bims-celmim 2026-09-13 papers

bims-celmim

Biomed News

on Cellular and mitochondrial metabolism

Issue of 2026–09–13
thirty-one papers selected by
Marc Segarra Mondejar, AINA

InsP3R signaling and actomyosin-dependent mitochondrial dynamics play essential roles in mitochondrial stress-induced longevity.
Vitamin C is a physiological modulator for mitochondrial calcium uptake.
Redox state of Protein Kinase A RIα coordinates lysosomal calcium signaling and mitochondrial homeostasis.
Malic enzyme 1 senses L-lactate to determine tumor heterogeneity.
A mitochondria-targeted ratiometric fluorescent probe for visualizing NO generation coupled with mitochondrial pH variations during autophagy.
Autofluorescence lifetime imaging resolves cell heterogeneity within peripheral blood mononuclear cells.
Reaction-based near-infrared fluorescent probes for monitoring NADH-associated redox remodeling in ferroptosis.
MCAT-mediated mitochondrial fatty acid metabolism regulates Lauren subtype divergence and suppresses gastric cancer progression through ROS/P53-dependent mitophagy and ferroptosis.
Adipocyte-derived β-hydroxybutyrate confers metabolic resilience in multiple myeloma.
Anesthesia, perimortem conditions, and brain harvest method govern the measured metabolome: analysis of substandard samples generates flawed metabolite levels.
A simple, anesthesia-free infusion technique for in vivo metabolic tracing.
Rational design of a near-infrared fluorescent probe for highly specific sensing carboxylesterase 2 and its applications in bioimaging.
4D spatiotemporal landscape of mitochondrial phenotypes across cellular states unlocked through representation learning.
Macrophages tune NK cell IFNγ production through direct lipid transfer.
Rotenone-induced oxidative stress triggers peroxisomal alterations in BV-2 microglial cells.
Glutaminase contributes to MYC-induced cell-autonomous autophagy and to Ras V12 -dependent non-autonomous autophagy in the Drosophila wing disc epithelium.
Tryptophan-kynurenine pathway dysregulation and its association with inflammatory biomarkers.
Deubiquitinases in mitophagy: therapeutic control of mitochondrial quality.
H4K5 lactylation exacerbates acute myocarditis by driving a positive feedback loop between inflammation and metabolic dysfunction.
Spatially resolved lactate-glycolysis transcriptional programs are associated with neutrophil-enriched immune remodeling in lung adenocarcinoma.
Linking cellular metabolism to mitochondrial outer membrane potential.
Calmodulin controls spatial and temporal specificity of calcium-induced calcium release.
Metabolic regulation of calcium homeostasis via SERCA succination.
Differential activation of TCA cycle activity and PDH flux by dichloroacetate in skeletal muscle measured by hyperpolarized [2-13C,3-2H3]pyruvate.
Lactate-Mediated Lysine Lactylation in Renal Fibrosis: Current Progress and Challenges.
Mitochondrial ecosystem restoration in Alzheimer's disease: from mechanisms to multi-target therapeutic strategies.
Mitochondrial Raf1 regulates glutamine catabolism.
Heme as a Versatile Signaling Molecule: Coordinating Mitochondrial Metabolism with Global Cellular Responses.
Mechanistic trade-offs between local and long-range signaling activity in natural and synthetic morphogens.
Mitochondrial NMNAT3 reduces amyloid aggregates in Drosophila and alters the amyloid processing in the 3xTgAD mouse.
Tetrazine-based bioorthogonal reactions to image hypoxia in cancer cells.

Nat Commun. 2026 Aug 13. pii: 9729. [Epub ahead of print]17(1):

InsP3R signaling and actomyosin-dependent mitochondrial dynamics play essential roles in mitochondrial stress-induced longevity.

Gaomin Feng, Elizabeth M Ruark, Alexandra G Mulligan, Eric K F Donahue, Anthony L Hoang, Brianne Jacquet-Cribe, Li Peng, Kristopher Burkewitz.

Certain forms of mitochondrial impairment confer longevity, while disease-associated mitochondrial dysfunction triggers pathogenesis. The adaptive pathways that distinguish benefit from pathology remain unclear. Here we reveal that longevity induced by mitochondrial Complex I/nuo-6 mutation in C. elegans is dependent on the endoplasmic reticulum (ER) Ca2+ channel, InsP3R. To explain this connection, we test multiple candidate links between Ca2+ and mitochondrial homeostasis previously established in vitro, including mitochondrial calcium uniporter (MCU)-dependent stimulation of respiration and cytosolic pathways regulating mitochondrial dynamics. We find that MCU is dispensable for both respiration and longevity in Complex I mutants. Conversely, transcriptomic profiling and imaging reveal InsP3R impairment results in maladaptive expansion of compromised mitochondrial networks. We provide evidence that this aberrant mitochondrial expansion results from disruption of a conserved, InsP3R-dependent actin remodeling network centered on Arp2/3. Disruption of actin remodeling or autophagy mimics the mitochondrial expansion and longevity suppression of InsP3R mutants. Conversely, driving mitochondrial fragmentation ameliorates mitochondrial expansion and rescues longevity in InsP3R mutants, supporting a model in which InsP3R-dependent actin remodeling is required for segregation and clearance of mitochondria. These findings identify an inter-organelle signaling axis linking ER calcium release and cytoskeletal remodeling to adaptive mitochondrial responses associated with longevity.

DOI: https://doi.org/10.1038/s41467-026-76514-3
Biochem Biophys Res Commun. 2026 Sep 02. pii: S0006-291X(26)01300-8. [Epub ahead of print]835 154536

Vitamin C is a physiological modulator for mitochondrial calcium uptake.

Jialong Li, Kozo Hamada.

  Mitochondrial calcium homeostasis is critical for bioenergetics, cell signaling, and cell survival and death, but its regulatory mechanism remains largely unknown. Here, a mitochondria-targeted genetically encoded calcium indicator has revealed that physiological concentrations of ascorbic acid (vitamin C) suppress mitochondrial calcium uptake in both intact living cells and permeabilized cells and enhance intracellular calcium signaling compared with ascorbate-deprived conditions. Mechanistic analyses indicate that this effect is mediated by a reduction in mitochondrial membrane potential, the primary driving force for mitochondrial calcium uptake. These findings uncover an unrecognized role of ascorbic acid in mitochondrial calcium homeostasis. Given the roles of mitochondrial calcium in neurodegeneration and cancer cell bioenergetics, our findings provide new insights into disease pathophysiology and potential therapeutic strategies.

Keywords:  Ca(2+) signaling; Genetically encoded Ca(2+) indicator; Mitochondria-associated ER membranes; Mitochondrial Ca(2+) homeostasis; Mitochondrial Ca(2+) uniporter; Mitochondrial membrane potential

DOI:  https://doi.org/10.1016/j.bbrc.2026.154536
Proc Natl Acad Sci U S A. 2026 Sep 15. 123(37): e2600754123

Redox state of Protein Kinase A RIα coordinates lysosomal calcium signaling and mitochondrial homeostasis.

Lorena Fernandez-Mosquera, Philip Eaton.

  Protein Kinase A (PKA) Regulatory RIα cysteine redox state regulates docking to D-AKAP1 and may control Drp1 phosphorylation, a principal mediator of mitochondrial fission. RIα C17S knock-in (KI) mice, unable to form disulfides and therefore mimicking the reduced kinase, exhibited enlarged dysfunctional mitochondria. Unexpectedly, this abnormal mitochondrial morphology, which was accompanied by reduced respiration, decreased membrane potential, increased reactive oxygen species and impaired treadmill performance, was not explained by altered Drp1 Ser637 phosphorylation. Transcriptomic analysis revealed decreased mitochondrial biogenesis without loss of total mitochondrial mass, consistent with impaired mitochondrial turnover. KI cells showed impaired lysosomal proteolysis, altered lysosomal calcium homeostasis, reduced RIα-lysosome colocalization and markedly diminished TRPML1 abundance. Pharmacological modulation of lysosomal calcium pathways restored lysosomal calcium signaling in KI cells, whereas activation of TRPML1 signaling impaired mitochondrial respiration in wildtype cells toward KI levels. Together, these findings support a role for disulfide-RIα in coordinating lysosomal calcium signaling and mitochondrial quality control, such that loss of this oxidation state promotes accumulation of dysfunctional mitochondria.

Keywords:  PKA; calcium; lysosome; mitochondria; redox

DOI:  https://doi.org/10.1073/pnas.2600754123
Signal Transduct Target Ther. 2026 Sep 11. pii: 386. [Epub ahead of print]11(1):

Malic enzyme 1 senses L-lactate to determine tumor heterogeneity.

Si-Yi Cao, Kewen Hu, Shijing Huang, Xiao-Lin Guan, Jian Wang, Yuan Shen, Hui Ming, Aihong Gu, Chao Wang, Xiao Shen, Qing Wu, Zhengjun Chen, Miao Yin, Wenyu Wen, Qun-Ying Lei.

L-lactate is generally elevated in tumors and acts as a signaling molecule that promotes tumor progression. Here, we reveal that malic enzyme 1 (ME1) functions as a previously unrecognized sensor of L-lactate through direct binding at arginine 155 (R155), thereby potentiating malignancy. Mechanistically, L-lactate binding promotes the nuclear translocation of ME1, a process involving reduced acetylation at lysine 362 (K362) and facilitated by nuclear import of karyopherin-α 4 (KPNA4). Nuclear accumulation of ME1 enhances metastatic potential, which is correlated with increased interaction with hepatoma-derived growth factor (HDGF) and acquisition of an epithelial‒mesenchymal transition (EMT)-related phenotype. Under nutrient-deficient conditions, L-lactate promotes the assembly of a ME1-lactate dehydrogenase B (LDHB) complex, which enhances oxidative phosphorylation (OXPHOS) and increases ATP production, suggesting a metabolic adaptive mechanism that supports tumor cell survival. Notably, the ME1R155A mutation, which disrupts L-lactate binding, abolishes the protumorigenic effect of the L-lactate-ME1 axis on tumor progression in vivo. In conclusion, our findings identify ME1 as a direct sensor of L-lactate and support a model in which lactate-mediated signaling and metabolic adaptation converge on ME1 to regulate tumor cell plasticity in a context-dependent manner under heterogeneous metabolic conditions. These insights advance our understanding of the spatiotemporal control of metabolic adaptation in cancer and reveal a potential therapeutic target.

DOI: https://doi.org/10.1038/s41392-026-02839-6
Talanta. 2026 Sep 06. pii: S0039-9140(26)01222-1. [Epub ahead of print]312(Pt C): 130566

A mitochondria-targeted ratiometric fluorescent probe for visualizing NO generation coupled with mitochondrial pH variations during autophagy.

Liguo Ji, Aoxiang Fu, Yingying Yang, Yixuan Wang, Yuying Zhang, Shaoli Cui, Na Gao, Linlin Yang, Wanbing Shang, Tangqiang Sun, Zhijun Yang, Guangjie He.

  Autophagy is a vital cytoprotective pathway against oxidative stress, and the regulatory function of reactive oxygen species (ROS) in autophagy has been thoroughly investigated. However, nitric oxide (NO), a representative reactive nitrogen species, exerts dual contradictory effects on autophagy, and the underlying reason for such discrepancy remains ambiguous. Existing studies indicate that the biological activity of NO is highly dependent on mitochondrial microenvironmental pH; the pH fluctuation during autophagy further modulates NO-mediated protein modification and downstream autophagic signaling. Nevertheless, conventional fluorescent probes can only separately detect NO or mitochondrial pH, lacking the capacity to synchronously track the two parameters in mitochondria, which severely restricts the exploration of the coupling relationship between NO and pH during autophagy. Herein, we constructed a benzindolium-functionalized mitochondria-targeted ratiometric fluorescent probe for simultaneous visualization of mitochondrial NO and pH. The probe possesses donor-acceptor structures whose spectral properties are modulated by ambient pH via protonation and deprotonation, and it only responds to pH variation in the presence of NO, guaranteeing the specificity of dual-parameter imaging. Spectral characterizations confirm the distinct ratiometric fluorescence shifts triggered by NO and pH co-stimulation. Cellular imaging experiments based on rapamycin-induced and ischemia-reperfusion-induced autophagy models demonstrate that autophagy activation is accompanied by upregulated mitochondrial NO and synchronous mitochondrial pH alternation. Distinct from single-analyte probes reported previously, this probe enables real-time synchronous ratiometric imaging of mitochondrial NO and pH in living cells. This work provides a reliable visual tool to monitor the dynamic coupling of NO and mitochondrial pH during autophagy, laying a foundation for further dissecting the disparate regulatory effects of NO on autophagy under varied pathological microenvironments.

Keywords:  Autophagy imaging; ICT modulation; Mitochondrial targeting; Nitric oxide; Ratiometric fluorescent probe; Triazole

DOI:  https://doi.org/10.1016/j.talanta.2026.130566
Biophotonics Discov. 2026 Jul;3(3): 035003

Autofluorescence lifetime imaging resolves cell heterogeneity within peripheral blood mononuclear cells.

Jeremiah M Riendeau, Lucia Hockerman, Elizabeth Maly, Kayvan Samimi, Melissa C Skala.

   Significance: Standard methods to characterize peripheral blood mononuclear cells (PBMCs) are often destructive, lack metabolic information, or do not provide single-cell resolution. Label-free tools that nondestructively measure single-cell metabolism within PBMCs can provide new layers of information to characterize disease state and cell therapy potential.
Aim: We aim to determine whether nondestructive fluorescence lifetime imaging microscopy (FLIM) of the endogenous metabolic cofactors nicotinamide adenine dinucleotide (phosphate) (reduced form) and flavin adenine dinucleotide (oxidized form), or optical metabolic imaging (OMI), can identify immune cell subsets and activation state within heterogeneous PBMC cultures.
Approach: OMI measured single-cell metabolism of PBMCs from three different human donors in the quiescent or activated (phorbol 12-myristate 13-acetate and ionomycin) state. Fluorescent antibodies were used as ground truth labels for single-cell classifiers of immune cell subtypes.
Results: OMI identified quiescent versus activated PBMCs with 94% accuracy at only 2 h post-stimulation, identified monocytes within quiescent and activated PBMCs with 96% and 88% recall, respectively, and identified NK cells within quiescent and activated PBMCs with 74% recall.
Conclusion: OMI identifies activation state and immune cell subpopulations within PBMCs, enabling single-cell and label-free measurements of metabolic heterogeneity within complex PBMC samples. Therefore, OMI could enhance PBMC immunophenotyping for diagnostic and therapeutic applications.

Keywords:  autofluorescence; fluorescence lifetime imaging microscopy; immune cells; label-free imaging; metabolism; optical imaging; peripheral blood mononuclear cells

DOI:  https://doi.org/10.1117/1.BIOS.3.3.035003
Bioorg Chem. 2026 Sep 07. pii: S0045-2068(26)01029-1. [Epub ahead of print]182 110493

Reaction-based near-infrared fluorescent probes for monitoring NADH-associated redox remodeling in ferroptosis.

Yanbo Li, Yating Sha, Danyi He, Yishu Yu, Yaru You, Tianqing Ye, Haiying Liu, Jianbo Wang, Jingjing Li, Mingxi Fang.

  Nicotinamide adenine dinucleotide (NADH) plays a central role in cellular redox balance and metabolic regulation, yet its dynamic behavior during ferroptosis remains insufficiently understood. Herein, we report reaction-based fluorescent probes, QX-I and QX-II, for imaging NADH-associated redox changes. Two probes were constructed by conjugating a responsive group (methyl-quinolinium salt) with an electron-withdrawing Xanthene moiety. The conjugated Xanthene structure not only shifts the emission wavelength of the probes into the near-infrared region, but also endows probe QX-I (modified with a single N-ethyl group) with advantages such as high fluorescence enhancement, rapid response, high sensitivity, and good selectivity. This probe enables visualization of endogenous NADH fluctuations in HepG2 and 4 T1 cells under metabolic regulation. Notably, QX-I was further employed to investigate NADH-related dynamic changes during ferroptosis. Cell and in vivo experiments demonstrated a decoupling relationship between lipid peroxidation and NADH-related redox states during ferroptosis inhibition. Overall, this study provides an effective tool for monitoring NADH-related redox remodeling and offers new insights into ferroptosis-associated redox metabolism.

Keywords:  Biosensing; Ferroptosis; In vivo imaging; NADH-activated fluorescent probe; Redox metabolism

DOI:  https://doi.org/10.1016/j.bioorg.2026.110493
Cell Death Differ. 2026 Sep 08.

MCAT-mediated mitochondrial fatty acid metabolism regulates Lauren subtype divergence and suppresses gastric cancer progression through ROS/P53-dependent mitophagy and ferroptosis.

Yufei Wang, Meng Zhu, Xin Yin, Tianyi Fang, Lei Zhang, Yujuan Jiao, Hongxin Wang, Zipu Dong, Tengteng Liu, Yingwei Xue.

Gastric cancer (GC) displays marked heterogeneity under the Lauren classification, yet the metabolic determinants of subtype divergence remain unclear. Here, we identify Malonyl-CoA:ACP transacylase (MCAT), a Lauren subtype-associated gene encoding a key mitochondrial fatty acid synthesis (mtFAS) enzyme, as a subtype-specific tumor suppressor in GC. Integrative multi-omics profiling revealed that MCAT expression is enriched in intestinal-type GC and correlates with favorable prognosis. Mechanistically, MCAT overexpression drives metabolic reprogramming through mitochondrial free fatty acid overload, suppressing β-oxidation while elevating mitochondrial reactive oxygen species (ROS), which triggers P53 phosphorylation at Ser15. This event concurrently activates PINK1/Parkin-mediated mitophagy and suppresses the SLC7A11/GPX4 axis to induce ferroptosis. Genetic rescue experiments confirmed that P53-Ser15 phosphorylation is essential for both mitophagy and ferroptosis induction. Endogenous MCAT levels are sufficient to determine basal ROS/P53/mitophagy/ferroptosis axis activity, and knockdown in high-expressing cells reverses these phenotypes, supporting a physiological, threshold-dependent role. In vivo, MCAT overexpression suppresses tumor growth and enhances mitophagy and ferroptosis markers. Collectively, these findings establish MCAT as a metabolic switch that links mtFAS to ROS/P53-dependent cell death, providing a potential biomarker and therapeutic target for GC.

DOI: https://doi.org/10.1038/s41418-026-01867-7
Nat Commun. 2026 Aug 11. pii: 9611. [Epub ahead of print]17(1):

Adipocyte-derived β-hydroxybutyrate confers metabolic resilience in multiple myeloma.

Chen Song, Peng Yang, Yu Li, Tao Xia, Rui Li, Mengmeng Guo, Wenjun Li, Chenfeng Liu, Tiantian Jia, Yansheng Wang, Xunxia Bao, Qi Wang, Yuan Yao, Qian Dai, Huan Liu, Zongwei Li.

Multiple myeloma (MM) remains an incurable blood cancer. Obesity is a known risk factor, but how adipocytes promote MM progression is not fully understood. Here, we uncover a metabolic crosstalk between adipocytes and MM cells that promotes MM cell survival under glucose deprivation. We show that glucose restriction activates AMPK, disrupting HSP90-IRF4 binding and rendering IRF4 susceptible to TRIM21-mediated proteasomal degradation. Paradoxically, the same stress stimulates adipocytes to produce β-hydroxybutyrate (β-OHB). MM cells utilize β-OHB through OXCT1-mediated ketolysis, fueling NAT10-dependent acetylation of IRF4 at K87, which restores IRF4-HSP90 binding and sustains tumor cell survival. Genetic ablation of the rate-limiting ketogenic enzyme Hmgcs2 in adipocytes abrogates this protective effect. Importantly, combining an AMPK activator (metformin) with an OXCT1 inhibitor (pimozide) or a NAT10 inhibitor (remodelin) shows synergistic anti-tumor activity in vivo. Our findings position adipocyte-derived β-OHB as a critical metabolic adaptor and highlight a potential combination therapy for MM.

DOI: https://doi.org/10.1038/s41467-026-76595-0
Oxf Open Neurosci. 2026 ;5 kvag011

Anesthesia, perimortem conditions, and brain harvest method govern the measured metabolome: analysis of substandard samples generates flawed metabolite levels.

Gerald A Dienel.

  Metabolism and energetics are closely integrated with brain function, and understanding how metabolic dysfunction contributes to neurological disease may help improve therapeutic approaches. Characterization of in situ metabolite levels, spatial distributions, and metabolomes requires special attention to anesthesia use, perimortem conditions, and tissue harvest. Anesthesia, CO2 asphyxiation, vascular perfusion, and decapitation alter metabolism, thereby substantially changing the metabolome, lipidome, and neurotransmitter profile. Analysis of flawed samples produces artifactual data, raising concerns about conclusions regarding the cellular basis of metabolism, metabolite shuttling, pathway activities, labeled metabolite profiling and imaging, and relationships between metabolism, function, and neurological disorders. Appropriate procedures for in vivo metabolic assays and tissue harvest are widely-unrecognized but essential components of metabolic and metabolomic studies.

Keywords:  Alzheimer’s disease; Postmortem ischemia; [13c]glucose metabolite profiling; brain harvest; metabolome; neuronal glycolytic upregulation

DOI:  https://doi.org/10.1093/oons/kvag011
Sci Adv. 2026 Sep 11. 12(37): eaeg1157

A simple, anesthesia-free infusion technique for in vivo metabolic tracing.

Yumi Kim, Samantha Caldwell, Meredith Long, Dominique Abrahams, Margi Baldwin, Gina M DeNicola.

Accurate metabolic flux analysis requires tracer delivery that preserves physiological metabolism. Current methods may distort metabolism through isoflurane anesthesia, surgical stress, or complex procedures. We demonstrate that isoflurane anesthesia profoundly alters serum and tissue metabolism across multiple pathways. In serum, acylcarnitines and fatty acids were broadly decreased, whereas amino acid metabolites and select nucleotide species were increased. Across multiple organs, isoflurane induced coordinated metabolic remodeling and distinct tissue-specific responses, including glycolytic remodeling in the brain and amino acid accumulation in the pancreas. To address these metabolic disturbances, we established a nonsurgical tail vein catheterization method completed in minutes under brief isoflurane anesthesia that enables multihour tracer infusion in awake, freely moving mice. Using U-13C6-cystine infusion, this method achieved robust cysteine labeling and downstream labeling comparable to jugular infusion while maintaining circulating cystine pools closer to physiological levels. This platform provides a practical approach for in vivo stable isotope tracing under more physiological conditions.

DOI: https://doi.org/10.1126/sciadv.aeg1157
J Mater Chem B. 2026 Sep 08.

Rational design of a near-infrared fluorescent probe for highly specific sensing carboxylesterase 2 and its applications in bioimaging.

Chia-Hung Li, Tsai-Xuan Lin, Shu-Pao Wu.

Carboxylesterase 2 (CES2) is a clinically significant serine hydrolase that governs the metabolic activation and detoxification of numerous ester-containing drugs and prodrugs. Despite its pivotal role in liver and colorectal cancer progression, direct in situ imaging of CES2 activity remains challenging due to the scarcity of probes with high isoform selectivity. To address this, we herein present XM-CE, a rationally engineered near-infrared (NIR) fluorescent probe specifically optimized for the highly sensitive and selective monitoring of CES2 activity. By integrating a CES2-responsive ester trigger with the XM-OH fluorophore, XM-CE yields a pronounced fluorescence turn-on response at 635 nm upon enzymatic hydrolysis. The probe demonstrates exceptional sensitivity with a limit of detection (LOD) of 0.023 U mL-1, alongside superior biocompatibility. These attributes enable high-resolution, real-time visualization of endogenous CES2 dynamics in living cells, zebrafish larvae, and tumor-bearing murine models. Collectively, our findings establish XM-CE as a robust analytical tool for mapping tissue-specific expression and monitoring enzyme regulation in vivo, offering significant potential for advancing biomedical research and clinical diagnostics.

DOI: https://doi.org/10.1039/d6tb01204c
Cell. 2026 Sep 10. pii: S0092-8674(26)01001-9. [Epub ahead of print]

4D spatiotemporal landscape of mitochondrial phenotypes across cellular states unlocked through representation learning.

Dhruv Agarwal, Zichen Wang, Eric Arkfeld, Andre Modolo, Parth Natekar, Hiroyuki Hakozaki, Mehul Arora, Gillian McMahon, Siddharth Nahar, Manav Doshi, Johannes Schöneberg.

  Mitochondria are four-dimensional (4D: x, y, z, and time) organelles essential for cellular function. Characterizing their 4D phenotypic landscape across diverse cellular states requires both 4D imaging and analytical frameworks. We present MitoSpace, a self-supervised deep learning model trained without labels on terabytes of single-cell lattice light-sheet microscopy data of mitochondria under mechanistically distinct perturbations. MitoSpace learns latent representations that outperform predefined features in drug classification and capture interpretable variation in mitochondrial morphology and dynamics. Regression probes predict mitochondrial membrane potential from the learned representations (R2 = 0.91), establishing a quantitative mapping between form and function at the single-cell level. MitoSpace also generalizes zero-shot to unseen perturbations and human lung organoids. Dimensionality ablation reveals that representation quality improves monotonically from 2D to 3D to 4D, demonstrating the importance of volumetric and temporal information. The model, dataset, and interactive explorer are publicly available, providing a foundation for 4D phenotypic screening.

Keywords:  contrastive learning; drug mechanism of action; foundation model; high-content phenotypic screening; lattice light-sheet microscopy; live-cell 4D imaging; mitochondria; mitochondrial dynamics; mitochondrial membrane potential; self-supervised learning

DOI:  https://doi.org/10.1016/j.cell.2026.08.028
Nat Commun. 2026 Aug 08. pii: 9527. [Epub ahead of print]17(1):

Macrophages tune NK cell IFNγ production through direct lipid transfer.

Cathal Keane, Shauna Mayock, Carrie Corkish, Ella Rogerson, Cristhiane Favero de Aguiar, Ya Gao, Sarah Kenny, Lorraine Brennan, Suzanne M Cloonan, David K Finlay.

Natural killer (NK) cells are critical effectors of innate immunity, but their activity is strongly influenced by metabolic state. While intrinsic NK metabolism has been studied extensively, less is known about how surrounding immune cells shape NK cell function. Here, we identify a direct metabolic communication axis between macrophages and NK cells. Using co-culture and in vivo models, we show that lipopolysaccharide-stimulated macrophages induce lipid accumulation in NK cells that suppresses mTORC1 activity and the production of IFNγ. This lipid accumulation is visualised as increased lipid droplets content in NK cells, generated using fatty acids synthesised within the macrophages. Genetic and pharmacological approaches show that fatty acid transfer from macrophages to NK cells requires cell-cell contact and is associated with CD36 protein transfer via trogocytosis. Blocking fatty acid synthesis specifically in macrophages prevents lipid accumulation in NK cells and restores both mTORC1 activity and IFNγ production. These findings define a previously unrecognized mechanism of macrophage-NK cell cross-regulation, revealing how metabolic exchange constrains NK effector function and establishing a feedback circuit with implications for hyperinflammation and immunotherapy.

DOI: https://doi.org/10.1038/s41467-026-76444-0
Front Cell Neurosci. 2026 ;20 1941513

Rotenone-induced oxidative stress triggers peroxisomal alterations in BV-2 microglial cells.

Alessio Valenza, Maurizio Muzzi, Francesca Rendina, Irene Montali, Daniele Pensabene, Anna Fracassi, Marco Segatto, Sandra Moreno.

   Introduction: Peroxisomes are highly dynamic organelles that contribute to cellular homeostasis by coordinating lipid metabolism, reactive oxygen species handling, and adaptive responses to metabolic stress. Their plasticity is particularly relevant in the nervous system, where peroxisomes cooperate with mitochondria to maintain redox and metabolic balance in neuronal and glial cells. Peroxisome proliferator-activated receptor alpha (PPARα), together with its coactivator PGC-1α, represents a major transcriptional regulator of peroxisomal and mitochondrial metabolic programs.
Methods: BV2 microglial cells were exposed to rotenone to investigate how mitochondrial oxidative stress influences the peroxisomal compartment. Mitochondrial and peroxisomal morphology, intracellular distribution, oxidative damage, and the expression of proteins involved in peroxisomal metabolism and PPARα signaling were evaluated.
Results: Rotenone induced a stress-associated microglial phenotype characterized by cytoskeletal remodeling, mitochondrial network disruption, and oxidative damage. These alterations were accompanied by a coordinated reorganization of the peroxisomal compartment, including increased abundance of peroxisomal membrane markers, redistribution of peroxisomes toward the perinuclear region, and enhanced expression of enzymes associated with peroxisomal fatty acid oxidation. An increased spatial association between peroxisomes and mitochondria was also observed, suggesting that peroxisomal remodeling forms part of a broader inter-organelle adaptation to mitochondrial dysfunction. These changes occurred together with increased nuclear phosphorylated PPARα and enhanced PGC-1α immunoreactivity, supporting the engagement of a PPARα-PGC-1α-related transcriptional response.
Discussion: Overall, our findings suggest that mitochondrial dysfunction in microglial cells activates a PPARα-associated adaptive program that promotes peroxisomal remodeling and strengthens mitochondria-peroxisome coordination. This response may represent an attempt to preserve lipid and redox homeostasis during cellular stress and identifies PPARα-regulated peroxisomal pathways as potentially relevant components of microglial metabolic adaptation in neurodegenerative conditions.

Keywords:  microglia; mitochondria; oxidative stress; peroxisomes; rotenone

DOI:  https://doi.org/10.3389/fncel.2026.1941513
bioRxiv. 2026 Sep 02. pii: 2026.08.31.748041. [Epub ahead of print]

Glutaminase contributes to MYC-induced cell-autonomous autophagy and to Ras V12 -dependent non-autonomous autophagy in the Drosophila wing disc epithelium.

Francesca Destefanis, Lorenzo Conci, Shivani Bajaj, Valeria Manara, Paola Bellosta.

MYC-driven metabolic reprogramming supports rapid cell growth but also creates metabolic demands that require adaptive mechanisms to maintain cellular homeostasis. Here, combining clonal analysis in Drosophila wing imaginal discs with studies in Schneider S2 cells, we identify glutamine metabolism as a component of Myc-induced autophagy. Myc increased the expression of genes involved in glutamine utilization, including glutaminase (GLS), and enhanced ammonia production, a metabolic by-product of glutaminolysis. Genetic depletion of GLS in clones suppressed the accumulation of Myc-induced Atg8a-positive structures and reduced autophagic flux, demonstrating that glutaminase contributes to the autophagic response elicited by Myc. Exogenous NH₄Cl was sufficient to induce Atg8a-positive structures and partially restored their accumulation following GLS depletion, supporting ammonia as a downstream contributor to this response. Mechanistically, Myc-induced autophagy in clones required the core autophagy factor Atg5 but was not suppressed by activation of Rheb/TOR signaling or Atg1 depletion, indicating reduced dependence on canonical TOR-Atg1 regulation. We further found that Myc activity is required for Ras V12 -driven epithelial overgrowth and that Ras V12 cells induce a pronounced non-cell-autonomous accumulation of Atg8a-positive structures in wild-type cells surrounding Ras V12 clones. Depletion of either Myc or Gls in Ras V12 cells strongly reduced this neighboring autophagic response. Together, our findings identify Gls-dependent glutamine metabolism as a previously unrecognized component of Myc-induced autophagy and extend this relationship to Ras-transformed epithelia, linking the metabolic state of transformed cells to autophagy in the surrounding tissue.
Graphical abstract: Myc increases glutaminase (Gls)-dependent glutamine catabolism, promoting ammonia production and Atg5-dependent autophagy in Drosophila epithelial cells. In Ras V12- transformed epithelia, Myc and Gls are also required for the induction of autophagy in neighboring wild-type cells, suggesting that metabolic signals generated by transformed cells can elicit a non-cell-autonomous autophagic response. Solid arrows indicate experimentally supported relationships, whereas the dashed arrow denotes a proposed metabolic signal whose identity remains to be established.

DOI: https://doi.org/10.64898/2026.08.31.748041
Biomed Khim. 2026 Sep;72(4): 287-295

Tryptophan-kynurenine pathway dysregulation and its association with inflammatory biomarkers.

K M Gharab, M A Bik, D E Onmaz, S Abusoglu, A Unlu.

  In this study we have evaluated a potential value of tryptophan (Trp) and kynurenine pathway (KP) metabolites as biomarkers in different types of acute inflammation and investigated their possible association with classical inflammatory markers (CRP, ESR, and WBC). The study included 100 patients with elevated inflammatory parameters and 50 healthy controls. Chromatographic separation and analysis of samples were performed in positive electrospray ionization mode using a LC-MS/MS API 3200 device. We found that Trp levels decreased significantly in the patient groups, while levels of kynurenine (KYN) and kynurenic acid (KYNA) increased significantly. The Trp/KYN ratio was reduced considerably in the presence of inflammation. Moderate positive correlations were found between KP metabolites and CRP, ESR, and WBC values. It was observed that KP activity increased independently of the source of inflammation. The findings suggest that KP metabolites alone are not definitive for diagnosing inflammation but can serve as complementary biomarkers reflecting the biological severity of inflammation and the immune-metabolic response. Assessing Trp metabolism, particularly when combined with classical markers, can contribute to the molecular understanding of inflammation.

Keywords:  3-hydroxykynurenine; LC-MS/MS; inflammation; kynurenic acid; kynurenine; tryptophan

DOI:  https://doi.org/10.18097/PBMCE0050
Trends Pharmacol Sci. 2026 Sep 12. pii: S0165-6147(26)00206-3. [Epub ahead of print]

Deubiquitinases in mitophagy: therapeutic control of mitochondrial quality.

Yang Xu, Bahareh Behrouz, Andrew Lee, Gang Xin, Nuo Sun.

Mitochondrial quality control is essential for maintaining cellular and tissue homeostasis. Mitophagy, the selective autophagic removal of damaged mitochondria, is a central component of this process, and defects in mitophagy are increasingly linked to neurodegeneration, cardiovascular disease, cancer, and inherited mitochondrial disorders. Ubiquitin-dependent tagging of outer mitochondrial membrane proteins is a major mechanism for marking damaged mitochondria for clearance; however, recent advances reveal that mitochondrial deubiquitinases (DUBs) shape ubiquitin signaling at damaged mitochondria, thereby influencing the efficiency and selectivity of mitochondrial turnover. Moreover, DUBs are emerging as context-dependent editors of the mitochondrial ubiquitin code that link mitophagy to disease pathogenesis and therapeutic intervention. Here, we synthesize current understanding of mitochondrial DUBs in physiology and disease and discuss emerging pharmacological strategies to guide the development of mitophagy-targeted therapeutics.

DOI: https://doi.org/10.1016/j.tips.2026.08.009
Front Immunol. 2026 ;17 1896701

H4K5 lactylation exacerbates acute myocarditis by driving a positive feedback loop between inflammation and metabolic dysfunction.

Yawei Zhao, Yue Cai, Song Shen, Yuchen Wen, Tianyue Li, Lina Kang, Biao Xu, Xuan Sun.

  Acute myocarditis is a non-ischemic cardiomyopathy with rapid onset and high mortality. Immunometabolic reprogramming of macrophages is a key pathological feature. However the understanding of its mechanisms remains to be clarified. In this study, we found that acute myocarditis induced an increase in glycolysis and lactate accumulation. Inhibition of lactate production ameliorated myocardial injury. Further, we demonstrated that lactate promoted a pro-inflammatory transition of macrophages, thereby amplifying the inflammatory response. Inhibition of lactate in macrophage shifted its phenotype from a pro-inflammatory to an anti-inflammatory subtype. We also observed a significant increase in H4K5 lactylation in macrophages. Next, we identified that H4K5la drove the transcriptional expression of the Rap1, which in turn upregulated the TNF/NF-κB signaling. This lactate-dependent H4K5la was enriched in inflammatory pathways, forming a positive feedback loop that amplified inflammation. Inhibition of Rap1 reduced cardiac inflammation and broke this loop. These consequently lowered H4K5la levels and delayed ventricular remodeling. Collectively, this study reveals the role of H4K5la in promoting inflammatory cascades in myocarditis, and provides a potential therapeutic target for inflammatory cardiomyopathy.

Keywords:  H4K5la; acute myocarditis; histone lactylation; immune metabolism; macrophage

DOI:  https://doi.org/10.3389/fimmu.2026.1896701
Med Oncol. 2026 Sep 08. pii: 270. [Epub ahead of print]43(10):

Spatially resolved lactate-glycolysis transcriptional programs are associated with neutrophil-enriched immune remodeling in lung adenocarcinoma.

Yixian Liang, Jing Tan, Jiali Zhang, Binyu Wang, Danfei Shi, Longfei Ji, Xinmin Li, Daojun Yu, Yong Li.

  Metabolic reprogramming characterized by enhanced glycolysis and lactate production plays a critical role in tumor progression and immune regulation. However, the cellular distribution and spatial organization of lactate-glycolysis activity within the lung adenocarcinoma (LUAD) microenvironment remain incompletely understood. We integrated single-cell RNA sequencing, spatial transcriptomics, and bulk transcriptomic datasets from TCGA and GEO cohorts to characterize lactate-glycolysis-associated metabolic heterogeneity in LUAD. AUCell-based scoring was used to quantify metabolic activity at single-cell resolution. Associations with immune infiltration and clinical outcomes were evaluated, and key findings were validated using spatial transcriptomics, quantitative PCR, and immunohistochemistry. Cells exhibiting high lactate-glycolysis activity were predominantly enriched in fibroblasts and neutrophils, indicating that this metabolic program extends beyond malignant cells. A metabolism-associated gene signature, comprising RPS2, GAPDH, and LDHA, was consistently correlated with immune remodeling and an unfavorable prognosis. Spatial transcriptomics further revealed the co-localization of GAPDH and LDHA with neutrophil-enriched regions. These findings were supported by experimental validation in clinical specimens. Our study reveals that lactate-glycolysis reprogramming in LUAD is spatially structured and closely associated with neutrophil-enriched immune remodeling. This metabolism-associated immune regulatory pattern provides insight into the organization of the tumor microenvironment and may have implications for metabolic- and immune-oriented therapeutic strategies in lung adenocarcinoma.

Keywords:  Glycolysis; Lactate metabolism; Lung adenocarcinoma; Single-cell transcriptome; Spatial transcriptome; Tumor immune microenvironment

DOI:  https://doi.org/10.1007/s12032-026-03390-8
Mitochondrion. 2026 Sep 10. pii: S1567-7249(26)00108-X. [Epub ahead of print] 102218

Linking cellular metabolism to mitochondrial outer membrane potential.

Kaitlin Abrantes, Bethel G Beyene, Nina A Bautista, Wendy Fitzgerald, Tatiana K Rostovtseva, Sergey M Bezrukov, Megha Rajendran.

  The voltage-dependent anion channel (VDAC) of the mitochondrial outer membrane (MOM) responds to transmembrane voltage through intrinsic gating and voltage-dependent interactions with cytosolic proteins, such as α-synuclein and β-tubulin. Despite this characteristic voltage sensitivity found in vitro, the existence of a substantial MOM potential (ΔΨMOM) in vivo remains controversial. Using pH sensors targeted to the cytosol and the intermembrane space (IMS), we measured the difference in proton concentration across the MOM and calculated a ΔΨMOM of ~33 mV, positive from the IMS side in HeLa cells; in contrast, HEK-293 cells lacked substantial ΔΨMOM. Hexokinase 2 (HK2) is known to be overexpressed in cancer cells. Consistent with the previously proposed role of VDAC- HK complexation in ΔΨMOM generation, we observed lower HK2 expression in HEK-293 cells than in HeLa cells. In addition, by studying pH changes in the IMS and cytosol in response to changes in glucose and glucose-6-phosphate concentrations in HeLa cells, we establish a relationship between ΔΨMOM and metabolic activity in cancer cells. Thus, our results demonstrate the metabolism-dependent generation of ΔΨMOM and provide strong evidence that VDAC regulation by voltage, observed in in vitro studies, is highly relevant to cell physiology.

Keywords:  Hexokinase; VDAC; Voltage-dependent anion channel; pH sensors

DOI:  https://doi.org/10.1016/j.mito.2026.102218
PLoS Comput Biol. 2026 Sep 10. 22(9): e1013752

Calmodulin controls spatial and temporal specificity of calcium-induced calcium release.

Joanna Jędrzejewska-Szmek, Kim T Blackwell.

Calcium dynamics controls learning and memory, and abnormal calcium dynamics have been implicated in neurodegenerative disorders, such as Alzheimer's disease (AD). Calcium dynamics are influenced by calcium-induced calcium release (CICR), which is mediated by ryanodine receptors (RyR) located on endoplasmic reticulum (ER) membrane. Calmodulin, one of the most abundant proteins in the brain, inhibits RyR2, expressed in the dendrites of hippocampal CA1 neurons, with several reported consequences: relief of this inhibition is responsible for heart failure, and enhancing calmodulin to RyR binding (Nakamura Y, Yamamoto T, Xu X, Kobayashi S, Tanaka S, Tamitani M, et al. Enhancing calmodulin binding to ryanodine receptor is crucial to limit neuronal cell loss in Alzheimer disease. Sci Rep. 11(1), 2021.) alleviates cell loss and AD-like neuronal hyperexcitability. To investigate the role of calmodulin in aging and AD, we built a sophisticated reaction-diffusion model of a dendritic branch with ER. We showed that relieving calmodulin inhibition of RyR2 increased spatial and temporal spread of calcium transients in the dendrite. This effect was also visible in a model of old age, where disinhibition of half of the RyR2 population increased spatial spread of calcium transients by a factor of 2, and disinhibition of RyR2 combined with increased concentration of calcium buffering molecules increased duration of calcium transients. Lower activation of plasma membrane calcium ATPase (PMCA), which is also activated by calmodulin and inhibited by β-Amyloid oligomers, and not RyR2 disinhibition, led to an increase in resting intracellular calcium concentration as observed in AD. Overall, our research demonstrates that changes in calmodulin that are associated with AD and aging, by regulation of RyR2 (in old age) and PMCA (in AD), underlie changes in calcium dynamics that might have consequences for learning and memory.

DOI: https://doi.org/10.1371/journal.pcbi.1013752
Sci Adv. 2026 Sep 11. 12(37): eaeh2771

Metabolic regulation of calcium homeostasis via SERCA succination.

Su Jin Ham, Yena Kim, Sehyeon Kim, Sunhoe Bang, Young Hoon Koh, Soung-Hun Roh, Hyung Seo Park, Jongkyeong Chung.

Although calcium homeostasis is disrupted in metabolic diseases, its metabolic regulation remains unclear. Here, we identify a mechanism by which fumarate suppresses sarco/endoplasmic reticulum (ER) calcium ion-adenosine triphosphatase (SERCA) activity via succination of a conserved cysteine residue, impairing ER calcium uptake and promoting metabolic dysfunction in Drosophila. In mammalian cells, high glucose or fumarate inhibits SERCA activity and increases ER calcium release and cytosolic and mitochondrial calcium levels. Mechanistically, we show that fumarate covalently modifies SERCA2b at Cys875 and that a Cys875Ser mutant resists fumarate-induced inhibition. In Drosophila, knock-in flies with the corresponding Cys875Ser mutation preserve ER calcium homeostasis and are protected from hyperglycemia, glucose intolerance, and reduced survival on a high-sugar diet. These effects are phenocopied by pharmacological fumarate reduction or allosteric SERCA activation. Collectively, these findings suggest that fumarate-mediated SERCA inhibition provides a mechanistic link between glucose metabolism and calcium homeostasis, with potential relevance to metabolic dysfunction.

DOI: https://doi.org/10.1126/sciadv.aeh2771
iScience. 2026 Sep 18. 29(9): 117325

Differential activation of TCA cycle activity and PDH flux by dichloroacetate in skeletal muscle measured by hyperpolarized [2-13C,3-2H3]pyruvate.

Sung-Han Lin, Andrew Cho, Mai T Huynh, Zohreh Erfani, Blanka Kucejova, Sasanka Wathukara Dewage, Thomas Jue, Xiaorong Fu, Zoltán Kovács, Shawn C Burgess, Jae Mo Park.

  Despite the central role of skeletal muscle bioenergetics in whole-body metabolic health, assessing mitochondrial oxidative phosphorylation and tricarboxylic acid (TCA) cycle activity in vivo remains a major challenge. While hyperpolarized [1-13C]pyruvate has been used to probe pyruvate dehydrogenase (PDH) flux to approximate TCA cycle activity, this approach relies on the unreliable assumption that PDH and TCA cycle fluxes are tightly coupled. Here, we demonstrate that hyperpolarized [2-13C,3-2H3]pyruvate can track label-incorporation into TCA cycle-derived glutamate in rat skeletal muscle. Following intravenous dichloroacetate administration, we observed a greater increase in hyperpolarized [1-13C]acetyl-L-carnitine relative to [5-13C]glutamate, suggesting disproportionately increased PDH flux relative to TCA cycle flux. A similar trend was also observed in ex vivo GC-MS analysis of skeletal muscle tissue collected from rats injected with [U-13C3]pyruvate. Together, these findings highlight the complex interplay between PDH and TCA cycle fluxes and establish hyperpolarized [2-13C,3-2H3]pyruvate as a robust agent for assessing mitochondrial metabolism in skeletal muscle.

Keywords:  TCA cycle; acetyl-L-carnitine; dichloroacetate; hyperpolarized; oxidative phosphorylation; pyruvate; pyruvate dehydrogenase; skeletal muscle

DOI:  https://doi.org/10.1016/j.isci.2026.117325
FASEB J. 2026 Sep 15. 40(17): e72276

Lactate-Mediated Lysine Lactylation in Renal Fibrosis: Current Progress and Challenges.

Weili Wang, Kai Xu, Yachen Xu, Xinru Ge, Yong Lv.

  Renal fibrosis constitutes the core pathological hallmark of chronic kidney disease (CKD) progression. Its intricate pathogenesis and the paucity of efficacious clinical interventions have elevated it to a critical global public health concern. Recently, the intersection of metabolic reprogramming and epigenetic regulation has illuminated that aberrant lactate accumulation associated with dysregulated glycolysis and the ensuing imbalance of histone and non-histone lysine lactylation (Kla) may represent an important molecular link between renal cellular metabolic perturbations and the fibrotic cascade. The dynamic landscape of Kla is regulated by lactate itself, alongside "writers" (lactoyltransferases), "erasers" (delactylases), and site-specific "readers." Currently, Kla marks have been extensively mapped across the core histones H2A, H2B, H3, and H4. Notably, histone H3 lysine 18 lactylation (H3K18la), histone H3 lysine 14 lactylation (H3K14la), histone H4 lysine 12 lactylation (H4K12la), and histone H4 lysine 16 lactylation (H4K16la) represent the most rigorously investigated loci within the context of renal fibrosis, where they have been implicated in pathological processes, including tubular epithelial-to-mesenchymal transition, perturbation of the renal inflammatory microenvironment, and mitochondrial impairment. Beyond histone modifications, the biological significance of non-histone Kla is increasingly being recognized. Investigations into specific loci, such as acyl-coenzyme A synthetase family member 2 K182 lactylation (ACSF2-K182la) and PBX homeobox 1 K40 lactylation (PBX1-K40la), are emerging as areas of growing research interest in renal fibrosis. This review systematically synthesizes the metabolic foundations, molecular mechanisms, pathological roles, disease correlations, and targeted therapeutic strategies associated with both histone and non-histone Kla. By integrating cutting-edge discoveries and delineating the challenges confronting contemporary research, we endeavor to provide a comprehensive academic overview. Ultimately, we aim to deepen the mechanistic understanding of Kla in CKD-related renal fibrosis and to inform future investigations into its translational potential for novel diagnostics and therapeutics.

Keywords:  chronic kidney disease; histone lysine lactylation; lactate; renal fibrosis

DOI:  https://doi.org/10.1096/fj.202602239R
Front Cell Dev Biol. 2026 ;14 1886145

Mitochondrial ecosystem restoration in Alzheimer's disease: from mechanisms to multi-target therapeutic strategies.

Dandan Song.

  Alzheimer's disease (AD), the most prevalent cause of dementia, lacks definitive cures despite decades of research focused on amyloid-beta (Aβ) and tau pathologies. Emerging evidence positions mitochondrial dysfunction not merely as a downstream consequence, but as the epicenter linking aging, metabolic failure, and neuroinflammation in AD pathogenesis. This study synthesizes the latest advances in mitochondrial-targeted therapies, framing them within a "Mitochondrial Ecological Restoration" perspective. I analyze the molecular mechanisms by which mitochondrial-targeted therapies modulate oxidative stress, mitochondrial dynamics, mitophagy and neuroinflammation, and evaluate their translational potential. Accumulating evidence indicates that strategies ranging from antioxidants (e.g., MitoQ) to mitophagy enhancement (e.g., Spautin-1) and biogenesis activation (e.g., PGC-1α Activator) have demonstrated efficacy in preclinical models. These interventions theoretically interrupt the pathological cycle between proteotoxicity and bioenergetic crisis. While challenges in blood-brain barrier (BBB) penetration and target specificity persist, the field is shifting from single-target scavenging to combinatorial ecosystem repair. Future success will require precise delivery systems, early biomarkers, and a paradigm shift toward treating the neuron as a metabolic ecosystem, though substantial translational challenges remain.

Keywords:  Alzheimer’s disease; TPP+ Conjugates; mitochondrial dysfunction; mitochondrial ecosystem restoration; mitochondrial targeted therapy

DOI:  https://doi.org/10.3389/fcell.2026.1886145
Cell Rep. 2026 Sep 09. pii: S2211-1247(26)01053-3. [Epub ahead of print]45(9): 117975

Mitochondrial Raf1 regulates glutamine catabolism.

Ronald L Shanderson, Ian D Ferguson, Luca Ducoli, Weili Miao, Suhas Srinivasan, Zurab Siprashvili, Albert M Li, Mary Grace Velasco, Yang Li, Christine N Hoang, Jiangbin Ye, Paul A Khavari.

  Raf kinases are central to mitogenic signaling and cancer, yet the full complement of functionally important Raf-proximal proteins across subcellular compartments remains undefined. Here, proximity-dependent biotinylation (BioID) of Raf1 in Raf1-dependent cancer cells recovered proteins localized to the mitochondrial matrix. Mitochondrial purification and super-resolution microscopy confirmed that a pool of Raf1 resides within mitochondria. There, Raf1 associated with glutaminase (GLS) across diverse human cancers and enabled glutaminolysis, a major source of biosynthetic precursors in tumor cells. These effects required Raf1 kinase activity but were independent of canonical MAP kinase pathway signaling, and matrix-targeted kinase-dead Raf1 impaired both glutaminolysis and in vivo tumorigenesis. Raf1 therefore acts inside mitochondria, where it engages GLS to drive glutamine catabolism and support tumor growth, revealing a non-canonical, metabolic arm of Raf signaling.

Keywords:  CP: metabolism; MAPK; Raf1; glutaminase; metabolic reprograming

DOI:  https://doi.org/10.1016/j.celrep.2026.117975
J Biol Chem. 2026 Sep 07. pii: S0021-9258(26)02390-2. [Epub ahead of print] 113518

Heme as a Versatile Signaling Molecule: Coordinating Mitochondrial Metabolism with Global Cellular Responses.

Iva Chitrakar, Breann L Brown.

  Heme is an essential iron-containing cofactor that supports diverse biological processes, including oxygen transport, mitochondrial respiration, and xenobiotic metabolism. Beyond these canonical functions, accumulating evidence has established heme as a dynamic signaling molecule that couples mitochondrial metabolic state to cellular stress responses, gene expression, and metabolic adaptation. Heme biosynthesis is compartmentalized between mitochondria and the cytosol, requiring tightly coordinated synthesis, trafficking, sensing, and degradation to maintain cellular homeostasis and prevent heme toxicity. In this review, we examine mechanisms by which heme regulates mitochondrial protein quality control, respiratory chain assembly, and metabolic feedback to coordinate organellar function with cellular energy demands. We further discuss how heme is trafficked to extramitochondrial compartments, where it modulates cytoplasmic stress signaling, iron homeostasis, transcriptional networks, and metabolic programs through interactions with proteins, including the BACH1 transcription factor, REV-ERB nuclear receptors, and the glycolytic enzyme GAPDH. We also highlight ongoing debates surrounding mitochondrial heme trafficking and identify critical unanswered questions regarding the identity of intracellular heme chaperones and mitochondrial heme sensors. Finally, we discuss how dysregulation of heme synthesis, trafficking, sensing, and degradation contributes to diverse pathologies. Collectively, recent advances establish heme as a central regulator of mitochondrial communication and cellular homeostasis, underscoring the therapeutic potential of targeting heme signaling pathways in human disease.

Keywords:  heme; iron; mitochondria; oxidative stress; porphyrin; unfolded protein response

DOI:  https://doi.org/10.1016/j.jbc.2026.113518
Sci Adv. 2026 Sep 11. 12(37): eaef4578

Mechanistic trade-offs between local and long-range signaling activity in natural and synthetic morphogens.

Gavin Schlissel, Anders S Hansen, Pulin Li.

Hedgehog family morphogens present an interesting paradox: Despite being hydrophobic because of dual-lipid modifications, they form spatial concentration gradients that are highly conserved and essential for many aspects of metazoan development. Using live-cell single-molecule tracking and engineered synthetic signaling ligands, we isolated the distinct contribution of each lipid modification to Hedgehog diffusion and signaling potency. We found that although both lipid modifications enhance signaling potency, they do so through different mechanisms. Palmitate directly promotes receptor engagement, whereas cholesterol topologically confines secreted morphogens on the cell surface, effectively using the lipid membrane as a nonsignaling co-receptor that enriches ligands locally at the cost of restricting long-range diffusion. Our results on the function of cholesterol point to an intrinsic trade-off between signaling potency and gradient formation, with implications for the evolution and mechanism of nonsignaling co-receptors.

DOI: https://doi.org/10.1126/sciadv.aef4578
Mitochondrial Commun. 2026 ;4 1-9

Mitochondrial NMNAT3 reduces amyloid aggregates in Drosophila and alters the amyloid processing in the 3xTgAD mouse.

Zhu Yi, Naynika Juvvadi, Grace Zhai, Carlos T Moraes, Milena Pinto.

Alzheimer's disease is a progressive neurological disorder characterized by two main neuropathological hallmarks: neurofibrillary tangles and amyloid plaques. Both are protein aggregates, composed mainly of hyperphosphorylated Tau and the amyloid fragment Aβ, respectively. NMNAT (Nicotinamide mononucleotide adenylyltransferase) is an endogenous enzyme involved in the conversion of NMN to NAD. It is known for its neuroprotective functions, particularly against axonal degeneration. We have previously shown that different isoforms of NMNAT can protect cells from neurotoxic stress caused by protein aggregates by acting as chaperones. Accordingly, the mitochondrial-localized isoform NMNAT3 exhibits potent chaperone activity, which antagonizes the aggregation of a wide spectrum of pathological amyloid client proteins in culture, including Tau and amyloid beta. Although mostly cytosolic, Aβ has also been detected in mitochondria and mitochondrial membranes. To investigate whether NMNAT3 could serve as a neuroprotective factor in amyloid pathology in vivo, we overexpressed NMNAT3 in two different models: a Drosophila model overexpressing APP and PS1 in developing photoreceptors, and the 3xTg-AD mouse, in which NMNAT3 was expressed in forebrain neurons and which accumulates neurofibrillary tangles and plaques in the hippocampus and cortex. When expressed in the Drosophila eye, APP accumulated in a location- and time-dependent manner, and co-expression of NMNAT3 decreased the total number of aggregates. When expressed in the mouse brain, NMNAT3 did not affect amyloid plaque number or volume; nonetheless, it altered APP processing, leading to the accumulation of oligomers and soluble C-terminal fragments. We conclude that the effects of NMNAT3 on APP differ between models, likely due to differences in access to the sites of protein aggregation and the neuronal environments between flies and mice.

DOI: https://doi.org/10.1016/j.mitoco.2026.01.001
iScience. 2026 Sep 18. 29(9): 117290

Tetrazine-based bioorthogonal reactions to image hypoxia in cancer cells.

Sara Boumya, Chiara Boero, Edoardo De Luigi, Federica Foglietta, Gustavo Ferreira-Alves, Daniele Mancardi, Barbara Lupo, Francesca Spyrakis, Loretta Lazzarato, Marta Serafini.

  Suboptimal oxygen supply in solid tumors controls a variety of cancer hallmarks and impairs responsiveness to anticancer treatments. Yet, tools to visualize hypoxia in cancer are still limited. Here we present an application of the tetrazine-dienophile inverse-electron demand Diels-Alder (IEDDA) reaction for hypoxia visualization. In this approach, trans-cyclooctene-clickable 2-nitroimidazoles work in combination with tetrazine-functionalized probes for live imaging of differential levels of hypoxia in two-dimensional (2D) and three-dimensional (3D) models. We used tetrazine-based fluorescent probes to determine oxygen levels in cell monolayers, spheroids, and patient-derived organoids, and applied a "click-to-release" approach to evaluate the diffusion of the released probe in the surrounding peripheral regions, allowing to quantify the bystander effect. Given the compatibility of the tetrazine-dienophile click reaction with living organisms, the combination of clickable 2-nitroimidazoles with tetrazine-based reporters opens a new avenue for in vivo hypoxia imaging.

Keywords:  3D cellular models; bystander effect; click chemistry; fluorescence; hypoxia; tetrazine bioorthogonal reactions

DOI:  https://doi.org/10.1016/j.isci.2026.117290