bims-camemi Biomed News
on Mitochondrial metabolism in cancer
Issue of 2025–09–21
sixty papers selected by
Christian Frezza, Universität zu Köln



  1. Nature. 2025 Sep 17.
      The regulation of metabolic processes by proteins is fundamental to biology and yet is incompletely understood. Here we develop a mass spectrometry (MS)-based approach that leverages genetic diversity to nominate functional relationships between 285 metabolites and 11,868 proteins in living tissues. This method recapitulates protein-metabolite functional relationships mediated by direct physical interactions and local metabolic pathway regulation while nominating 3,542 previously undescribed relationships. With this foundation, we identify a mechanism of regulation over liver cysteine utilization and cholesterol handling, regulated by the poorly characterized protein LRRC58. We show that LRRC58 is the substrate adaptor of an E3 ubiquitin ligase that mediates proteasomal degradation of CDO1, the rate-limiting enzyme of the catabolic shunt of cysteine to taurine1. Cysteine abundance regulates LRRC58-mediated CDO1 degradation, and depletion of LRRC58 is sufficient to stabilize CDO1 to drive consumption of cysteine to produce taurine. Taurine has a central role in cholesterol handling, promoting its excretion from the liver2, and we show that depletion of LRRC58 in hepatocytes increases cysteine flux to taurine and lowers hepatic cholesterol in mice. Uncovering the mechanism of LRRC58 control over cysteine catabolism exemplifies the utility of covariation MS to identify modes of protein regulation of metabolic processes.
    DOI:  https://doi.org/10.1038/s41586-025-09535-5
  2. Sci Adv. 2025 Sep 19. 11(38): eadw9095
      Cellular iron levels must be tightly regulated to ensure sufficient iron for essential enzymatic functions while avoiding the harmful generation of toxic species. Here, to better understand how iron levels are controlled, we carry out genome-wide mutagenesis screens in human cells. Alongside mapping known components of iron sensing, we determine the relative contributions of iron uptake, iron recycling, ferritin breakdown, and mitochondrial flux in controlling the labile iron pool. We also identify SETD2, a histone methyltransferase, as a chromatin modifying enzyme that controls intracellular iron availability through ferritin breakdown. Functionally, we show that SETD2 inhibition or cancer-associated SETD2 mutations render cells iron deficient, thereby driving resistance to ferroptosis and potentially explaining how some tumors evade antitumoral immunity.
    DOI:  https://doi.org/10.1126/sciadv.adw9095
  3. Sci Adv. 2025 Sep 19. 11(38): eadw2539
      Adipocyte hypertrophy during obesity triggers chronic inflammation, leading to metabolic disorders. However, the role of adipocyte-specific inflammatory signaling in metabolic syndrome remains unclear. The linear ubiquitin chain assembly complex, LUBAC, is an E3-ligase that generates nondegradative linear ubiquitination (Lin-Ub). LUBAC regulates NF-κB/MAPK-driven inflammation and prevents cell death triggered by immune receptors like TNF receptor-1. Here, we show that mice lacking HOIP, the Lin-E3 ligase catalytic subunit of LUBAC, in adipocytes (HoipA-KO) display lipodystrophy and heightened susceptibility to obesity-induced metabolic syndrome, particularly metabolic dysfunction-associated steatotic liver disease (MASLD). Mechanistically, loss of HOIP attenuates TNF-induced NF-κB activation and promotes cell death in human adipocytes. Inhibiting caspase-8-mediated cell death is sufficient to prevent lipodystrophy and MASLD in HoipA-KO obese mice. HOIP expression in adipose tissue positively correlates with metabolic fitness in obese individuals. Overall, our findings reveal a fundamental developmental role for Lin-Ub in adipocytes by mitigating cell death-driven adipose tissue inflammation and protecting against obesity-related metabolic syndrome.
    DOI:  https://doi.org/10.1126/sciadv.adw2539
  4. bioRxiv. 2025 Sep 11. pii: 2025.09.10.675369. [Epub ahead of print]
      Although oncogenic alterations influence tumor metabolism, how they impose distinct metabolic programs within a shared tissue context remains poorly defined. Here, we developed a rapid mitochondrial profiling platform to compare metabolites and proteins in genetic models of primary liver cancer (PLC). Analyses of six genetically distinct PLCs revealed that mitochondrial energy metabolism is largely dictated by oncogene identity. Kras -driven tumors required creatine metabolism to buffer energy demands during early tumorigenesis, whereas c-MYC -driven tumors relied on oxidative phosphorylation. Among c-MYC -driven PLCs, Pten -deficient tumors accumulated mitochondrial phosphoethanolamine, a precursor for phosphatidylethanolamine (PE) synthesis. Inhibition of PE synthesis selectively impaired the growth of Pten -deficient tumors and extended survival, in part through enhanced infiltration of CD8⁺ T cells and sensitization to TNFα-mediated cytotoxicity. Mechanistically, loss of PE elevated surface TNF receptor 2 (TNFR2), promoting TNFα signaling and pro-inflammatory response. These findings uncover genotype-specific mitochondrial metabolic liabilities and establish PE synthesis as a tumor-intrinsic mechanism of immune evasion in PLC.
    DOI:  https://doi.org/10.1101/2025.09.10.675369
  5. Biol Chem. 2025 Sep 15.
      Mitochondria are essential for cellular metabolism, serving as the primary source of adenosine triphosphate (ATP). This energy is generated by the oxidative phosphorylation (OXPHOS) system located in the inner mitochondrial membrane. Impairments in this machinery are linked to serious human diseases, especially in tissues with high energy demands. Assembly of the OXPHOS system requires the coordinated expression of genes encoded by both the nuclear and mitochondrial genomes. The mitochondrial DNA encodes for 13 protein components, which are synthesized by mitochondrial ribosomes and inserted into the inner membrane during translation. Despite progress, key aspects of how mitochondrial gene expression is regulated remain elusive, largely due to the organelle's limited genetic accessibility. However, emerging technologies now offer new tools to manipulate various stages of this process. In this review, we explore recent strategies that expand our ability to target mitochondria genetically.
    Keywords:  RNA; gene expression; genetic tools; mitochondria
    DOI:  https://doi.org/10.1515/hsz-2025-0170
  6. Nat Metab. 2025 Sep 16.
      Iron sustains cancer cell plasticity, yet it also sensitizes the mesenchymal, drug-tolerant phenotype to ferroptosis. This posits that iron compartmentalization must be tightly regulated. However, the molecular machinery governing organelle Fe(II) compartmentalization remains elusive. Here, we show that BDH2 is a key effector of inter-organelle Fe(II) redistribution and ferroptosis vulnerability during melanoma transition from a melanocytic (MEL) to a mesenchymal-like (MES) phenotype. In MEL cells, BDH2 localizes at the mitochondria-lysosome contacts (MLCs) to generate the siderophore 2,5-dihydroxybenzoic acid (2,5-DHBA), which ferries iron into the mitochondria. Fe(II) transfer by BDH2 supports mitochondrial bioenergetics, which is required to maintain lysosomal acidification and MLC formation. Loss of BDH2 alters lysosomal pH and MLC tethering dynamics, causing lysosomal iron sequestration, which primes MES cells for ferroptosis. Rescuing BDH2 expression, or supplementing 2,5-DHBA, rectifies lysosomal pH and MLCs, protecting MES cells from ferroptosis and enhancing their ability to metastasize. Thus, we unveil a BDH2-dependent mechanism that orchestrates inter-organelle Fe(II) transfer, linking metabolic regulation of lysosomal pH to the ferroptosis vulnerability of the mesenchymal, drug-tolerant cancer cells.
    DOI:  https://doi.org/10.1038/s42255-025-01352-4
  7. FEBS Open Bio. 2025 Sep 19.
      Tryptophan (Trp) is the largest and most structurally complex amino acid, yet it is the least abundant in the proteome. Its distinct indole ring and high carbon content allow it to give rise to several biologically active metabolites, including serotonin, kynurenine (Kyn), and indole-3-pyruvate (I3P). Dysregulation of Trp metabolism has been implicated in a range of diseases, from depression to cancer. Investigating Trp and its metabolites in healthy tissues provides insight into how disease-associated disruptions may be targeted selectively while preserving essential physiological functions. Whereas previous studies have typically focused on individual organs or single metabolic branches, our analysis spans 12 peripheral organs, the central nervous system, and serum in male and female (C57BL/6) mice across three life stages: young (3 weeks), adult (54 weeks), and aged (74 weeks). We identified striking tissue-, sex-, and age-specific differences in Trp metabolism, including elevated levels of I3P and Kyn, both linked to tumor growth, in aging males. We also compared Trp metabolite profiles in tissues from mice fed a control defined diet versus a Trp-deficient diet for three weeks. This intervention led to a marked reduction in circulating Trp and its metabolites, with more modest effects observed in the liver and central nervous system. These findings underscore the importance of organ-specific and diet-sensitive analyses of Trp metabolism for understanding its role in both normal physiology and disease. Establishing baseline levels of Trp metabolites across tissues may also provide a foundation for identifying organ-specific metabolic reprogramming in cancer and other illnesses.
    Keywords:  atlas; indole‐3‐pyruvate; kynurenine; metabolism; serotonin; tryptophan
    DOI:  https://doi.org/10.1002/2211-5463.70123
  8. Nature. 2025 Sep 17.
      Neuroendocrine and tuft cells are rare chemosensory epithelial lineages defined by the expression of ASCL1 and POU2F3 transcription factors, respectively. Neuroendocrine cancers, including small cell lung cancer (SCLC), frequently display tuft-like subsets, a feature linked to poor patient outcomes1-9. The mechanisms driving neuroendocrine-tuft tumour heterogeneity and the origins of tuft-like cancers are unknown. Using multiple genetically engineered animal models of SCLC, we demonstrate that a basal cell of origin (but not the accepted neuroendocrine origin) generates neuroendocrine-tuft-like tumours that highly recapitulate human SCLC. Single-cell clonal analyses of basal-derived SCLC further uncovered unexpected transcriptional states, including an Atoh1+ state, and lineage trajectories underlying neuroendocrine-tuft plasticity. Uniquely in basal cells, the introduction of genetic alterations enriched in human tuft-like SCLC, including high MYC, PTEN loss and ASCL1 suppression, cooperates to promote tuft-like tumours. Transcriptomics of 944 human SCLCs revealed a basal-like subset and a tuft-ionocyte-like state that altogether demonstrate notable conservation between cancer states and normal basal cell injury response mechanisms10-13. Together, these data indicate that the basal cell is a probable origin for SCLC and other neuroendocrine-tuft cancers that can explain neuroendocrine-tuft heterogeneity, offering new insights for targeting lineage plasticity.
    DOI:  https://doi.org/10.1038/s41586-025-09503-z
  9. bioRxiv. 2025 Sep 07. pii: 2025.09.02.673805. [Epub ahead of print]
      Renal cell carcinoma (RCC) is a heterogeneous malignancy in which clear cell RCC (ccRCC) represents the most aggressive subtype. Survivin (BIRC5), an inhibitor of apoptosis and key regulator of mitosis, is frequently overexpressed in RCC and associated with poor prognosis, yet its broader role in kidney cancer biology remains poorly defined. Here, we analyzed transcriptomic data from the TCGA-KIRC cohort and found that advanced-stage ccRCC exhibits widespread dysregulation of cell cycle pathways, with 1,484 genes upregulated and 479 genes downregulated in stage IV compared to stage I tumors. To define survivin's functional contribution, we performed loss-of-function and pharmacologic inhibition studies in RENCA cells. Survivin knockdown or treatment with the small molecule inhibitor YM155 significantly reduced proliferation, S-phase entry, and Cyclin D1 expression, while also impairing both collective and single-cell migration. Beyond cell cycle control, survivin depletion induced notable changes in mitochondrial morphology and bioenergetics, including increased mitochondrial content coupled with reduced oxygen consumption, suggesting accumulation of dysfunctional mitochondria due to impaired clearance. Collectively, these findings identify survivin as a multifaceted oncogenic driver in RCC that integrates cell cycle progression, cytoskeletal organization, and mitochondrial homeostasis. By revealing survivin's dual roles in proliferative and metabolic adaptation, this work highlights survivin as both a prognostic biomarker and a therapeutic vulnerability, supporting future strategies that combine survivin inhibition with metabolic or cell cycle-directed therapies for advanced kidney cancer.
    Keywords:  Survivin; migration; mitochondria; proliferation; renal cell carcinoma
    DOI:  https://doi.org/10.1101/2025.09.02.673805
  10. Nature. 2025 Sep 17.
      Brown and beige adipocytes express uncoupling protein 1 (UCP1), a mitochondrial protein that dissociates respiration from ATP synthesis and promotes heat production and energy expenditure. However, UCP1-/- mice are not obese1-5, consistent with the existence of alternative mechanisms of thermogenesis6-8. Here we describe a UCP1-independent mechanism of thermogenesis involving ATP-consuming metabolism of monomethyl branched-chain fatty acids (mmBCFA) in peroxisomes. These fatty acids are synthesized by fatty acid synthase using precursors derived from catabolism of branched-chain amino acids9 and our results indicate that β-oxidation of mmBCFAs is mediated by the peroxisomal protein acyl-CoA oxidase 2 (ACOX2). Notably, cold exposure upregulated proteins involved in both biosynthesis and β-oxidation of mmBCFA in thermogenic fat. Acute thermogenic stimuli promoted translocation of fatty acid synthase to peroxisomes. Brown-adipose-tissue-specific fatty acid synthase knockout decreased cold tolerance. Adipose-specific ACOX2 knockout also impaired cold tolerance and promoted diet-induced obesity and insulin resistance. Conversely, ACOX2 overexpression in adipose tissue enhanced thermogenesis independently of UCP1 and improved metabolic homeostasis. Using a peroxisome-localized temperature sensor named Pexo-TEMP, we found that ACOX2-mediated fatty acid β-oxidation raised intracellular temperature in brown adipocytes. These results identify a previously unrecognized role for peroxisomes in adipose tissue thermogenesis characterized by an mmBCFA synthesis and catabolism cycle.
    DOI:  https://doi.org/10.1038/s41586-025-09517-7
  11. Mol Cell. 2025 Sep 18. pii: S1097-2765(25)00713-0. [Epub ahead of print]85(18): 3351-3352
      In this issue of Molecular Cell, Xiang et al.1 provided insights into the mechanism and structure-guided engineering of DdCBE for mitochondrial DNA base editing. More precise editing was achieved by better defining the editing window.
    DOI:  https://doi.org/10.1016/j.molcel.2025.08.028
  12. Trends Cancer. 2025 Sep 16. pii: S2405-8033(25)00204-3. [Epub ahead of print]
      The tumor microenvironment (TME) imposes profound metabolic and functional constraints on immune cells, with mitochondrial dysfunction emerging as a pivotal driver of immunosuppression. While mitochondrial metabolism is well recognized for its role in energy production and cellular homeostasis, its dynamic regulation of immune cell activation, differentiation, and exhaustion within the TME remains underexplored. In this review we summarize insights into how TME stressors such as hypoxia, nutrient competition, and metabolic byproducts subvert mitochondrial dynamics, redox balance, and mitochondrial DNA (mtDNA) signaling in T cells, natural killer (NK) cells, and macrophages, thereby directly impairing their antitumor efficacy. We emphasize that the restoration of mitochondrial fitness in immune cells, achieved by targeting metabolites in the TME and mitochondrial quality control, represents a pivotal axis for adoptive cell therapies (ACTs) and TME reprogramming.
    Keywords:  ROS; chimeric antigen receptor (CAR); metabolism; mitochondria; tumor immunotherapy
    DOI:  https://doi.org/10.1016/j.trecan.2025.08.006
  13. Nat Aging. 2025 Sep 18.
      The mechanisms of aging are becoming increasingly well mapped; however, there remains ongoing debate about the ultimate and proximate causes of aging. The recent development of highly precise aging clocks led to a resurgence of arguments in support of a biological program of aging. However, the declining force of natural selection after the onset of reproduction means that cellular function could deteriorate without requiring a specific program. Here, we argue that aging clocks do not imply an intrinsic program but rather reflect the stochastic accumulation of molecular errors and damage. Damage accumulates due to insufficient maintenance and repair and contributes to system-wide entropy. In support of this, cross-species comparisons indicate that enhanced DNA repair capacity is a key determinant of exceptional longevity in mammals. By better understanding the nature of the stochasticity that governs the aging process, we will have a stronger mechanistic basis for developing geroprotective interventions to promote healthy aging in humans.
    DOI:  https://doi.org/10.1038/s43587-025-00975-2
  14. bioRxiv. 2025 Sep 09. pii: 2025.06.09.658730. [Epub ahead of print]
      Proper heme biosynthesis is essential for numerous cellular functions across nearly all life forms. In humans, dysregulated heme metabolism is linked to multiple blood diseases, neurodegeneration, cardiovascular disease, and metabolic disorders. Erythroid heme production begins with the rate-limiting enzyme Aminolevulinic Acid Synthase (ALAS2) in the mitochondrion. Although prior studies discuss the regulation of ALAS2 in the nucleus and cytoplasm, its modulation as a mature mitochondrial matrix enzyme remains poorly understood. We report that heme binds mature human ALAS2 with high affinity, acting as a reversible mixed inhibitor that reduces enzymatic activity. Structure-based modeling reveals two flexible regions of ALAS2 interact with heme, locking the enzyme in an inactive conformation and occluding the active site. Our work reveals a negative feedback mechanism for heme synthesis, offering insights into the spatial regulation of ALAS2 and the maturation of the essential heme cofactor.
    DOI:  https://doi.org/10.1101/2025.06.09.658730
  15. J Biol Chem. 2025 Sep 16. pii: S0021-9258(25)02585-2. [Epub ahead of print] 110733
      Deoxynucleotides (dNTPs) in post-mitotic tissues rely on deoxynucleoside salvage pathways in order to repair and replicate nuclear and mitochondrial DNA (mtDNA). Previous work from our laboratory showed in perfused rat heart and isolated mitochondria that the only substrate for TTP synthesis is thymidine. When thymidylate (TMP) is provided to bypass thymidine kinase 2 (TK2) the substrate is readily dephosphorylated to thymidine before salvage occurs suggesting compartmentalization within the heart mitochondrial matrix. The goal of this work extends these findings in the heart to mitochondria from other post-mitotic tissues, including rat liver, kidney, and brain. Using AZT to block mitochondrial thymidine kinase 2, we demonstrate that TMP cannot serve as a precursor for TTP synthesis in isolated mitochondria from any of these tissues unless it is de-phosphorylated to thymidine first. Broken mitochondria incubated with labeled TMP showed similar results as intact mitochondria, suggesting the findings are not related to TMP transport across the inner mitochondrial membrane. Further, using proximity labeling with immunofluorescence microscopy we provide evidence supporting the hypothesis that TMP compartmentation is accounted for by the interaction of TK2 and CMPK2 in the mitochondria. Differential fraction experiments provide additional evidence that association with TK2 allows CMPK2 to display TMPK2 activity. Together, the results indicate that a two-step phosphorylation of thymidine to TDP occurs because the proximity of TK2 and CMPK2 in the mitochondria prevents TMP from diffusing from the two enzymes.
    Keywords:  cytidine monophosphate kinase 2; mitochondrial disease; mitochondrial metabolism; nucleoside/nucleotide biosynthesis; nucleoside/nucleotide metabolism; thymidine kinase 2
    DOI:  https://doi.org/10.1016/j.jbc.2025.110733
  16. Nat Metab. 2025 Sep 19.
      The consumption of sugar-sweetened beverages (SSBs), which contain high levels of fructose and glucose, has been causally and mechanistically linked to an increased risk of colorectal cancer (CRC). However, the effects of SSB consumption on advanced stages of disease progression, including metastasis, remain poorly understood. Here we show that exposure of CRC cells to a glucose and fructose formulation-reflecting the composition of both high-fructose corn syrup and sucrose found in SSBs-enhances cellular motility and metastatic potential compared to glucose alone. Given that CRC cells grow poorly in fructose alone, and cells in vivo are not physiologically exposed to fructose without glucose, we excluded the fructose-only condition from our studies unless needed as a control. Mechanistically, the combination of glucose and fructose elevates the NAD⁺/NADH ratio by activation of the reverse reaction of sorbitol dehydrogenase in the polyol pathway. This redox shift relieves NAD⁺ limitations and accelerates glycolytic activity, which in turn fuels activation of the mevalonate pathway, ultimately promoting CRC cell motility and metastasis. Our findings highlight the detrimental impact of SSBs on CRC progression and suggest potential dietary and therapeutic strategies to mitigate metastasis in patients with CRC.
    DOI:  https://doi.org/10.1038/s42255-025-01368-w
  17. bioRxiv. 2025 Sep 04. pii: 2025.08.31.673254. [Epub ahead of print]
      Dietary protein is a key regulator of metabolic health in humans and rodents. Many of the benefits of protein restriction are mediated by reduced consumption of dietary branched-chain amino acids (BCAAs; leucine, valine and isoleucine), and restriction of the BCAAs is sufficient to extend healthspan and lifespan in mice. While the BCAAs have often been considered as a group, it has become apparent that they have distinct metabolic roles, and we recently found that restriction of isoleucine is sufficient to extend the healthspan and lifespan of male and female mice. Here, we test the effect of lifelong restriction of the BCAA valine on healthy aging. We find that valine restriction (Val-R) improves metabolic health in C57BL/6J mice, promoting leanness and glycemic control in both sexes. To investigate the molecular mechanisms engaged by Val-R with aging, we conducted multi-tissue transcriptional profiling and gene network analysis. While Val-R had a significantly greater molecular impact in the liver, muscle, and brown adipose tissue of female mice than males, there was a stronger gene enrichment with phenotypic traits in male mice. Further, we found that phenotypic changes are associated with a multi-tissue downregulation of the longevity associated PI3K-Akt signaling pathway. Val-R reduces frailty in both sexes and extends the lifespan of male by 23%, but does not extend female lifespan, corresponding with a male-specific downregulation of PI3K-Akt signaling. Our results demonstrate that Val-R improves multiple aspects of healthspan in mice of both sexes and extends lifespan in males, suggests that interventions that mimic Val-R may have translational potential for aging and age-related diseases.
    Keywords:  aging; branched-chain amino acids; frailty; lifespan; metabolic health; mice; valine
    DOI:  https://doi.org/10.1101/2025.08.31.673254
  18. Mol Metab. 2025 Sep 12. pii: S2212-8778(25)00156-5. [Epub ahead of print] 102249
      Circadian rhythms are integral to maintaining metabolic health by temporally coordinating physiology across tissues. However, the mechanisms underlying circadian cross-tissue coordination remain poorly understood. In this study, we uncover a central role for the liver clock in regulating circadian rhythms in white adipose tissue (WAT). Using a hepatocyte-specific Bmal1 knockout mouse model, we show that hepatic circadian control modulates lipid metabolism in WAT. In addition, by utilizing a model where functional clocks are restricted to the hepatocytes, we demonstrate that the liver clock alone integrates feeding cues to modulate circadian gene expression in WAT, including Cebpa, a key regulator of adipogenesis. We show that the hepatocyte clock regulates adipocyte Cebpa rhythmicity through secreted proteins. Further investigation identified one of the contributing mediators to be the adaptor protein 14-3-3η (Ywhah). The clinical relevance of the liver clock for systemic metabolic function is supported by human cohort data, which revealed a gene regulatory network, consisting of several clock-controlled liver genes, linked to cardiometabolic risk. These findings provide evidence for how the hepatocyte clock coordinates WAT physiology and highlights the core clock system as a potential therapeutic target to improve cardiometabolic health.
    Keywords:  Cardiometabolic disease; Circadian rhythms; Cross-tissue communication; Lipid metabolism
    DOI:  https://doi.org/10.1016/j.molmet.2025.102249
  19. bioRxiv. 2025 Sep 07. pii: 2025.09.03.674000. [Epub ahead of print]
      Primary mitochondrial cardiomyopathies are an unmet clinical challenge, as there are no therapies that directly address the underlying mitochondrial dysfunction. We previously reported that the cardiomyocyte-specific deletion of the mitochondrial phosphate carrier (SLC25A3), which imports phosphate required for ATP synthesis, produces a model of mitochondrial cardiomyopathy in which total cardiac ATP levels are preserved despite defective mitochondrial ATP production. This was accompanied by increased glycolytic activity and reduced mitochondrial flux, leading us to hypothesize that pharmacologically enhancing glycolysis might be protective when the mitochondrial energy machinery is intrinsically impaired. To test this, we turned to meclizine, an FDA-approved antihistamine previously shown to shift metabolism toward glycolysis. Chronic meclizine treatment in SLC25A3-deficient mice attenuated cardiac hypertrophy, improved systolic function, and restored mitochondrial ultrastructure. Unexpectedly, meclizine suppressed glycolytic enzyme expression and reduced lactate accumulation, suggesting that meclizine does not induce a glycolytic shift in SLC25A3-deleted hearts. Instead, proteomic and functional analyses revealed preservation of mitochondrial cristae architecture via MICOS upregulation and improved NAD+/NADH homeostasis through uncoupled electron flux and NAD+ regeneration. Together, these findings identify meclizine as a clinically approved compound that promotes cardioprotection in mitochondrial disease not by driving glycolysis, but by preserving mitochondrial membrane organization and redox balance, highlighting mitochondrial quality and NAD+ redox homeostasis as therapeutic targets for primary mitochondrial cardiomyopathies.
    DOI:  https://doi.org/10.1101/2025.09.03.674000
  20. Nat Cell Biol. 2025 Sep 16.
      The microbiome affects eukaryotic host cells via many metabolites, including the well-studied queuine as substrate for host tRNA queuosine modification. The microbial metabolite pre-queuosine 1 (preQ1) is produced in the bacterial tRNA queuosine biosynthesis pathway, with unknown effects on host cell biology. Here we show that preQ1 strongly represses cell proliferation in both human and mouse cells. Queuine reverses this effect by competing with preQ1 to modify the same tRNA. PreQ1 is detectable in the plasma and tissues of mice, and its injection suppresses tumour growth in a mouse cancer model. Mechanistically, preQ1 reduces cognate tRNA levels specifically, as well as codon-dependent translation of housekeeping genes. We identify the endoplasmic reticulum-localized inositol-requiring enzyme 1 (IRE1) ribonuclease as the enzyme responsible for the selective degradation of preQ1-modified tRNAs on translating ribosomes. Our results identify two microbial metabolites competing for host tRNA modification, which elicits translation quality control and impacts cell proliferation.
    DOI:  https://doi.org/10.1038/s41556-025-01750-6
  21. Cell Rep. 2025 Sep 12. pii: S2211-1247(25)01059-9. [Epub ahead of print]44(9): 116288
      The histocompatibility barrier prevents the transfer of both normal and tumor cells between individuals; however, clonally transmissible cancers in dogs, Tasmanian devils, and soft-shell clams can naturally transmit as allografts. To understand if cancer cells can more generally evolve to escape the histocompatibility barrier, we have serially passaged a mouse melanoma into increasingly mismatched mouse strains until a transplantable tumor emerged. The transplantable melanoma cells are characterized by an antiviral immune signature and the upregulation of endogenous retrotransposable elements (RTEs), major histocompatibility complex class I (MHC class I), programmed cell death ligand-1 (PD-L1), and Qa-1 non-classical MHC molecules. Knockout of the RNA sensor retinoic acid-inducible gene I (RIG-I) reduces expression of PD-L1 and Qa-1, and antibody-mediated blockade of PD-L1 and Qa-1 induces tumor rejection. Thus, an immune antiviral signature linked to RTEs upregulation facilitates escape of the melanoma from allogeneic rejection, simultaneously making the tumor sensitive to PD-L1 and Qa-1 antagonism. A similar immune signature is found in human melanomas that respond to PD-L1 blockade.
    Keywords:  CP: Cancer; CP: Immunology; Qa-1; RIG-I; melanoma; non-classical MHC; transplantable
    DOI:  https://doi.org/10.1016/j.celrep.2025.116288
  22. J Am Chem Soc. 2025 Sep 14.
      Copper is an essential element for sustaining life. However, disruptions in copper homeostasis underpin disease, as illustrated by cuproptosis, an emerging form of cell death resulting from aberrant accumulation of copper pools in loosely bound, labile forms. Along these lines, activity-based sensing (ABS) offers a powerful strategy for tracking labile copper fluxes with metal and oxidation state selectivity by exploiting analyte reactivity for analyte detection. Traditional ABS probes for Cu(I), the major oxidation state of copper in cells, are selective but require O2 as a coadditive, thus limiting their temporal resolution and sensitivity. Here, we present the design, synthesis, and biological evaluation of a first-generation ABS strategy for direct Cu(I) sensing by leveraging alkyne-directed cleavage reactivity. Copper Alkyne Probe-1 (CAP-1) features a rapid response to changes in intracellular Cu(I) pools with over 400-fold selectivity for Cu(I) over competing biological metals. We apply this probe to identify novel metal-metal crosstalk in cuproptosis, where we observe that Mn(II) exposure sensitizes cells to cuproptosis through upregulating the mitochondrial reductase FDX1 and depleting reduced glutathione, thus synergistically elevating labile Cu(I) levels. By revealing an interplay between copper and manganese in regulating cell death, this work provides a starting point for broader investigations of metal-metal nutrient crosstalk in biology and medicine.
    DOI:  https://doi.org/10.1021/jacs.5c09297
  23. Nat Biomed Eng. 2025 Sep 16.
      Chimeric antigen receptor (CAR) T cell therapy for solid tumours is challenging because of the immunosuppressive tumour microenvironment and a complex manufacturing process. Cellular manufacturing protocols directly impact CAR T cell yield, phenotype and metabolism, which correlates with in vivo potency and persistence. Although metabolic fitness is a critical quality attribute, how T cell metabolic requirements vary throughout the manufacturing process remains unexplored. Here we use optical metabolic imaging (OMI), a non-invasive, label-free method to evaluate single-cell metabolism. Using OMI, we identified the impacts of media composition on CAR T cell metabolism, activation strength and kinetics, and phenotype. We demonstrate that OMI parameters can indicate cell cycle stage and optimal gene transfer conditions for both viral transduction and electroporation-based CRISPR/Cas9. In a CRISPR-edited anti-GD2 CAR T cell model, OMI measurements allow accurate prediction of an oxidative metabolic phenotype that yields higher in vivo potency against neuroblastoma. Our data support OMI as a robust, sensitive analytical tool to optimize manufacturing conditions and monitor cell metabolism for increased CAR T cell yield and metabolic fitness.
    DOI:  https://doi.org/10.1038/s41551-025-01504-7
  24. Nature. 2025 Sep 17.
      The mechanistic target of rapamycin complex 1 (mTORC1) integrates growth factor (GF) and nutrient signals to stimulate anabolic processes connected to cell growth and inhibit catabolic processes such as autophagy1,2. GF signalling through the tuberous sclerosis complex regulates the lysosomally localized small GTPase RAS homologue enriched in brain (RHEB)3. Direct binding of RHEB-GTP to the mTOR kinase subunit of mTORC1 allosterically activates the kinase by inducing a large-scale conformational change4. Here we reconstituted mTORC1 activation on membranes by RHEB, RAGs and Ragulator. Cryo-electron microscopy showed that RAPTOR and mTOR interact directly with the membrane. Full engagement of the membrane anchors is required for optimal alignment of the catalytic residues in the mTOR kinase active site. Converging signals from GFs and nutrients drive mTORC1 recruitment to and activation on lysosomal membrane in a four-step process, consisting of (1) RAG-Ragulator-driven recruitment to within ~100 Å of the lysosomal membrane; (2) RHEB-driven recruitment to within ~40 Å; (3) RAPTOR-membrane engagement and intermediate enzyme activation; and (4) mTOR-membrane engagement and full enzyme activation. RHEB and membrane engagement combined leads to full catalytic activation and structurally explains GF and nutrient signal integration at the lysosome.
    DOI:  https://doi.org/10.1038/s41586-025-09545-3
  25. Nat Metab. 2025 Sep 15.
      Excessive consumption of the simple sugar fructose, which induces excessive hepatic lipogenesis and gut dysbiosis, is a risk factor for cardiometabolic diseases. Here we show in male mice that the gut microbiome, when adapted to dietary fibre inulin, catabolizes dietary fructose and mitigates or reverses insulin resistance, hepatic steatosis and fibrosis. Specifically, inulin supplementation, without affecting the host's small intestinal fructose catabolism, promotes the small intestinal microbiome to break down incoming fructose, thereby decreasing hepatic lipogenesis and fructose spillover to the colonic microbiome. Inulin also activates hepatic de novo serine synthesis and cystine uptake, augmenting glutathione production and protecting the liver from fructose-induced lipid peroxidation. These multi-modal effects of inulin are transmittable by the gut microbiome, where Bacteroides acidifaciens acts as a key player. Thus, the gut microbiome, adapted to use inulin (a fructose polymer), efficiently catabolizes dietary monomeric fructose, thereby protecting the host. These findings provide a mechanism for how fibre can facilitate the gut microbiome to mitigate the host's exposure to harmful nutrients and disease progression.
    DOI:  https://doi.org/10.1038/s42255-025-01356-0
  26. Cell Metab. 2025 Sep 16. pii: S1550-4131(25)00381-X. [Epub ahead of print]
      Acute myeloid leukemia (AML) commonly relapses after initial chemotherapy response. We assessed metabolic adaptations in chemoresistant cells in vivo before overt relapse, identifying altered branched-chain amino acid (BCAA) levels in patient-derived xenografts (PDXs) and immunophenotypically identified leukemia stem cells from AML patients. Notably, this was associated with increased BCAA transporter expression with low BCAA catabolism. Restricting BCAAs further reduced chemoresistant AML cells, but relapse still occurred. Among the persisting cells, we found an unexpected increase in protein production. This was accompanied by elevated translation of 2-oxoglutarate- and iron-dependent oxygenase 1 (OGFOD1), a known ribosomal dioxygenase that adjusts the fidelity of tRNA anticodon pairing with coding mRNA. We found that OGFOD1 upregulates protein synthesis in AML, driving disease aggressiveness. Inhibiting OGFOD1 impaired translation processing, decreased protein synthesis and improved animal survival even with chemoresistant AML while sparing normal hematopoiesis. Leukemic cells can therefore persist despite the stress of chemotherapy and nutrient deprivation through adaptive control of translation. Targeting OGFOD1 may offer a distinctive, translation-modifying means of reducing the chemopersisting cells that drive relapse.
    Keywords:  BCAA; OGFOD1; Ribo-seq; acute myeloid leukemia; chemoresistance; metabolism; protein biosynthesis; ribosome pausing; translation accuracy
    DOI:  https://doi.org/10.1016/j.cmet.2025.08.008
  27. Sci Adv. 2025 Sep 19. 11(38): eadz9606
      Studies on the impact of metabolism on cell fate decisions are seeing a renaissance. However, a key challenge remains to distinguish signaling functions of metabolism from its canonical bioenergetic and biosynthetic roles, which underlie cellular homeostasis. Here, we tackled this challenge using mouse embryonic axis segmentation as an experimental model. First, we found that energetically subminimal amounts of glucose can support ongoing segmentation clock activity, providing evidence that glycolysis exerts a signaling function. Using a dynamical systems approach based on entrainment, we identified fructose 1,6-bisphosphate (FBP) as the potential signaling metabolite. Functionally, we demonstrated that glycolytic flux/FBP control the segmentation clock period and Wnt signaling in an anticorrelated manner. Critically, we showed that the slow segmentation clock phenotype caused by elevated glycolysis is mediated by Wnt signaling rather than cellular bioenergetic and biosynthetic state. Combined, our results demonstrate a modular organization of metabolic functions, revealing a signaling module of glycolysis that can be decoupled from its canonical metabolic functions.
    DOI:  https://doi.org/10.1126/sciadv.adz9606
  28. Dokl Biochem Biophys. 2025 Sep 14.
      Ferroptosis, an iron-dependent form of regulated cell death, represents an emerging therapeutic vulnerability in colorectal cancer (CRC). However, the epigenetic mechanisms controlling ferroptosis sensitivity in CRC remain poorly understood. Here, we identify histone deacetylase 3 (HDAC3) as a pivotal epigenetic suppressor of ferroptosis. Both pharmacological inhibition and genetic knockdown of HDAC3 significantly enhanced ferroptosis sensitivity, as evidenced by elevated intracellular ferrous iron (Fe2+) and lipid peroxidation. Mechanistically, inhibition of HDAC3 reduced the expression of nuclear factor erythroid 2-related factor 2 (NRF2), a master antioxidant transcription factor, thereby leading to downregulation of glutathione peroxidase 4 (GPX4), a central ferroptosis defense gene. Notably, NRF2 knockdown abolished GPX4 downregulation by HDAC3 inhibition, whereas GPX4 overexpression rescued the ferroptotic phenotype caused by HDAC3 depletion. Collectively, these findings define an HDAC3-NRF2-GPX4 axis that suppresses ferroptosis in CRC, and highlight HDAC3 as a potential therapeutic target for ferroptosis-based cancer treatment.
    Keywords:  GPX4; HDAC3; NRF2; colorectal cancer; ferroptosis
    DOI:  https://doi.org/10.1134/S1607672925600496
  29. J Biol Chem. 2025 Sep 11. pii: S0021-9258(25)02565-7. [Epub ahead of print] 110713
      Provitamin A carotenoids are metabolized to retinoids, critical for vision and transcriptional regulation, through oxidative cleavage by carotenoid oxygenases. β-Carotene, a symmetric carotenoid, undergoes central cleavage by β-carotene oxygenase 1 (BCO1), generating two molecules of retinaldehyde. In contrast, the metabolism of asymmetric carotenoids, such as α-carotene (β,ε-carotene) and β-cryptoxanthin (β,β-carotene-3-ol), produces noncanonical apocarotenoid derivatives in addition to retinaldehyde. Here, we dissect the enzymatic pathways and transport mechanisms governing these metabolic fates in mice. We demonstrate that α-carotene is cleaved exclusively by BCO1 to yield retinaldehyde and α-retinaldehyde, bypassing mitochondrial processing. β-Cryptoxanthin, however, undergoes an initial eccentric cleavage by mitochondrial BCO2, followed by cytosolic BCO1-mediated central cleavage, producing only retinaldehyde. This divergence arises from differential subcellular trafficking: β-cryptoxanthin is transported to mitochondria via Aster-B, while α-carotene is excluded. Downstream, α-retinol is esterified by lecithin:retinol acyltransferase (LRAT), trafficked in chylomicrons, and stored as α-retinyl esters in the liver under ISX-mediated transcriptional control. Notably, α-retinol is not mobilized into circulation via retinol binding protein 4 (RBP4), and, genetic ablation of its receptor, STRA6 does not alter α-retinyl ester storage in lung tissue. Intriguingly, α-retinyl esters accumulate in the eyes of STRA6-deficient mice yet fail to participate in the visual cycle due to exclusion from RPE65-mediated isomerization. These findings establish α-retinoids as metabolic tracers of BCO1 activity and chylomicron-mediated vitamin A delivery and reveal mechanistic safeguards that prevent incorporation of noncanonical retinoids into the visual cycle.
    Keywords:  Lipid Transport; Metabolism; Retinoids; Vision; Vitamin A
    DOI:  https://doi.org/10.1016/j.jbc.2025.110713
  30. J Clin Invest. 2025 Sep 16. pii: e193745. [Epub ahead of print]135(18):
      Inactivation of cyclin-dependent kinase 12 (CDK12) defines an immunogenic molecular subtype of prostate cancer characterized by genomic instability and increased intratumoral T cell infiltration. This study revealed that genetic or pharmacologic inactivation of CDK12 and its paralog CDK13 robustly activates stimulator of interferon genes (STING) signaling across multiple cancer types. Clinical cohort analysis showed that reduced CDK12/13 expression correlates with improved survival and response to immune checkpoint blockade (ICB). Mechanistically, CDK12/13 depletion or targeted degradation induced cytosolic nucleic acid release, triggering STING pathway activation. CDK12/13 degradation delayed tumor growth and synergized with anti-PD-1 therapy in syngeneic tumor models, enhancing STING activity and promoting CD8+ T cell infiltration and activation within tumors. Notably, the antitumor effects of this combination required STING signaling and functional CD8+ T cells. These findings establish STING activation as the key driver of T cell infiltration and the immune-hot tumor microenvironment in CDK12-mutant cancers, suggesting that dual CDK12/13 inhibitors and degraders activate antitumor immunity and potentiate responses to immunotherapies.
    Keywords:  Cancer; Cancer immunotherapy; Cell biology; Oncology; Therapeutics
    DOI:  https://doi.org/10.1172/JCI193745
  31. Trends Immunol. 2025 Sep 16. pii: S1471-4906(25)00215-7. [Epub ahead of print]
      Mitochondrial lipid metabolism plays a pivotal role in tumor immunosurveillance and immune evasion. This review explores how mitochondrial regulation shapes immune cell metabolism within the tumor microenvironment (TME), focusing on the antitumor effects of the mitochondrial-fueled immune response and the detrimental impact of impaired mitochondrial function on immune cell cytotoxicity. Although current studies support this dual role, critical gaps remain, including how immune cells adapt differently to the lipid-rich TME, and how therapies can target lipid metabolism without harming immune memory. By synthesizing current findings and highlighting these uncertainties, this review highlights mitochondrial lipid metabolism as a promising therapeutic axis in cancer immunotherapy.
    Keywords:  immunometabolism; lipid metabolism; mitochondria; tumor metabolic reprogramming
    DOI:  https://doi.org/10.1016/j.it.2025.08.005
  32. Mol Cell. 2025 Sep 18. pii: S1097-2765(25)00709-9. [Epub ahead of print]85(18): 3443-3459.e11
      Increasing brain complexity is a major step in the evolution of species. Here, we show that, in the transition from amphibians to reptiles, the DNA repair protein RAD23B acquires a metalloadaptor function that allows it to serve as a central hub for both metabolism and protection of genomic integrity. More specifically, RAD23B gains an allosteric H274/H323 copper-binding site to enable the transfer of copper from the universal copper transporter 1 (CTR1) uptake protein to all known copper metallochaperone pathways, while simultaneously making its canonical functions in DNA repair copper dependent. This layer of nutrient regulation allows organisms to withstand elevated levels of potentially toxic copper while augmenting metabolism in cells with high energetic needs across both physiology and disease, including neurons in the locus coeruleus, a key brain structure that regulates sleep, and cancer cells.
    Keywords:  Amniota evolution; CTR1/SLC31A1; Rad23b; metalloadaptor; metalloallostery; mitochondrial metabolism; sleep and wake behavior; transition metal signaling
    DOI:  https://doi.org/10.1016/j.molcel.2025.08.024
  33. Mol Cell. 2025 Sep 18. pii: S1097-2765(25)00712-9. [Epub ahead of print]85(18): 3353-3354
      Damage to polyunsaturated fats causes ferroptotic cell death. In this issue, Deng et al.1 show that the incorporation of the fatty acid DHA into membranes is controlled by the protein UBXD8, as a natural mechanism to prevent overloading cells with dangerous fat, preventing ferroptosis.
    DOI:  https://doi.org/10.1016/j.molcel.2025.08.027
  34. Nat Genet. 2025 Sep 15.
    SenNet Consortium
      Cellular senescence is a complex biological process that plays a pathophysiological role in aging and age-related diseases. The biological understanding of senescence at the cellular and tissue levels remains incomplete due to the lack of specific biomarkers as well as the relative rarity of senescent cells, their phenotypic heterogeneity and dynamic features. This Review provides a comprehensive overview of multiomic approaches for the characterization and biological understanding of cellular senescence. The technical capability and challenges of each approach are discussed, and practical guidelines are provided for selecting tools for identifying, characterizing and spatially mapping senescent cells. The importance of computational analyses in multiomics research, including senescent cell identification, signature detection and interactions of senescent cells with microenvironments, is highlighted. Moreover, tissue-specific case studies and experimental design considerations for individual organs are presented. Finally, future directions and the potential impact of multiomic approaches on the biological understanding of cellular senescence are discussed.
    DOI:  https://doi.org/10.1038/s41588-025-02314-y
  35. Genome Biol. 2025 Sep 18. 26(1): 284
       BACKGROUND: Synthetic lethal interactions are attractive therapeutic candidates as they enable selective targeting of cancer cells in which somatic alterations have disrupted one member of a synthetic lethal gene pair while leaving normal tissues untouched, thus minimising off-target toxicity. Despite this potential, the number of well-established and validated synthetic lethal gene pairs is modest.
    RESULTS: We generate a dual-guide CRISPR/Cas9 Library and analyse 472 predicted synthetic lethal pairs in 27 cancer cell Lines from melanoma, pancreatic and lung cancer Lineages. We report a robust collection of 117 genetic interactions within and across cancer types and explore their candidacy as therapeutic targets. We show that SLC25A28 is an attractive target since its synthetic lethal paralog partner SLC25A37 is homozygously deleted pan-cancer. We generate knockout mice for Slc25a28 revealing that, except for cataracts in some mice, these animals are normal; suggesting inhibition of SLC25A28 is unlikely to be associated with profound toxicity.
    CONCLUSIONS: We provide and validate an extensive collection of synthetic lethal interactions across cancer types.
    Keywords:  CRISPR; Epistasis; High-throughput screening; Synthetic lethality
    DOI:  https://doi.org/10.1186/s13059-025-03737-w
  36. Nat Metab. 2025 Sep 16.
      N-Lactoyl-phenylalanine (Lac-Phe) is a lactate-derived circulating metabolite that reduces feeding and obesity, but the molecular mechanisms that underlie the metabolic benefits of Lac-Phe remain unknown. Here we show that Lac-Phe directly inhibits hypothalamic neurons that express Agouti-related protein (AgRP), resulting in an indirect activation of anorexigenic neurons in the paraventricular nucleus of the hypothalamus (PVH). Both AgRP inhibition and PVH activation are required to mediate Lac-Phe-induced hypophagia. Lac-Phe-mediated inhibition of AgRP neurons occurs through activation of the ATP-sensitive potassium (KATP) channel, whereas inhibition of the KATP channel blunts the effects of Lac-Phe to suppress feeding. Together, these results reveal the molecular and neurobiological mechanisms by which Lac-Phe mediates metabolic improvements and suggest this exercise-induced metabolite might have therapeutic benefits in various human diseases.
    DOI:  https://doi.org/10.1038/s42255-025-01377-9
  37. Cell Rep. 2025 Sep 12. pii: S2211-1247(25)01017-4. [Epub ahead of print]44(9): 116246
      We developed the AVID (ATP visualization in vivo directly) mouse, a genetically encoded biosensor mouse enabling real-time, multiscale imaging of ATP dynamics across the whole body, organs, and cellular compartments in living animals. AVID revealed previously undetectable localized ATP depletion near the central vein of the liver after myocardial infarction, spatially linked to kynurenic acid accumulation-a phenomenon invisible to conventional bulk metabolomics. By seamlessly integrating macroscopic organ-level imaging with microscopic spatial metabolomics, AVID establishes a new framework for spatial systems metabolism. Beyond myocardial infarction, this platform offers broad applicability to study organ-organ metabolic communication, spatial metabolic heterogeneity, and localized metabolic shifts across diverse physiological and pathological contexts, providing a transformative resource for metabolic research.
    Keywords:  ATP dynamics; CP: Metabolism; FRET; GO-ATeam biosensor; disease progression; energy metabolism; in vivo imaging; multiscale imaging; myocardial infarction; organ-organ interaction; spatial systems metabolism
    DOI:  https://doi.org/10.1016/j.celrep.2025.116246
  38. Commun Biol. 2025 Sep 19. 8(1): 1348
      Ion transport within mitochondria influences their structure, energy production, and cell death regulation. TMBIM5, a conserved calcium/proton exchanger in the inner mitochondrial membrane, contributes to mitochondrial structure, ATP synthesis, and apoptosis regulation. The relationship of TMBIM5 with the mitochondrial calcium uniporter complex formed by MCU, MICU1-3, and EMRE remains undefined. We generated Tmbim5-deficient Drosophila that exhibit disrupted cristae architecture, premature mitochondrial permeability transition pore opening, reduced calcium uptake, and mitochondrial swelling - resulting in impaired mobility and shortened lifespan. Crossing these with flies lacking mitochondrial calcium uniporter complex proteins was generally detrimental, but partial MICU1 depletion ameliorated the Tmbim5-deficiency phenotype. In human cells, MICU1 rescues morphological defects in TMBIM5-knockout mitochondria, while TMBIM5 overexpression exacerbates size reduction in MICU1-knockout mitochondria. Both proteins demonstrated opposing effects on submitochondrial localization and coexisted in the same macromolecular complex. Our findings establish a functional interplay between TMBIM5 and MICU1 in maintaining mitochondrial integrity, with implications for understanding calcium homeostasis mechanisms.
    DOI:  https://doi.org/10.1038/s42003-025-08839-6
  39. Cell Rep Med. 2025 Sep 16. pii: S2666-3791(25)00429-X. [Epub ahead of print]6(9): 102356
      Triple-negative breast cancer (TNBC) is an aggressive subtype of breast cancer, associated with poor response to therapies and high mortality. We identify that phosphodiesterase 7A (PDE7A) is overexpressed in the majority of TNBCs, and a higher level of PDE7A associates with poor prognosis. The phosphatidylinositol 3-kinase (PI3K)/AKT pathway, via the transcription factor IRF1, stimulates the expression of PDE7A in TNBC cells. PDE7A inhibition attenuates TNBC growth in both cell culture and mouse models of TNBC. Inhibition of PDE7A suppresses de novo pyrimidine biosynthesis, in part through the downregulation of the enzyme dihydroorotate dehydrogenase (DHODH). DHODH suppression attenuates TNBC tumor growth, mirroring the effects of PDE7A inhibition, and ectopic DHODH expression rescues PDE7A-inhibition-induced tumor suppression. Pharmacological co-targeting of PDE7A and DHODH potently inhibits TNBC tumor growth and metastasis. These findings identify the PDE7A → DHODH →de novo pyrimidine biosynthesis pathway as a key driver of TNBC, offering additional therapeutic opportunities for TNBC patients.
    Keywords:  DHODH; PDE7A; phosphodiesterases; pyrimidine biosynthesis; triple-negative breast cancer
    DOI:  https://doi.org/10.1016/j.xcrm.2025.102356
  40. Nat Commun. 2025 Sep 17. 16(1): 8287
      The cellular plasticity of neuroblastoma is defined by a mixture of two major cell states, adrenergic and mesenchymal, which may contribute to therapy resistance. However, how neuroblastoma cells switch cellular states during therapy remains largely unknown, and how to eradicate neuroblastoma regardless of its cell state is a clinical challenge. To better understand the cellular plasticity of neuroblastoma in chemoresistance, we define the transcriptomic and epigenetic map of adrenergic and mesenchymal types of neuroblastomas using human and murine models treated with indisulam, a selective RBM39 degrader. We show that cancer cells not only undergo a bidirectional switch between adrenergic and mesenchymal states, but also acquire additional cellular states, reminiscent of the developmental pliancy of neural crest cells. These cell state alterations are coupled with epigenetic reprogramming and dependency switching of cell state-specific transcription factors, epigenetic modifiers, and targetable kinases. Through targeting RNA splicing, indisulam induces an inflammatory tumor microenvironment and enhances the anticancer activity of natural killer cells. The combination of indisulam with anti-GD2 immunotherapy results in a durable, complete response in high-risk transgenic neuroblastoma models, providing an innovative, rational therapeutic approach to eradicate tumor cells regardless of their potential to switch cell states.
    DOI:  https://doi.org/10.1038/s41467-025-63979-x
  41. bioRxiv. 2025 Sep 05. pii: 2025.09.05.674553. [Epub ahead of print]
      Genetically encoded DNA recorders convert transient biological events into stable genomic mutations, offering a means to reconstruct past cellular states. However, current approaches to log historical events by modifying genomic DNA have limited capacity to record the magnitude of biological signals within individual cells. Here, we introduce MitoScribe, a mitochondrial DNA (mtDNA)-based recording platform that uses mtDNA base editors (DdCBEs) to write graded biological signals into mtDNA as neutral, single-nucleotide substitutions at a defined site. Taking advantage of the hundreds to thousands of mitochondrial genome copies per cell, we demonstrate MitoScribe enables reproducible, highly sensitive, non-destructive, durable, and high-throughput measurements of molecular signals, including hypoxia, NF-κB activity, BMP and Wnt signaling. We show multiple modes of operation, including multiplexed recordings of two independent signals, and coincidence detection of temporally overlapping signals. Coupling MitoScribe with single-cell RNA sequencing and mitochondrial transcript enrichment, we further reconstruct signaling dynamics at the single-cell transcriptome level. Applying this approach during the directed differentiation of human induced pluripotent stem cells (iPSCs) toward mesoderm, we show that early heterogeneity in response to a differentiation cue predicts the later cell state. Together, MitoScribe provides a scalable platform for high-resolution molecular recording in complex cellular contexts.
    DOI:  https://doi.org/10.1101/2025.09.05.674553
  42. Phys Rev E. 2025 Aug;112(2-1): 024409
      The mammalian target of rapamycin (mTOR) signaling pathway, a crucial nutrient sensor in cells, plays pivotal roles in maintaining metabolic homeostasis, cancer development, and aging-related physiological and pathological processes. Despite its significance, the regulatory mechanisms of mTOR signaling, particularly its physical properties, remain poorly understood. Here, we constructed an insulin-induced mTOR signaling model and identified time- and dose-dependent biphasic behaviors. Our findings demonstrate that the indirect negative feedback of mTORC1 on mTORC2 is central to generating these behaviors. By integrating concepts from potential landscape theory, entropy production, and dominant kinetic paths, we quantified the transitions between various cellular states-normal, tumor, prosurvival, and aging-from a physical properties perspective. Potential landscape and entropy analyses suggest that the levels of mTORC1 and mTORC2 regulate cellular fate transitions between multiple attractors, including normal, tumor, prosurvival, and aging. Dominant kinetic path analysis further revealed that the transition from normal state to tumor state requires crossing the aging state barrier, which inhibits tumor formation. The optimal transition paths between different states are irreversible. Despite the minimal action along these paths, the system still drives the transition paths to bypass the saddle points between the lowest states. This phenomenon arises from the driving forces in nonequilibrium systems, which depend not only on gradient forces within potential wells but also on curl forces. Our study provides new insights into the nonequilibrium dynamics of mTOR signaling in cell fate decisions. It enhances our understanding of tumorigenesis and aging from a physical perspective, offers guidance for targeted and personalized treatments, and suggests potential clues to uncover the physiological and pathological significance of mTOR signaling.
    DOI:  https://doi.org/10.1103/tgzc-vr4q
  43. Aging Adv. 2025 Sep;2(3): 108-111
      Mitochondrial epigenetics, a burgeoning field bridging mitochondrial biology and epigenetic regulation, has emerged as a critical determinant of aging and age-related diseases. While nuclear epigenetics is well-characterized, the mechanisms governing mitochondrial DNA (mtDNA) regulation, including nucleoid dynamics, non-coding RNAs (ncRNAs), and metabolite-driven modifications, remain underexplored. This review synthesizes evidence that mitochondrial epigenetics influences cardiovascular pathogenesis through altered DNA methylation and histone acetylation patterns, which dysregulate oxidative phosphorylation and nucleoid stability. In neurodegenerative diseases, endoplasmic reticulum-mitochondrial contact points, disrupted by aging, impair calcium homeostasis and promote neuronal apoptosis, while oxidative stress exacerbates mtDNA instability through inefficient repair mechanisms. Cancer cells exploit mitochondrial metabolic reprogramming, where shifts in acetyl-CoA and α-ketoglutarate levels modulate epigenetic enzymes, fostering drug resistance. Potential therapeutic targets include pharmacological modulation of Mitochondrial transcription factor A acetylation/phosphorylation to enhance mtDNA transcription and dietary interventions to boost NAD+ levels, thereby improving mitochondrial function. Transgenerational studies reveal matrilineal inheritance of mtDNA methylation patterns and stress-induced epigenetic memory, though technical limitations in detecting mtDNA methylation persist. Clinically, mitochondrial epigenetic biomarkers like mtDNA hydroxymethylation and lncRNA expression (e.g., Mitoregulin) show promise for early diagnosis and treatment monitoring. Despite advances, challenges include standardizing methods for mtDNA methylation analysis and translating preclinical findings into therapies. This perspective review underscores the need for integrative approaches combining single-cell sequencing and CRISPR-based technologies to dissect mitochondrial-nuclear crosstalk, ultimately paving the way for precision medicine strategies targeting mitoepigenetic pathways to mitigate age-related decline.
    Keywords:  aging; epigenetics; methylation; mitochondria; mitochondrial nucleoid; mtDNA
    DOI:  https://doi.org/10.4103/agingadv.agingadv-d-25-00006
  44. Nat Cell Biol. 2025 Sep 19.
      Thousands of nuclear pore complexes (NPCs) cover the nuclear surface of mammalian cells and establish selective transport conduits that biochemically segregate the nucleoplasm and cytoplasm. Although the molecular composition and structure of archetypical NPCs are well understood, distinct NPCs composed of varying nucleoporins exist in different cell types and even within individual cells. Furthermore, the integration of NPCs within mechanosensitive networks impacts their dilation state. However, whether (and how) the dilation or compositional plasticity of NPCs impacts their primary role as selective transport channels remains unclear. Based on our current understanding of NPC plasticity, we propose here that nuclear membrane tension and the resulting dilation of nuclear pores is a determinant of the compositional plasticity of NPCs, thus providing a framework to interpret how nucleoporins may influence cell fate decisions and explain the tissue-specificity of some NPC-related diseases.
    DOI:  https://doi.org/10.1038/s41556-025-01768-w
  45. ACS Chem Biol. 2025 Sep 16.
      Histone methylation depends on one-carbon metabolism, with methyl groups donated by methionine-, serine-, and glucose-derived intermediates. To dissect the metabolic origins of histone methylation, we developed Relative Quantitative Methyl Isotopomer Distribution Mass Spectrometry (RQMID-MS), a high-resolution mass spectrometry-based method that uses diagnostic low-mass fragment ions to quantify methyl group transfer from isotope-labeled precursors. Using this method, we mapped methylation sources to histone lysines in glioblastoma cells under nutrient and oxygen stress. Methionine was the dominant methyl donor under replete condition. Under combined serine and methionine depletion or prolonged methionine depletion alone, glucose emerged as a key compensatory source, particularly in U87 cells with elevated 3-phosphoglycerate dehydrogenase (PHGDH) expression. In contrast, U251 cells favored exogenous serine and glycine, correlating with higher levels of serine hydroxymethyltransferase 2 (SHMT2) expression. Hypoxia initially enhanced glucose-derived methylation but later suppressed it, likely due to impaired vitamin B12-dependent remethylation of homocysteine. RQMID-MS enables precise tracking of methyl donor routing to histones and offers a robust platform for studying metabolic and epigenetic crosstalk in cancer and beyond.
    DOI:  https://doi.org/10.1021/acschembio.5c00528
  46. Cancer Discov. 2025 Sep 19.
      Although p53 plays a central role in tumor suppression, how it is regulated in T cells to exert antitumor effects remains unclear. Here, we show that activation of T cell-intrinsic p53 via carboxyl-terminal domain (CTD) acetylation during immunotherapy activates the IFN-γ pathway, promotes CD8+ T cell infiltration, and elicits CD8+ T cell-dependent antitumor immunity. Using T cell-specific knockin mouse models, we demonstrate that loss of CTD acetylation in T cells abrogates CD8+ T cell-dependent antitumor immunity whereas expression of CTD acetylation-mimicking p53 in T cells enhances this immune response. Moreover, we identify IFNG as a direct target of T cell-intrinsic p53 and uncover a positive feedback loop between p53 and the IFN-γ pathway for enhancing T cell-dependent antitumor immunity. Our study reveals that CTD acetylation-mediated activation of T cell-intrinsic p53 promotes antitumor immunity in response to immunotherapy, highlighting a non-tumor cell-autonomous mechanism of p53 action by regulating adoptive immune responses.
    DOI:  https://doi.org/10.1158/2159-8290.CD-25-0649
  47. Free Radic Biol Med. 2025 Sep 11. pii: S0891-5849(25)00975-X. [Epub ahead of print]
      Oxidative stress is a critical initiating factor in vitiligo, yet the early molecular events linking redox imbalance to melanocyte immune activation remain unclear. Here, we demonstrate that sub-lethal hydrogen peroxide (H2O2, 0.1 mM) exposure in human epidermal melanocytes induces a robust pro-inflammatory response independent of apoptosis or pyroptosis. This response is driven by the selective cytosolic release of mitochondrial DNA (mtDNA), which activates the cyclic GMP-AMP synthase-stimulator of interferon genes (cGAS-STING) pathway. Mechanistically, voltage-dependent anion channel 1 (VDAC1) oligomerization cooperates with mitochondrial permeability transition pore (mPTP) opening to mediate mtDNA release. Both genetic VDAC1 knockdown and pharmacological inhibition blocked mtDNA leakage and downstream cytokine production. In H2O2-induced vitiligo mice, intradermal administration of the VDAC1 oligomerization inhibitor VBIT-4 restored melanin pigmentation, reduced CD8+ T cell infiltration, and alleviated cutaneous inflammation. These findings identify VDAC1-dependent mtDNA release as a key driver of innate immune activation in melanocytes and highlight VDAC1 as a potentially druggable therapeutic target for early intervention in vitiligo.
    Keywords:  VDAC1 oligomerization; cGAS-STING; melanocytes; mitochondrial DNA; sublethal oxidative stress; vitiligo
    DOI:  https://doi.org/10.1016/j.freeradbiomed.2025.09.018
  48. bioRxiv. 2025 Sep 04. pii: 2025.08.31.673338. [Epub ahead of print]
      TFE3 translocation renal cell carcinoma (tRCC), an aggressive kidney cancer driven by TFE3 gene fusions, is frequently misdiagnosed owing to morphologic overlap with other kidney cancer subtypes. Conventional liquid biopsy assays that detect tumor DNA via somatic mutations or copy number alterations are unsuitable for tRCC, since it often lacks recurrent genetic alterations and because fusion breakpoints are highly variable between patients. We reasoned that epigenomic profiling could more effectively detect tRCC, because the driver fusion constitutes an oncogenic transcription factor that alters gene regulation. By defining a TFE3-driven epigenomic signature in tRCC cell lines and detecting it in patient plasma using chromatin immunoprecipitation and sequencing, we distinguished tRCC from clear cell RCC (AUC=0.87) and healthy controls (AUC=0.91) at low tumor fractions (<1%). This work establishes a framework for non-invasive epigenomic detection, diagnosis and monitoring of tRCC, with implications for other mutationally quiet, fusion-driven cancers.
    SIGNIFICANCE: Translocation renal cell carcinoma (tRCC) is an aggressive fusion-driven subtype of kidney cancer that is frequently misdiagnosed due to morphologic overlap with other kidney cancer subtypes. Conventional liquid biopsy assays targeting DNA alterations are suboptimal for use in tRCC due to its paucity of genomic changes. We demonstrate the utility of cell-free chromatin profiling to noninvasively detect and monitor tRCC with high accuracy, a method that could have applicability to other genomically quiet cancers.
    DOI:  https://doi.org/10.1101/2025.08.31.673338
  49. Semin Oncol. 2025 Sep 12. pii: S0093-7754(25)00105-8. [Epub ahead of print]52(6): 152413
      Melanoma is a particularly aggressive type of skin cancer due to its rapid growth and capacity to metastasize. There is substantial metabolic reprogramming in melanoma that is linked to its malignant characteristics, including therapeutic resistance. This review intended to provide a detailed overview of the central metabolic pathways reprogrammed in melanoma, including the Warburg effect and the complex interactions between glycolysis and oxidative phosphorylation, which ultimately influence energy production, biosynthesis, and adaptation to the tumor microenvironment. We also discuss the molecular pathways that regulate these metabolic pathways and the effect these metabolic processes have on crucial elements of melanoma progression, including invasion, metastasis, and survival during nutrient deprivation and hypoxia. Furthermore, we discuss the importance of metabolism beyond glucose, including glutamine metabolism, changes in lipid metabolism, and alterations in one-carbon and nucleotide biosynthesis, as well as mechanisms critical for the proliferation and survival of melanoma cells. An emphasis is placed on the active metabolic crosstalk between melanoma cells and the immune system within the tumor microenvironment, where melanoma cells utilize nutrient competition and the production of immunosuppressive metabolites to alter and block the function of anti-tumor immune cells, thereby facilitating immune evasion and therapy resistance. Lastly, we critically assess developments targeting melanoma metabolism, including pharmacological inhibition of key metabolic enzymes and pathways, as well as metabolic modulation to enhance the efficacy of conventional and immunotherapies. Although promising, this area is complex and subject to contextual effects and metabolic heterogeneity, indicating that we still have a way to go in annotating robust and clinically relevant metabolic targets. We sought to consolidate current knowledge about melanoma metabolism and highlight the challenges, future directions, and complexity of a potential therapeutic vulnerability in the rapidly evolving field of cancer research.
    Keywords:  Bioenergetics; Melanoma; Metabolism; Pathogenesis; Therapy
    DOI:  https://doi.org/10.1016/j.seminoncol.2025.152413
  50. EMBO J. 2025 Sep 16.
      Cellular metabolism plays a pivotal role in regulating the effector functions and fate decisions of immune cells, shaping immune responses in homeostasis and disease. Metabolic pathways also serve as critical signaling hubs governing immune cell behavior. Deregulated metabolic pathways contribute to immune dysfunction, fueling disease progression and creating challenges for therapeutic interventions. The recent development of advanced technologies to delineate immunometabolic regulation has revolutionized our understanding of immune cell biology. These tools, ranging from quantitative single-cell metabolomics to in vivo spatial tissue profiling and DC-based metabolic therapy, have shifted the focus from broad nutrient pathways to a detailed exploration of metabolic reprogramming within disease microenvironments, revealing how metabolic changes drive immune cell activation, differentiation, and effector responses. The integration of immunometabolic insights into clinical practice holds strong potential for advancing precision medicine and developing targeted therapies that restore immune balance in pathological conditions. Here, we summarize emerging cutting-edge technologies related to immunometabolism and critically reflect on their current limitations. Finally, we discuss potential needs for developing novel methods that can uncover the intricate interplay between metabolism and immune cell function.
    Keywords:  Dendritic Cells; Immunometabolism; Metabolic Reprogramming; T Cells; Technological Advances
    DOI:  https://doi.org/10.1038/s44318-025-00569-z
  51. bioRxiv. 2025 Sep 01. pii: 2025.08.28.672849. [Epub ahead of print]
      Renal cell carcinomas comprise multiple molecularly distinct cancers but most are treated empirically with therapies designed for clear cell RCC (ccRCC), the most common subtype, due to incomplete understanding of subtype-specific biology. We analyzed single-cell transcriptomes and chromatin accessibility profiles from translocation renal cell carcinoma (tRCC), an aggressive RCC defined by oncogenic TFE3 gene fusions. Unexpectedly, despite arising from a proximal tubule cell of origin similar to ccRCC, tRCCs display markedly distinct oncogenic programs and an immunosuppressive tumor microenvironment. tRCCs exhibit six conserved tumor meta-programs, including epithelial-mesenchymal transition and proximal tubule identity programs whose balance is regulated by TFE3 fusion activity. The fusion-driven EMT program drives a suppressive TME marked by progenitor-exhausted CD8+ T cells, anti-inflammatory SPP1+ macrophages, and matrix-associated fibroblasts (mCAFs). Our findings highlight unique TFE3 fusion-driven biology in tRCC, explaining its reduced immunotherapy responsiveness relative to ccRCC, and suggesting strategies for targeting fusion-driven oncogenic programs and TME reprogramming.
    DOI:  https://doi.org/10.1101/2025.08.28.672849
  52. bioRxiv. 2025 Sep 04. pii: 2025.08.30.673205. [Epub ahead of print]
      Mutations in isocitrate dehydrogenase (IDHm) define a distinct molecular class of gliomas. IDHm converts α-ketoglutarate (α-KG) to the oncometabolite D-2-hydroxyglutarate (D-2HG), which drives tumorigenesis. The IDHm inhibitor vorasidenib suppresses D-2HG production and extends progression-free survival in some, but not all, IDHm glioma patients. Here, using clinically relevant patient-derived IDHm models and patient tissue, we show that phosphoglycerate dehydrogenase (PHGDH) drives intrinsic resistance to vorasidenib by promiscuously converting α-KG to D-2HG and maintaining D-2HG concentration despite IDHm inhibition. Silencing PHGDH sensitizes resistant models to vorasidenib, while conversely, overexpressing PHGDH induces vorasidenib resistance in sensitive models. Importantly, deuterium metabolic imaging of D-2HG production from diethyl-[3,3'- 2 H]-α-ketoglutarate provides an early readout of response and resistance to vorasidenib that is not available by anatomical imaging in vivo. Collectively, we have identified PHGDH-driven D-2HG production as an intrinsic mechanism of resistance to vorasidenib and diethyl-[3,3'- 2 H]α-ketoglutarate as a non-invasive tracer for interrogating intrinsic resistance in IDHm gliomas.
    STATEMENT OF SIGNIFICANCE: Vorasidenib, which suppresses D-2HG production, is the first precision therapy to be approved for IDHm glioma patients. We show that PHGDH-driven restoration of D-2HG production mediates intrinsic resistance to vorasidenib in IDHm gliomas. Importantly, deuterium metabolic imaging of D-2HG production from diethyl-[3,3'- 2 H]-α-ketoglutarate enables non-invasive assessment of resistance in IDHm gliomas.
    DOI:  https://doi.org/10.1101/2025.08.30.673205
  53. Nat Chem Biol. 2025 Sep 15.
      KRAS is one of the most frequently mutated oncogenes in cancer. Targeting mutant KRAS directly has been challenging because of minor structural changes caused by mutations. Despite recent success in targeting KRAS-G12C, targeted therapy for another hotspot mutant, KRAS-G12V, has not been described. We used CRISPR-Cas9 genome-wide knockout screens to identify genes that specifically modulate mutant KRAS harboring the G12V substitution. Our top hit, a fatty acid elongase (ELOVL6), showed remarkable selectivity in diminishing KRAS-G12V protein expression and aberrant oncogenic signaling associated with mutant KRAS. Our studies reveal that ELOVL6 can be targeted to control the production of phospholipids exploited by KRAS mutants for function-targeted and trigger-targeted degradation of the protein. Our results demonstrate the basis for a first-in-class small-molecule inhibitor to selectively clear KRAS-G12V from cancer cells.
    DOI:  https://doi.org/10.1038/s41589-025-01998-x
  54. Cell Syst. 2025 Sep 18. pii: S2405-4712(25)00226-1. [Epub ahead of print] 101393
      Our understanding of metabolic thermodynamics is limited by the lack of genome-scale data on the standard Gibbs free energy change (ΔrG°) of metabolic reactions. Here, we present dGbyG, a graph neural network (GNN)-based model for predicting ΔrG° with superior accuracy, versatility, robustness, and generalization ability. Integration of dGbyG predictions into metabolic networks facilitated model curation, improved flux prediction accuracy, and identified thermodynamic driver reactions (TDRs) with substantial negative values of the reaction Gibbs free energy change (ΔrG). TDRs showed distinctive network topological features and heterogeneous enzyme expression, implying coupling between reaction thermodynamics and network topology for efficient metabolic regulation. We also discovered a universal pattern of thermodynamics in linear metabolic pathways, explained by a multi-objective optimization model balancing the needs to maximize pathway flux and minimize enzyme and metabolite loads. Our work expands accessible thermodynamic data and elucidates optimality principles in metabolism at the genome scale. A record of this paper's transparent peer review process is included in the supplemental information.
    Keywords:  Gibbs free energy; Pareto optimality; genome-scale metabolic networks; graph neural networks; machine learning; thermodynamics
    DOI:  https://doi.org/10.1016/j.cels.2025.101393
  55. bioRxiv. 2025 Sep 08. pii: 2025.09.03.674106. [Epub ahead of print]
      MYC amplification contributes to poor survival and outcome in pancreatic ductal adenocarcinoma (PDAC). Here we show that in PDAC cell lines with amplified MYC, MondoA is required for viability, facilitating proliferation while suppressing apoptosis in vitro and in vivo . Transcriptional and genomic profiling demonstrates that loss of MondoA leads to altered expression of direct MondoA targets as well as MYC target genes and is accompanied by shifts in genomic occupancy of MYC, MNT, and the MondoA paralog ChREBP. This altered genomic binding by MYC network members is associated with transcriptional perturbation of multiple metabolic and stress pathways, as well as global changes in N6-methyladenosine modification (m 6 A) of mRNA. MondoA inhibition disrupts coordination between MYC network members and the Integrated Stress Response (ISR), resulting in decreased translation of ATF4 mRNA, discordant gene regulation of shared targets of MYC and ATF4 and, ultimately, apoptosis. Re-establishing ATF4 protein expression rescues the diminished viability due to loss of MondoA expression or activity, providing direct evidence of a link between deregulated MYC and the transcriptional machinery of the ISR. Lastly, we find that small-molecule inhibition of MondoA is lethal in a subset of PDAC cell lines, including patient-derived organoids, suggesting that the ability to target MYC via chemical inhibition of MondoA transcriptional activity may have broad efficacy.
    Significance Statement: This report investigates mechanisms underlying the dependence of MYC-amplified pancreatic cancer cells on the MYC network member MondoA which, as a heterodimer with MLX, is a nutrient-sensing transcription factor. We show this dependency is linked to genomic crosstalk between MYC, components of the proximal MYC network, and the master regulator of the integrated stress response, ATF4. Moreover, we find that small molecule inhibitors of MondoA-MLX transcriptional activity abrogate survival of MYC-amplified PDAC lines and patient derived organoids. The significance of this work relates to its focus on a unique vulnerability intrinsic to MYC, an oncogenic driver associated with a wide range of cancers, which is considered to be "undruggable".
    DOI:  https://doi.org/10.1101/2025.09.03.674106
  56. EMBO Rep. 2025 Sep 16.
      mTOR (mechanistic target of rapamycin) kinase is a pivotal regulator of cellular growth and metabolism, integrating signals from nutrients and growth factors. It functions through the assembly of two distinct complexes, mTORC1 and mTORC2, which differ in their substrate specificity and regulation. While the regulation of mTORC1 is well-characterized, less is known about the modulators of mTORC2 signaling. In this study, we identify tyrosine phosphatase PTPN22 as an mTORC2-associated protein. We provide evidence that PTPN22 is essential for the activation of the mTORC2/AKT axis, independent of cell lineage. Loss of PTPN22 results in impaired AKT phosphorylation in response to both basal and growth factor signals. Mechanistically, PTPN22 functions as a scaffolding protein that promotes the mSIN-RICTOR interaction, thereby maintaining mTORC2 complex integrity. Notably, this adaptor function of PTPN22 is independent of its tyrosine phosphatase activity. Functionally, we demonstrate that PTPN22 is required for cell growth and survival in both cellular models and nude mouse xenografts. Together, these findings reveal a non-catalytic role for phosphatase PTPN22 in mTORC2 assembly and function.
    Keywords:  AKT; PTPN22; Rictor; mSIN; mTOR
    DOI:  https://doi.org/10.1038/s44319-025-00576-5