bims-celmim 2025-11-02 papers

bims-celmim

Biomed News

on Cellular and mitochondrial metabolism

Issue of 2025–11–02
25 papers selected by
Marc Segarra Mondejar, AINA

HIF2α inhibits glutaminase clustering in mitochondria to sustain growth of clear cell Renal Cell Carcinoma.
Accumulation of succinate suppresses de novo purine synthesis through succinylation-mediated control of the mitochondrial folate cycle.
Autophagy-senescence interplay in kidney disease: mechanistic insights and therapeutic potential.
Dihydroorotate dehydrogenase inhibition activates STING pathway and pyroptosis to enhance NK cell-dependent tumor immunotherapy.
Two-point calibration protocol for the Förster Resonance Energy Transfer indicator Pyronic in neurons.
Ultrastructural evaluation of lithium-induced autophagic and mitochondrial stress in 3D endometrial and neuroblastoma spheroids.
African swine fever virus hijacks host pyrimidine metabolism to promote viral replication.
Ammonia metabolism and ammonia-induced cell death: role in cancer therapy.
Leucine inhibits degradation of outer mitochondrial membrane proteins to adapt mitochondrial respiration.
Screening of targets related to amino acid metabolism in glioma to identify the tumor-promoting effects of its core gene ASL.
Induction of a metabolic switch from glucose to ketone metabolism programs ketogenic diet-induced therapeutic vulnerability in lung cancer.
Amino acid dysregulation in cerebrospinal fluid of stroke patients serving as diagnostic biomarkers in post-neurosurgical bacterial meningitis.
L-Glutamate enables the EGFR-MEK-ERK-mTFB2 axis to enhance mitochondrial biogenesis in intestinal stem cells.
Unveiling Metabolic Signatures as Potential Biomarkers in Common Cancers: Insights from Lung, Breast, Colorectal, Liver, and Gastric Tumours.
The neuron-astrocyte metabolic unit as a cornerstone of brain energy metabolism in health and disease.
Structural basis of apoptosis induction by the mitochondrial voltage-dependent anion channel.
p53-mediated regulation of electron transport chain and nucleotide synthesis during Newcastle disease virus infection.
Close-up of vesicular ER exit sites by volume electron imaging using FIB-SEM.
Metabolic rewiring prevents neurodegeneration caused by chronic mitochondrial dysfunction.
An eNOS-like nanomaterial for specific reversal of cerebral ischemia-reperfusion injury.
Developing Endogenous Autophagy Reporters in Caenorhabditis elegans to Monitor Basal and Starvation-Induced Autophagy.
Mitochondrial organization in the developing proximal tubule is controlled by LRRK2.
Light-evoked activity and BDNF regulate mitochondrial dynamics and mitochondrial localized translation in CNS axons.
Mechanism-based peroxiredoxin 3 inhibitors exploit a covalent warhead for cancer therapy.
Cell wash-free fluorescent probes based on phenothiazine and phenoxazine with high photostability and large stokes shifts for targeted imaging of subcellular organelles.

JCI Insight. 2025 Oct 30. pii: e182711. [Epub ahead of print]

HIF2α inhibits glutaminase clustering in mitochondria to sustain growth of clear cell Renal Cell Carcinoma.

Wencao Zhao, Sara M Demczyszyn, Nathan J Coffey, Yanqing Jiang, Boyoung Kim, Schuyler Bowers, Caitlyn E Bowman, Michael C Noji, Cholsoon Jang, M Celeste Simon, Zoltan Arany, Boa Kim.

  Clear cell renal cell carcinomas (ccRCC) are largely driven by HIF2α and are avid consumers of glutamine. However, inhibitors of glutaminase1 (GLS1), the first step in glutaminolysis, have not shown benefit in phase III trials, and HIF2α inhibition, recently FDA-approved for treatment of ccRCC, shows significant but incomplete benefits. This highlights the need to better understand the interplay between glutamine metabolism and HIF2α in ccRCC. Here, we report that glutamine deprivation rapidly redistributes GLS1 into isolated clusters within mitochondria in diverse cell types, but not in ccRCC. GLS1 clustering occurs rapidly within 1 to 3 hours, is reversible, is specifically triggered by reduced intracellular glutamate, and is dependent on mitochondrial fission. Clustered GLS1 markedly enhances glutaminase activity and promotes cell death under glutamine-deprived conditions. HIF2α prevents GLS1 clustering, independently of its transcriptional activity, thereby maintaining low GLS activity and protecting ccRCC cells from glutamine deprivation-induced cell death. Forced clustering of GLS1, using constitutively clustering mutants, restores high GLS activity, promotes apoptosis, and suppresses ccRCC tumor growth in vivo. These findings reveal multiple insights into cellular glutamine handling, including a previously unrecognized process by which HIF2α promotes ccRCC: by suppressing GLS1 clustering and maintaining low GLS activity. This mechanism provides a potential explanation for the lack of clinical efficacy of GLS inhibitors in ccRCC and suggests a therapeutic avenue to combine HIF2α inhibition with strategies that restore GLS1 clustering.

Keywords:  Cancer; Cell biology; Metabolism; Mitochondria

DOI:  https://doi.org/10.1172/jci.insight.182711
Mol Cell. 2025 Oct 28. pii: S1097-2765(25)00819-6. [Epub ahead of print]

Accumulation of succinate suppresses de novo purine synthesis through succinylation-mediated control of the mitochondrial folate cycle.

Mushtaq A Nengroo, Austin T Klein, Heather S Carr, Olivia Vidal-Cruchez, Umakant Sahu, Daniel J McGrail, Nidhi Sahni, Niklas B Thompson, Peter A Faull, Peng Gao, John M Asara, Hardik Shah, Marc L Mendillo, Issam Ben-Sahra.

  The de novo purine synthesis pathway is fundamental for nucleotide production, yet the role of mitochondrial metabolism in modulating this process remains underexplored. Here, we identify that succinate dehydrogenase (SDH) is essential for maintaining de novo purine synthesis. Genetic or pharmacological inhibition of SDH suppresses purine synthesis, contributing to a decrease in cell proliferation. Mechanistically, SDH inhibition elevates succinate, which in turn promotes the succinylation of serine hydroxymethyltransferase 2 (SHMT2) within the mitochondrial tetrahydrofolate (THF) cycle. This post-translational modification lowers formate output, depriving cells of one-carbon units needed for purine assembly. In turn, cancer cells activate the purine salvage pathway, a metabolic compensatory adaptation that represents a therapeutic vulnerability. Notably, co-inhibition of SDH and purine salvage induces pronounced antiproliferative and antitumoral effects in preclinical models. These findings reveal a signaling role for mitochondrial succinate in tuning nucleotide metabolism and highlight a dual-targeted strategy to exploit metabolic dependencies in cancer.

Keywords:  TCA cycle; cancer; formate; mitochondrial metabolism; nucleotide metabolism; succinate

DOI:  https://doi.org/10.1016/j.molcel.2025.10.002
Mol Biol Rep. 2025 Oct 29. 53(1): 22

Autophagy-senescence interplay in kidney disease: mechanistic insights and therapeutic potential.

Jiajun Sang, Kexin Zhang, Qiming Fan, Chengxia Kan, Ruiyan Pan, Xiaodong Sun, Zhentao Guo.

  Autophagy and cellular senescence are intimately linked processes that play pivotal roles in renal homeostasis, aging, and disease progression. Autophagy preserves intracellular integrity by degrading damaged organelles, misfolded proteins, and metabolic waste through lysosomal pathways, thereby maintaining energy balance and delaying senescence. However, with advancing age or persistent stress, autophagic activity declines, leading to the accumulation of senescent cells, mitochondrial dysfunction, and chronic inflammation. In the kidney, a metabolically demanding organ, this imbalance contributes to the pathogenesis of chronic kidney disease (CKD) and acute kidney injury (AKI). Senescent cells secrete a senescence-associated secretory phenotype, which amplifies inflammation, fibrosis, and tissue remodeling. The bidirectional interplay between impaired autophagy and cellular senescence exacerbates renal tubular atrophy, glomerulosclerosis, and interstitial fibrosis, thereby promoting CKD progression and maladaptive repair following AKI. Emerging therapeutic strategies, including autophagy activators, senolytics, antioxidants, and stem cell based interventions, have shown promise in restoring cellular homeostasis and delaying renal aging. Nonetheless, challenges remain in achieving cell type specific modulation while avoiding the deleterious effects of excessive activation. This review highlights recent advances in understanding the mechanistic interplay between autophagy and senescence in renal physiology and disease, outlines their contributions to CKD and AKI, and explores evolving therapeutic strategies aimed at restoring autophagic flux and eliminating senescent cells. Targeting the autophagy senescence axis represents a compelling avenue for precision therapy in kidney disease and may redefine future approaches in nephrology.

Keywords:  AKI; Autophagy; CKD; Cellular senescence

DOI:  https://doi.org/10.1007/s11033-025-11180-0
Mol Biomed. 2025 Oct 27. 6(1): 87

Dihydroorotate dehydrogenase inhibition activates STING pathway and pyroptosis to enhance NK cell-dependent tumor immunotherapy.

Yongrui Hai, Ruizhuo Lin, Weike Liao, Shuo Fu, Renming Fan, Guiquan Ding, Junyan Zhuang, Bingjie Zhang, Yi Liu, Junke Song, Gaofei Wei.

  Cancer cells rely heavily on de novo pyrimidine synthesis. Inhibiting pyrimidine metabolism directly suppresses tumor growth and fosters immune activation within the tumor microenvironment. Dihydroorotate dehydrogenase (DHODH) is a key enzyme in the de novo pyrimidine synthesis pathway. Inhibiting DHODH can reverse immune suppression and trigger a mild innate immune response. However, the impact of DHODH inhibition on natural killer (NK) cells remains to be explored. In this study, we found that DHODH inhibition promoted NK cell infiltration into tumors efficiently. Mechanistically, DHODH suppression induced mitochondrial oxidative stress, leading to mitochondrial DNA (mtDNA) release into the cytoplasm through voltage-dependent anion channel (VDAC) oligomerization and caspase-3 activation. This subsequently activated the stimulator of interferon gene (STING) pathway, triggered ferroptosis, and induced gasdermin E (GSDME) mediated pyroptosis in cancer cells. These changes collectively facilitated NK cell recruitment. Furthermore, infiltrated NK cells enhanced GSDME-dependent pyroptosis in tumor cells through granzyme release, establishing a positive feedback loop that amplified anti-tumor immunity. Additionally, we developed EA6, a novel DHODH inhibitor that is more effective at promoting NK cell infiltration. In summary, this study reveals that targeting pyrimidine metabolism activates a novel mechanism involving pyroptosis-ferroptosis crosstalk and STING pathway activation to enhance NK cell-mediated immunity. These finding opens new avenues for enhancing the efficacy of targeted nucleotide metabolism in cancer therapy.

Keywords:  CGAS-STING pathway; DHODH; NK cells; Pyrimidine metabolism; Pyroptosis

DOI:  https://doi.org/10.1186/s43556-025-00339-7
Neurophotonics. 2025 Jun;12(Suppl 2): S22807

Two-point calibration protocol for the Förster Resonance Energy Transfer indicator Pyronic in neurons.

Felipe Baeza-Lehnert, Yasna Contreras-Baeza, Camila Aburto, Alejandro San Martín.

   Significance: Pyruvate is a nodal intermediate in cellular metabolism, positioned at the crossroads between glycolysis and fermentative metabolism. It is exchanged between the intracellular and extracellular compartments through the proton-coupled monocarboxylate transporters and between the cytosol and mitochondria through the mitochondrial pyruvate carrier, where it serves as a primary carbon source for respiration.
Aim: Our goal is to present a detailed protocol for quantifying cytosolic pyruvate concentration in neurons at single-cell resolution using a minimally invasive, two-point calibration approach with the Förster Resonance Energy Transfer (FRET)-based genetically encoded fluorescent indicator Pyronic.
Approach: This protocol is based on a noninvasive pharmacological two-point calibration approach, where Pyronic's dynamic range ( ΔRMAX ) is established by withdrawing all extracellular substrates to deplete intracellular pyruvate ( RMIN ) and by inducing Pyronic saturation ( RMAX ) through the combination of inhibition of pyruvate export, stimulation of its production, and blockade of its mitochondrial consumption. The protocol also incorporates the previously published KD values for Pyronic obtained from in vitro experiments. This procedure does not require the use of detergents to permeabilize the cells.
Results: Implementing this protocol enables the measurement of absolute cytosolic pyruvate concentrations. This quantitative parameter facilitates comparisons of pyruvate metabolism across different cells, samples, and experimental batches, thereby enabling the comparison between a plethora of experimental conditions.
Conclusion: The FRET-based fluorescent indicator Pyronic can be reliably calibrated using a minimally invasive, pharmacology-based two-point calibration protocol in neurons, thus providing a robust and quantitative method to study pyruvate metabolism under various physiological and pathological scenarios.

Keywords:  Pyronic; calibration; fluorescence; metabolism; neurons; pyruvate; quantification

DOI:  https://doi.org/10.1117/1.NPh.12.S2.S22807
Sci Rep. 2025 Oct 28. 15(1): 37652

Ultrastructural evaluation of lithium-induced autophagic and mitochondrial stress in 3D endometrial and neuroblastoma spheroids.

Berna Yıldırım, Agnes Ansa Archibong-Omon, Ayhan Bilir.

  Lithium chloride (LiCl), a widely used mood stabilizer, has been reported to modulate selective autophagy pathways, including mitophagy. However, its ultrastructural effects in three-dimensional (3D) tumor models remain incompletely characterized. In this study, we examined the subcellular alterations induced by LiCl in 3D spheroid cultures derived from Ishikawa endometrial cancer and SH-SY5Y neuroblastoma cells. Spheroids were treated with 1, 10, or 50 mM LiCl and analyzed using transmission electron microscopy (TEM). The analysis revealed double-membrane-bound vesicles surrounding degenerating mitochondria, along with cytoplasmic vacuolization and membrane remodeling. These morphological features are suggestive of mitophagic activity, accompanied by stress-related ultrastructural remodeling. Although molecular validation (e.g., LC3B or PINK1/Parkin Western blotting) was not performed, the observed ultrastructural profiles are consistent with organelle-selective autophagy. These findings underscore the dose-dependent cellular responses to LiCl and support the value of 3D cancer spheroids as models to explore non-canonical autophagy-related stress pathways. Future studies incorporating molecular markers such as LC3B, PINK1, Parkin, and Lamin B1 will be essential to confirm these observations.

Keywords:  3D cancer spheroids; Endometrial cancer; Lithium chloride; Mitophagy; Transmission electron microscopy

DOI:  https://doi.org/10.1038/s41598-025-21569-3
J Virol. 2025 Oct 31. e0098525

African swine fever virus hijacks host pyrimidine metabolism to promote viral replication.

Zebu Song, Yilin Chen, Hui Guo, Guihong Zhang, Lang Gong, Zezhong Zheng.

  African swine fever (ASF) is a highly contagious disease of pigs caused by the African swine fever virus (ASFV), posing a significant threat to global swine production. As an obligate intracellular parasite, ASFV relies on host metabolic networks to fulfill its replication requirements. However, the precise mechanisms by which it manipulates nucleotide metabolism remain unclear. In this study, untargeted metabolomic analysis of ASFV-infected porcine alveolar macrophages revealed significant perturbations in purine and pyrimidine metabolism, glycolysis, the pentose phosphate pathway (PPP), and the glutamate and aspartate metabolic pathways. Functional validation demonstrated that ASFV depends on de novo pyrimidine biosynthesis for viral genome replication. Notably, ASFV employs a dual strategy to sustain the supply of nucleotide precursors: (i) it hijacks the PPP to generate ribose-5-phosphate and NADPH for redox balance, and (ii) it enhances glutamine uptake and catabolism to provide the nitrogen and carbon needed for nucleotide biosynthesis and tricarboxylic acid cycle replenishment. Furthermore, although aspartate is essential for pyrimidine synthesis, ASFV circumvents dependence on extracellular aspartate by activating a cytosolic GOT1-mediated synthesis pathway. Collectively, these findings elucidate how ASFV reprograms host nucleotide metabolism to support its replication, offering new insights into virus-host metabolic interactions and identifying potential targets for antiviral therapy.IMPORTANCEAfrican swine fever (ASF) is a devastating disease that causes substantial economic losses in the global pig industry. This study demonstrates that the African swine fever virus (ASFV) reprograms host cell metabolism to produce the essential building blocks required for its replication. Specifically, ASFV manipulates host nucleotide biosynthetic pathways to secure both the substrates for DNA synthesis and the reducing power necessary to mitigate oxidative stress. Elucidating these metabolic interactions not only deepens understanding of ASFV pathogenesis but also highlights promising metabolic targets for antiviral therapy. By elucidating how ASFV hijacks nucleotide biosynthesis within infected cells, our findings pave the way for innovative strategies to combat ASF.

Keywords:  African swine fever virus; aspartate; glutamine; metabolic hijacking; pyrimidine metabolism

DOI:  https://doi.org/10.1128/jvi.00985-25
Cell Commun Signal. 2025 Oct 30. 23(1): 468

Ammonia metabolism and ammonia-induced cell death: role in cancer therapy.

Yan Xu, Jiafeng Wang, Aixiang Wu, Mengchuan Wang.

  Ammonia has long been regarded as the end-toxic product of hepatic metabolism. Under normal physiological conditions, ammonia is metabolized through the urea cycle; however, its metabolic imbalance is closely related to various diseases, including hepatic encephalopathy, liver fibrosis, and cancer. Ammonia-induced cell death, specifically the selective death of immune cells, has emerged in recent years as a new form of cell death in the field of tumor biology, offering a new perspective on the regulation of tumor cell fate. This review creatively focuses on the role of ammonia in tumorigenesis, development, and treatment resistance. We systematically reviewed the sources and dynamic balance of ammonia in the tumor microenvironment and found that it plays a key role in tumor metabolic reprogramming by regulating glutamine metabolism, mitochondrial function, and lysosomal stability in tumor cells. Ammonia can also induce the selective death of immune cells, reshape the immune cell map in the tumor microenvironment, and regulate the anti-tumor immune response. Mechanistically, we analyzed the multi-level network of ammonia metabolism regulation, including the role of glutamine synthetase, the mTOR signaling pathway, and epigenetic modification in ammonia death. In addition, this review emphasizes the importance of ammonia as a potential target for cancer therapy and proposes multimodal strategies combining metabolic regulation and immunotherapy to achieve precision in cancer treatment. Finally, the comprehensive map of ammonia in the tumor ecosystem was constructed, highlighting its potential clinical value as a new anti-cancer target.

Keywords:  Ammonia; Apoptosis; Autophagy; Immunotherapy; Metabolic reprogramming; Tumor microenvironment

DOI:  https://doi.org/10.1186/s12964-025-02504-5
Nat Cell Biol. 2025 Oct 31.

Leucine inhibits degradation of outer mitochondrial membrane proteins to adapt mitochondrial respiration.

Qiaochu Li, Konstantin Weiss, Fuateima Niwa, Jan Riemer, Thorsten Hoppe.

The mitochondrial proteome is remodelled to meet metabolic demands, but how metabolic cues regulate mitochondrial protein turnover remains unclear. Here we identify a conserved, nutrient-responsive mechanism in which the amino acid leucine suppresses ubiquitin-dependent degradation of outer mitochondrial membrane (OMM) proteins, stabilizing key components of the protein import machinery and expanding the mitochondrial proteome to enhance metabolic respiration. Leucine inhibits the amino acid sensor GCN2, which selectively reduces the E3 ubiquitin ligase cofactor SEL1L at mitochondria. Depletion of SEL1L phenocopies the effect of leucine, elevating OMM protein abundance and mitochondrial respiration. Disease-associated defects in leucine catabolism and OMM protein turnover impair fertility in Caenorhabditis elegans and render human lung cancer cells resistant to inhibition of mitochondrial protein import. These findings define a leucine-GCN2-SEL1L axis that links nutrient sensing to mitochondrial proteostasis, with implications for metabolic disorders and cancer.

DOI: https://doi.org/10.1038/s41556-025-01799-3
Sci Rep. 2025 Oct 31. 15(1): 38161

Screening of targets related to amino acid metabolism in glioma to identify the tumor-promoting effects of its core gene ASL.

Shisong Wang, Jun Lu, Jingyou Li, Zihao Yan, Zhongxue Yu, Lian Chen, Chen Zhu, Jingyu Zou.

  Gliomas, notably high-grade variants, dominate the spectrum of central nervous system (CNS) malignancies, characterized by aggressive behavior and diffuse invasion. Despite advances in tumor immunology, patient outcomes are stagnant. Amino acid metabolism is pivotal in glioma progression, driving the quest for metabolic targets. Bioinformatics allows deep dives into large-scale patient data from TCGA, CGGA, and GEO. Comparative studies on glioma amino acid metabolism have identified genes associated with tumor characteristics and patient survival. This yields an amino acid metabolism-based risk score model, which elucidates key biological processes and signaling pathways. Our holistic strategy clarifies amino acid metabolism's role in glioma onset, paves the way for targeted therapies. Precise analysis and strategic targeting of metabolic pathways hold great promise for improving glioma treatment, offering hope to patients battling this relentless CNS malignancy.

Keywords:  ASL; Amino acid metabolism; Glioma; NF-κB

DOI:  https://doi.org/10.1038/s41598-025-22105-z
Cell Metab. 2025 Oct 24. pii: S1550-4131(25)00435-8. [Epub ahead of print]

Induction of a metabolic switch from glucose to ketone metabolism programs ketogenic diet-induced therapeutic vulnerability in lung cancer.

Zhengwei Wu, Zhenxun Wang, Seow Qi Ng, Jessica Alice Lidster, Paul Schwerd-Kleine, Zi Jin Cheryl Phua, Kai Lay Esther Peh, Yin Ying Ho, Ju Yuan, S Shathishwaran, Xun Hui Yeo, Ying Zhang, Yui Hei Jasper Chiu, Li Yieng Eunice Lau, Tony Kiat Hon Lim, Angela Takano, Eng Huat Tan, Anders Jacobsen Skanderup, Vinay Tergaonkar, Weiping Han, Ying Swan Ho, Daniel Shao Weng Tan, Wai Leong Tam.

  Tumor-initiating cells (TICs) preferentially reside in poorly vascularized, nutrient-stressed tumor regions, yet how they adapt to glucose limitation is unclear. We show that lung TICs, unlike bulk tumor cells, can switch from glucose to ketone utilization under glucose deprivation. Ex vivo ketone supplementation or a prolonged ketogenic diet supports TIC growth and tumor-initiating capacity. Integrated metabolomics, genomics, and flux analyses reveal that ketones fuel ketolysis, fatty acid synthesis, and de novo lipogenesis. Paradoxically, ketogenic diet intervention creates metabolic vulnerabilities in TICs, sensitizing them toward inhibition of the ketone transporter monocarboxylate transporter 1 (MCT1), regulated by its chaperone protein CD147, as well as toward pharmacological blockade of fatty acid synthase (FASN). Loss of CD147 ablates TICs under glucose limitation conditions in vitro and in vivo. These findings uncover a nutrient-responsive metabolic switch in lung TICs and provide mechanistic insight into how dietary manipulation can influence cancer progression and enhance the efficacy of targeted therapies.

Keywords:  CD147; MCT1; glucose stress; ketogenic diet; ketone metabolism; lung cancer; metabolic reprogramming; monocarboxylate transporter; tumor-initiating cells

DOI:  https://doi.org/10.1016/j.cmet.2025.10.001
Sci Rep. 2025 Oct 27. 15(1): 37461

Amino acid dysregulation in cerebrospinal fluid of stroke patients serving as diagnostic biomarkers in post-neurosurgical bacterial meningitis.

Wei Chen, Yuanyuan Chen, Bohang Liu, Lu Ding, Chaojie Wang, Hongwei Cheng, Lei Ye.

  Post-neurosurgical bacterial meningitis (PNBM) is a severe complication following neurosurgical operations. However, clinical diagnosis of PNBM is difficult because of the complicated pathological conditions. This study aims to investigate alterations in amino acid metabolism in hemorrhagic stroke patients with PNBM through targeted metabolomics analysis. Cerebrospinal fluid (CSF) samples were collected from 66 hemorrhagic stroke patients who underwent neurosurgical operation in our department. Baseline data were retrospectively analyzed for two patient groups: the post-neurosurgical bacterial meningitis group (PNBM, n = 40) and the non-post-neurosurgical bacterial meningitis (non-infected control group, n = 26), classified based on established diagnostic criteria for intracranial infection. A targeted analysis of 36 amino acids and their derivatives in CSF was performed using liquid chromatography-mass spectrometry (LC-MS). Candidate biomarkers were identified through Student's t-test, fold change (FC) analysis, Variable Importance in Projection (VIP), and logistic Least Absolute Shrinkage and Selection Operator (LASSO) regression. The diagnostic performance was evaluated using Receiver Operating Characteristic (ROC) curve analysis. Twenty-one amino acids and their derivatives were found to be significantly downregulated in the PNBM group. Logistic LASSO regression identified Glycine (porginal=2.24 × 10-20, fold change = 0.34, AUC = 0.91), L-Threonine (porginal=5.05 × 10-28, fold change = 0.39, AUC = 0.92), and L-Homoserine (porginal=2.18 × 10-17, fold change = 0.28, AUC = 0.92) as potential biomarkers for diagnosing PNBM in the context of hemorrhagic stroke. Metabolic pathway analysis, corrected for false discovery rate, revealed three CSF-based amino acid metabolic pathways potentially associated with PNBM. In conclusion, these altered amino acids offer new insights into the pathophysiology of PNBM and providing helpful information on potential therapeutic targets in PNBM in the context of hemorrhagic stroke.

Keywords:  Amino acids; Bacterial meningitis; Hemorrhagic stroke; Metabolomics; Operation

DOI:  https://doi.org/10.1038/s41598-025-21286-x
Stem Cell Res Ther. 2025 Oct 31. 16(1): 599

L-Glutamate enables the EGFR-MEK-ERK-mTFB2 axis to enhance mitochondrial biogenesis in intestinal stem cells.

Cai-Xia Dou, Hao-Zhan Qu, Ying-Chao Qin, Xiao-Fan Wang, Jia-Yi Zhou, Xiu-Qi Wang, Hui-Chao Yan.

BACKGROUND: Intestinal stem cells (ISCs) sustain epithelial homeostasis through rapid mitochondrial metabolism, however, how they sense nutrient signals to regulate mitochondrial function remains unclear.
METHODS: We examined the role of L-glutamate (Glu) in regulating cell mitochondrial biosynthesis using in vivo piglets, ex vivo porcine intestinal organoids (IOs), and in vitro IPEC-J2 cells.
RESULTS: Glu enhanced jejunal development in weaned piglets. Isobaric tags for relative and absolute quantitation (iTRAQ) analysis revealed the significant enrichment of mitochondrial functions and activation of EGFR-MEK-ERK-mTFB2 signaling pathway in the jejunum. In vitro, 5 mM Glu promotes mitochondrial biosynthesis and potentiates the EGFR-MEK-ERK-mTFB2 axis. Whereas inhibition of EGFR with Osimertinib and silencing EGFR abolished these effects in IOs and IPEC-J2 cells. Colocalization and biochemical studies demonstrated interaction between Glu and EGFR in IOs.
CONCLUSIONS: Glu promotes mitochondrial biogenesis and ISC expansion by activating the EGFR-MEK-ERK-mTFB2 axis, highlighting a nutrient-sensing mechanism that couples energy availability to ISC function.

DOI: https://doi.org/10.1186/s13287-025-04718-3
Biomolecules. 2025 Sep 28. pii: 1376. [Epub ahead of print]15(10):

Unveiling Metabolic Signatures as Potential Biomarkers in Common Cancers: Insights from Lung, Breast, Colorectal, Liver, and Gastric Tumours.

Kha Wai Hon, Rakesh Naidu.

  Reprogramming is a hallmark of cancer, enabling tumour cells to sustain rapid proliferation, resist cell death, and adapt to hostile microenvironments. This review explores the expression profiles of key metabolic enzymes and transporters involved in glucose, amino acid, and lipid metabolism across the five most deadly cancers worldwide: lung, breast, colorectal, liver, and gastric cancers. Through a comparative analysis, we identify consistent upregulation of glycolytic enzymes such as LDHA, PKM2, and HK2, as well as nutrient transporters like GLUT1, ASCT2, and LAT1, which contribute to cancer progression, metastasis, and therapy resistance. The role of enzymes involved in glutaminolysis (e.g., GLS1, GDH), one-carbon metabolism (e.g., SHMT2, PHGDH), and fatty acid synthesis (e.g., FASN, ACLY) is also examined, with emphasis on their emerging relevance as diagnostic, prognostic, and predictive biomarkers. While several metabolic proteins show strong potential for clinical translation, only a few, such as tumour M2-pyruvate kinase (TuM2-PK) and serum LDH measurement, have progressed into clinical use or trials. This review addresses some of the challenges in biomarker development. Ultimately, our findings underscore the importance of metabolic proteins not only as functional drivers of malignancy but also as promising candidates for biomarker discovery. Advancing their clinical implementation could significantly enhance early detection, treatment stratification, and personalized oncology.

Keywords:  biomarker; breast cancer; colorectal cancer; gastric cancer; liver cancer; lung cancer; metabolic proteins

DOI:  https://doi.org/10.3390/biom15101376
Nat Metab. 2025 Oct 30.

The neuron-astrocyte metabolic unit as a cornerstone of brain energy metabolism in health and disease.

Juan P Bolaños, Pierre J Magistretti.

Over the past years, substantial advances have deepened our understanding of the cellular and molecular drivers of brain energy metabolism. Enabled by transformative technologies offering cellular-level resolution, these insights have revealed a highly regulated and dynamic metabolic interplay among brain cell types, particularly between neurons and astrocytes. In this Review, we shed light on the intricate ways in which neurons and astrocytes operate as a metabolically coupled unit, optimized to sustain the energetic demands of neurotransmission while ensuring neuroprotection. We highlight intercellular cooperation as a key determinant of brain function and provide examples of how disruption of the neuron-astrocyte metabolic unit contributes to numerous diseases of the nervous system, underscoring the critical importance of continued fundamental research to dissect the regulatory principles and vulnerabilities of this intercellular metabolic axis and identify potential therapeutic targets.

DOI: https://doi.org/10.1038/s42255-025-01404-9
Nat Commun. 2025 Oct 27. 16(1): 9481

Structural basis of apoptosis induction by the mitochondrial voltage-dependent anion channel.

Melina Daniilidis, Umut Günsel, Georgios Broutzakis, Kira D Leitl, Robert Janowski, Kai Fredriksson, Dierk Niessing, Christos Gatsogiannis, Franz Hagn.

The voltage-dependent anion channel (VDAC) is the main gateway for metabolites across the mitochondrial outer membrane. VDAC oligomers are connected to apoptosis induced by various stimuli. However, the mechanistic and structural basis of apoptosis induction by VDAC remains poorly understood. Here, using cryo-EM and NMR we show that VDAC1 oligomerization or confinement in small lipid nanodiscs triggers the exposure of its N-terminal α-helix (VDAC1-N) which becomes available for partner protein binding. NMR and X-ray crystallography data show that VDAC1-N forms a complex with the BH3 binding groove of the anti-apoptotic Bcl2 protein BclxL. Biochemical assays demonstrate that VDAC1-N exhibits a pro-apoptotic function by promoting pore formation of the executor Bcl2 protein Bak via neutralization of BclxL. This mechanism is reminiscent of BH3-only sensitizer Bcl2 proteins that are efficient inducers of Bax/Bak-mediated mitochondrial outer membrane permeabilization and ultimately apoptosis. The VDAC pathway most likely responds to mitochondrial stress or damage.

DOI: https://doi.org/10.1038/s41467-025-65363-1
J Virol. 2025 Oct 31. e0157625

p53-mediated regulation of electron transport chain and nucleotide synthesis during Newcastle disease virus infection.

Changrun Zhao, Ning Tang, Jing Wang, Yang Qu, Lei Tan, Cuiping Song, Xusheng Qiu, Ying Liao, Tingrong Luo, Chan Ding, Yingjie Sun.

  Mitochondria and their electron transport chain (ETC) constitute the central machinery for cellular energy metabolism and biosynthetic regulation. Disruption of the ETC leads to reactive oxygen species (ROS) production and metabolic imbalance, but its precise role in viral replication and infection remains to be elucidated. In this study, we used Newcastle disease virus (NDV), an important avian pathogen and a promising oncolytic virus, as a model to explore its relationship with cellular mitochondrial metabolism. We demonstrate that NDV infection induces varying degrees of mitochondrial fragmentation, membrane potential dissipation, and ROS production, especially in p53-null H1299 cells compared to p53-wild-type A549 cells. ETC impairment restricts NDV replication primarily by limiting aspartate and pyrimidine nucleotide biosynthesis, rather than through ROS-mediated cytotoxicity or energy depletion. Notably, NDV replication in p53-null cells is highly sensitive to ETC complexes I and III inhibition, which can be rescued by exogenous aspartate or uridine supplementation. Mechanistically, p53 serves as a metabolic buffer, protecting mitochondrial function and maintaining precursor availability during viral infection. These findings elucidate the selective and differential utilization of mitochondrial ETC components by NDV and reveal that p53 status shapes cellular susceptibility to NDV-induced metabolic stress. Our work highlights mitochondrial metabolism and p53 as potential targets for antiviral and oncolytic strategies against NDV.IMPORTANCEThis study uncovers the intricate relationship between Newcastle disease virus (NDV) infection and host cell mitochondrial metabolism, with a particular emphasis on the pivotal regulatory role of p53. As both an important avian pathogen and a promising oncolytic virus, NDV disrupts mitochondrial function and the electron transport chain, leading to p53-mediated alterations in cellular energy metabolism and redox homeostasis. Our findings not only deepen the understanding of NDV-mitochondria interactions but also highlight the central role of p53 in viral infection and oncolytic mechanisms. These insights provide a theoretical foundation and novel therapeutic targets for antiviral and anticancer strategies based on p53 or mitochondrial pathways.

Keywords:  NDV; electron transport chain; mitochondrial metabolism; nucleotide synthesis; p53; reactive oxygen species

DOI:  https://doi.org/10.1128/jvi.01576-25
J Cell Biol. 2026 Jan 05. pii: e202504178. [Epub ahead of print]225(1):

Close-up of vesicular ER exit sites by volume electron imaging using FIB-SEM.

Athul Nair, Akhil Nair, Patrick Stock, Arkash Jain, Elliott Somerville, Anwesha Sanyal, Jose Inacio Costa-Filho, Tom Kirchhausen.

The architecture of ER exit sites (ERES), the first sites of membrane remodeling in protein secretion, remains unclear, with descriptions ranging from vesicular clusters to extended tubular structures. We addressed this divergence by visualizing ERES in cells not overexpressing secretory cargo using large-scale volume-focused ion beam scanning EM (FIB-SEM) after high-pressure freeze substitution. Automated segmentation in EM (ASEM), our 3D U-Net pipeline trained with sparsely labeled 50-70-nm COPI vesicles near the Golgi, accurately detected them in HeLa, SVG-A, and iPSC-derived neurons. Using the same model, we identified abundant clusters of ∼5-40 larger vesicles (∼65-85 nm) confined within ∼250 nm3 regions adjacent to flattened ER domains, consistent with vesicular ERES. Similar assemblies also appeared alongside tubular networks and varicosities extending from enlarged ER domains, previously described as the sole ERES in HeLa cells. These findings reveal that vesicular ERES are widespread and morphologically diverse, resolving longstanding contradictions in early secretory pathway organization.

DOI: https://doi.org/10.1083/jcb.202504178
Curr Biol. 2025 Oct 27. pii: S0960-9822(25)01263-1. [Epub ahead of print]

Metabolic rewiring prevents neurodegeneration caused by chronic mitochondrial dysfunction.

Shlesha Richhariya, Daniel Shin, Matthias Schlichting, Michael Rosbash.

  The mitochondrial fission-fusion cycle is often disrupted in neurodegenerative diseases, but this important, dynamic process is not well characterized in healthy long-lived neurons of animals. We used an efficient cell-type-specific CRISPR strategy to knock out key fission and fusion genes in specific Drosophila neurons. Neither process is essential for neuronal survival and function, but the fusion knockouts had a larger impact than that of fission, especially in older animals. Mutations in the human mitochondrial inner membrane fusion gene Opa1 often cause the disease optic atrophy. Importantly, knockout of Opa1 in neurons causes a dramatic age-dependent transcriptomic response. This response resembles those of cancer cells and includes the upregulation of glycolytic genes, including Lactate dehydrogenase (Ldh). A novel double knockout strategy indicates that Ldh enhances the reduced ATP levels of the fusion mutants and is essential to prevent age-dependent neurodegeneration. This neuroprotective upregulation of Ldh is largely mediated by the transcription factor ATF4. The identified relationship-dysfunctional mitochondrial fusion alters metabolism-is reminiscent of Warburg's original cancer hypothesis, albeit in neurons. These data underscore the similarity of the two molecular programs, which promote growth in cancer and viability in the case of neurodegeneration.

Keywords:  ATF4; CRISPR; Drosophila; Warburg effect; mitochondrial dynamics; neurodegeneration

DOI:  https://doi.org/10.1016/j.cub.2025.09.063
Nat Commun. 2025 Oct 27. 16(1): 9456

An eNOS-like nanomaterial for specific reversal of cerebral ischemia-reperfusion injury.

Shuya Wang, Yuting Xiang, Xiaojing Shi, Tingli Xiong, Ruishi Li, Wenxuan Zheng, Wensheng Chen, Qiaohui Chen, Yongqi Yang, Jue Wang, Qiong Huang, Kelong Ai.

The protective role of NO has been widely verified in cerebrovascular diseases. However, the beneficial effects of NO depend on its concentration and reactive oxygen species (ROS) level, which makes current NO donors face great difficulties in treating cerebral ischemia-reperfusion injury (CIRI). Here, a tailored MoS2-based NO donor (MSNO) was constructed with defect-rich MoS2, in which the abundant S edge sites in the defects form -SNO, and the Mo sites can also bind NO to form Mo-NO. Combined with MSNO's own strong ability to eliminate ROS, MSNO could provide pure NO at suitable concentrations like eNOS and avoid the generation of highly toxic ONOO-. After intravenous injection, MSNO with suitable nano-size could penetrate the blood-brain barrier of ischemia-reperfusion injured brain tissue, and effectively treat CIRI through multiple effects: inhibiting calcium overload, alleviating mitochondrial damage and endoplasmic reticulum stress, and inhibiting the inflammatory storm.

DOI: https://doi.org/10.1038/s41467-025-64518-4
Int J Mol Sci. 2025 Oct 20. pii: 10178. [Epub ahead of print]26(20):

Developing Endogenous Autophagy Reporters in Caenorhabditis elegans to Monitor Basal and Starvation-Induced Autophagy.

Kincső Bördén, Tibor Vellai, Tímea Sigmond.

  Autophagy (cellular self-eating) is a tightly regulated catabolic process of eukaryotic cells during which parts of the cytoplasm are sequestered and subsequently delivered into lysosomes for degradation by acidic hydrolases. This process is central to maintaining cellular homeostasis, the removal of aged or damaged organelles, and the elimination of intracellular pathogens. The nematode Caenorhabditis elegans has proven to be a powerful genetic model for investigating the regulation and mechanism of autophagy. To date, the fluorescent autophagy reporters developed in this organism have predominantly relied on multi-copy, randomly integrated transgenes. As a result, the interpretation of autophagy dynamics in these models has required considerable caution due to possible overexpression artifacts and positional effects. In addition, starvation-induced autophagy has not been characterized in detail using these reporters. Here, we describe the development of two endogenous autophagy reporters, gfp::mCherry::lgg-1/atg-8 and gfp::atg-5, both inserted precisely into their endogenous genomic loci. We demonstrate that these single-copy reporters reliably track distinct stages of the autophagic process. Using these tools, we reveal that (i) the transition from the earliest phagophore to the mature autolysosome is an exceptionally rapid event because the vast majority of the detected fluorescent signals are autolysosome-specific, (ii) starvation triggers autophagy only after a measurable lag phase rather than immediately, and (iii) the regulation of starvation-induced autophagy depends on the actual life stage, and prevents excessive flux that could otherwise compromise cellular survival. We anticipate that these newly developed reporter strains will provide refined opportunities to further dissect the physiological and pathological roles of autophagy in vivo.

Keywords:  ATG-5; C. elegans; LGG-1; TOR; autophagy; endogenous reporters; starvation

DOI:  https://doi.org/10.3390/ijms262010178
Nat Commun. 2025 Oct 30. 16(1): 9611

Mitochondrial organization in the developing proximal tubule is controlled by LRRK2.

Mohsina Khan, Kyle Bond, Elyse Grilli, Daniel Cameron, Liyang Zhao, Sunder Sims-Lucas, Andrew P McMahon, Thomas J Carroll, Leif Oxburgh.

The proximal tubule of the nephron performs energy-demanding functions such as resorption of water, amino acids and glucose. Formation of the energy-producing machinery is an essential step in proximal tubule epithelial cell differentiation, and this report asks how mitochondria are localized within these cells. We show that mitochondria move from the apical to basolateral side of the proximal tubule cell coincident with the initiation of lumen flow and that proximal tubules deficient in filtration maintain mitochondria in the apical position. Mitochondrial localization depends on the activity of LRRK2 and modeling fluid flow on cultured proximal tubule epithelial cells demonstrates that LRRK2 activity is regulated by fluid shear stress, explaining how onset of flow in the newly differentiated proximal tubule may trigger the apical-to-basolateral dissemination of mitochondria. These findings indicate that mitochondrial redistribution is one component of a cellular program in the nascent proximal tubule that drives function and that this process is triggered by flow.

DOI: https://doi.org/10.1038/s41467-025-64598-2
iScience. 2025 Oct 17. 28(10): 113563

Light-evoked activity and BDNF regulate mitochondrial dynamics and mitochondrial localized translation in CNS axons.

Alexander Kreymerman, Jessica E Weinstein, Nirmal Vadgama, Sahil H Shah, Michael M Nahmou, Kinsley C Belle, Marco H Ji, Xin Xia, Anne Faust, Yolandi Van Der Merwe, David N Buickians, In-Jae Cho, Star K Huynh, Sonya Verma, Kristina Russano, Xiao-Lu Jin, Ioannis Karakikes, Michael B Steketee, Jeffrey L Goldberg.

  Mitochondria coordinate well-described maintenance functions within neuronal axons and dendrites. However, less is known about how mitochondria are regulated during axon development and maturation. Here, we demonstrate that within the developing visual system, retinal ganglion cell (RGC) axons in the retina and optic nerve exhibit increases in mitochondria size, number, and total area in vivo. Our findings indicate that these developmental changes in mitochondria are driven by neuronal activity associated with eye opening and by brain-derived neurotrophic factor (BDNF). These events occur in concert with downstream gene and protein expression changes consistent with mitochondrial biogenesis and energetics pathways. We further demonstrate that activity- and BDNF-regulated transcripts are localized and translated at mitochondria within RGC axons in vivo, concomitant with the regulation of mitochondrial dynamics. These data highlight the previously undescribed regulation of mitochondrial dynamics in axonal maturation, dependent on mechanisms involving neuronal activity and neurotrophic factor signaling, coordinated with mitochondrial-localized translation.

Keywords:  Biological sciences; Natural sciences; Neuroscience; Systems neuroscience

DOI:  https://doi.org/10.1016/j.isci.2025.113563
Sci Adv. 2025 Oct 31. 11(44): eady4492

Mechanism-based peroxiredoxin 3 inhibitors exploit a covalent warhead for cancer therapy.

Kimberly J Nelson, Terrence L Smalley, Terri Messier, Rajesh Gumpena, Uma Gandhi, Stephanie Milczarek, Aida Habibovic, Hattie Hoffman, Victoria Gibson, Robert J Hondal, W Todd Lowther, Brian Cunniff.

Covalent inhibitors that are approved and marketed drugs exploit a wide array of warheads and reactions with amino acid side chain-based nucleophiles. Thiostrepton (TS) inhibits the peroxidase activity of the mitochondrial antioxidant protein peroxiredoxin 3 by forming a covalent crosslink between the two active site cysteine residues. Peroxiredoxin 3 inactivation increases reactive oxygen species levels, induces cancer cell death in preclinical models, and shows promise in an ongoing clinical trial for malignant mesothelioma using direct pleural infusion. We report the identification of the minimal fragment of TS that contains tandem dehydro-alanine (DHA) moieties and maintains anticancer activity while losing interactions with three alternative targets of intact TS. Biochemical, kinetic, cellular, and structural studies demonstrate that this fragment is a mechanism-based peroxiredoxin inhibitor. These findings represent a promising start toward a pro-oxidant approach for cancer therapy. Moreover, the data support that the DHA moiety should be added to the covalent warhead arsenal.

DOI: https://doi.org/10.1126/sciadv.ady4492
Mater Today Bio. 2025 Dec;35 102399

Cell wash-free fluorescent probes based on phenothiazine and phenoxazine with high photostability and large stokes shifts for targeted imaging of subcellular organelles.

Zhichao Wang, Jinxiao Lyu, Yongjie Sun, Fang Liu, Lanqing Li, Shaoping Li, Xuanjun Zhang.

  Most organelle-targeting probes require the removal of excess dye to enhance the signal-to-noise ratio before microscopic imaging experiments. However, this washing step may cause cellular damage and interfere with the continuous observation of cellular activities. Here, we report a series of wash-free probes based on small molecule phenothiazine/phenoxazine. Simple modification of phenothiazine/phenoxazine by nitro group significantly enhances the polarity-sensitive characteristic, which are well-suited for wash-free cellular imaging. These probes feature low molecular weight, excellent photostability, and large Stokes shifts (up to 191 nm). By conjugation with targeting groups, a series of probes are developed for specific imaging in different organelles such as lysosomes, mitochondria, the endoplasmic reticulum, lipid droplets, and the plasma membrane, without any washing step. Moreover, by simply replacing S atom in the central core with O atom, the emission of probes shifts from red to green-yellow. Using these two probes, high-contrast, dual-color wash-free imaging can be achieved. Among them, the PXZ-Lipid probe was successfully applied for real-time monitoring of dynamic changes in lipid droplets within living cells. This work establishes a general strategy for designing small-molecule, wash-free fluorescent probes based on phenothiazine/phenoxazine scaffolds, enabling real-time, multi-organelle imaging with minimal cellular disturbance.

Keywords:  Fluorescent probe; Organelle-targeting; Phenothiazine and phenoxazine; Polarity sensitive; Wash free fluorescent imaging

DOI:  https://doi.org/10.1016/j.mtbio.2025.102399