bims-celmim 2025-04-27 papers

bims-celmim

Biomed News

on Cellular and mitochondrial metabolism

Issue of 2025–04–27
27 papers selected by
Marc Segarra Mondejar

Endoplasmic Reticulum Stress and Its Role in Metabolic Reprogramming of Cancer.
Deciphering the Controversial Role of TP53 Inducible Glycolysis and Apoptosis Regulator (TIGAR) in Cancer Metabolism as a Potential Therapeutic Strategy.
Role of lactate dehydrogenase A in the regulation of podocyte metabolism and glucose uptake under hyperglycemic conditions.
TMBIM-2 links neuronal mitochondrial stress to systemic adaptation via calcium signaling.
Neuroprotection by Mitochondrial NAD Against Glutamate-Induced Excitotoxicity.
Hypoxic conditions by Raman microspectroscopy - Reprogramming of fatty acids and glucose metabolism during colon cancer progression.
Mitochondrial NADPH fuels mitochondrial fatty acid synthesis and lipoylation to power oxidative metabolism.
Metabolic reprogramming in polycystic kidney disease and other renal ciliopathies.
Origin and evolution of mitochondrial inner membrane composition.
Proteomic analysis of hippocampus reveals metabolic reprogramming in a piglet model of mild hypoxic ischemic encephalopathy.
REDOX Imbalance and Oxidative Stress in the Intervertebral Disc: The Effect of Mechanical Stress and Cigarette Smoking on ER Stress and Mitochondrial Dysfunction.
Role of BOLA3 in the mitochondrial Fe-S cluster clarified by metabolomic analysis.
Age-associated reduction in ER-Mitochondrial contacts impairs mitochondrial lipid metabolism and autophagosome formation in the heart.
Protocol to quantitatively assess glycolysis and related carbon metabolic fluxes using stable isotope tracing in Crabtree-positive yeasts.
Asymmetric cell division of ALDH1-positive cancer stem cells generates glycolytic metabolically diverse cell populations.
Mitochondrial protein OPA1 is required for the expansion of effector CD8 T cells.
PPARα regulates ER-lipid droplet protein Calsyntenin-3β to promote ketogenesis in hepatocytes.
Comparative analysis of STP6 and STP10 unravels molecular selectivity in sugar transport proteins.
Human RCC1L is involved in the maintenance of mitochondrial nucleoids and mtDNA.
New insights into tryptophan metabolism in cancer.
IDH status dictates oHSV mediated metabolic reprogramming affecting anti-tumor immunity.
DHODH modulates immune evasion of cancer cells via CDP-Choline dependent regulation of phospholipid metabolism and ferroptosis.
Combined inhibition of de novo glutathione and nucleotide biosynthesis is synthetically lethal in glioblastoma.
Cell Painting PLUS: expanding the multiplexing capacity of Cell Painting-based phenotypic profiling using iterative staining-elution cycles.
Neuronal autophagy controls excitability via ryanodine receptor-mediated regulation of calcium-activated potassium channel function.
Conformational plasticity of mitochondrial VDAC2 controls the kinetics of its interaction with cytosolic proteins.
Hepatic gluconeogenesis and PDK3 upregulation drive cancer cachexia in flies and mice.

Metabolites. 2025 Mar 24. pii: 221. [Epub ahead of print]15(4):

Endoplasmic Reticulum Stress and Its Role in Metabolic Reprogramming of Cancer.

Salvatore Zarrella, Maria Rosaria Miranda, Verdiana Covelli, Ignazio Restivo, Sara Novi, Giacomo Pepe, Luisa Tesoriere, Manuela Rodriquez, Alessia Bertamino, Pietro Campiglia, Mario Felice Tecce, Vincenzo Vestuto.

  Background/Objectives: Endoplasmic reticulum (ER) stress occurs when ER homeostasis is disrupted, leading to the accumulation of misfolded or unfolded proteins. This condition activates the unfolded protein response (UPR), which aims to restore balance or trigger cell death if homeostasis cannot be achieved. In cancer, ER stress plays a key role due to the heightened metabolic demands of tumor cells. This review explores how metabolomics can provide insights into ER stress-related metabolic alterations and their implications for cancer therapy. Methods: A comprehensive literature review was conducted to analyze recent findings on ER stress, metabolomics, and cancer metabolism. Studies examining metabolic profiling of cancer cells under ER stress conditions were selected, with a focus on identifying potential biomarkers and therapeutic targets. Results: Metabolomic studies highlight significant shifts in lipid metabolism, protein synthesis, and oxidative stress management in response to ER stress. These metabolic alterations are crucial for tumor adaptation and survival. Additionally, targeting ER stress-related metabolic pathways has shown potential in preclinical models, suggesting new therapeutic strategies. Conclusions: Understanding the metabolic impact of ER stress in cancer provides valuable opportunities for drug development. Metabolomics-based approaches may help identify novel biomarkers and therapeutic targets, enhancing the effectiveness of antitumor therapies.

Keywords:  biochemical pathways; cancer; drug discovery; endoplasmic reticulum stress; metabolomics; tumor microenvironment; unfolded protein response

DOI:  https://doi.org/10.3390/metabo15040221
Cells. 2025 Apr 15. pii: 598. [Epub ahead of print]14(8):

Deciphering the Controversial Role of TP53 Inducible Glycolysis and Apoptosis Regulator (TIGAR) in Cancer Metabolism as a Potential Therapeutic Strategy.

Fatima I AlMaazmi, Lara J Bou Malhab, Leen ElDohaji, Maha Saber-Ayad.

  Tumor metabolism has emerged as a critical target in cancer therapy, revolutionizing our understanding of how cancer cells grow, survive, and respond to treatment. Historically, cancer research focused on genetic mutations driving tumorigenesis, but in recent decades, metabolic reprogramming has been recognized as a hallmark of cancer. The TP53 inducible glycolysis and apoptosis regulator, or TIGAR, affects a wide range of cellular and molecular processes and plays a key role in cancer cell metabolism by regulating the balance between glycolysis and antioxidant defense mechanisms. Cancer cells often exhibit a shift towards aerobic glycolysis (the Warburg effect), which allows rapid energy production and gives rise to biosynthetic intermediates for proliferation. By inhibiting glycolysis, TIGAR can reduce the proliferation rate of cancer cells, particularly in early-stage tumors or specific tissue types. This metabolic shift may limit the resources available for rapid cell division, thereby exerting a tumor-suppressive effect. However, this metabolic shift also leads to increased levels of reactive oxygen species (ROS), which can damage the cell if not properly managed. TIGAR helps protect cancer cells from excessive ROS by promoting the pentose phosphate pathway (PPP), which generates NADPH-a key molecule involved in antioxidant defense. Through its actions, TIGAR decreases the glycolytic flux while increasing the diversion of glucose-6-phosphate into the PPP. This reduces ROS levels and supports biosynthesis and cell survival by maintaining the balance of nucleotides and lipids. The role of TIGAR has been emerging as a prognostic and potential therapeutic target in different types of cancers. This review highlights the role of TIGAR in different types of cancer, evaluating its potential role as a diagnostic marker and a therapeutic target.

Keywords:  P53; ROS; cancer metabolism; gastric cancer; ketogenic diet; pancreatic cancer; pentose phosphate pathway

DOI:  https://doi.org/10.3390/cells14080598
Sci Rep. 2025 Apr 23. 15(1): 14162

Role of lactate dehydrogenase A in the regulation of podocyte metabolism and glucose uptake under hyperglycemic conditions.

Audzeyenka Irena, Grochowalska Klaudia, Szrejder Maria, Kulesza Tomasz, Rachubik Patrycja, Rogacka Dorota, Piwkowska Agnieszka.

  Lactate is a cellular product of glycolytic metabolism, serving as both an additional oxidative energy substrate and a signaling molecule in metabolic regulation. Plasma lactate levels are elevated in diabetes, and chronic extracellular lactic acidosis is recognized as a negative prognostic marker for the disease. The development of diabetic kidney disease is closely associated with podocyte injury, which forms a crucial layer of the glomerular filtration barrier. Given that high extracellular glucose concentrations also induce lactate production and excretion in podocytes, we hypothesize that an appropriate LDH expression pattern is crucial for maintaining proper podocyte metabolism and function. Our research shows that hyperglycemia significantly decreases lactate dehydrogenase activity in podocytes. Specifically, reduced LDHA expression under hyperglycemic conditions contributes to metabolic disturbances in these cells. Lower LDH activity results in decreased glycolytic activity, altered expression of monocarboxylate transporters, reduced insulin-dependent glucose uptake, and a decrease in the number of podocyte foot processes. These findings underscore the essential role of LDHA in the metabolic adaptation of podocytes to elevated glucose levels typical of diabetes. By elucidating the molecular mechanisms underlying podocyte injury, our study provides new insights into potential therapeutic targets for preventing or mitigating diabetic kidney disease.

Keywords:  Glucose uptake; Glycolysis; Hyperglycemia; Insulin; Lactate; Lactate dehydrogenase

DOI:  https://doi.org/10.1038/s41598-025-98797-0
J Cell Biol. 2025 May 05. pii: e202503004. [Epub ahead of print]224(5):

TMBIM-2 links neuronal mitochondrial stress to systemic adaptation via calcium signaling.

Yu Sun, Terytty Yang Li.

Mitochondrial function is critical for neuronal activity and systemic metabolic adaptation. In this issue, Li et al. (https://doi.org/10.1083/jcb.202408050) identify TMBIM-2 as a key regulator of calcium dynamics, coordinating the neuronal-to-intestinal mitochondrial unfolded protein response (UPRmt), pathogen-induced aversive learning, and aging.

DOI: https://doi.org/10.1083/jcb.202503004
Cells. 2025 Apr 12. pii: 582. [Epub ahead of print]14(8):

Neuroprotection by Mitochondrial NAD Against Glutamate-Induced Excitotoxicity.

Bruna S Paiva, Diogo Neves, Diogo Tomé, Filipa J Costa, Inês C Bruno, Diogo Trigo, Raquel M Silva, Ramiro D Almeida.

  Excitotoxicity is a pathological process that occurs in many neurological diseases, such as stroke or epilepsy, and is characterized by the extracellular accumulation of high concentrations of glutamate or other excitatory amino acids (EAAs). Nicotinamide adenine dinucleotide (NAD) depletion is an early event following excitotoxicity in many in vitro and in vivo excitotoxic-related models and contributes to the deregulation of energy homeostasis. However, the interplay between glutamate excitotoxicity and the NAD biosynthetic pathway is not fully understood. To address this question, we used a primary culture of rat cortical neurons and found that an excitotoxic glutamate insult alters the expression of the NAD biosynthetic enzymes. Additionally, using a fluorescent NAD mitochondrial sensor, we observed that glutamate induces a significant decrease in the mitochondrial NAD pool, which was reversed when exogenous NAD was added. We also show that exogenous NAD protects against the glutamate-induced decrease in mitochondrial membrane potential (MMP). Glutamate excitotoxicity changed mitochondrial retrograde transport in neurites, which seems to be reversed by NAD addition. Finally, we show that NAD and NAD precursors protect against glutamate-induced cell death. Together, our results demonstrate that glutamate-induced excitotoxicity acts by compromising the NAD biosynthetic pathway, particularly in the mitochondria. These results also uncover a potential role for mitochondrial NAD as a tool for central nervous system (CNS) regenerative therapies.

Keywords:  NAD metabolism; excitotoxicity; glutamate; mitochondria

DOI:  https://doi.org/10.3390/cells14080582
Spectrochim Acta A Mol Biomol Spectrosc. 2025 Apr 19. pii: S1386-1425(25)00581-5. [Epub ahead of print]339 126275

Hypoxic conditions by Raman microspectroscopy - Reprogramming of fatty acids and glucose metabolism during colon cancer progression.

Monika Kopeć, Karolina Beton-Mysur, Jakub Surmacki, Beata Brożek-Płuska.

  Cellular respiration is the primary metabolic process for producing the energy (ATP) needed for survival. Disruptions in this process can lead to various diseases, including colon cancer. This paper reviews the current understanding of how excess fatty acids (FAs) and glucose (Glc) alter metabolic pathways. We focused on the impact of unsaturated fatty acids (UFAs) (eicosapentaenoic acid (EPA), linoleic acid (LA)), saturated fatty acid (SFA) (palmitic acid (PA)), and glucose on healthy human colon cells (CCD-18 Co) and cancerous colon cells (Caco-2) using Raman microspectroscopy. Our study examined the metabolic abnormalities in mitochondria and lipid droplets caused by the external intake of FAs and glucose. The results indicate that the peaks at 750 cm-1, 1004 cm-1, 1256 cm-1, 1444 cm-1, and 1656 cm-1 can serve as Raman biomarkers for monitoring metabolic pathways in colon cancer. We proved that oxidative metabolism towards glycolysis allows maintaining redox homeostasis and enables the survival and proliferation of cancer cells in hypoxic conditions. Our findings show that comparing control cells with cells supplemented with UFAs, SFA, and glucose can help detect metabolic abnormalities. Specifically, supplementation with UFAs reduces the intensity of the bands at 750 cm-1 and 1004 cm-1, while SFA and glucose increase their intensity. For the bands at 1256 cm-1, 1444 cm-1, and 1656 cm-1, palmitic acid and glucose decrease the intensity, whereas linoleic acid increases it. This paper introduces new experimental techniques, such as Raman microspectroscopy and imaging, to track and understand the metabolic changes in colon cells caused by FAs and glucose under hypoxic conditions.

Keywords:  Colon cancer biomarkers; Fatty acids; Glucose; Hypoxia; Raman microspectroscopy

DOI:  https://doi.org/10.1016/j.saa.2025.126275
Nat Cell Biol. 2025 Apr 21.

Mitochondrial NADPH fuels mitochondrial fatty acid synthesis and lipoylation to power oxidative metabolism.

Dohun Kim, Rushendhiran Kesavan, Kevin Ryu, Trishna Dey, Austin Marckx, Cameron Menezes, Prakash P Praharaj, Stewart Morley, Bookyong Ko, Mona H Soflaee, Harrison J Tom, Harrison Brown, Hieu S Vu, Shih-Chia Tso, Chad A Brautigam, Andrew Lemoff, Marcel Mettlen, Prashant Mishra, Feng Cai, Doug K Allen, Gerta Hoxhaj.

Nicotinamide adenine dinucleotide phosphate (NADPH) is a vital electron donor essential for macromolecular biosynthesis and protection against oxidative stress. Although NADPH is compartmentalized within the cytosol and mitochondria, the specific functions of mitochondrial NADPH remain largely unexplored. Here we demonstrate that NAD+ kinase 2 (NADK2), the principal enzyme responsible for mitochondrial NADPH production, is critical for maintaining protein lipoylation, a conserved lipid modification necessary for the optimal activity of multiple mitochondrial enzyme complexes, including the pyruvate dehydrogenase complex. The mitochondrial fatty acid synthesis (mtFAS) pathway utilizes NADPH for generating protein-bound acyl groups, including lipoic acid. By developing a mass-spectrometry-based method to assess mammalian mtFAS, we reveal that NADK2 is crucial for mtFAS activity. NADK2 deficiency impairs mtFAS-associated processes, leading to reduced cellular respiration and mitochondrial translation. Our findings support a model in which mitochondrial NADPH fuels the mtFAS pathway, thereby sustaining protein lipoylation and mitochondrial oxidative metabolism.

DOI: https://doi.org/10.1038/s41556-025-01655-4
EMBO Mol Med. 2025 Apr 22.

Metabolic reprogramming in polycystic kidney disease and other renal ciliopathies.

Sara Clerici, Alessandra Boletta.

  Primary cilia are solitary organelles formed by a microtubule-based skeleton protruding in a single copy on the surface of most cells. Alterations in their function cause a plethora of human conditions collectively called the ciliopathies. The kidney is frequently and severely affected in the ciliopathies, presenting with a spectrum of phenotypes. Cyst formation is a common trait of all renal ciliopathies. Besides this common manifestation, however, the renal ciliopathies present with profoundly different phenotypes, resulting in either polycystic kidney disease (PKD) or nephronophthisis (NPH) phenotypes. The past decade has seen a surge of studies highlighting metabolic reprogramming as a major feature of PKD, with a distinct involvement of mitochondrial dysfunction. This discovery has brought forward the development of novel therapeutic approaches. More recent evidence suggests that primary cilia modulate the mitochondrial production of energy in response to environmental cues. Here, we summarize the evidence available to date and propose a more general involvement of metabolic and mitochondrial alterations in the renal ciliopathies that might in principle help defining the profoundly different, and potentially opposite, manifestations observed.

Keywords:  Cilia; Ciliopathies; Kidney Cysts; Metabolism; Mitochondria

DOI:  https://doi.org/10.1038/s44321-025-00239-x
J Cell Sci. 2025 May 01. pii: jcs263780. [Epub ahead of print]138(9):

Origin and evolution of mitochondrial inner membrane composition.

Kailash Venkatraman, Nicolas-Frédéric Lipp, Itay Budin.

  Unique membrane architectures and lipid building blocks underlie the metabolic and non-metabolic functions of mitochondria. During eukaryogenesis, mitochondria likely arose from an alphaproteobacterial symbiont of an Asgard archaea-related host cell. Subsequently, mitochondria evolved inner membrane folds known as cristae alongside a specialized lipid composition supported by metabolic and transport machinery. Advancements in phylogenetic methods and genomic and metagenomic data have suggested potential origins for cristae-shaping protein complexes, such as the mitochondrial contact site and cristae-organizing system (MICOS). MICOS protein homologs function in the formation of cristae-like intracytoplasmic membranes (ICMs) in diverse extant alphaproteobacteria. The machinery responsible for synthesizing key mitochondrial phospholipids - which cooperate with cristae-shaping proteins to establish inner membrane architecture - could have also evolved from a bacterial ancestor, but its origins have been less explored. In this Review, we examine the current understanding of mitochondrial membrane evolution, highlighting distinctions between prokaryotic and eukaryotic mitochondrial-specific proteins and lipids and their differing roles in shaping cristae and ICM architecture, and propose a model explaining the concurrent specialization of the mitochondrial lipidome and inner membrane structure in eukaryogenesis. We discuss how advancements across a range of disciplines are shedding light on how multiple membrane components co-evolved to support the central functions of eukaryotic mitochondria.

Keywords:  Cardiolipin; Cristae; Curvature; Evolution; Mitochondria; Phospholipids

DOI:  https://doi.org/10.1242/jcs.263780
PLoS One. 2025 ;20(4): e0320869

Proteomic analysis of hippocampus reveals metabolic reprogramming in a piglet model of mild hypoxic ischemic encephalopathy.

Dawn B Lammert, Regina F Fernandez, Xiuyun Liu, Jingyao Chen, Raymond C Koehler, Susanna Scafidi, Joseph Scafidi.

Neonatal hypoxic-ischemic encephalopathy (HIE) remains a leading cause of long-term neurologic morbidity. Fifty percent of HIE cases are mild and do not have clearly defined therapeutic interventions. Emergent evidence now demonstrates that up to 25% of children with mild HIE suffer motor and developmental delay by 18 months and 35% have cognitive impairments by age 5 years. Interestingly, the hippocampus, which is responsible for learning and memory, does not show overt injury but does demonstrate volume changes on imaging that correlate with cognitive and behavioral outcomes. Although there is extensive data regarding pathophysiological changes following moderate and severe HIE, there is a paucity of understanding regarding the extent, duration, and compensatory adaptations in the mild neonatal HIE brain. We performed hippocampal proteomic analysis using a swine model of mild neonatal hypoxia-asphyxia. Hippocampi were collected at 24 or 72 hours after injury, and proteomics was performed by liquid chromatography tandem mass spectrometry (LC-MS/MS). Pathway analysis demonstrated that several metabolic pathways are temporally regulated after mild HIE. Specifically, amino acid, carbohydrate, and one-carbon metabolism increased at 24 hours while fat metabolism and oxidative phosphorylation decreased at 24 hours. Downregulation of oxidative phosphorylation was more pronounced at 72 hours. Our data demonstrate that metabolic reprogramming occurs after mild HIE, and these changes persist up to 72 hours after injury. These results provide new evidence that mild HIE disrupts brain metabolism, emphasizing the need for a better understanding of the underlying pathophysiology of mild HIE and development of targeted therapeutic interventions for this population.

DOI: https://doi.org/10.1371/journal.pone.0320869
Cells. 2025 Apr 19. pii: 613. [Epub ahead of print]14(8):

REDOX Imbalance and Oxidative Stress in the Intervertebral Disc: The Effect of Mechanical Stress and Cigarette Smoking on ER Stress and Mitochondrial Dysfunction.

Hui Li, Joshua Kelley, Yiqing Ye, Zhi-Wei Ye, Danyelle M Townsend, Jie Zhang, Yongren Wu.

  Low back pain is a widespread condition that significantly impacts quality of life, with intervertebral disc degeneration (IDD) being a major contributing factor. However, the underlying mechanisms of IDD remain poorly understood, necessitating further investigation. Environmental risk factors, such as mechanical stress and cigarette smoke, elevate reactive oxygen species levels from both endogenous and exogenous sources, leading to redox imbalance and oxidative stress. The endoplasmic reticulum (ER) and mitochondria, two key organelles responsible for protein folding and energy production, respectively, are particularly vulnerable to oxidative stress. Under oxidative stress conditions, ER stress and mitochondrial dysfunction occur, resulting in unfolded protein response activation, impaired biosynthetic processes, and disruptions in the tricarboxylic acid cycle and electron transport chain, ultimately compromising energy metabolism. Prolonged and excessive ER stress can further trigger apoptosis through ER-mitochondrial crosstalk. Given the unique microenvironment of the intervertebral disc (IVD)-characterized by hypoxia, glucose starvation, and region-specific cellular heterogeneity-the differential effects of environmental stressors on distinct IVD cell populations require further investigation. This review explores the potential mechanisms through which environmental risk factors alter IVD cell activities, contributing to IDD progression, and discusses future therapeutic strategies aimed at mitigating disc degeneration.

Keywords:  ER–mitochondrial crosstalk; cellular dysfunction; endoplasmic reticulum stress; environmental risk factors; intervertebral disc degeneration; low back pain; mitochondrial dysfunction; reactive oxygen species; redox imbalance

DOI:  https://doi.org/10.3390/cells14080613
Mol Genet Metab. 2025 Apr 18. pii: S1096-7192(25)00104-0. [Epub ahead of print]145(2): 109113

Role of BOLA3 in the mitochondrial Fe-S cluster clarified by metabolomic analysis.

Hiroyuki Iijima, Atsuko Imai-Okazaki, Yoshihito Kishita, Ayumu Sugiura, Masaru Shimura, Kei Murayama, Yasushi Okazaki, Akira Ohtake.

  BOLA3 is one of the proteins involved in the assembly and transport of [4Fe-4S] clusters, which are incorporated into mitochondrial respiratory chain complexes I and II, aconitase, and lipoic acid synthetase. Pathogenic variants in the BOLA3 gene cause a rare condition known as multiple mitochondrial dysfunctions syndrome 2 with hyperglycinemia, characterized by life-threatening lactic acidosis, nonketotic hyperglycinemia, and hypertrophic cardiomyopathy. The aim of this study was to elucidate the biochemical characteristics of patients with BOLA3 variants and to clarify the role of BOLA3 protein in humans. The characteristics, clinical course, and biochemical data of eight Japanese patients with BOLA3 pathogenic variants were collected. In addition, metabolomic analyses were performed using capillary electrophoresis time-of-flight mass spectrometry, blue native polyacrylamide gel electrophoresis (BN-PAGE)/Western blot analysis of mitochondrial respiratory chain complexes, and in-gel enzyme staining of mitochondrial respiratory chain complexes of fibroblasts from all eight patients. Metabolomic data were compared between the eight patients with BOLA3 variants and three control samples using Welch's t-test. In the metabolomic analysis, levels of lactic acid, pyruvic acid, alanine, tricarboxylic acid (TCA) cycle intermediates (such as α-ketoglutaric acid and succinic acid), branched-chain amino acids, and metabolites of lysine and tryptophan were significantly elevated in the BOLA3 group. Data collected during the patients' lives showed increased lactic acid and glycine levels. In BN-PAGE/Western blot analysis and in-gel enzyme staining, bands for complexes I and II were barely detectable in all eight cases. These results indicate that BOLA3 variants decrease the activity of lipoic acid-dependent proteins (pyruvate dehydrogenase complex, α-ketoglutarate dehydrogenase, 2-oxoadipate dehydrogenase, branched-chain ketoacid dehydrogenase, and the glycine cleavage system), as well as mitochondrial respiratory chain complexes I and II, but do not affect aconitase. Thus, it is believed that BOLA3 is involved in transporting [4Fe-4S] clusters to respiratory chain complexes I and II and lipoic acid synthetase, but does not interfere with aconitase. These findings suggest that while lipoic acid supplementation or vitamin cocktails may provide benefits, the impaired [4Fe-4S] cluster pathway itself should be targeted for treatment to improve the extensive metabolic abnormalities caused by BOLA3 deficiency.

Keywords:  BOLA3; Lipoic acid; Mitochondria; TCA cycle

DOI:  https://doi.org/10.1016/j.ymgme.2025.109113
Cell Death Differ. 2025 Apr 20.

Age-associated reduction in ER-Mitochondrial contacts impairs mitochondrial lipid metabolism and autophagosome formation in the heart.

Weilong Hong, Xue Zeng, Ruiyan Ma, Yu Tian, Huimin Miu, Xiaoping Ran, Rui Song, Zhenchun Luo, Dapeng Ju, Daqing Ma, Milad Ashrafizadeh, Sujit Kumar Bhutia, João Conde, Gautam Sethi, He Huang, Chenyang Duan.

The accumulation of dysfunctional giant mitochondria is a hallmark of aged cardiomyocytes. This study investigated the core mechanism underlying this phenomenon, focusing on the disruption of mitochondrial lipid metabolism and its effects on mitochondrial dynamics and autophagy, using both naturally aging mouse models and etoposide-induced cellular senescence models. In aged cardiomyocytes, a reduction in endoplasmic reticulum-mitochondrial (ER-Mito) contacts impairs lipid transport and leads to insufficient synthesis of mitochondrial phosphatidylethanolamine (PE). A deficiency in phosphatidylserine decarboxylase (PISD) further hinders the conversion of phosphatidylserine to PE within mitochondria, exacerbating the deficit of PE production. This PE shortage disrupts autophagosomal membrane formation, leading to impaired autophagic flux and the accumulation of damaged mitochondria. Modulating LACTB expression to enhance PISD activity and PE production helps maintain mitochondrial homeostasis and the integrity of aging cardiomyocytes. These findings highlight the disruption of mitochondrial lipid metabolism as a central mechanism driving the accumulation of dysfunctional giant mitochondria in aged cardiomyocytes and suggest that inhibiting LACTB expression could serve as a potential therapeutic strategy for mitigating cardiac aging and preserving mitochondrial function.

DOI: https://doi.org/10.1038/s41418-025-01511-w
STAR Protoc. 2025 Apr 22. pii: S2666-1667(25)00192-3. [Epub ahead of print]6(2): 103786

Protocol to quantitatively assess glycolysis and related carbon metabolic fluxes using stable isotope tracing in Crabtree-positive yeasts.

Shreyas Niphadkar, Sreesa Sreedharan, Vineeth Vengayil, Sunil Laxman.

  Crabtree-positive yeasts rapidly consume glucose via glycolysis, making it difficult to experimentally estimate their actual glycolytic rate or flux. We present a stable isotope labeling and liquid chromatography-tandem mass spectrometry (LC-MS/MS)-based protocol to quantitatively estimate glycolytic and related carbon metabolic fluxes using Saccharomyces cerevisiae. This approach defines time windows to capture glucose metabolic intermediate production before label saturation, enabling a comparison of glycolytic flux changes across different cells. This protocol provides a reliable, quantitative approach to study dynamic metabolic fluxes in these cells. For complete details on the use and execution of this protocol, please refer to Vengayil et al., 2024.1.

Keywords:  metabolism; metabolomics; model organisms; systems biology

DOI:  https://doi.org/10.1016/j.xpro.2025.103786
Sci Rep. 2025 Apr 22. 15(1): 13932

Asymmetric cell division of ALDH1-positive cancer stem cells generates glycolytic metabolically diverse cell populations.

Shoma Tamori, Chika Matsuda, Takahiro Kasai, Shigeo Ohno, Kazunori Sasaki, Kazunori Akimoto.

Metabolic heterogeneity in various cancer cells within a tumor causes resistance to medical therapies and promotes tumor recurrence and metastasis. However, the mechanisms by which tumors acquire metabolic heterogeneity are poorly understood. Here, we revealed that PKCλ-dependent asymmetric division of ALDH1-positive cancer stem cells (CSCs) led to an uneven distribution of glycolytic capacity, which is crucial for understanding metabolic heterogeneity within a tumor. The rate-limiting enzyme PFKP and the metabolic probe CDG in glycolysis codistributed with the ALDH1A3 protein during the post-cell division phase, highlighting a mechanism for acquiring metabolic diversity. PKCλ deficiency reduced the asymmetric distribution of these proteins in ALDH1high cells with high ALDH1 activity, suggesting a fundamental role for PKCλ in metabolic heterogeneity. We identified 28 distinct distribution patterns combining PFKP and CDG distributions, demonstrating the complexity of glycolytic heterogeneity. Furthermore, validation and prediction of cell distribution patterns via a probabilistic model confirmed that PKCλ deficiency diminished glycolytic diversity in individual cells within a cancer cell colony generated from an ALDH1-positive CSC. These findings suggest that PKCλ-dependent asymmetric cell division of ALDH1-positive CSCs is crucial for glycolytic heterogeneity in cancer cells within a tumor, potentially offering new therapeutic targets against tumor resistance and metastasis.

DOI: https://doi.org/10.1038/s41598-025-97985-2
Cell Rep. 2025 Apr 21. pii: S2211-1247(25)00381-X. [Epub ahead of print]44(5): 115610

Mitochondrial protein OPA1 is required for the expansion of effector CD8 T cells.

Benjamin A S Willett, Scott B Thompson, Vincent Chen, Anza Dareshouri, Conner L Jackson, Tonya Brunetti, Angelo D'Alessandro, Jared Klarquist, Travis Nemkov, Ross M Kedl.

  Short-lived effector cells are characterized metabolically by a highly glycolytic state, driving energy and biomass acquisition, whereas memory-fated T cells have historically been described as meeting these requirements through mitochondrial metabolism. Here, we show that the mitochondrial protein optic atrophy 1 (OPA1) is critical for rapidly dividing CD8 T cells in vivo, the requirement for which is most pronounced in effector CD8 T cells. More specifically, OPA1 supports proper cell cycle initiation and progression and the viability and survival of CD8 T cells during clonal expansion. Use of mice deficient in the mitochondrial membrane fusion proteins Mitofusin 1 and 2 (MFN1/2) in both in vivo proliferation/differentiation assays and ex vivo metabolic analysis indicates that the requirement for OPA1 during cell division supersedes its role in mitochondrial fusion. We conclude that OPA1 is critical for the generation and accumulation of short-lived effector cells that arise during the response to infection.

Keywords:  CD8; CP: Immunology; Mitofusins; Opa1; T cell; metabolism

DOI:  https://doi.org/10.1016/j.celrep.2025.115610
Proc Natl Acad Sci U S A. 2025 Apr 29. 122(17): e2426338122

PPARα regulates ER-lipid droplet protein Calsyntenin-3β to promote ketogenesis in hepatocytes.

Lauren F Uchiyama, Alexander Nguyen, Kevin Qian, Liujuan Cui, Khoi T Pham, Xu Xiao, Yajing Gao, Yuta Shimanaka, Marcus J Tol, Laurent Vergnes, Karen Reue, Peter Tontonoz.

  Ketogenesis requires fatty acid flux from intracellular (lipid droplets) and extrahepatic (adipose tissue) lipid stores to hepatocyte mitochondria. However, whether interorganelle contact sites regulate this process is unknown. Recent studies have revealed a role for Calsyntenin-3β (CLSTN3β), an endoplasmic reticulum-lipid droplet contact site protein, in the control of lipid utilization in adipose tissue. Here, we show that Clstn3b expression is induced in the liver by the nuclear receptor PPARα in settings of high lipid utilization, including fasting and ketogenic diet feeding. Hepatocyte-specific loss of CLSTN3β in mice impairs ketogenesis independent of changes in PPARα activation. Conversely, hepatic overexpression of CLSTN3β promotes ketogenesis in mice. Mechanistically, CLSTN3β affects LD-mitochondria crosstalk, as evidenced by changes in fatty acid oxidation, lipid-dependent mitochondrial respiration, and the mitochondrial integrated stress response. These findings define a function for CLSTN3β-dependent membrane contacts in hepatic lipid utilization and ketogenesis.

Keywords:  hepatocyte; ketogenesis; ketogenic diet; lipid metabolism

DOI:  https://doi.org/10.1073/pnas.2426338122
Proc Natl Acad Sci U S A. 2025 Apr 29. 122(17): e2417370122

Comparative analysis of STP6 and STP10 unravels molecular selectivity in sugar transport proteins.

Camilla Gottlieb Andersen, Laust Bavnhøj, Søren Brag, Anastasiia Bohush, Adriana Chrenková, Jan Heiner Driller, Bjørn Panyella Pedersen.

  The distribution of sugars is crucial for plant energy, signaling, and defense mechanisms. Sugar Transport Proteins (STPs) are Sugar Porters (SPs) that mediate proton-driven cellular uptake of glucose. Some STPs also transport fructose, while others remain highly selective for only glucose. What determines this selectivity, allowing STPs to distinguish between compounds with highly similar chemical composition, remains unknown. Here, we present the structure of Arabidopsis thaliana STP6 in an inward-occluded conformational state with glucose bound and demonstrate its role as both a glucose and fructose transporter. We perform a comparative analysis of STP6 with the glucose-selective STP10 using in vivo and in vitro systems, demonstrating how different experimental setups strongly influence kinetic transport properties. We analyze the properties of the monosaccharide binding site and show that the position of a single methyl group in the binding site is sufficient to shuffle glucose and fructose specificity, providing detailed insights into the fine-tuned dynamics of affinity-induced specificity for sugar uptake. Altogether, these findings enhance our understanding of sugar selectivity in STPs and more broadly SP proteins.

Keywords:  STP10; STP6; plant sugar uptake; sugar porter family; sugar transport

DOI:  https://doi.org/10.1073/pnas.2417370122
Sci Rep. 2025 Apr 21. 15(1): 13811

Human RCC1L is involved in the maintenance of mitochondrial nucleoids and mtDNA.

Emi Matsumoto, Taeko Sasaki, Tetsuya Higashiyama, Narie Sasaki.

  Mitochondrial DNA (mtDNA) is organized with proteins into mitochondrial nucleoid (mt-nucleoid). The mt-nucleoid is a unit for the maintenance and function of mtDNA. The regulator of chromosome condensation 1-like protein (RCC1L) performs various functions in mitochondria, including translation, but its involvement in regulating mt-nucleoid maintenance is unknown. Herein, we found that human RCC1L was required to maintain mt-nucleoids and mtDNA. Human RCC1L has three splicing isoforms: RCC1LV1, RCC1LV2, and RCC1LV3. Knockout (KO) cells lacking all RCC1L isoforms, which were lethal without pyruvate and uridine, exhibited a decrease in mt-nucleoids and mtDNA, along with swollen and fragmented mitochondria. Among the three RCC1L isoforms, only RCC1LV1 recovered all phenotypes observed in RCC1L KO cells. As the treatment of wild-type cells with chloramphenicol, a mitochondrial translation inhibitor, did not lead to the decrease in mt-nucleoids accompanied by mtDNA depletion, the decrease in mt-nucleoids and mtDNA in RCC1L KO cells was not solely attributed to impaired mitochondrial translation. Using conditional RCC1L KO cells, we observed a rapid decrease in mt-nucleoids and mtDNA during a specific period following RCC1L loss. Our findings indicate that RCC1L regulates the maintenance of mt-nucleoids and mtDNA besides its role in mitochondrial translational regulation.

Keywords:  Mitochondrial DNA; Mitochondrial nucleoid; RCC1L

DOI:  https://doi.org/10.1038/s41598-025-98397-y
Trends Cancer. 2025 Apr 23. pii: S2405-8033(25)00076-7. [Epub ahead of print]

New insights into tryptophan metabolism in cancer.

Zhe Qi Liu, M Teresa Ciudad, Tracy L McGaha.

  Tryptophan (Trp) is an essential amino acid and key intermediate in a range of biological processes. Early studies identified altered Trp utilization in cancer cells favoring cancer survival and growth. Seminal findings linking Trp metabolism and suppression of immunity led to an explosion of interest ultimately culminating in clinical trials targeting these pathways in melanoma. The failure of these trials led to a clinical retreat in this approach; however, recent insights into the complex interplay of the various Trp circuits and between tumor cells, immune cells, and the microbiota have shown that reconsideration of Trp metabolism is needed. Here, we discuss recent developments in our understanding of Trp metabolism and apparent contradictions in the field. We also discuss adaptations that occur when Trp pathways are manipulated, which may impact therapy responses.

Keywords:  kynurenine; metabolism; microbiome; tryptophan; tumor immunity

DOI:  https://doi.org/10.1016/j.trecan.2025.03.008
Nat Commun. 2025 Apr 24. 16(1): 3874

IDH status dictates oHSV mediated metabolic reprogramming affecting anti-tumor immunity.

Upasana Sahu, Matthew P Mullarkey, Sara A Murphy, Joshua C Anderson, Vasanta Putluri, Abu Hena Mostafa Kamal, Jun Hyoung Park, Tae Jin Lee, Alexander L Ling, Benny A Kaipparettu, Ashok Sharma, Nagireddy Putluri, Pamela L Wenzel, Christopher D Willey, E Antonio Chiocca, James M Markert, Balveen Kaur.

Identification of isocitrate dehydrogenase (IDH) mutations has uncovered the crucial role of metabolism in gliomagenesis. Oncolytic herpes virus (oHSV) initiates direct tumor debulking by tumor lysis and activates anti-tumor immunity, however, little is known about the role of glioma metabolism in determining oHSV efficacy. Here we identify that oHSV rewires central carbon metabolism increasing glucose utilization towards oxidative phosphorylation and shuttling glutamine towards reductive carboxylation in IDH wildtype glioma. The switch in metabolism results in increased lipid synthesis and cellular ROS. PKC induces ACSL4 in oHSV treated cells leading to lipid peroxidation and ferroptosis. Ferroptosis is critical to launch an anti-tumor immune response which is important for viral efficacy. Mutant IDH (IDHR132H) gliomas are incapable of reductive carboxylation and hence ferroptosis. Pharmacological blockade of IDHR132H induces ferroptosis and anti-tumor immunity. This study provides a rationale to use an IDHR132H inhibitor to treat high grade IDH-mutant glioma patients undergoing oHSV treatment.

DOI: https://doi.org/10.1038/s41467-025-58911-2
Nat Commun. 2025 Apr 24. 16(1): 3867

DHODH modulates immune evasion of cancer cells via CDP-Choline dependent regulation of phospholipid metabolism and ferroptosis.

Da Teng, Kenneth D Swanson, Ruiheng Wang, Aojia Zhuang, Haofeng Wu, Zhixin Niu, Li Cai, Faith R Avritt, Lei Gu, John M Asara, Yaqing Zhang, Bin Zheng.

The ability of cancer cells to evade immune destruction is governed by various intrinsic factors including their metabolic state. Here we demonstrate that inactivation of dihydroorotate dehydrogenase (DHODH), a pyrimidine synthesis enzyme, increases cancer cell sensitivity to T cell cytotoxicity through induction of ferroptosis. Lipidomic and metabolomic analyses reveal that DHODH inhibition reduces CDP-choline level and attenuates the synthesis of phosphatidylcholine (PC) via the CDP-choline-dependent Kennedy pathway. To compensate this loss, there is increased synthesis from phosphatidylethanolamine via the phospholipid methylation pathway resulting in increased generation of very long chain polyunsaturated fatty acid-containing PCs. Importantly, inactivation of Dhodh in cancer cells promotes the infiltration of interferon γ-secreting CD8+ T cells and enhances the anti-tumor activity of PD-1 blockade in female mouse models. Our findings reveal the importance of DHODH in regulating immune evasion through a CDP-choline dependent mechanism and implicate DHODH as a promising target to improve the efficacy of cancer immunotherapies.

DOI: https://doi.org/10.1038/s41467-025-59307-y
Cell Rep. 2025 Apr 19. pii: S2211-1247(25)00367-5. [Epub ahead of print]44(5): 115596

Combined inhibition of de novo glutathione and nucleotide biosynthesis is synthetically lethal in glioblastoma.

Suresh Udutha, Céline Taglang, Georgios Batsios, Anne Marie Gillespie, Meryssa Tran, Johanna Ten Hoeve, Thomas G Graeber, Pavithra Viswanath.

  Understanding the mechanisms by which oncogenic events alter metabolism will help identify metabolic weaknesses that can be targeted for therapy. Telomerase reverse transcriptase (TERT) is essential for telomere maintenance in most cancers. Here, we show that TERT acts via the transcription factor forkhead box O1 (FOXO1) to upregulate glutamate-cysteine ligase (GCLC), the rate-limiting enzyme for de novo biosynthesis of glutathione (GSH, reduced) in multiple cancer models, including glioblastoma (GBM). Genetic ablation of GCLC or pharmacological inhibition using buthionine sulfoximine (BSO) reduces GSH synthesis from [U-13C]-glutamine in GBMs. However, GCLC inhibition drives de novo pyrimidine nucleotide biosynthesis by upregulating the glutamine-utilizing enzymes glutaminase (GLS) and carbamoyl-phosphate synthetase 2, aspartate transcarbamoylase, and dihydroorotatase (CAD) in an MYC-driven manner. Combining BSO with the glutamine antagonist JHU-083 is synthetically lethal in vitro and in vivo and significantly extends the survival of mice bearing intracranial GBM xenografts. Collectively, our studies advance our understanding of oncogene-induced metabolic vulnerabilities in GBMs.

Keywords:  CP: Cancer; CP: Metabolism; TERT; brain tumors; cancer; glioblastoma; glutamine metabolism; glutathione; in vivo stable isotope tracing; metabolic synthetic lethality; metabolomics; nucleotide biosynthesis; telomerase reverse transcriptase

DOI:  https://doi.org/10.1016/j.celrep.2025.115596
Nat Commun. 2025 Apr 24. 16(1): 3857

Cell Painting PLUS: expanding the multiplexing capacity of Cell Painting-based phenotypic profiling using iterative staining-elution cycles.

Elena von Coburg, Marlene Wedler, Jose M Muino, Christopher Wolff, Nils Körber, Sebastian Dunst, Shu Liu.

Phenotypic changes in the morphology and internal organization of cells can indicate perturbations in cell functions. Therefore, imaging-based high-throughput phenotypic profiling (HTPP) applications such as Cell Painting (CP) play an important role in basic and translational research, drug discovery, and regulatory toxicology. Here we present the Cell Painting PLUS (CPP) assay, an efficient, robust and broadly applicable approach that further expands the versatility of available HTPP methods and offers additional options for addressing mode-of-action specific research questions. An iterative staining-elution cycle allows multiplexing of at least seven fluorescent dyes that label nine different subcellular compartments and organelles including the plasma membrane, actin cytoskeleton, cytoplasmic RNA, nucleoli, lysosomes, nuclear DNA, endoplasmic reticulum, mitochondria, and Golgi apparatus. In this way, CPP significantly expands the flexibility, customizability, and multiplexing capacity of the original CP method and, importantly, also improves the organelle-specificity and diversity of the phenotypic profiles due to the separate imaging and analysis of single dyes in individual channels.

DOI: https://doi.org/10.1038/s41467-025-58765-8
Proc Natl Acad Sci U S A. 2025 Apr 29. 122(17): e2413651122

Neuronal autophagy controls excitability via ryanodine receptor-mediated regulation of calcium-activated potassium channel function.

Gaga Kochlamazashvili, Aarti Swaminathan, Alexander Stumpf, Amit Kumar, York Posor, Dietmar Schmitz, Volker Haucke, Marijn Kuijpers.

  Glutamate-mediated neuronal hyperexcitation plays a causative role in eliciting seizures and promoting epileptogenesis. Recent data suggest that altered autophagy can contribute to the occurrence of epilepsy. We examined the role of autophagy in neuronal physiology by generating knockout mice conditionally lacking the essential autophagy protein ATG5 in glutamatergic neurons. We demonstrate that conditional genetic blockade of neuronal autophagy results in action potential narrowing, axonal hyperexcitability, and an increase in kainate-induced epileptiform bursts ex vivo, indicative of a lower threshold for the induction of epileptic seizures. Neuronal hyperexcitability in hippocampal slices from conditional ATG5 knockout mice is due to elevated activity of the large conductance calcium-activated potassium channel BKCa downstream of calcium influx via the endoplasmic reticulum (ER)-localized calcium channel ryanodine receptor (RYR). Consistently, pharmacological blockade of RYR or BKCa function rescued hyperexcitability and reduced the frequency of kainate-induced epileptiform bursts in ATG5 cKO brain slices. Our findings reveal a physiological role for neuronal autophagy in the regulation of neuronal excitability via the control of RYR-mediated calcium release, and thereby, calcium-activated potassium channel function in the mammalian brain.

Keywords:  action potential; autophagy; neuronal excitability; potassium channel; ryanodine receptor

DOI:  https://doi.org/10.1073/pnas.2413651122
Sci Adv. 2025 Apr 25. 11(17): eadv4410

Conformational plasticity of mitochondrial VDAC2 controls the kinetics of its interaction with cytosolic proteins.

William M Rosencrans, Harisankar Khuntia, Motahareh Ghahari Larimi, Radhakrishnan Mahalakshmi, Tsyr-Yan Yu, Sergey M Bezrukov, Tatiana K Rostovtseva.

The voltage-dependent anion channel (VDAC) is a key conduit of the mitochondrial outer membrane for water-soluble metabolites and ions. Among the three mammalian isoforms, VDAC2 is unique because of its embryonic lethality upon knockout. Using single-molecule electrophysiology, we investigate the biophysical properties that distinguish VDAC2 from VDAC1 and VDAC3. Unlike the latter, VDAC2 exhibits dynamic switching between multiple high-conductance, anion-selective substates. Using α-synuclein (αSyn)-a known VDAC1 cytosolic regulator-we found that higher-conductance substates correlate with increased on-rates of αSyn-VDAC2 interaction but shorter blockage times, maintaining a consistent equilibrium constant across all substates. This suggests that αSyn detects VDAC2's dynamic structural variations before final binding. We explored the dependence of VDAC2's unique amino-terminal extension and cysteines on substate behavior, finding that both structural elements modulate substate occurrence. The discovered conformational flexibility enables VDAC2 recognition by diverse binding partners, explaining its critical physiological role via dynamical adaptation to mitochondrial metabolic conditions.

DOI: https://doi.org/10.1126/sciadv.adv4410
Nat Metab. 2025 Apr;7(4): 823-841

Hepatic gluconeogenesis and PDK3 upregulation drive cancer cachexia in flies and mice.

Ying Liu, Ezequiel Dantas, Miriam Ferrer, Ting Miao, Mujeeb Qadiri, Yifang Liu, Aram Comjean, Emma E Davidson, Tiffany Perrier, Tanvir Ahmed, Yanhui Hu, Marcus D Goncalves, Tobias Janowitz, Norbert Perrimon.

Cachexia, a severe wasting syndrome characterized by tumour-induced metabolic dysregulation, is a leading cause of death in people with cancer, yet its underlying mechanisms remain poorly understood. Here we show that a longitudinal full-body single-nuclei-resolution transcriptome analysis in a Drosophila model of cancer cachexia captures interorgan dysregulations. Our study reveals that the tumour-secreted interleukin-like cytokine Upd3 induces fat-body expression of Pepck1 and Pdk, key regulators of gluconeogenesis, disrupting glucose metabolism and contributing to cachexia. Similarly, in mouse cancer cachexia models, we observe IL-6-JAK-STAT-signalling-mediated induction of Pck1 and Pdk3 expression in the liver. Increased expression of these genes in fly, mouse, and human correlates with poor prognosis, and hepatic expression of Pdk3 emerges as a previously unknown mechanism contributing to metabolic dysfunction in cancer cachexia. This study highlights the conserved nature of tumour-induced metabolic disruptions and identifies potential therapeutic targets to mitigate cachexia in people with cancer.

DOI: https://doi.org/10.1038/s42255-025-01265-2