Nature Metabolism

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.

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.

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.

Joint single-cell transcriptomic-metabolomic profiling remains technically intractable. Here we present CHIMERA (Cell-level Hybrid Inference of Metabolome Embedded on RNA Atlas), a data-driven framework that learns transcriptome-to-metabolome mappings from spatially paired multi-omics data and transfers them to unpaired scRNA-seq. CHIMERA generates quantitative, database-independent single-cell metabolite abundances and, by pairing them with the measured transcriptome of the same cells, enables joint co-embedding of genes and metabolites for the discovery of differential metabolites and co-regulated gene-metabolite modules. Using 10x Visium paired with MALDI-MSI from murine liver sections and a matched scRNA-seq reference, CHIMERA achieves a per-metabolite median Pearson r = 0.285 with positive cross-section generalization. On an independent Liver Cell Atlas Western-diet cohort, CHIMERA recovers metabolic reprogramming that recapitulate published non-alcoholic fatty liver disease pathophysiology. Applied to a Rarres2 (chemerin) knock-down hepatocellular carcinoma model, CHIMERA uncovers metabolic heterogeneity among tumour-associated macrophages, resolving four metabolic subclusters (MC-0 to MC-3); Rarres2 appears to drive macrophage polarization from an LAM-like MC-3 state toward Spp1+ like MC-0/MC-2 by modulating a co-regulated gene-metabolite module--a dual-omics phenotype undetectable by either modality alone. CHIMERA is the first data-driven framework for quantitative single-cell metabolome inference, opening joint transcriptomic- metabolomic analyses inaccessible to either experimental or knowledge-based computational approaches.

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.

Hypoxia disrupts mitochondrial respiration and increases the NADH/NAD+ ratio, causing reductive stress. To maintain redox homeostasis, mammalian cells divert electrons toward fermentation. While fermentation in mammals typically involves lactate production, we identify the fermentation of branched-chain amino acids (BCAAs) as an alternative electron sink activated by hypoxia. The resulting metabolites are excreted in urine as a distinct mechanism for alleviating reductive stress. BCAA fermentation is catalyzed by lactate dehydrogenase (LDH) enzymes and is highly responsive to the NADH/NAD+ ratio. Consequently, BCAA fermentation products are sensitive biomarkers for reductive stress in human contexts ranging from resistance exercise to severe hypoxemia. Furthermore, we find that mouse sperm have evolved highly efficient BCAA fermentation, providing a specific metabolic strategy to support the anaerobic electron flow that facilitates flagellar hypermotility across mammalian sperm. Our work highlights an under-appreciated fate of BCAAs in response to reductive stress.

Lipids constitute one of the largest and most diverse classes of cellular molecules, sustaining membrane architecture, energy storage, and signaling. Consequently, their dysregulation underlies a broad spectrum of human disease. However, the genetic mechanisms governing lipid homeostasis have remained largely inaccessible, owing to the lack of approaches capable of systematically linking defined genetic perturbations to large-scale changes in cellular lipidome composition. Here we introduce LipoGrid, a spatial mass spectrometry platform that resolves the genetic architecture of lipid metabolism at single-cell resolution. LipoGrid arrays CRISPR/Cas9-perturbed cells on a micropatterned grid and sequentially captures lipidomic and gRNA identity from the same cells, complemented by single-cell RNA sequencing of matched cell populations subjected to the same perturbations. Using this approach, we quantified the relative abundance of 158 distinct lipid species across 143 target genes in a rigorously controlled experimental framework. We find that most gene knockouts produced measurable alterations in lipid composition, often affecting specific lipid classes and molecular subspecies. The screen accurately recapitulated established gene-lipid relationships, including enzyme-substrate specificities, lipid pathway regulators, and disease-associated loss-of-function phenotypes, thereby demonstrating the sensitivity and accuracy of LipoGrid. By jointly profiling transcriptomic and lipidomic responses, we further uncover compensatory feedback mechanisms that buffer the impact of genetic perturbations on the cellular lipidome. Collectively, these findings establish LipoGrid as a scalable multimodal platform for systematically mapping gene-lipid interactions and reveal the regulatory networks linking gene perturbation, transcriptional adaptation, and lipidome remodeling. HighlightsO_LIMicropatterned single-cell growth enables spatial lipidomic perturbation screens C_LIO_LILipoGrid maps 143 gene knockouts to 158 lipid species and transcriptomic states C_LIO_LIPerturbed lipidomes reveal compensatory feedback and lipid-class-specific uptake C_LIO_LIRecovers enzyme substrate specificities and disease-linked lipid signatures C_LI

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.

Neurons engage compensatory pathways that promote survival when confronted with mitochondrial dysfunction. Indeed, we recently showed that Drosophila neurons upregulate Ldh transcription to help survive the loss of the key mitochondrial fusion gene Opa1. Here, we further characterize this metabolic flexibility and show that it reflects a more general increase in glycolytic activity. A distinct mitochondrial perturbation, TFAM overexpression, similarly induces glycolytic gene expression including Ldh and also elevates lactate levels. LDH is also required to maintain neuronal function under TFAM overexpression. Notably, raising NAD+/NADH ratio by expressing the bacterial NADH oxidase LbNOX does not substitute for LDH function. On the contrary, it further compromises neuronal function in Opa1-deficient and TFAM-overexpressing neurons. Moreover, mitochondria-targeted LbNOX expression alone induces mitochondrial dysfunction and the compensatory glycolytic response. Together, these findings indicate that LDH-mediated rescue does not reflect an increase in NAD+/NADH ratio but is part of a broader neuroprotective metabolic reprogramming which enables neurons to withstand diverse forms of mitochondrial impairment.

Lysosomes are acidic organelles that fuel cancer progression by facilitating nutrient acquisition and metabolic adaptation, yet the determinants through which cancer cells sustain specialized lysosomal functions are not fully delineated. Notably, assimilation of dietary antioxidants within lipoproteins, a lysosome-dependent process, protects tumors from ferroptosis, an oxidative form of cell death, raising the possibility that tumors evolve mechanisms to enhance this process. Here, we applied genetic screens to identify regulators of lysosome-dependent lipoprotein assimilation and ferroptosis resistance and identified ZNF217, a frequently amplified transcriptional regulator in human cancers, as a driver of tumor lysosomal function and ferroptosis resistance. ZNF217 promoted lipoprotein assimilation through transcriptional maintenance of RAB11FIP4, an endolysosomal protein. Loss of either ZNF217 or RAB11FIP4 impaired lysosomal acidification across multiple cancer types, leading to defective lipoprotein assimilation, increased lipid peroxidation, ferroptosis sensitivity, and impaired tumor growth. Mechanistically, RAB11FIP4 boosts lysosomal acidity through maintenance of RAB7A activity. Finally, disruption of ZNF217 in breast cancer cell lines and patient-derived organoids, a tumor context linked to ZNF217 expression, reduced lysosomal acidity and impaired cancer growth through increased ferroptosis sensitivity. Together, we identify transcriptional regulation of lysosomal acidification as a key metabolic adaptation that enables extracellular antioxidant acquisition and tumor progression.

Background and aimsCardiovascular-kidney-metabolic (CKM) syndrome stages confer graded CVD risk, but the underlying stage-specific molecular mechanisms remain undefined. MethodsIn 355,724 UK Biobank participants (median follow-up 13.5 years), we mapped CKM stages (0-3) to incident CVD. Using proteomics (n=37,785) and metabolomics (n=190,112), we identified stage-specific biomarkers via LASSO and XGBoost-SHAP. Mediation analyses were performed to quantify the proportion of the CKM-CVD association that was statistically accounted for by these biomarkers. The proportion of the protective association between cardiovascular health (Lifes Crucial 9 [LC9]) and incident CVD that was mediated by the same molecules was quantified. ResultsCVD risk increased across CKM stages. Beyond 11 pan-stage proteins (e.g., RTN4R,LEP) and 29 pan-stage metabolites (e.g.,GlycA), stage-specific molecular signatures emerged, whose pathway enrichment revealed a shift from metabolic/extracellular matrix dysregulation (Stage 1) to inflammation (Stage 2) to hypoxia/fibrosis (Stage 3). The proportion of the CKM-CVD risk association statistically accounted for by these molecules shifted accordingly: ADM (42.9%) in Stage 1, FABP4 (24.6%) in Stage 2, and HAVCR1 (28.0%) in Stage 3. High CVH (LC9[≥]80) was associated with approximately 80% lower CVD risk in Stages 0-2; a proportion of this protective association was statistically accounted for by the same stage-specific molecules. ConclusionsThese findings reveal a stage-ordered molecular continuum--from ECM remodeling to inflammation to fibrosis--that redefines CKM-driven CVD risk, and the strong protection of high CVH in early stages was statistically accounted for in part by these stage-specific molecules, generating the hypothesis that CVH may reduce risk through these modifiable pathways and providing a molecular framework for future stage-adapted intervention trials.

Animals rely on color to navigate complex environments, yet how eyeless organisms use chromatic information to guide food choice remains poorly understood. Here, we show that Caenorhabditis elegans exhibits robust color dependent foraging driven by microbial chromophores, preferentially consuming red while avoiding blue chromoprotein expressing bacteria across bacterial backgrounds and wild isolates. This discrimination persists in darkness and independently of photoreceptor, revealing a mechanism beyond canonical photoreception. Purified chromoproteins and bacterial metabolite fractions independently reproduce preference, demonstrating complementary chromatic and post ingestive metabolic cues. Mechanistically, blue chromoproteins generate singlet oxygen, producing oxidative stress and remodeling bacterial tryptophan and pterin metabolism, whereas red food promotes serotonin production and feeding-associated neuropeptide signaling. Disrupting serotonin biosynthesis or neuropeptide processing abolishes color preference. Together, our findings reveal a previously unrecognized, novel sensory strategy in which wavelength-selective pigment photochemistry transforms microbial color into metabolic information that is integrated through gut brain neuroendocrine signaling to guide foraging behavior in an eyeless animal.

A central challenge in microbial ecology is understanding how competing guilds coexist and why community structures unexpectedly drift away from theoretical steady states. While polyphosphate accumulation provides energy and redox buffering in many heterotrophs, how competing lineages occupying the same ecological niche without polyphosphate synthesis manage equivalent intracellular redox imbalances remains unposed. Using an enhanced biological phosphorus removal macrocosm, we integrated quantitative stoichiometry with metaproteomics to resolve alternative metabolic strategies that underpin cellular homeostasis in heterotrophs. We show that glycogen-accumulating organisms (GAOs) achieve baseline metabolic parity with polyphosphate-accumulating organisms (PAOs) through a parallel redox-buffering mechanism: heterotrophic CO2/HCO3- re-assimilation via the ethylmalonyl-CoA pathway. This inorganic carbon fixation couples structural carbon conservation with tight redox control, mitigating intracellular electron overflow and eliminating the long-assumed GAO bioenergetic inferiority. The bioenergetic efficiency of GAOs is further fortified by fine-tuned metabolic wiring, featuring energy-efficient high affinity acetate activation, ferredoxin-centered biochemistry, and energy-neutral polyhydroxyalkanoates (PHA) mobilization. Strikingly, minor formate co-feeding disrupted this established PAO/GAO parity. Stoichiometric simulations revealed that this formate supplementation creates an asymmetric bioenergetic niche that grants per-cycle energy gains exclusively to GAOs. Decoupled from hydraulic throughput, solids retention time control retains cells carrying accumulated intracellular inventory, translating subtle per-cycle stoichiometric edges into a multi-generational ratchet and drives a rapid community shift from PAO/GAO co-dominance to GAO dominance. By exposing limitations of traditional single-substrate and single-cycle steady-state models, our findings reveal how inorganic resource management and generational metabolic compounding govern community assembly in biomass-retaining microbial ecosystems.

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.

MTCH2 (mitochondrial carrier homolog 2) is a noncanonical member of the solute carrier family with five transmembrane (TM) helices, localized to the mitochondrial outer membrane. MTCH2's atypical topology creates a membrane-accessible hydrophilic groove, predicted to be necessary for its protein insertase and lipid scramblase activities. MTCH2 is linked to lipid metabolism and obesity and is required for starvation-induced mitochondrial hyperfusion. Here, we show that MTCH2 is a stable component of a complex containing the Armadillo (ARM) repeat-containing protein, ARMC1, and the DnaJ/Hsp40 chaperone protein, DNAJC11. Protein crosslinking, protein structural modeling, and molecular dynamics simulations demonstrate that the ARMC1 alpha-helical C-terminal domain (CTD) inserts into and stably interacts with the MTCH2 hydrophilic groove and blocks its lipid scramblase activity. We observe that starvation-induced mitochondrial fatty acid oxidation (FAO) is negatively regulated by the ARMC1-MTCH2 interaction. In ARMC1-deficient cells, FAO is stimulated compared to wild-type cells and lipid droplet abundance is significantly reduced. The altered lipid phenotype of ARMC1-/- cells is strictly dependent on MTCH2 and is reversed by ARMC1 expression in a manner dependent on its CTD. Beyond this metabolic axis, we also identify a function for ARMC1 in regulating lysosomal distribution and autophagic flux that is independent of its CTD and interaction with MTCH2. Thus, our data support a model in which the MTCH2-ARMC1 interaction functions as a metabolic switch during starvation to regulate the balance between fat storage and fat burning.

Metabolism is spatially compartmentalized across scales, from distinct tissues to cells and orga-nelles. However, most approaches for studying metabolic activity obscure spatial organization and intra-compartment heterogeneity within bulk biochemical measurements. On the other hand, multi-isotope mass spectrometry coupled with scanning electron microscopy (MIMS-EM) maps the fates of labeled nutrients in situ at nanometer-scale resolution, preserving ultrastructural con-text. Here we adapt MIMS-EM for Caenorhabditis elegans, where the compact metazoan body plan uniquely enables visualization of virtually all tissue types and their resident organelles within a single cross-sectional image. Using pulse-chase labeling of dietary carbon and nitrogen, we apply this approach to understanding the metabolic program induced in early stages of dietary restriction (DR). While DR is widely proposed to enhance organismal healthspan by enhancing broadscale turnover, proteomic studies have suggested more nuanced models. MIMS-EM across intact animals reveals that DR induces non-uniform effects between tissues and car-bon/nitrogen resources, accelerating carbon turnover in the muscle and hypodermis, but not in-testine. At the organelle scale, MIMS-EM revealed heterogeneity within mitochondrial networks that was independent of diet and stable over time. Spatial analysis of isotope signatures within intestinal mitochondrial networks also indicated greater similarity between neighboring mitochon-dria than distal mitochondria, supporting models of local mitochondrial mixing. Collectively, these results reveal that DR induces compartment- and resource-specific remodeling strategies across an intact animal while establishing C. elegans MIMS-EM as a powerful platform for multi-scale, integrative models of nutrient handling.

Pregnancy is accompanied by profound endocrine remodeling, yet the mechanisms by which maternal hormonal signals establish long-term tissue homeostasis remain largely unknown. Here we identify maternal progesterone signaling as a developmental cue that establishes lifelong oral homeostasis through a hormone-lipid-microbiome axis. We show that the membrane progesterone receptor mPR{delta} is selectively expressed in the developing and maternal submandibular glands, where it mediates non-genomic progesterone signaling to promote epithelial differentiation by driving the selective mobilization of docosahexaenoic acid (DHA). Loss of this pathway disrupts salivary gland maturation, reshapes the oral microbial ecosystem through the selective expansion of Pasteurellaceae, and causes local inflammation as well as systemic metabolic dysfunction. Mechanistically, antibiotic treatment abolishes these phenotypes, whereas transfer of the oral microbiota recapitulates disease, demonstrating that developmental defects in the host are translated into long-term pathology through the oral microbiome. Remarkably, maternal--but not adult--DHA supplementation restores salivary gland development and microbial homeostasis and prevents adult disease phenotypes, identifying a critical developmental window during which oral homeostasis is durably established. Collectively, these findings reveal a previously unrecognized maternal endocrine mechanism that establishes lifelong host-microbiome homeostasis and identify developmental programming as a fundamental principle linking maternal physiology to adult health. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=188 SRC="FIGDIR/small/743932v1_ufig1.gif" ALT="Figure 1"> View larger version (56K): org.highwire.dtl.DTLVardef@ba90c4org.highwire.dtl.DTLVardef@7644a5org.highwire.dtl.DTLVardef@94c998org.highwire.dtl.DTLVardef@3f49a4_HPS_FORMAT_FIGEXP M_FIG C_FIG

Circadian rhythms in mammals are generated by negative feedback loops, in which CLOCK and BMAL1 bind to E-box to activate transcription of Period (Per) and Cryptochrome (Cry) and the E-box-dependent transactivation is inhibited by PER and CRY proteins. Although the core transcriptional feedback loop of the circadian clock has been well defined, how this machinery interfaces with broader nuclear regulatory systems remains incompletely understood. Here, we identify nardilysin (NRDC), a metalloendopeptidase previously implicated in nuclear transcriptional regulation and metabolic homeostasis, as an unexpected modulator of the circadian clock. NRDC deficiency led to elevated PER2 protein levels in the liver and enhanced PER2 dynamics in cell-autonomous circadian oscillators, and was accompanied by a significant shortening of behavioral rhythms in mice. Biochemical analyses demonstrated that NRDC selectively associates with PER2 and CRY2 and antagonizes PER2-mediated repression of CLOCK-BMAL1-dependent transcription. Genome-wide chromatin immunoprecipitation analyses reveal that NRDC is enriched at promoter-proximal E-box-containing regions, frequently co-localizing with CLOCK binding sites. Together, these findings uncover a previously unrecognized link between circadian timing and protease-based nuclear regulation, positioning NRDC as a critical modulator of PER2 function and circadian period determination.

In eukaryotic cells, the function of each organelle depends on its unique protein composition. Protein targeting errors threaten organelle identity and function, yet how mistargeting errors are detected and resolved remains poorly understood. Here, we show that mitochondrial import stress drives widespread rerouting of mitochondrial proteins to the endoplasmic reticulum (ER), with strong enrichment for hydrophobic oxidative phosphorylation (OXPHOS) components. Using proximity proteomics, a split-fluorescence reporter system, and genome-wide CRISPR screening, we find that mistargeted proteins partition into distinct classes with divergent fates, ranging from stable ER residence to rapid degradation by ER-associated degradation (ERAD). The clearance of these mislocalized proteins involves partially redundant ERAD branches, with the ubiquitin ligase MARCHF6 playing a central role. Together, these findings establish the ER as a key organelle for handling mistargeted mitochondrial proteins and reveal how ER quality control maintains proteostasis during mitochondrial dysfunction.

Human genetic variation is a major determinant of organ metabolism, yet how naturally occurring variants shape quantitative metabolic phenotypes remains unclear. We present VariantFlux, a workflow that integrates ancestry-aware variant interpretation into genome-scale metabolic modelling to generate personalised, variant-constrained kidney reconstructions. Using the Human1 v1.19 model, we built a kidney-specific baseline model constrained by 482 metabolites and analysed 2,547 individuals from the 1000 Genomes Project, in whom [~]50% of metabolic genes were predicted damaging by at least three computational tools. These variants, whose burden differed subtly across ancestries, were translated into gene-dosage-anchored flux constraints for homozygous knockouts and graded heterozygous knockdowns. Despite widespread perturbation, >97% of models preserved baseline growth, indicating strong metabolic robustness. Yet individual genomes exhibited distinct flux-rewiring patterns, with frequent individual-specific gain-of-flux events and fewer shared loss-of-flux reactions. Limited ancestry clustering suggests metabolic responses are driven mainly by unique variant combinations. VariantFlux links human genomes to organ-level flux phenotypes, enabling precision medicine, pharmacogenomics, and disease risk prediction. Conceptual advanceWe present VariantFlux, a genotype-first framework that integrates predicted variant effects directly into genome-scale metabolic networks to generate personalised, organ-specific flux phenotypes. Unlike association-based metabolomics studies, this bottom-up approach enables exploratory, mechanistic prediction of how naturally occurring genetic variation reshapes human metabolism.