelial tumorigenesis and therapy resistance. Using integrated steady-state metabolomics, transcriptomics and [U-13C6]glucose tracing, we defined how Hippo pathway activation reorganizes nutrient utilization and carbon flux in vivo and assessed how the resulting Yki-driven metabolic network aligns with mammalian cancer metabolism. Yki tumors exhibited a Warburg-like state with increased glycolytic throughput and enhanced conversion of glucose-derived carbon to lactate, accompanied by transcriptional upregulation of key glycolytic and lactate-production enzymes. Glucose carbon was also redirected into redox-supporting and anabolic nodes, including activation of the glycerol-3-phosphate shuttle and increased labeling of alanine and serine. Mitochondrial metabolism was reorganized into a non-canonical, segmented TCA network centered on -ketoglutarate, which accumulated and acted as a drain into glutamate/glutamine and 2-hydroxyglutarate rather than supporting complete oxidative turnover. Despite reduced abundance of pentose phosphate intermediates, non-oxidative PPP carbon rearrangements and ribose labeling were maintained, enabling robust glucose contribution to pyrimidine nucleotide pools, including strongly labeled dTTP. Together, these data establish a comprehensive map of Yki-driven central carbon partitioning in vivo and highlight conserved principles of tumor carbon allocation shared across oncogenic contexts and mammalian cancer metabolism.

Intermuscular adipose tissue (IMAT) expansion is closely associated with cardiometabolic disease (CMD), yet its cellular organization and regulatory mechanisms remain poorly defined. Using bulk transcriptomics on human IMAT, we identified a distinct gene signature and functional regulators including adipogenic transcription factor early B-cell factor 2 (EBF2). By mapping this human signature to the spatial transcriptome of IMAT from mice with CMD, we unraveled discrete stromal niches surrounding muscle fibers, characterized by IMAT expansion and the coordinated activation of adipogenic, extracellular matrix, inflammatory, and metabolic pathways. Spatial analyses showed that fibro-adipogenic progenitor (FAP) abundance does not predict adipocyte formation, supporting a model of localized and context-dependent lineage transitions. Cross-species comparison revealed partial conservation of human IMAT gene programs, validating the mouse model and highlighting species-specific features. Functional experiments in human primary myoblasts showed that EBF2 is sufficient to induce adipogenic reprogramming. Our findings establish IMAT as an active, spatially organized remodeling niche and identify lineage plasticity as a central mechanism driving its expansion in metabolic disease.

It is generally accepted that hepatic gluconeogenesis, the synthesis of glucose from non-carbohydrate substrates is active in the fasted state and inactive in the fed state. In contrast, de novo lipogenesis is active in the fed state and is inactive in the fasted state. Here, we used targeted single cell RNA-seq, HCR RNA-FISH, and PrimeFlow in normal physiological mouse liver, and identified a subpopulation of periportal hepatocytes that simultaneously co-express both gluconeogenic and lipogenic genes in the fed state. Euglycemic-hyperinsulinemic clamps further demonstrated that this novel hepatocyte subpopulation is naturally insulin resistant. Spatial metabolic imaging coupled with stable isotope tracing analyses revealed individual hepatocytes that simultaneously undergo both gluconeogenesis and de novo lipogenesis. These dual-positive hepatocytes were also present in human hepatocytes from humanized mouse livers. Moreover, the number of dual-positive hepatocytes increased in high-fat diet-fed mice, suggesting a paradigm shift in our understanding of how the liver becomes insulin resistant.

Type 2 diabetes and prediabetes affect hundreds of millions of people globally, yet the metabolic networks underlying disease development remain poorly understood. Using untargeted liquid chromatography-mass spectrometry (LC-MS/MS), we profiled a total of 15,470 (900 known) serum metabolite features across the human diabetes spectrum (the most comprehensive coverage reported to date). Weighted coexpression network analysis of samples from people with normal glucose tolerance, prediabetes, and type 2 diabetes, collected at baseline and 2 hours after an oral glucose tolerance test, revealed tightly coregulated modules strongly associated with glycemic dysregulation, insulin resistance, and islet dysfunction. Notably, short-chain organic acids, particularly crotonic acid, emerged as hubs of the diabetes-associated networks, accumulating progressively with disease severity. Reanalysis of extracellular vesicle proteomics from the same cohort showed that 16.5% of circulating proteins were crotonylated, with approximately 40% correlated with crotonic acid and other hub metabolites, establishing a metabolome-crotonylome axis as a novel mechanism in diabetes development.

mTORC1 integrates growth factor and nutrient signals to regulate cellular metabolism, yet there are no metabolites known to directly regulate mTORC1 activity in cells. Cryo-EM studies revealed that inositol hexakisphosphate (IP6) associates with the FAT domain of mTOR, suggesting that inositol phosphates may directly modulate mTOR activity. We previously showed that higher-order inositol phosphates enhance mTORC1 kinase activity and stability in vitro. Here, we investigated whether inositol phosphate metabolism regulates mTORC1 signaling in pancreatic {beta}-cells. Suppression or acute inhibition of inositol phosphate multikinase (IPMK), as well as knockdown of inositol trisphosphate kinase 1 (ITPK1), selectively reduced cellular IP5 levels without altering IP6 and resulted in impaired basal and insulin-stimulated mTORC1 signaling, particularly under physiological glucose and low growth factor conditions. Combined inhibition of IPMK and ITPK1 nearly abolished IP5 and reduced IP6, demonstrating that these enzymes compensate to supply IP5 for IP6 synthesis. Importantly, depletion of IP5 did not impair PI3K/Akt activation but accelerated termination of the mTORC1 signal, indicating a role for IP5 in stabilizing the active mTORC1 complex. Reduction of inositol phosphate levels did not prevent insulin- or glucose-induced mTORC1 activation, revealing that IP5 primarily regulates signal persistence rather than initiation. Together, these findings identify IP5 as a metabolic regulator that prolong mTORC1 activity in {beta}-cells, providing a mechanism by which cellular metabolic state modulates sustained mTORC1 signaling. Significance StatementmTORC1 is a central metabolic regulator whose chronic activation contributes to metabolic disease, yet mechanisms that sustain mTORC1 activity after its activation are poorly understood. We show that enzymes controlling inositol phosphate metabolism regulate the stability of mTORC1 signaling in pancreatic {beta}-cells by maintaining cellular levels of inositol pentakisphosphate (IP5). Reducing IP5 impairs basal and sustained mTORC1 signaling without affecting upstream growth factor or energy-sensing pathways, revealing a mechanism that controls signal duration rather than activation. These findings identify IP5 as a metabolic regulator of mTORC1 and suggest that targeting inositol phosphate metabolism may provide a strategy to modulate mTORC1 activity in metabolic disease.

Lethal sterile inflammatory diseases are linked to amino acid metabolism, but the role of serine remains unclear. Here, we show that dysregulated serine metabolism and reduced plasma serine levels correlate with disease severity of acute pancreatitis (AP) in patients and mouse models. Elevating serine levels via exogenous serine supplementation or pancreatic phosphoglycerate dehydrogenase (PHGDH) overexpression mitigates pancreatic injury, whereas a serine deprivation diet or pancreatic PHGDH knockdown exacerbates AP. Serine prevents cell death and oxidative stress in pancreatic acinar cells, human induced pluripotent stem cells-derived pancreatic organoids and mouse pancreatic tissue. Serine enhances cysteine and glutathione biosynthesis primarily by promoting solute carrier family 7 member 11 (SLC7A11)-dependent cystine uptake rather than by serving as a direct substrate. Mechanistically, the E3 ubiquitin ligase NEDD4 mediates ubiquitination and degradation of SLC7A11, whereas serine binds to NEDD4 and thereby inhibits SLC7A11 degradation. Similarly to serine, pharmacological inhibition of NEDD4 alleviates lipid peroxidation and pancreatic injury. These findings identify serine as a critical signaling regulator of SLC7A11 stability and oxidative stress, and provides a new therapeutic strategy for AP and associated sterile inflammatory disorders. HighlightsAcute pancreatitis (AP) is linked to abnormal serine metabolism and serine depletion. Serine prevents cell death in AP acinar cells, human pancreatic organoids and mice. Serine promotes SLC7A11-dependent cystine uptake and glutathione levels in acinar cells. Serine reduces NEDD4-mediated ubiquitination of SLC7A11. In briefSerine protects against cell death and pancreatic injury in acute pancreatitis by stabilizing SLC7A11 through disruption of NEDD4-mediated ubiquitination in acinar cells.

Dementia affects approximately 60 million people worldwide, yet molecular mechanisms linking early neuropathological changes to clinical progression remain poorly understood. We performed targeted and untargeted metabolomics in plasma and cerebrospinal fluid (CSF) from 166 memory clinic patients spanning no cognitive impairment, mild cognitive impairment due to Alzheimers disease (AD), AD dementia, and mixed AD-cerebrovascular dementia. Using a data-driven approach, we identified a CSF polyol signature characterized by elevated sorbitol, meso-erythritol, and d-glucose/erythritol ratio consistently associated with phosphorylated tau (pTau) and total tau (tTau), but not amyloid-{beta}. This association was validated in an independent CSF metabolomics (n=687) and proteomics (n=737) cohorts. Structural equation modelling confirmed that polyol metabolites predict tau burden, with less than 3% attenuation following genetic adjustment, establishing a non-genetic, metabolically driven mechanism. These findings define a tau-dominant, amyloid-independent metabolic axis in neurodegeneration, implicating the polyol pathway as a potentially modifiable therapeutic target.

Citrate is a central metabolite linking tricarboxylic acid (TCA) cycle activity to energy and lipid metabolism and supports the synthesis of inflammatory mediators, including itaconate, in macrophages. While citrate is primarily generated endogenously, extracellular citrate levels are elevated under pathological conditions such as citrate transporter disorder. Cells import extracellular citrate through SLC13 transporters, including the sodium-dependent citrate transporter NaCT (encoded by SLC13A5). However, whether macrophages take up extracellular citrate and how this affects metabolism and function remains unclear. Here, we combined mass spectrometry and tracing approaches to investigate the metabolic fate of citrate in human macrophage cell lines, primary, and iPSC-derived macrophages. We demonstrate that cells take up extracellular citrate, which was enhanced under metabolic stress conditions. Exogenous citrate was not substantially utilized as a carbon source but selectively altered glutamine metabolism and responses to bacterial infection with Salmonella enterica Typhimurium and Legionella pneumophila Corby. Our work identifies extracellular citrate as a context-dependent regulator in macrophages that decouples uptake from metabolic utilization. HighlightsO_LIMacrophages import extracellular citrate via SLC13 transporters C_LIO_LIExtracellular citrate accumulates under hypoxia and inflammatory activation C_LIO_LIExtracellular citrate does not fuel central carbon metabolism in human macrophages C_LIO_LICitrate modulates glutamine immunometabolism and modulates immune responses C_LI eTOC blurbVo{beta}-Willenbockel et al. demonstrate that human macrophages accumulate extracellular citrate without using it as a major carbon source. Instead, citrate modulates glutamine utilization, inflammatory responses, and host-pathogen interactions revealing a context-dependent regulatory role for extracellular metabolites in immune cell function.

Glycosuria, whether genetically induced or triggered by SGLT2 inhibitors, activates compensatory glucose-producing pathways that limit glucose lowering in type 2 diabetes. To define these pathways, we studied renal Glut2 knockout mice, which progressively lose Slc5a2 (encoding SGLT2) expression yet maintain normoglycemia despite marked urinary glucose loss. Metabolic profiling and isotope tracing revealed coordinated adaptations in mannose and glutamine metabolism during glycosuria. Skeletal muscle reduced glucose utilization and instead oxidized mannose, while whole-body glycolysis declined, establishing a systemic glucose-sparing state. Disruption of glutamine transport or mannose utilization caused hypoglycemia in mice treated with an SGLT2 inhibitor, demonstrating dependence on these substrates to maintain glucose homeostasis during glycosuria. Multiomic profiling revealed increased expression and chromatin accessibility of mannose and glutamine transport pathways. These findings identify a kidney-driven metabolic program that preserves systemic glucose homeostasis during glycosuria and may inform strategies to optimize the glucose-lowering efficacy of SGLT2 inhibitors.

Neutrophils are the most abundant leukocytes in humans and play a central role in immune regulation. Although traditionally viewed as terminally differentiated cells with limited plasticity, growing evidence indicates that neutrophils exhibit substantial functional heterogeneity in response to stress. To date, however, most studies have focused on transcriptional and signaling changes, while metabolic heterogeneity, especially beyond central carbon metabolism, remains poorly characterized. Here, we systematically investigate metabolic reprogramming in neutrophils under three stress conditions: granulocyte colony-stimulating factor (G-CSF) treatment, hematopoietic stem cell transplantation (HSCT), and pancreatic ductal adenocarcinoma (PDAC). Using condition-specific genome-scale metabolic (GSM) models, we identify distinct metabolic vulnerabilities across neutrophil states. Vitamin metabolism emerged as a key differentiating feature between G-CSF- and HSCT-treated neutrophils, whereas PDAC-associated neutrophils displayed globally enhanced metabolic activity coupled with restricted metabolite exchange fluxes. Furthermore, solute carrier (SLC) family transporters were identified as major metabolic regulators underlying stress-induced neutrophil reprogramming. Together, our findings demonstrate that neutrophil heterogeneity extends beyond transcriptional programs to encompass profound metabolic specialization, highlighting metabolism as a critical dimension of neutrophil plasticity in health and disease.

Interest in fasting-based dietary interventions to improve metabolic health is growing. Caloric restriction (CR) with one meal per day includes an extended fasting component that contributes to its metabolic and longevity benefits, yet the specific role of fasting within CR remains unclear. Here, we compared mice under CR with those subjected to a fasting-refeeding-fasting (FRF) regimen while controlling pre-fasting food intake and fasting duration. Simultaneous comparison of diet induced changes in plasma insulin and free fatty acids, hepatic mTOR signaling and ketogenesis, total body metabolic rhythms with kinetics of food digestion suggested that gastric emptying served as a primary metabolic trigger in acute fasting. In contrast, in CR, fasting responses were actively regulated and suggested anticipatory mechanisms. At the transcriptomic level, CR enhanced circadian rhythmicity and metabolic gene coordination, whereas FRF disrupted it. In agreement with the expression data, CR improves glucose and fatty acid metabolism while fasting leads to glucose intolerance and fat accumulation in the liver induced glucose intolerance and hepatic steatosis. These findings reveal that CR engages clock-aligned, anticipatory metabolic control, while fasting-refeeding cycles rely on direct nutrient cues. This mechanistic distinction between active and passive metabolic regulation may underlie the superior metabolic and longevity outcomes of caloric restriction.

Despite decades of biochemical study, a comprehensive map of the mammalian metabolome remains elusive. Mass spectrometry-based metabolomics detects thousands of small molecule-associated signals in mammalian tissues, but it is currently unclear how many of these reflect products of endogenous metabolism. Here, we leverage systematic in vivo isotope tracing to infer the biosynthetic origins of unidentified metabolites. We administered 26 different isotopically labelled nutrients to mice, measured circulating and tissue metabolite labelling by mass spectrometry, and developed a statistical framework to infer the number of carbon atoms incorporated from each of these precursors into more than 4,000 putative metabolites. We show this information can be harnessed for biosynthesis-aware structure elucidation using a multimodal AI model that co-embeds isotopic labelling patterns with chemical structures. This approach revealed several previously unrecognized families of mammalian metabolites, including cysteine-derived alkylthiazolidines, dithioacetal mercapturic acid derivatives, short-chain N-acyltaurines, acylglycyltaurines, and N-oxidized taurines. It further uncovered a family of mevalonate-derived isoprenoid metabolites that includes 2,3-dihydrofarnesoic acid, which is markedly depleted in both mouse and human aging. Age-related depletion of these isoprenoids is driven by impaired coenzyme A synthesis. Our work establishes the biosynthetic precursors for thousands of unidentified metabolites and reveals multiple previously unrecognized branches of mammalian metabolism.

Hepatocytes undergo extensive proliferation to facilitate liver repair after injury, yet early adaptive changes prior to proliferation remain unclear. Here, we report that during early acetaminophen (APAP)-induced liver injury, hepatocytes exhibit transient proliferation suppression, most pronounced in mid-zone hepatocytes due to zonal APAP metabolism. Using spatial transcriptomics (ST), immunohistochemistry, and functional studies, we identified a unique mid-zone stress-response program. Central to this adaptation is the Atf4-Chop axis, which actively suppresses proliferation via the cell cycle inhibitor Btg2, prioritizing cytoprotection over cell division. This transient arrest is a critical survival strategy: halting energy-intensive proliferation during peak injury allows mid-zone hepatocytes to redirect resources towards protection, enhancing their survival in early APAP-induced liver injury. Thus, Atf4-Chop-mediated quiescence preserves a hepatocyte reservoir necessary for subsequent regenerative proliferation and effective repair. Our findings reveal a key adaptive trade-off in mid-zone hepatocytes where transient proliferation arrest promotes early survival to enable repair.

Aging arises from interconnected molecular defects, yet upstream regulatory mechanisms that coordinate these hallmarks remain incompletely defined. While epitranscriptomic regulation has emerged as a critical layer of gene control, the contribution of tRNA-specific modifications to aging remains largely unexplored. Here, we systematically profile tRNA modifications across multiple organs, species, and senescence models and identify mannosyl-queuosine (manQ), a wobble-position modification of tRNAAsp, as the first tRNA-specific modification that consistently declines with age. ManQ depletion is evolutionarily conserved and tightly correlates with functional deterioration. Mechanistically, loss of manQ impairs translational fidelity, leading to proteome imbalance, collapse of proteostasis, and aberrant expression of senescence-associated proteins, including GPNMB. These translational defects intersect with established aging hallmarks and accelerate cellular and organismal aging. We further demonstrate that circulating queuine, a microbiota-derived precursor required for manQ biosynthesis, declines with age in rodents and humans. Queuine deficiency promotes senescence, whereas supplementation restores manQ levels, improves translational accuracy, suppresses p16/p21-driven senescence programs, and re-establishes proteostatic balance. Across species, queuine supplementation extends lifespan and enhances healthspan. In Drosophila, it increases median lifespan by 47% and improves stress resistance and memory. In naturally aging mice, long-term oral administration extends lifespan by 15.3%, reduces DNA methylation age, improves cognitive and motor performance, strengthens antioxidant defenses, remodels the gut microbiota, and alleviates inflammation and metabolic dysfunction without detectable toxicity. Collectively, these findings establish tRNA epitranscriptomic remodeling as a previously unrecognized layer of aging regulation and identify restoration of manQ through queuine supplementation as a multi-system strategy to delay aging.

The transition from metabolic health to type 2 diabetes unfolds through progressive insulin resistance (IR), yet the gold-standard hyperinsulinemic-euglycemic clamp is inapplicable at population scale and fasting insulin is not uniformly available. Several surrogate measures have been described in the literature, but whether these surrogates identify the same individuals, and whether continuous glucose monitoring (CGM) or NMR metabolomics carry information beyond conventional markers, remains unresolved. Here, we analyzed IR surrogates in 10,114 non-diabetic adults (35-75 y) from the Human Phenotype Project (HPP), integrated with 14-day CGM, dual x-ray absorptiometry (DEXA) body composition, liver and carotid ultrasound, sleep monitoring, and NMR metabolomics and established sex-specific, age-resolved reference ranges. IR surrogates were moderately inter-correlated but captured distinct metabolic facets. We next focused on DEXA-derived visceral adipose tissue (VAT), one of the strongest correlates of clamp-measured insulin resistance. Our analysis showed that VAT can be reliably predicted from anthropometric measurements alone (R{superscript 2} = 0.659). However, it is only modestly predicted by CGM features alone (R2 = 0.078). Among CGM-derived features, markers of glycemic variability were stronger predictors of VAT than conventional mean-glucose metrics. Residual-based analyses identified individuals whose visceral adiposity was substantially higher than expected given their BMI or HbA1c levels. Notably, 1.2% of adults in the HPP cohort exhibited elevated visceral adiposity despite having both a normal BMI (< 25 kg/m{superscript 2}) and normoglycemic HbA1c (< 5.7%). These discordant subpopulations harbored adverse profiles across lipid, hepatic, vascular, sleep, and metabolomic domains. NMR lipoprotein subfractions (VLDL, HDL) discriminated discordant phenotypes. A CGM variability-only model separated discordant individuals at AUC = 0.63, with negligible gain from adding mean glucose. Findings were validated in an independent cohort with available fasting insulin data. Together, these results establish normative IR surrogate reference ranges, quantify the fraction of metabolically at-risk individuals missed by conventional BMI and HbA1c screening, and highlight CGM variability metrics and NMR lipoprotein profiling as complementary tools for early metabolic risk stratification. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=112 SRC="FIGDIR/small/26352290v1_ufig1.gif" ALT="Figure 1"> View larger version (68K): org.highwire.dtl.DTLVardef@1f491a6org.highwire.dtl.DTLVardef@18660a9org.highwire.dtl.DTLVardef@133fa14org.highwire.dtl.DTLVardef@1675463_HPS_FORMAT_FIGEXP M_FIG C_FIG

Diet deeply influences health and disease risk by reshaping cellular metabolism. In the intestine, dietary nutrients directly affect intestinal stem cell (ISC) behavior, yet the regulatory mechanisms linking metabolism to transcriptional control remain poorly defined. Because mitochondria function as central metabolic hubs, we focused on mitochondrial signaling to understand how nutrient utilization governs ISC function. Using the MITO-Tag mouse, we isolated metabolites specifically from ISC mitochondria and found that the sugar-derived metabolite UDP-GlcNAc was reduced in ISCs from mice fed a high-fat diet. Moreover, we identified that reducing O-GlcNAcylation (OGN) rapidly increased stem cell frequency, proliferation, regenerative capacity, and the abundance of PPAR target proteins. Mechanistically, these effects depend on PPAR signaling, as genetic loss of Ppar-d/a blocks the ISC phenotypes induced by reduced OGN. These results reveal an OGN-PPAR signaling axis that translates dietary metabolic cues into transcriptional programs governing fuel utilization and ISC behavior in the intestine. Collectively, our findings highlight that OGN is a previously unrecognized regulator of PPAR signaling in intestinal stem cells.

Dietary fat composition modulates host physiology and the gut microbiome, but the long-term effects of specific fat sources and the extent to which these changes resolve after dietary reversal remain incompletely defined. Here, we present a longitudinal multi-omic resource of mice maintained for one year on a purified control diet, seven high-fat diets differing in predominant fat source, or reversal regimens in which animals were switched from high-fat to control diet after 4 or 9 months. We further incorporated two cohorts with distinct pre-existing microbiome configurations to determine how baseline community structure shapes diet-induced remodeling of the gut microbiome ecosystem. By integrating longitudinal phenotyping, fecal metagenomics, fecal metabolomics, plasma metabolomics and lipidomics, and intestinal single-cell RNA sequencing, we defined the shared and dietary fat-specific responses across host and microbiome compartments. Baseline microbiome composition strongly influenced microbial responses to diet, indicating that pre-existing community structure is a major determinant of dietary ecosystem remodeling. Although many altered features shifted toward baseline after dietary reversal, only approximately half of diet-associated microbial changes recovered within the study window. A subset of taxa exhibited persistent alterations, including sustained depletion of Lactobacillus johnsonii and Bifidobacterium pseudolongum and sustained enrichment of Alistipes finegoldii, consistent with a "microbiome memory" of prior high-fat diet exposure. This memory effect is mirrored in the host, by sustained suppression of major histocompatibility complex class II (MHC-II) gene expression in intestinal epithelial cells after dietary reversal. These findings indicate that dietary fats leave a lasting imprint on the host-microbiome interactome that survives dietary intervention. Together, these data establish a resource for defining how dietary fat source, baseline microbiome composition, and dietary history shape host-microbiome states. The entire resource is available online as an RShiny app.