bims-camemi Biomed News
on Mitochondrial metabolism in cancer
Issue of 2026–10–04
fifty-four papers selected by
Christian Frezza, Universität zu Köln



  1. Science. 2026 Oct;394(6819): eadz4797
      Adipocyte lipid metabolism is coordinated by circadian rhythms, diet, and environmental temperature, but how these diverse signals are molecularly integrated remains unknown. We showed that these cues converge on the orphan mitochondrial transporter SLC25A34 to orchestrate lipid cycling. During the sleep phase, the adipocyte clock suppresses Slc25a34 expression through the REV-ERB transcriptional repressors. Entering the active phase, consuming lipid-rich diets, or exposure to cold abolishes REV-ERB repression, and lipolytic signals stimulate Slc25a34 transcription through the peroxisome proliferator-activated receptors. SLC25A34 is proposed to import oxaloacetate into mitochondria, dually supporting the tricarboxylic acid cycle and cytosolic acetyl-coenzyme A (acetyl-CoA) production. Elevated cytosolic acetyl-CoA then fuels the synthesis of lipids and promotes the transcription of genes enhancing mitochondrial oxidation. Thus, SLC25A34 confers circadian, dietary, and temperature control of adipocyte lipid metabolism.
    DOI:  https://doi.org/10.1126/science.adz4797
  2. Cell. 2026 Oct 01. pii: S0092-8674(26)01068-8. [Epub ahead of print]189(20): 6307-6324.e7
    MitoCarta Tree of Life Consortium
      Oxidative phosphorylation (OXPHOS) is a key metabolic process that couples redox energy to ATP production. While some core OXPHOS complex subunits are found across all domains of life, many have diverged or expanded across evolution-as seen in the protozoan pathogen Acanthamoeba castellanii. By integrating cryo-electron microscopy of unenriched mitochondrial lysate with mass spectrometry proteomics, we resolved the structures of endogenous mitochondrial ATP synthase (complex V), Hsp60, and respiratory complex III from Acanthamoeba. We capture Acanthamoeba ATP synthase in an IF1-inhibited state and reveal how Acanthamoeba-specific subunits and extensions stabilize the molecular machine, which includes a β subunit extension that interfaces with the peripheral stalk. Additionally, we characterize an active malate dehydrogenase (MDH) dimer structurally integrated within the ATP synthase peripheral stalk, thus revealing a direct protein tether between OXPHOS and the tricarboxylic acid cycle. Together, these findings provide structural insight into lineage-specific adaptations in Acanthamoeba that may tune protozoan metabolism.
    Keywords:  ATP synthase; Acanthamoeba; complex V; cryo-EM; crystallography; malate dehydrogenase; mitochondria; oxidative phosphorylation; respiratory complexes; tricarboxylic acid cycle
    DOI:  https://doi.org/10.1016/j.cell.2026.08.057
  3. bioRxiv. 2026 Sep 22. pii: 2026.09.21.753355. [Epub ahead of print]
      The citric acid cycle (TCA cycle) is the common terminal pathway for the oxidation of all nutrients. Citrate oxidation to oxaloacetate produces CO 2 , and citrate synthase (CS) uses nutrient-derived acetyl groups to regenerate citrate and fuel cycle turning. However, the essentiality of cycle fueling and turning in vivo remains unclear. Here, we use hematopoiesis, the most proliferative system in the body, as a model to show that, contrary to common assumptions, TCA cycle turning is dispensable for respiration, survival, and proliferation of stem and progenitor cells in vivo and its loss promotes stem cell function. Hematopoietic-specific Cs deletion in adult mice blocked citrate cycling without reducing the frequency of hematopoietic stem (HSC) and progenitor cells. HSCs and progenitor cells adapted to TCA cycle loss by markedly increasing nutrient consumption and biosynthesis. Disruption of cycle turning increased HSC regeneration, myeloid progenitor proliferation, and myelopoiesis in vivo. HSCs without a turning TCA cycle outcompeted wild-type HSCs within the same environment. The effect of CS deletion on HSC function was not phenocopied by genetic ablation of cytosolic citrate use and was rescued by ablation of glutamine use in biosynthesis. Therefore, TCA cycle turning restrains nutrient uptake, biosynthesis, cell proliferation, and stem cell function. These results suggest an explanation for the reduction in cycle activity observed in many normal proliferating cells and cancer cells.
    DOI:  https://doi.org/10.64898/2026.09.21.753355
  4. Redox Biol. 2026 Sep 23. pii: S2213-2317(26)00411-8. [Epub ahead of print]97 104412
      Renal ischemia-reperfusion injury (IRI) is initiated by a burst of mitochondrial reactive oxygen species generated when ischemia-accumulated succinate is rapidly oxidised upon reperfusion, driving reverse electron transport and triggering lipid peroxidation-dependent tubular cell death. Here, we identify the mitochondrial matrix protease CLPP as an unexpected regulator of renal redox resilience. CLPP deficiency reduced succinate-driven mitochondrial H2O2 production and protected kidneys from functional decline, tubular necrosis, mitochondrial ultrastructural damage, and lipid peroxidation following IRI. Protection was most pronounced in females, in which CLPP loss established a constitutive antioxidant and detoxification programme prior to injury, characterised by increased glutathione and γ-glutamylcysteine abundance, enhanced NADPH-generating pentose phosphate pathway activity, sustained sulphur amino acid metabolism, and elevated capacity for lipid aldehyde detoxification. During reperfusion, these adaptations preserved thiol-redox buffering, limited 4-hydroxynonenal accumulation, and reduced oxidative modification of cysteine residues on proteins involved in complement, coagulation, fibrinolysis, and inflammatory signalling, thereby restricting ferroptotic lipid damage and downstream thrombo-inflammatory amplification. Although reduced reverse electron transport-derived ROS contributed to this phenotype, it was insufficient to account for the sex bias. While CLPP deficiency amplified an endogenous female antioxidant programme, male kidneys, lacking equivalent glutathione-centred preconditioning, showed only marginal benefit. These findings establish mitochondrial proteostasis as a determinant of sex-dependent redox adaptation and identify CLPP as a candidate target for preconditioning against predictable ischaemic insults, including kidney transplantation and cardiac surgery.
    Keywords:  Ferroptosis; Glutathione metabolism; Lipid peroxidation; Mitochondrial CLPP protease; Mitochondrial dysfunction; NRF2; Renal ischemia-reperfusion injury; Renal preconditioning; Sex differences
    DOI:  https://doi.org/10.1016/j.redox.2026.104412
  5. Nature. 2026 Sep 30.
      Lysosomal adaptation to environmental changes is critical for cellular and metabolic homeostasis and requires coordination by the mTORC1 kinase, which conveys nutritional and stress signals into distinct, substrate-specific outputs1,2. The FLCN-FNIP complex (FLCN:FNIP) serves as a crucial regulator of lysosomal function by selectively controlling the ability of mTORC1 to inhibit transcription factor EB (TFEB), a master regulator of catabolic programs and a known oncogene3. Yet how FLCN:FNIP activity is regulated has remained unclear. Here we identify a nutrient-independent lysosomal signalling pathway that regulates FLCN through v-ATPase-driven recruitment of TBK1 or ULK1 (TBK1/ULK1) to lysosomes, via the TAX1BP1 adaptor. This enables TBK1/ULK1-mediated FNIP1 phosphorylation at S296, resulting in inhibition of FLCN and nuclear translocation of TFEB. Recurrent ATP6V1B2 v-ATPase mutations, found in patients with follicular lymphoma, constitutively activate this pathway, leading to hyperactivation of TFEB and follicular lymphoma proliferation. Our work uncovers a lysosomal signalling pathway that is critical for lysosomal adaptation and tumorigenesis.
    DOI:  https://doi.org/10.1038/s41586-026-11093-3
  6. Mol Cell. 2026 Oct 01. pii: S1097-2765(26)00627-1. [Epub ahead of print]86(19): 3862-3863
      Glioma cells experience profound metabolic stress in hypoxic tumor regions, where mitochondrial respiration is constrained and redox balance becomes difficult to maintain. A recent study by Vettore and colleagues1 in Molecular Cell identifies nicotinamide nucleotide transhydrogenase as a key mitochondrial enzyme that connects NADH oxidation to NADPH production, thereby supporting proline synthesis and growth under hypoxia. This work highlights how distinct redox pools are coordinated in cancer cells and suggests that NNT-dependent metabolism may represent a vulnerability in hypoxic tumors.
    DOI:  https://doi.org/10.1016/j.molcel.2026.09.007
  7. Cell. 2026 Oct 01. pii: S0092-8674(26)01076-7. [Epub ahead of print]189(20): 6243-6245
      Our textbook view of mitochondria, which has been shaped by studies in animals and yeast, fails to do justice to the organelle's broader eukaryotic diversity. While most mitochondria retain a tiny genome, the overwhelming majority of their proteins are nuclear-encoded and vary extensively across lineages. To map this diversity, the MitoCarta Tree of Life Consortium developed experimental and computational workflows to generate high-accuracy mitochondrial proteomes across diverse eukaryotes-helping to lay a foundation for comparative mitochondrial biology with broad implications for physiology, evolution, and disease.
    DOI:  https://doi.org/10.1016/j.cell.2026.09.007
  8. bioRxiv. 2026 Sep 22. pii: 2026.09.18.752622. [Epub ahead of print]
      Despite long-standing epidemiological associations, the mechanism linking folate availability to gestational neural tube defects remains unclear, partly because measuring and interpreting metabolic activity in dynamic biological systems remains challenging. Here, we apply a deep-learning-based graph-guided variational autoencoder (MeRN; Metabolic Representation Network) to infer single-cell metabolic activity and states from scRNA-seq data of mouse embryogenesis. By analyzing folate-deficient embryogenesis from E7.0-E9.0, we identify a transient state within the nascent neural lineage that is acutely sensitive to folate availability, leading to an interconnected disruption between key bioenergetic pathways and de novo purine biosynthesis. Moreover, metabolically induced growth defects lead to permanent morphological disruptions along the dorsal-ventral axis, which we confirm by generating whole-embryo fate maps using a prime-editing-based lineage recorder (PEtracer). Collectively, our results establish a highly scalable framework for interpreting dynamic changes in embryonic metabolism and elucidating the mechanistic bases underlying environmentally linked congenital disorders.
    Research highlights: Developing embryos adopt metabolic states that are distinct from cell lineageMetabolic states are organized temporally and spatially along key body axesNeural tube development depends on a rapid transition between metabolic statesActivation of transient neural metabolic states is highly sensitive to disrupted folate absorptionThe floor plate is preferentially resistant to folate deprivation and distorts subsequent neural patterning.
    DOI:  https://doi.org/10.64898/2026.09.18.752622
  9. Science. 2026 Oct;394(6819): 29-30
      An orphan protein integrates circadian, dietary, and environmental signals to control brown fat metabolism.
    DOI:  https://doi.org/10.1126/science.ael7271
  10. bioRxiv. 2026 Sep 24. pii: 2026.09.17.751504. [Epub ahead of print]
      Metabolism shapes cellular function and state, yet measuring single-cell metabolic states at scale remains a challenge. We present Metabolic Representation Net (MeRN), a graph-guided variational autoencoder that leverages prior metabolic knowledge as a topology graph to learn latent representations of metabolic state and reaction activity from single-cell transcriptomes. MeRN's scalable estimation of reaction activity enables the definition of data-driven pathways (DDPs): context-specific metabolic modules supported by transcriptomic evidence and agnostic of standard pathway definitions. Using DDPs, we introduce the weakest link analysis to identify metabolic network rewiring. MeRN recovers metabolic zonation in the mouse intestine, links a folate deficiency-induced break in de novo purine synthesis to embryonic neural tube defects, shows cytokines with similar non-metabolic effects can elicit divergent T cell metabolism, and identifies metabolic drivers of T cell exhaustion and therapy response in human cancers. Our results establish MeRN as a unified method for metabolic analysis of single-cell transcriptomes.
    Research highlights: MeRN leverages the metabolic topology to comprehensively predict reaction- and pathway-level metabolic activitiesMeRN enables data-driven pathways (DDPs) that capture empirically supported cell-type-specific metabolic modules, agnostic of standard pathway definitions MeRN-based DDPs identify metabolic network rewiring of de novo purine synthesis due to folate deficiency during embryonic neural tube development MeRN identifies human pan-cancer metabolic drivers of T cell exhaustion and Treg-specific metabolic adaptations.
    DOI:  https://doi.org/10.64898/2026.09.17.751504
  11. bioRxiv. 2026 Sep 09. pii: 2026.09.04.749519. [Epub ahead of print]
      Elevated sulfur-containing amino acids (SAA; methionine and cystine) are linked to human mortality. While methionine restriction (MR) extends lifespan in animals, it is often ignored that traditional longevity-promoting MR diets also lack cystine. When dietary cystine is eliminated, host redirects substrates from methionine cycle and generates cysteine via cystathionine γ-lyase (CTH) in transsulfuration pathway, leaving it unclear which SAA controls aging. Here, we show that selective cysteine restriction in Caenorhabditis elegans enhanced lifespan and stress survival independently of methionine. Notably, cysteine-free diets (methionine-replete or restricted) in Cth- deficient mice induced pro-metabolic effects, whereas MR with normal cysteine was ineffective. Sustained 70% cysteine reduction in aged Cth - /- mice reprogrammed the immunometabolic axis, conferring healthspan benefits. Thus, lowering cysteine while keeping the methionine pool intact enhances healthy lifespan.
    DOI:  https://doi.org/10.64898/2026.09.04.749519
  12. Nat Commun. 2026 08 31. pii: 10359. [Epub ahead of print]17(1):
      The nutrient-sensing mechanistic target of rapamycin complex 1 (mTORC1) signaling pathway controls cellular and organismal growth and metabolism, and aberrant activation is linked to human disease, including metabolic disease. Cellular studies have established regulatory mechanisms influencing mTORC1 activation, but the physiological signals that control mTORC1 at the organismal and tissue levels are less well-defined. mTORC1 is dynamically regulated by fasting and feeding in metabolic tissues, with both nutrients and insulin proposed to activate mTORC1 in response to feeding. Here, studies employing a liver-specific genetic mouse model demonstrate that AKT-mediated TSC2 phosphorylation is the predominant mechanism of hepatic mTORC1 induction by insulin but is dispensable for activation by feeding. Furthermore, postprandial activation of hepatic mTORC1 requires dietary protein, which dictates the insulin-responsiveness of the pathway. Contrary to dogma, hepatic mTORC1 signaling was not elevated in response to diet-induced obesity, despite overt impairments in insulin and glucose homeostasis, and blocking hepatic AKT-TSC-mTORC1 signaling did not affect these metabolic phenotypes. Evidence is also provided supporting a role for glucagon in hepatic mTORC1 suppression during fasting. This study reveals a hierarchy of physiological signals regulating hepatic mTORC1.
    DOI:  https://doi.org/10.1038/s41467-026-77216-6
  13. J Mol Biol. 2026 Sep 26. pii: S0022-2836(26)00414-6. [Epub ahead of print] 170041
      Cancer cells rely on aerobic glycolysis to fuel proliferation, yet how lipid metabolism dynamically regulates glycolysis remains incompletely understood. Here, we identify pyruvate kinase M2 (PKM2) is regulated by auto-S-fatty acylation. Using bioorthogonal chemical reporters, we demonstrate that PKM2 is S-fatty acylated at a conserved cysteine residue (Cys474), preferentially incorporating C18 stearate and C16 palmitate. This modification destabilizes PKM2's active tetramer, thereby suppressing pyruvate kinase activity and altering the abundance of glycolytic intermediates. Genetic ablation of PKM2 S-fatty acylation (C474S mutant) enhances mitochondrial respiration, alters glycolytic metabolite abundance, and impairs lung cancer cell growth in vitro and in vivo. Our findings establish PKM2 auto-S‑fatty acylation as a mechanism that links fatty acid availability to glycolysis and tumor cell growth, highlighting a potential vulnerability in cancers dependent on aerobic glycolysis.
    Keywords:  PKM2; S-fatty acylation; auto-acylation; cancer metabolism; glycolysis
    DOI:  https://doi.org/10.1016/j.jmb.2026.170041
  14. Cell. 2026 Oct 01. pii: S0092-8674(26)01072-X. [Epub ahead of print]189(20): 6214-6216
      In this issue of Cell, Chen et al. chart mitochondrial proteome diversity across eukaryotes, revealing an unexpectedly complex ancestral proteome alongside extensive lineage-specific innovation. Their broad phylogenetic reconstruction provides new insights into the mitochondrial proteome of the last eukaryotic common ancestor while unearthing a wealth of unexplored mitochondrial biology outside of traditional model systems.
    DOI:  https://doi.org/10.1016/j.cell.2026.09.003
  15. bioRxiv. 2026 Sep 23. pii: 2026.09.19.752713. [Epub ahead of print]
      Communication between peroxisomes and mitochondria is essential for cellular metabolic homeostasis, yet how peroxisomal import stress impacts mitochondria function during aging and cellular senescence remains poorly defined. Using a genome-wide CRISPR screening in HEK293 cells under peroxisome import stress, we identified SCAF1 (SR-related CTD-associated factor 1) a known canonical nuclear pre-mRNA splicing factor, as an essential regulator of mitochondrial homeostasis. Under peroxisome stress SCAF1 undergoes proteolytic processing and translocates to the mitochondria, where its N-terminal region acts as an autonomous repressor module that blocks mitoribosomal subunit joining. Consequently, SCAF1 depletion accelerates subunit joining and elevates oxidative phosphorylation protein levels, whereas its overexpression in IMR90 fibroblast cells triggers robust cellular senescence characterized by increased senescence associated β gal staining. Together, our findings uncover a stress-responsive peroxisome-to-mitochondria signaling axis mediated by SCAF1 translocation. This pathway directly modulates mitoribosome assembly to maintain translational homeostasis, providing a precise molecular mechanism for how upstream peroxisomal decline drives downstream mitochondrial dysfunction and cellular senescence.
    DOI:  https://doi.org/10.64898/2026.09.19.752713
  16. bioRxiv. 2026 Sep 24. pii: 2026.09.23.753803. [Epub ahead of print]
      Dietary restriction (DR) protects against metabolic disease, extends lifespan, and is associated with remodeling of tissue reactive oxygen species (ROS). ROS control biological adaptation through reversible oxidation of protein cysteines, yet the targets of DR-initiated redox signaling are unknown. Here we generate OxiDR, a tissue-resolved atlas of the cysteine redox proteome that quantifies oxidation state under DR. Rather than oxidizing the proteome broadly, DR selectively targets a high-amplitude set of cysteines in a tissue-specific manner, allowing systematic classification of biological processes subject to DR-mediated redox regulation. Among the cysteines most highly oxidized upon DR is Cys19 of the core autophagy protein ATG5. We show oxidation of Cys19 is required for ATG5-mediated autophagosome formation and for autophagy triggered by nutrient restriction in human cells and mice. Reversible oxidation of this cysteine promotes ATG5 binding to ATG10, thus forming the ATG5-ATG12 conjugate that lipidates LC3B/ATG8 and matures the autophagosome. In mice, loss of this redox switch prevents effective initiation of autophagy upon nutrient restriction, resulting in gross tissue pathology and rapid onset of mortality. The autophagic response to nutrient restriction is thus gated by oxidation of a single cysteine.
    DOI:  https://doi.org/10.64898/2026.09.23.753803
  17. Sci Adv. 2026 Oct 02. 12(40): eaeh7186
      Maintenance of fissed mitochondria is viewed as a defining feature of Kirsten rat sarcoma viral oncogene homolog (KRAS)-mutant cancers. However, regulation of this process by accompanying comutations or environmental factors is not clearly defined. Here, by analyzing a subset of pancreatic cancer lesions driven by concurrent KrasG12D and GNAS complex locus gene (GNASR201C/H) mutations, we found that despite the presence of mutant Kras, hyperactive GnasR201C maintains mitochondria predominantly in a fused state, which is necessary for tumor growth. Multiplex proteomics, super-resolution microscopy, loss- and gain-of-function studies, coupled with metabolite rescue experiments, revealed that GnasR201C-regulated branched-chain amino acid (BCAA) pathway is a previously unidentified regulator of mitochondrial morphology. Mechanistically, the BCAA pathway, the associated tricarboxylic acid cycle, and aspartate metabolism converge on nicotinamide adenine dinucleotide (NADH-NAD+) metabolites to promote mitochondrial elongation. NAD+ availability is crucial for mitochondrial fusion, as facilitating NAD+ generation through alternative means promotes fusion. Collectively, we unraveled a new mechanism that drives mitochondrial fusion and showed that the combination of oncogenic signaling and metabolism can maintain distinct mitochondrial morphology within genetic subsets of KRAS-mutant pancreatic cancer.
    DOI:  https://doi.org/10.1126/sciadv.aeh7186
  18. Nat Aging. 2026 Sep 29.
      Aging paradoxically leads to both a decline in skeletal muscle mitochondrial function and a shift in muscle composition that favors fibers rich in mitochondria. Yet the biological rationale and mechanism underlying this phenomenon remain largely unknown. Here we show that synthesis of the mitochondrial membrane lipid, cardiolipin, causally links mitochondrial dysfunction to fiber-type adaptations in aging mouse and human skeletal muscle. By mimicking the aging decline of skeletal muscle cardiolipin levels in young mice using inducible tissue-specific cardiolipin synthase 1 (Crls1) deletion, we could reproduce key aging hallmarks, including the shift from glycolytic to oxidative fibers. This shift is mediated by mitochondria-to-nucleus signaling through the nuclear receptor, estrogen-related receptor γ, which promotes reactive oxygen species-sensitive glucose uptake and enhanced glycolytic rerouting to sustain antioxidant defenses. Restoring Crls1 expression in adult Crls1 knockout mice reestablishes cardiolipin levels, initiates reversal of muscle atrophy and fully rescues premature mortality. These findings reveal how changes in a mitochondrial membrane lipid cell autonomously orchestrate fiber-type adaptations in aging and myopathies.
    DOI:  https://doi.org/10.1038/s43587-026-01227-7
  19. Nat Cell Biol. 2026 Sep 28.
      The vertebrate central nervous system is enveloped by the meninges, consisting of the pia, arachnoid and dura layers. The arachnoid is hypothesized to give rise to the most common primary intracranial tumours, meningiomas. However, supporting molecular evidence is lacking. There are no effective medical therapies to treat meningiomas that are resistant to local interventions, encumbered by our limited understanding of their cellular origin. Here, to advance our understanding of meningioma biology, we generated a comprehensive reference single-cell and spatial transcriptomic atlas of human fetal meninges at postconceptional weeks 5-13. We found that the meningeal layers develop concurrently, and identified an inner CDH1-positive dura layer expressing tight-junction genes consistent with barrier function. Comparing meningiomas with fetal meninges, we show that, transcriptionally, meningioma cells resemble dura-lineage cells, and that common meningioma driver genes were expressed in the dura lineage. This raises the hypothesis that meningiomas could originate from dura-lineage cells.
    DOI:  https://doi.org/10.1038/s41556-026-02074-9
  20. Curr Biol. 2026 Oct 01. pii: S0960-9822(26)01123-1. [Epub ahead of print]
    MitoCarta Tree of Life Consortium
      Babesia are tick-transmitted apicomplexan parasites of widespread medical and veterinary importance. Although atovaquone, a first-line therapy for human babesiosis, targets one of the three proteins encoded by mitochondrial DNA, a full characterization of the nuclear-encoded mitochondrial proteome is lacking. Here, we combined organelle immunoprecipitation and density gradient separation to enrich mitochondria from Babesia divergens. Using protein mass spectrometry and protein correlation profiling, we generated B. divergens MitoCarta (BdMitoCarta), a high-confidence inventory of 525 mitochondrial proteins. The B. divergens mitoproteome is broadly conserved across Apicomplexa, which, as a clade, have undergone reductive evolution. As seen in other apicomplexans, metabolite transport and the TCA cycle have diverged, with loss of the pyruvate dehydrogenase complex, presence of malate:quinone oxidoreductase, and a class I fumarate hydratase. Specific to Babesia is the presence of two mitochondrial isocitrate dehydrogenase homologs. Using isolated mitochondria, we performed blue native PAGE complexome analysis and detected previously uncharacterized proteins co-migrating with the ATP synthase and mitochondrial ribosome. Our work has yielded the first mitochondrial proteome and complexome for Babesia, which we expect to be a valuable resource for understanding the evolution of apicomplexan parasites for future therapeutic development.
    Keywords:  ATP synthase; Apicomplexa; Babesia; Plasmodium; Toxoplasma; electron transport chain; isocitrate dehydrogenase; mitochondria; mitochondrial ribosome; proteome
    DOI:  https://doi.org/10.1016/j.cub.2026.08.072
  21. bioRxiv. 2026 Sep 13. pii: 2026.09.10.750701. [Epub ahead of print]
      The intrinsically slow pace of human development poses challenges for regenerative medicine and disease modeling. This trait is attributed to low metabolic rates, yet the endogenous mechanisms determining species-specific metabolic flux remain unknown. Here, we identify coupling between glycolytic NADH production and mitochondrial oxidation through the glycerol-3-phosphate (G3P) shuttle as a genetic bottleneck constraining human developmental tempo. Using stem cell-derived models of the segmentation clock, an oscillator whose period reflects developmental rate, we show that low expression of the G3P shuttle enzyme GPD1L limits NADH oxidation in human progenitors compared to mouse. Overexpressing GPD1L boosts metabolic flux, accelerating the segmentation clock, cell cycle, and differentiation across germ layers. G3P-mediated redox coupling is thus a genetically encoded, rate-limiting mechanism that sets the tempo of human development.
    DOI:  https://doi.org/10.64898/2026.09.10.750701
  22. Sci Adv. 2026 Oct 02. 12(40): eaei2831
      Triple-negative breast cancer (TNBC) develops in hypoxic, nutrient-limited tumors enriched with macrophages and cell death. We show that metabolically distinct TNBCs differentially exploit macrophage-derived nutrients, influencing tumor growth and therapeutic response. Prolonged hypoxia reprogrammed mouse and human macrophages, enabling them to release metabolites that rescued the growth of select TNBC cell lines during glutamine deprivation or glutamine metabolism inhibition. Hypoxic macrophages reduced glutamine consumption, increased arginine utilization, and secreted higher levels of ornithine, an intermediate of arginine metabolism. Exogenous ornithine, but not arginine, restored the growth of responsive TNBC cells. Mechanistically, TNBC cells diverted ornithine into proline biosynthesis, supporting oxidative pentose phosphate pathway activity. In vivo, depletion of tumor-associated myeloid cells reduced tumor growth and impaired proline synthesis in glutaminase inhibitor-resistant TNBC. These findings identify hypoxia-driven metabolic cross-talk between macrophages and TNBC cells, revealing ornithine-dependent proline metabolism as a mechanism by which macrophages sustain tumor growth under nutrient stress and contribute to resistance to glutamine-targeted therapies.
    DOI:  https://doi.org/10.1126/sciadv.aei2831
  23. Philos Trans R Soc Lond B Biol Sci. 2026 Oct 01. pii: 20250500. [Epub ahead of print]381(1960):
      Acquiring new cellular states entails metabolic reprogramming driven by changes in the expression of cytosolic and mitochondrial metabolic enzymes. Most mitochondrial proteins are synthesized in the cytosol and imported into the mitochondria in a linear form, after which they are folded by a network of mitochondrial chaperones and co-chaperones. Which mitochondrial protein is dependent upon which chaperone for its folding is largely unknown. HSPD1/HSPE1 (HSP60/HSP10) are evolutionarily conserved mammalian homologues of the bacterial proteins GroEL/GroES, forming a chamber-and-lid chaperonin to facilitate the folding of client proteins. The endogenous clients of HSP60 in mammalian cells are not fully known, nor are the HSP60 clients that require HSP10 for folding. We used gene knockdown and stable isotope labelling of amino acids in cell culture (SILAC)-based proteomics to identify HSPD1 client proteins. We found that HSPD1 supports the expression of methylenetetrahydrofolate dehydrogenase 2 (MTHFD2), a key mitochondrial one-carbon (1C) pathway enzyme, in cells and tumours. In addition, HSPD1 directly folds MTHFD2 independently of its co-chaperone HSPE1. HSPD1 interacts with MTHFD2 in mitochondria, and MTHFD2 is degraded by LONP1 in HSPD1 knockdown cells. Our data show that HSPD1 is an MTHFD2 chaperone and can fold an endogenous client protein independently of HSPE1, providing a link between mitochondrial protein folding and the 1C pathway. This article is part of the Theo Murphy meeting issue 'ProteostaSys: a systems view of proteostasis'.
    Keywords:  HSPD1; MTHFD2; cancer; chaperones; mitochondria; one-carbon
    DOI:  https://doi.org/10.1098/rstb.2025.0500
  24. Cancer Res. 2026 Sep 28.
      The mevalonate pathway generates sterols and isoprenoids essential for membrane biosynthesis and signaling. Increased activity of the mevalonate pathway is a common feature of cancer and has emerged as a potential therapeutic vulnerability. Here, we showed that the mevalonate pathway sustains de novo serine biosynthesis and aspartate production by maintaining NAD⁺ regeneration through ubiquinone-dependent electron transport. Statin-mediated inhibition of the mevalonate pathway impaired oxidative phosphorylation, lowered the NAD⁺/NADH ratio, suppressed serine and aspartate biosynthesis, and activated the GCN2-eIF2α-ATF4 amino acid deprivation response. The resulting depletion of serine-derived glycine and one-carbon units, together with reduced aspartate availability, limited purine and pyrimidine biosynthesis. Genetic and pharmacological disruption of ubiquinone synthesis recapitulated the metabolic defects, whereas expression of the bacterial NADH oxidase LbNOX restored the NAD⁺/NADH ratio and reversed the metabolic and growth defects induced by statin treatment. Importantly, impairment of NAD⁺ regeneration reduced PHGDH-dependent de novo serine synthesis, thereby sensitizing neuroblastoma cells to PHGDH inhibition. Accordingly, simvastatin enhanced the anti-proliferative effects of the PHGDH inhibitor NCT-503 in vitro and exhibited elevated anti-tumor activity in combination with NCT-503 in neuroblastoma xenograft models. Together, these findings establish ubiquinone-dependent NAD⁺ regeneration as a key mechanism linking the mevalonate pathway to amino acid and nucleotide biosynthesis and provide a mechanistic rationale for combined targeting of the mevalonate pathway and serine biosynthesis in cancer.
    DOI:  https://doi.org/10.1158/0008-5472.CAN-26-1063
  25. Mol Cell. 2026 Oct 01. pii: S1097-2765(26)00620-9. [Epub ahead of print]86(19): 4043-4057.e7
    MitoCarta Tree of Life Consortium
      The mitochondrial proteomes of Leishmania tarentolae and Trypanosoma brucei contain ∼1,700 proteins, most of which lack homologs in higher eukaryotes. Here, we integrate complexome profiling and cryo-electron microscopy to define conserved and lineage-specific macromolecular assemblies that support mitochondrial functions in these kinetoplastid protozoa. Comparative analyses reveal species- and life-stage-dependent differences in the abundance and composition of respiratory, metabolic, RNA processing, and other complexes, refining and expanding current annotations. Structures of L. tarentolae respiratory complex III2 (CIII2), complex IV2 (CIV2), and complex V (CV) identify nine previously unrecognized nuclear-encoded subunits and resolve five mitochondrially encoded proteins, including products of pan-edited mRNAs. These reconstructions uncover architectural innovations: a subunit 8 of ubiquinol cytochrome-c reductase (QCR8) N-terminal extension that plugs the vestigial mitochondrial processing peptidase (MPP)α/β cavity in CIII2, a CIV2 dimer stabilized by an extensive clade-restricted interface, and a CV dimer containing the mitochondrially encoded ATP6 subunit. Together, our findings reveal how kinetoplastids assemble specialized mitochondrial machinery while incorporating diverged components into core modules shared across eukaryotes.
    Keywords:  Leishmania; RNA editing; Trypanosoma; complexome profiling; cryo-EM; kinetoplastids; mass spectrometry; mitochondria; respiratory complexes
    DOI:  https://doi.org/10.1016/j.molcel.2026.08.031
  26. FEBS J. 2026 Sep 29.
      Phosphate is central to modern bioenergetics and to all theories for the origin of life. How phosphate entered metabolism is unknown, though microbial physiology and geochemical environments can provide important clues. Some bacteria obtain electrons and energy from phosphite (HPO3 2-), a reduced form of phosphate (HPO4 2-), that naturally occurs in serpentinizing (H2-producing) hydrothermal systems. Here we show that the insoluble, solid-state catalyst native palladium, which is naturally deposited in serpentinizing hydrothermal systems, catalyzes the oxidation of phosphite to phosphate and H2 in water at 25-100 °C in a highly exergonic reaction. Palladium awaruite (PdxNi3Fe), a common form of Pd0 in serpentinizing vents, also catalyzes phosphite-dependent phosphorylation. Phosphite oxidation over Pd0 generates a reactive but so far unidentified chemical intermediate, possibly metaphosphate, [PO3]-, that readily phosphorylates hydroxyl moieties in glycerol, ribose, glucose, serine, and cytidine at 25-100 °C in 2-72 h. The same conditions also generate (i) phosphoanhydride bonds in pyrophosphate, polyphosphates, and ADP, (ii) the phosphoramidate bond in phosphocreatine, (iii) and the acyl phosphate bond in acetyl phosphate, which is obtained overnight at 25 °C with 8% yield. The reactions proceed without sulfur, excluding thioester or metal sulfide intermediates. Phosphite-dependent phosphorylations under serpentinizing hydrothermal vent conditions are facile. They identify a natural, geochemical source of prebiotic phosphorylation and a novel source of metabolic energy at origins. The central role of phosphate in bioenergetics, metabolism, and nucleic acids could reflect metal-catalyzed, redox chemistry of phosphorus in the environment where metabolism (and life) arose.
    Keywords:  bioenergetics; origin of life; origin of metabolism; phosphite; serpentinization
    DOI:  https://doi.org/10.1111/febs.70737
  27. Nat Cell Biol. 2026 Sep 28.
      The meninges are increasingly recognized as key stromal and immune niches supporting cranial development. Here we constructed a paired single-nuclei RNA and Assay for Transposase-Accessible Chromatin atlas of human meningeal development from 6 to 21 postconception weeks across cranial regions. By integrating spatial transcriptomics, we resolved cell types across meningeal layers. Our multiomic atlas defines gene regulatory networks underlying blood-brain barrier endothelial identity during development. Within immune compartments, the data support a yolk sac origin for meningeal myeloid lineages, including perivascular macrophages primed for barrier immunity. We present two analytical tools: Nichefinder, for spatial label transfer and proximity analysis, and cell2home, for inferring chemotactic signalling. Using cell2home, we identify interactions potentially driving B cell migration from cranial marrow into prenatal meninges. We studied trisomy 21, and observed reduced fibroblast chemokine expression with enhanced JAK-STAT signalling. Together, this work provides a developmental atlas of the human meninges and defines cellular and regulatory programs shaping early barrier immunity.
    DOI:  https://doi.org/10.1038/s41556-026-02075-8
  28. Cell. 2026 Oct 01. pii: S0092-8674(26)01002-0. [Epub ahead of print]189(20): 6285-6306.e13
    MitoCarta Tree of Life Consortium
      Mitochondria arose from the endosymbiosis of a bacterium with an archaea-related host cell about 2 billion years ago. To understand their origins and evolution, we compared experimentally defined mitoproteomes from the MitoCarta Tree of Life project. Across eight organisms, we identified 8,619 distinct mitochondrial proteins within 3,199 families, of which 43% lack Pfam domains. We report 33 protein families conserved in eukaryotic pathogens yet absent in humans, representing promising candidate targets for protozoan infectious diseases. Leveraging our experimentally defined mitoproteomes, we retrained a classifier based on a protein language model to predict mitoproteomes of ∼200 eukaryotes. From this expanded set, we detail the evolutionary trajectories of mitochondria, ranging from clade-specific gene family expansions to extreme mitoproteome reductions seemingly en route to complete organelle loss. Finally, we reconstruct the last eukaryotic common ancestor (LECA) mitoproteome, revealing that LECA possessed a complex mitochondrion capable of both aerobic and anaerobic metabolism.
    Keywords:  calcium; eukaryogenesis; evolution; last eukaryotic common ancestor; mitochondria; mitoproteome; oxygen; parasite; pathogen; phylogenetics
    DOI:  https://doi.org/10.1016/j.cell.2026.08.029
  29. Cancer Cell. 2026 Sep 28. pii: S1535-6108(26)00399-5. [Epub ahead of print]
    PEACE Consortium
      Successful metastatic colonization requires cancer cells to survive multiple stresses during early organ adaptation, yet how metastasis-initiating cells overcome this bottleneck remains unknown. Here, we identify a transient MXD4-dependent proliferative pause that enables aggressive cancer cells to survive early brain colonization. Before vascular co-option-associated outgrowth, metastatic cells temporarily restrain proliferation through the MYC antagonist MXD4, buffering stresses encountered after extravasation. Genetic disruption of MXD4 compromises survival of micrometastases, preventing their progression to macrometastases. Analyses of human brain micrometastases validate this transient adaptive state in patients. Exploiting vulnerabilities associated with the proliferative pause reveals preventive therapeutic opportunities across experimental settings, including spontaneous brain metastasis models and minimal residual disease following neurosurgical resection. In addition, patient-derived organotypic cultures confirm the feasibility of targeting this state with clinically available drugs. These findings uncover a previously unrecognized adaptive stage during metastatic colonization and identify actionable vulnerabilities to prevent brain metastasis progression and relapse.
    Keywords:  autopsies; brain metastasis; metastasis initiating cells; micrometastasis; organ colonization; perivascular niche; prevention; relapse; vascular co-option; window of opportunity
    DOI:  https://doi.org/10.1016/j.ccell.2026.09.002
  30. Science. 2026 Oct;394(6819): 53-59
      Sex differences have traditionally been attributed to gonadal hormones, but accumulating evidence shows that sex chromosomes exert distinct, cell-autonomous effects on health, aging, and disease. XX and XY complements alter gene dosage, epigenetic programming, immune signaling, metabolism, and cellular stress responses, which shape aging and disease trajectories in women and men. This Review integrates mechanistic advances in sex chromosome biology-including escape from X chromosome inactivation, X reactivation, parent-of-X-origin, X-skew, X- and Y-linked gene functions, and Y loss-with aging, neurologic disease, immunity, cancer, and cardiometabolic disease. We highlight insights from mouse models, human studies, and emerging technologies that disentangle hormone-driven effects from chromosome-mediated effects and discuss translational implications for diagnostics, biomarkers, therapeutics, and clinical trial design, emphasizing the integration of sex chromosome biology into precision medicine.
    DOI:  https://doi.org/10.1126/science.aeh0145
  31. bioRxiv. 2026 Sep 24. pii: 2026.09.23.752387. [Epub ahead of print]
      Resistance to CDK4/6 inhibitors limits the durability of therapy for ER+ breast cancer. Despite the identification of mechanisms that regulate resistance, the metabolic adaptations that enable therapeutic escape remain poorly understood. Here, we identify a metabolic-epigenetic circuit that drives resistance by coordinately rewiring amino acid and glucose metabolism. CDK4/6 inhibitor-resistant ER+ tumor cells upregulate the leucine transporter SLC7A5, enhancing leucine uptake. SLC7A5 overexpression is sufficient to confer palbociclib resistance across ER+ cell lines, patient-derived organoids and xenografts. Stable isotope tracing in cell lines and in xenograft tumors revealed that leucine is catabolized through BCAT2 and HMGCL to increase acetyl-CoA levels, and elevated acetyl-CoA promotes H3K27 acetylation at the GLUT1 promoter, upregulating GLUT1 expression and glycolytic activity. Disrupting leucine transport, catabolism, or availability suppresses GLUT1 expression and restores therapeutic sensitivity in resistant models. In patients receiving palbociclib-based therapy, high SLC7A5 expression and coordinated SLC7A5-GLUT1 co-expression are associated with shorter progression-free survival. Together, these findings define a metabolic- epigenetic mechanism linking branched-chain amino acid catabolism to glycolysis and identify a biomarker-associated metabolic vulnerability in advanced ER+ breast cancer.
    Statement of Significance: Resistance to CDK4/6 inhibitors is nearly universal in ER+ breast cancer. We identify a metabolic- epigenetic circuit in which acetyl-coA derived from leucine catabolism promotes epigenetic changes at the GLUT1 promoter, thereby increasing glucose uptake and driving glycolysis. Disrupting leucine transport, catabolism, or availability suppresses this program and restores drug sensitivity, identifying crosstalk between amino acid metabolism and glycolysis in regulating drug resistance. High expression of the leucine transporter, SLC7A5, is associated with shorter progression-free survival, revealing a biomarker-associated metabolic vulnerability.
    DOI:  https://doi.org/10.64898/2026.09.23.752387
  32. Curr Biol. 2026 Oct 01. pii: S0960-9822(26)01005-5. [Epub ahead of print]
    MitoCarta Tree of Life Consortium
      Giardia lamblia is a microaerophilic protozoan parasite that infects nearly 280 million people worldwide each year. Giardia lacks a mitochondrial genome and mitochondrial enzymes for oxidative phosphorylation. However, it retains mitochondrion-related organelles (MROs) that house an iron-sulfur cluster (ISC) assembly pathway. To date, 32 MRO proteins have been identified with high confidence. Purifying MROs is extremely challenging due to their small size and low abundance. Here, as part of the MitoCarta Tree of Life Consortium, we used large-scale culture, density gradient fractionation, affinity purification, data-independent acquisition mass spectrometry (DIA-MS), protein-correlation profiling, and confocal microscopy to generate the Giardia MitoCarta (GlMitoCarta) inventory. GlMitoCarta consists of 59 proteins, 27 of which are new and 34 with unknown function. Metronidazole unexpectedly upregulates many components of the MRO. Immunoprecipitation (IP)-MS analysis reveals that MROX6 and MROX13, proteins of unknown function, reciprocally interact and share an overlapping interactome related to ISC biology. Further, we identify MOMTiP-4 as a likely MRO inner membrane solute transporter that structurally resembles and functionally complements the yeast SLC25A carrier, Mtm1. The GlMitoCarta resource is freely available and should serve as a valuable foundation for systematic and mechanistic studies of MRO biology and Giardia pathogenesis.
    Keywords:  Giardia; MOMTiP-4; Metamonada; MitoProteome; Mitochondrion Related Organelle; Mtm1; SLC25A39; iron-sulfur cluster assembly; metronidazole; perturbation profiling
    DOI:  https://doi.org/10.1016/j.cub.2026.07.074
  33. Cell. 2026 Oct 01. pii: S0092-8674(26)01067-6. [Epub ahead of print]189(20): 6246-6266.e19
    MitoCarta Tree of Life Consortium
      Acanthamoeba castellanii causes infectious blindness and resides in a key evolutionary outgroup to humans and fungi. Its divergent mitochondria are of outstanding interest due to their predicted aerobic and anaerobic functions with potential for drug targeting. However, a detailed delineation of its bioenergetic machinery, its activities, and their regulation remains lacking. Here, we integrate mitochondrial immunoprecipitation, density gradient purification, mass spectrometry, protein correlation profiling, and microscopy to generate a high-confidence inventory of the Acanthamoeba mitoproteome. The resulting AcMitoCarta contains 1,122 proteins, including 381 lacking readily identifiable homologs in human and yeast mitochondria. Complexome analysis highlights 20 macromolecular assemblies. Complementary proteomic and transcriptomic profiling reveals extensive rewiring of the organelle's bioenergetic machinery by oxygen, including induction of an anaerobic pyruvate:ferredoxin oxidoreductase-to-hydrogenase pathway under anoxia. We experimentally demonstrate that Acanthamoeba can produce H2 gas under anoxic conditions via a mitochondria-localized, oxygen-labile hydrogenase. AcMitoCarta establishes a framework for dissecting the interplay between aerobic and anaerobic energy metabolism.
    Keywords:  ATP synthase; Acanthamoeba; BN-PAGE-MS; HCP; HGT; HupA; HydA; HydE; HydF; HydG; MDH; NDH2; NirK; PFOR; SDHB; TFAM; complex I; hybrid cluster protein; mitochondria; mitochondrial ribosome
    DOI:  https://doi.org/10.1016/j.cell.2026.08.056
  34. Trends Endocrinol Metab. 2026 Oct 01. pii: S1043-2760(26)00247-X. [Epub ahead of print]
      Metabolic adaptation is often framed as differential gene expression, yet nutrient state also remodels which transcript isoforms from a gene contribute to physiology. This review presents isoform usage as an organizing principle of endocrine and metabolic regulation: a layer that connects nutrient sensing to transcript architecture, protein function, tissue specialization, and disease vulnerability. We synthesize evidence that fasting, feeding, insulin, and metabolite availability reshape isoform outputs across metabolic organs independently of total mRNA abundance. We then integrate functional examples, nutrient-responsive RNA-processing mechanisms, human genetic and disease data, and emerging RNA-targeted interventions. These findings suggest that metabolic disease reflects not only dysregulated gene expression but also failure to maintain the appropriate isoform state required for adaptive physiology.
    Keywords:  alternative splicing; isoform usage; metabolic adaptation; metabolic disease; nutrient sensing
    DOI:  https://doi.org/10.1016/j.tem.2026.09.008
  35. bioRxiv. 2026 Sep 08. pii: 2026.09.04.749543. [Epub ahead of print]
      Myeloid cells are essential mediators of host defense against Mycobacterium tuberculosis (Mtb), yet the metabolic programs that sustain their function during chronic infection remain poorly defined. Here, using scRNA-seq we identified a striking, coordinated decline in mitochondrial electron transport chain gene expression across diverse myeloid populations as Mtb disease progressed in mice. This transcriptional remodeling was associated with broad changes in immune and metabolic pathways, including reduced antigen presentation, interferon responses, protein synthesis, and glycolysis. Accordingly, loss of Complex I in macrophages ( Ndufs4 knockdown) reduced MHC-II surface expression, dysregulated inflammatory gene expression, and limited control of Mtb replication. Finally, analysis of single-cell transcriptomic data from Mtb-exposed human household contacts identified an almost identical transcriptional program enriched in IGRA+ individuals, supporting a role for mitochondrial respiratory remodeling in human TB. Together, these findings demonstrate that mitochondrial bioenergetic competence is required to sustain macrophage effector function during chronic Mtb infection and suggest that mitochondrial restoration may boost protective responses in TB patients.
    DOI:  https://doi.org/10.64898/2026.09.04.749543
  36. Nature. 2026 Sep 30.
      Severe respiratory viral disease varies widely among individuals and often reflects immunopathology rather than inadequate pathogen control, suggesting that previous immune history can prime the lungs towards disease tolerance. Here we show that nerve- and airway-associated macrophages (NAMs), a subset of interstitial macrophages, expand ephemerally after type 2 inflammation induced by Nippostrongylus brasiliensis. We therefore hypothesized that NAMs acquire epigenetically imprinted trained immunity and tested this using a heterologous challenge model in which mice that were previously infected with N. brasiliensis were challenged 4-6 weeks later with lethal H1N1 influenza. All of the N. brasiliensis-conditioned mice survived, whereas all of the unconditioned controls succumbed by days 5-6. Protection occurred without reduced viral burden or enhanced T cell responses, instead tracking with reduced immunopathology, amplified type 2 cues, increased efferocytosis and accelerated tissue repair. Using NAM-DTR mice, we show that conditioned NAMs are necessary and sufficient for protection: depletion or replacement with unconditioned NAMs abrogated survival, whereas adoptive transfer of conditioned NAMs conferred tolerance without enhancing viral clearance. Genomic analyses implicated an IL-4-STAT6-PPARγ and ARG1 chromatin program that imprints a pro-resolving and reparative NAM state driving tissue repair, type 2 immunity and efferocytosis during lethal respiratory viral infections. Finally, meta-analysis of human lung single-cell atlases from cohorts of healthy individuals and individuals with IPF and COPD revealed context-dependent NAM-like repair programs. These findings establish local trained immunity in lung-resident macrophages as a mechanism of disease tolerance and a therapeutic entry point for severe inflammatory respiratory infections.
    DOI:  https://doi.org/10.1038/s41586-026-11060-y
  37. bioRxiv. 2026 Sep 25. pii: 2026.09.24.753323. [Epub ahead of print]
      Metabolic reprogramming is a hallmark of cancer cells, and stem-like populations often upregulate aldehyde dehydrogenases (ALDHs). Functional studies have established essential roles for individual ALDH isoforms in tumor initiation, progression, and metastasis; however, the mechanisms by which these enzymes promote malignancy remain poorly understood. Here we show that aldehyde dehydrogenase 1B1 (ALDH1B1), a mitochondrial enzyme highly expressed in colorectal cancer (CRC) and pancreatic ductal adenocarcinoma (PDAC), generates γ-butyrobetaine (GBB) and γ-aminobutyric acid (GABA) in CRC cells. The biosynthesis of both aminocarboxylic acids has been attributed to the cytosolic enzyme ALDH9A1, and we demonstrate that mitochondrial GBB and GABA are functionally distinct from the cytosolic pools of these metabolites. We further demonstrate that mitochondrial GBB can function as an antiport substrate of carnitine-acylcarnitine translocase (CACT), the transporter that mediates fatty acid uptake into the mitochondrial inner matrix. This activity complements the role of cytosolic GBB as the biosynthetic precursor to carnitine. Accordingly, ALDH1B1 can markedly enhance mitochondrial fatty acid oxidation (FAO), a catabolic process that has been linked to CRC and PDAC stemness, progression, and metastasis. Our findings reveal an unexpected role for ALDH1B1 in carnitine metabolism, GABA biosynthesis, and FAO and illustrate how the compartmental reprogramming of metabolic pathways can promote tumor growth.
    DOI:  https://doi.org/10.64898/2026.09.24.753323
  38. Cell Metab. 2026 Oct 02. pii: S1550-4131(26)00380-3. [Epub ahead of print]
      Fungi are crucial components of the human gut microbiota. Here, we investigated the role of fungi in metabolic dysfunction-associated steatotic liver disease-associated hepatocellular carcinoma (MASLD-HCC). Rhizopus arrhizus was the top enriched fungus across the progression from MASLD to MASLD-HCC, accelerating tumorigenesis in multiple mouse models. R. arrhizus-conditioned medium increased cell proliferation while reducing cell cycle arrest and apoptosis in human MASLD-HCC cells. Kynurenic acid (KYNA) was identified as the crucial metabolite generated from R. arrhizus, and its upregulation was confirmed in portal vein, liver tissues, and stools of R. arrhizus-treated mice. KYNA promoted the proliferation of MASLD-HCC cells and accelerated tumorigenesis in mice. Mechanistically, KYNA directly bound to IQ motif containing GTPase activating protein 1 (IQGAP1) in tumor cells and activated the oncogenic mitogen-activated protein kinase (MAPK) signaling pathway, thereby facilitating MASLD-HCC development. In summary, R. arrhizus is a pathogenic fungus that promotes MASLD-HCC by producing KYNA. Blocking this host-fungi interaction is a potential therapeutic strategy to suppress MASLD-HCC.
    Keywords:  IQGAP1; MAPK; MASLD-HCC; Rhizopus arrhizus; fungal metabolites; gut mycobiota; kynurenic acid; liver cancer; metabolic dysfunction-associated steatotic liver disease; mycobiota; tumorigenesis
    DOI:  https://doi.org/10.1016/j.cmet.2026.09.005
  39. bioRxiv. 2026 Sep 24. pii: 2026.09.23.753957. [Epub ahead of print]
      Metastatic melanoma remains highly lethal despite advances in immunotherapy and MAPK-targeted therapy. The Rac1 P29S mutation, present in 4-9% of cutaneous melanomas, confers intrinsic resistance to BRAF and MEK inhibitors. Like other small GTPases, Rac1 lacks suitable pockets for small molecule inhibitor binding, motivating indirect approaches to suppressing its activity. We have previously shown that wild-type Rac1 is sensitive to inhibition of de novo GTP biosynthesis in cancer cells, particularly suppression of the rate-limiting inosine monophosphate dehydrogenase (IMPDH) enzymes. Therefore, we asked whether IMPDH inhibition could suppress Rac1 P29S and its associated phenotypes in melanoma. We found that IMPDH inhibition reduced Rac1 activity, impaired Rac1-dependent phenotypes, and induced S-phase arrest in Rac1 P29S -harboring cells. Moreover, IMPDH inhibition synergized with the BRAF inhibitor vemurafenib and the MEK inhibitor trametinib in Rac1 P29S melanoma cells. Dual BRAF and IMPDH inhibition also resulted in enhanced suppression of MEK and ERK phosphorylation in vitro. In syngeneic mouse models, the FDA-approved IMPDH inhibitor mycophenolate mofetil sensitized Rac1 P29S -expressing melanoma tumors to trametinib, including tumors made refractory by prior trametinib exposure. We further identified a feed-forward circuit in which Rac1 sustains IMPDH2 expression levels through JNK and c-Jun/AP1 signaling, potentially coupling the GTPase to its own nucleotide supply. These findings establish GTP biosynthesis as a targetable vulnerability in Rac1 P29S melanoma and support IMPDH inhibition as a rational partner for MAPK-targeted therapy.
    DOI:  https://doi.org/10.64898/2026.09.23.753957
  40. bioRxiv. 2026 Sep 08. pii: 2026.09.03.749265. [Epub ahead of print]
      A large portion of eukaryotic genomes is composed of transposable elements, which are usually kept repressed in young, healthy cells but can be derepressed in response to cell senescence and organismal aging. LINE-1 (L1) is the most abundant TE in the human genome by percent coverage, and its derepression has been implicated in inflammaging responses. However, whether L1 transcription itself is sufficient to drive aging-associated molecular phenotypes in healthy cells has not been extensively explored. Here, we leverage a multi-omic approach combining transcriptomics, proteomics, and secretomics of primary human IMR-90 fibroblasts transiently overexpressing a human L1Hs element in order to define the systems-level consequences of L1 transcription. Intriguingly, transient L1Hs overexpression induced widespread remodeling of the transcriptome, proteome and secretome, impacting pathways related to cell cycle regulation and interferon signaling. Interrogation of multiple independent L1 elements revealed both shared and distinct cellular responses to acute expression. Thus, our findings demonstrate that acute L1 expression induces coordinated molecular remodeling extending beyond canonical retrotransposition-associated pathways, rather than simply mimicking senescence or triggering antiviral signaling. This study establishes a comprehensive multi-omics resource for investigating the impact of L1 transcription in human cells and highlights the need to consider individual transposable element families as distinct regulators of cellular state during aging and disease.
    DOI:  https://doi.org/10.64898/2026.09.03.749265
  41. Philos Trans R Soc Lond B Biol Sci. 2026 Oct 01. pii: 20260194. [Epub ahead of print]381(1960):
      The mitochondrial chaperone and co-chaperone HSP60/HSP10 (HSPD1/ HSPE1), the mammalian homologues of bacterial GroEL/GroES, form a barrel-and-lid complex to fold newly imported or misfolded mitochondrial proteins. Several lines of evidence suggest that HSPD1 and HSPE1 have diverged in function. HSPD1 and HSPE1 are found in different clusters in the ecological network of gene expression in cancer. MTHFD2 was demonstrated to be an endogenous client protein of HSPD1 that does not require HSPE1 for its folding. Newly imported proteins show differential dependencies on HSP60 and HSP10 in isolated yeast mitochondria. Finally, HSPE1 was found to regulate a mitochondrial GTPase and modulate amyloid fibril formation independently of HSPD1. Nevertheless, the extent to which HSPD1 and HSPE1 have diverged in function has not been explored. Here, we show divergent transcriptomic and metabolic responses to the depletion of HSP60 versus HSP10 in cancer cells, and divergent activation of the mitochondrial unfolded protein response across tissues in Caenorhabditis elegans. Importantly, responses to HSP10 depletion were not nested within those of HSP60 depletion. We speculate that HSPE1 has diverged from HSPD1 and may have additional new cellular functions. This article is part of the Theo Murphy meeting issue 'ProteostaSys: a systems view of proteostasis'.
    Keywords:  cancer; chaperonin; development; mitochondria; mitochondrial UPR
    DOI:  https://doi.org/10.1098/rstb.2026.0194
  42. Cell. 2026 Oct 01. pii: S0092-8674(26)01000-7. [Epub ahead of print]189(20): 6267-6284.e9
    MitoCarta Tree of Life Consortium
      Plant mitochondria share many features with animal mitochondria but also possess unique traits, including presence of both circular and linear mitochondrial DNA, RNA editing, a branched electron transport chain, and metabolic pathways supporting photosynthesis. An accurate mitochondrial proteome is crucial for studying these conserved and lineage-specific functions. Here, we introduce a novel approach to defining plant mitoproteomes that combines serial mitochondrial enrichment, mass spectrometry, and protein correlation profiling. This approach allows us to experimentally define a mitochondrial protein inventory of 1,462 proteins with high sensitivity and specificity. Integration of our experimental inventory with literature and microscopy validation yields the Arabidopsisthaliana MitoCarta (AtMitoCarta) atlas of 1,609 mitochondrial proteins, including 236 newly defined proteins and 147 proteins of unknown functions. A comparative analysis across eukaryotic organisms reveals that 15% of mitochondrial protein families are plant specific, including expanded pentatricopeptide repeat proteins. The AtMitoCarta inventory and the experimental workflow applicable to wild-type plants will enable comparative studies of plant mitochondria.
    Keywords:  Arabidopsis; MitoCarta; calcium uniporter; mitochondria; pentatricopeptide repeat; protein correlation profiling; proteomics
    DOI:  https://doi.org/10.1016/j.cell.2026.08.027
  43. Nat Commun. 2026 08 29. pii: 10329. [Epub ahead of print]17(1):
      DNA damage from routine cellular processes or exogenous insults can have a lasting impact on gene regulation beyond genetic mutations1-5. The prevailing paradigm for the consequences of DNA damage repair revolves around restoration of the original genetic sequence, but long-term changes in chromatin configuration, gene expression and DNA modifications have not been analyzed. We introduce numerous, simultaneous Cas9-mediated DNA double strand breaks (DSBs) at defined locations in human glioblastoma cells and track both non-genetic and genetic alterations over time. Megabase-scale genomic alterations that endured two weeks after the initial damage were detected, involving a shift from transiently increased intra-TAD interactions to persistent long range cis and trans contacts, alterations in gene-expression and associated large structural variations. These findings reveal that widespread DNA damage, such as chemotherapy or radiotherapy, can trigger long-term genetic and non-genetic modifications which alter cellular function and may impact tumor outcome and the emergence of resistant cells.
    DOI:  https://doi.org/10.1038/s41467-026-77331-4
  44. Nat Cardiovasc Res. 2026 Sep 28.
      Cardiac regeneration is limited in the adult mammalian heart because of restricted cardiomyocyte proliferation and persistent fibrosis. We previously demonstrated that transient pharmacological inhibition of succinate dehydrogenase (SDH) with malonate promotes regeneration after myocardial infarction. Here, we integrate single-nucleus RNA sequencing and ATAC-seq to reveal multicellular transcriptional and epigenetic reprogramming underlying this response. Cell-specific Sdhb deletion dissected contributions of SDH inhibition; cardiomyocyte-specific Sdhb deletion transiently increased cardiomyocyte proliferation but did not improve post-myocardial infarction function, whereas myofibroblast-specific Sdhb deletion suppressed myofibroblast activation and fibrosis and improved cardiac function. SDH inhibition promoted reductive mitochondrial metabolism and remodeled H3K4me3-marked and H3K27me3-marked chromatin states in cardiomyocytes and fibroblasts. Integration of CUT&RUN, chromatin accessibility and transcriptional profiling identified regulatory targets linking metabolic and epigenetic remodeling to regenerative responses. Together, these findings establish SDH as a multicellular regulator of cardiac regeneration and define distinct cell-specific mechanisms contributing to the regenerative effects of transient pharmacological SDH inhibition.
    DOI:  https://doi.org/10.1038/s44161-026-00881-9
  45. Philos Trans R Soc Lond B Biol Sci. 2026 Oct 01. pii: 20250271. [Epub ahead of print]381(1960):
      Mitochondria are the powerhouse of the cell, playing vital roles in energy production and metabolism. Most mitochondrial proteins are encoded in the nuclear DNA and must be synthesized in the cytosol before being transported into the appropriate mitochondrial compartments. Mitochondrial protein import is not only essential for mitochondrial biogenesis but also a crucial regulatory step in mitochondrial proteostasis surveillance and stress response. Additionally, defects in mitochondrial protein import lead to mislocalization of precursor proteins to the cytosol, disrupting cytosolic proteostasis and contributing to various human diseases. This review summarizes recent findings demonstrating that mitochondrial protein import is a key regulator of cellular proteostasis. This article is part of the Theo Murphy meeting issue 'ProteostaSys: a systems view of proteostasis'.
    Keywords:  mitochondria; protein import; proteostasis; stress response
    DOI:  https://doi.org/10.1098/rstb.2025.0271
  46. Nature. 2026 Sep 30.
      γδ T cells are one of three lymphocyte lineages that utilize gene rearrangement to diversify their antigen receptors. Nonetheless, the cells' classification has remained uncertain, complicating our ability to understand the basis for their evolutionary conservation. Whereas many γδ T cells display hallmarks of adaptive immunity, others, including those in barrier tissues, make rapid, reportedly T cell receptor-independent responses that phenocopy innate immune cells1. Here we address this paradox and show that the phenotypes of tissue-intrinsic γδ T cells, including their rapid, innate-like responsiveness to tissue stress and carcinogenesis, acutely depend on the γδ T cell receptor (TCRγδ). Those dependencies emphasize the unique biology of γδ T cells and of the immunosurveillance modalities they mediate, with their clinical deployment evidently requiring environments conducive to TCRγδ signalling.
    DOI:  https://doi.org/10.1038/s41586-026-11076-4
  47. bioRxiv. 2026 Sep 25. pii: 2026.09.21.753167. [Epub ahead of print]
      Systemic iron sequestration occurs frequently in cancer due to inflammation-driven expression of the iron-regulatory hormone hepcidin. The impact of systemic iron availability on tumoral immunity is unclear. Here, we show that elevated serum hepcidin is associated with reduced survival and decreased intratumoral CD8+ T cells in patients with pancreas cancer. While hepcidin is not induced in murine tumor models, administration of a hepcidin mimetic phenocopies the T-cell-depleted tumor microenvironment seen in patients. Mechanistically, chronic antigen-driven mitochondrial dysfunction disrupts iron metabolism and selectively depletes high avidity CD8+ T cells during iron restriction. These findings establish a direct link between hepcidin-mediated iron sequestration and tumoral immunity and nominate systemic iron dysregulation as a therapeutic target to enhance anti-tumoral CD8+ T cell responses.
    DOI:  https://doi.org/10.64898/2026.09.21.753167
  48. Biophys J. 2026 Sep 26. pii: S0006-3495(26)00667-3. [Epub ahead of print]
      Cellular respiration depends on the rapid, lateral flow of protons along the inner mitochondrial membrane to drive ATP synthesis. The precise nanoscale thermodynamic forces confining protons to this "local circuit" remain highly debated. Previous attempts to model macroscopic interfacial proton diffusion have been hindered by parameter equifinality and geometric artifacts, preventing the deconvolution of structural water networks from lipid electrostatics. Here, we address this ambiguity using a constrained, high-resolution two-dimensional continuum model. By incorporating experimentally validated buffer proton consumption rates as strict biological priors, we break mathematical degeneracy and isolate the specific effective spatial components of planar lipid bilayers. Calibrating our model against time-resolved DOPG fluorescence kinetics, we decouple a universal structural water barrier (5.7kBT) from the specific -1e electrostatic trap (4.3kBT). Extrapolating these first principles, we predict the confinement architecture of cardiolipin, the signature -2e dimeric lipid of mitochondria. Our simulations reveal a deep 14.3kBT phenomenological potential well. Crucially, this massive barrier confines protons within 1 to 2 nanometres of the membrane surface, virtually abolishing vertical leakage into the bulk aqueous phase of the inter-membrane space. Our simulations suggest that this spatial confinement triggers "dimensional squeezing", preserving a robust lateral concentration gradient that actively accelerates radial proton wave propagation. Biologically, these findings reveal that cardiolipin does not merely prevent proton dissipation, we predict it functions as a highly efficient, quasi-two-dimensional nanoscale antenna that captures and rapidly channels protons directly to ATP synthase, ensuring the kinetic viability of eukaryotic energy production.
    DOI:  https://doi.org/10.1016/j.bpj.2026.09.037
  49. Cell Death Differ. 2026 Sep 30.
      Birt-Hogg-Dubé (BHD) and Tuberous Sclerosis (TSC) are inherited cancer syndromes associated with kidney cystogenesis and tumorigenesis and caused by mutations of the folliculin (FLCN) and TSC1/2 genes, respectively. We and others previously showed that Transcription Factors EB (TFEB) and E3 (TFE3) are the main drivers of the kidney phenotypes observed in mouse models of these conditions. These transcription factors are also responsible for the feedback hyperactivation of the mechanistic Target of Rapamycin Complex 1 (mTORC1), a known tumorigenic factor. This raises the question of whether TFEB/TFE3 exert their oncogenic activity by inducing mTORC1 or by mTORC1-independent pathways. To address this question, we generated kidney-specific mouse models in which we knocked out factors that differentially control mTORC1 and TFEB/TFE3, thus uncoupling their activities. Specifically, we generated three kidney-specific conditional knockout lines: (1) Depdc5-KO mice in which loss of GATOR1 activity leads to mTORC1 hyperactivation and TFEB/TFE3 inhibition, (2) RagC-KO mice in which TFEB/TFE3 are constitutively active and mTORC1 activity is partially inhibited due to impaired Rag heterodimer formation, and (3) Flcn/RagC double KO mice to test whether mTORC1 inhibition induced by RagC loss ameliorates the aggressive kidney phenotype of FLCN KO mice. Comparison between these models revealed that mTORC1 hyperactivation is a key driver of cystogenesis and tumorigenesis, while TFEB/TFE3 constitutive activation further enhances and accelerates pathology by establishing a transcriptional program that integrates metabolic and stress-response pathways. Together, our findings define an oncogenic mechanism by which both mTORC1 and TFEB/TFE3 hyperactivation cooperate in kidney tumorigenesis.
    DOI:  https://doi.org/10.1038/s41418-026-01881-9
  50. Curr Biol. 2026 Oct 02. pii: S0960-9822(26)01198-X. [Epub ahead of print]
      Kidney tubular epithelial cells adapt to physiological urinary flow through rapid metabolic remodeling,1,2 but the mechanisms coordinating this response remain poorly understood. Shear stress promotes lipid catabolism and mitochondrial activity in these cells,3,4 but how changes in mitochondrial dynamics contribute to this metabolic adaptation remains poorly understood.5,6,7,8,9 Here, we show that physiological shear stress rapidly remodels mitochondrial morphology in kidney epithelial cells in vitro and in the zebrafish pronephros, characterized by the emergence of a distinct pool of donut-shaped mitochondria. This remodeling is accompanied by a transient stabilization of mitochondria-endoplasmic reticulum (ER) contact sites (MERCs), occurring independently of any increase in overall ER volume. Using split-TurboID proximity labeling and mass spectrometry, we detected subtle changes in the molecular environment of MERCs during shear stress, including increased proximity of proteins implicated in lipid transfer and membrane contact-site biology. We further show that shear stress promotes the formation of ER-lipid droplet (LD)-mitochondria contact sites and facilitates the local transfer of fatty acids from LDs to mitochondria. This lipid transfer requires vacuolar membrane protein 1 (VMP1), a component of membrane contact sites, whose depletion perturbs LDs and compromises metabolic adaptation to shear stress. Together, our findings identify ER-LD-mitochondria contact sites as dynamic platforms that coordinate lipid transfer and mitochondrial remodeling during the early adaptation of kidney epithelial cells to physiological shear stress, highlighting membrane contact sites as important components of the cellular response to mechanical forces.
    Keywords:  contact sites; endoplasmic reticulum; kidney epithelial cells; lipid droplets; metabolic adaptation; mitochondria; shear stress; zebrafish
    DOI:  https://doi.org/10.1016/j.cub.2026.09.021
  51. J Evol Biol. 2026 Oct 01. pii: voag097. [Epub ahead of print]
      Somatic mutations contribute to tumorigenesis through mutation, selection, and clonal expansion within the native host. Quantifying oncogenic fitness-the extent to which specific somatic mutations promote tumorigenesis-is vital to understanding cancer initiation, progression, and therapeutic response. Perturbation of tumorigenesis by experimental alteration of oncogenes and tumor suppressors in genetically engineered mouse models has long served to inform human cancer research and such experimental systems have been argued to be necessary for definition of tumorigenic effects and fitness landscapes. However, such experimentally constrained systems do not recapitulate the evolutionary processes through which human cancers arise and are highly affected by interspecific differences in genetic background, physiology, and the environment. Here, we argue that large-scale human tumor genomic datasets can be viewed as repeated natural evolutionary experiments that enable inference of oncogenic potential and selective epistatic interactions within our own species. Using lung adenocarcinoma as an illustrative case, we show that inferred oncogenic potential and selective epistatic interactions vary across both somatic genetic and ecological contexts, including tobacco exposure. These observations highlight the value of evolutionary modeling of human tumor genomic data for accurate and precise characterization of oncogenic fitness landscapes, while situating such analyses within a broader context. Computational analyses can leverage human cancer genomic data as a primary resource for accessing oncogenic fitness landscapes, guiding experimental research, and refining therapeutic strategies. Comparative analyses across species can extend this framework by examining conserved and lineage-specific features of somatic selection in each cancer's native species, germline genetics, and environment with phylogenetic tools, thereby revealing both conserved and lineage-specific features of mutation, somatic selection, and epistasis.
    Keywords:  Comparative tumor genomics; Epistasis; Oncogenic selection; Orthologous driver genes; Somatic evolution
    DOI:  https://doi.org/10.1093/jeb/voag097
  52. FEMS Yeast Res. 2026 Sep 29. pii: foag049. [Epub ahead of print]
      Histone acetylation depends on acetyl-CoA, a central metabolic intermediate linking nutrient availability to chromatin regulation. Beyond bulk acetyl-CoA abundance, accumulating evidence indicates that chromatin-proximal acetyl-CoA production and acetate recycling provide spatial control over histone acetylation. In budding yeast, acetyl-CoA synthetase Acs2 supports nucleocytosolic acetyl-CoA production and associates with chromatin during transcriptional transitions, enabling local acetyl-CoA generation for histone acetyltransferases. Its mammalian ortholog, ACSS2, can accumulate in the nucleus in response to metabolic or signaling cues, where it recaptures acetate released by histone deacetylation to sustain promoter-localized histone acetylation. Acs2/ACSS2 also function within multi-enzyme or chromatin-associated assemblies, such as the yeast SESAME complex, coupling acetate metabolism with other metabolic and epigenetic pathways. These mechanisms influence gene expression, heterochromatin maintenance, senescence, and tumor-associated transcriptional programs. Together, these findings support a spatial model in which local metabolite production shapes epigenetic output independently of bulk metabolite abundance. Defining how such nuclear metabolic microenvironments are established and regulated may refine our understanding of metabolic control of chromatin and inform more selective therapeutic strategies.
    Keywords:  Acetyl-CoA metabolism; Acs2/ACSS2; Gene expression; Histone acetylation; Spatial control; chromatin dynamics
    DOI:  https://doi.org/10.1093/femsyr/foag049
  53. Nat Commun. 2026 09 11. pii: 10407. [Epub ahead of print]17(1):
      Antibody-producing plasmablasts (PB) and plasma cells (PC) are critical for humoral immunity, autoimmunity and vaccine responses. Despite the importance of environmental stressors in regulating humoral immune responses, the influence of pH on PB and PC differentiation remains elusive. Here, we identify SLC4A7/NBCn1, a Na+/HCO3- cotransporter, as a selective regulator of PB differentiation in vitro. SLC4A7 deletion also impairs the formation of antibody secreting cells (ASCs) and antibody responses in mice in vivo following immunization and influenza A virus infection. Mechanistically, SLC4A7 deletion results in intracellular acidification and lysosomal alkalinization, and is associated with impaired function of the mechanistic target of rapamycin complex 1 (mTORC1). Enforcing mTORC1 activation in SLC4A7-deficient B cells or B cells in which intracellular pH is acidified by blocking Na+/H+ exchanger (NHE) function restores PB differentiation in vitro. Moreover, ASC differentiation and antibody responses are impaired under conditions of extracellular acidosis in vitro and in a mouse model of metabolic acidosis. Altogether, we identify a critical relationship between intracellular pH regulation through SLC4A7 and mTORC1-dependent ASC differentiation and humoral immunity.
    DOI:  https://doi.org/10.1038/s41467-026-77588-9