bims-celmim 2025-11-16 papers

bims-celmim

Biomed News

on Cellular and mitochondrial metabolism

Issue of 2025–11–16
twenty-one papers selected by
Marc Segarra Mondejar, AINA

Calcium Regulation of Mitochondrial Metabolism.
The SLC1A1/EAAT3 dicarboxylic amino acid transporter is an epigenetically dysregulated nutrient carrier that sustains oncogenic metabolic programs.
Calcium transfer from the ER to other organelles for optimal signaling in Toxoplasma gondii.
Tumour sampling conditions perturb the metabolic landscape of clear cell renal cell carcinoma.
Single-cell imaging of liver metabolic dynamics using fluorescent biosensors.
Endosomal microautophagy is activated by specific cellular stresses in trout hepatocytes.
The function of Mak16 in ribosome biogenesis depends on its [4Fe-4S] cluster.
The tumor suppressor LACTB remodels mitochondria to promote cytochrome c release and apoptosis.
Ist2 promotes lipid transfer by Osh6 via its membrane tethering and lipid scramblase activities.
iGlucoSnFR2: A genetically encoded fluorescent sensor for measuring intracellular or extracellular glucose in vivo in mouse brain.
qMaLioffG: a genetically encoded green fluorescence lifetime-based indicator enabling quantitative imaging of intracellular ATP.
Neuronal differentiation regulator CEND1 coordinately suppresses tumor growth and energetics via AMPK signaling in brain glioma.
Glutamine metabolism reprogramming promotes bladder cancer progression via PYCR1: a multi-omics and functional validation study.
A glucose kinase-independent HK2 activity prevents TNF-induced cell death by phosphorylating RIPK1.
Inducing ferroptosis to impede metastasis by inhibiting the calcium channel TRPC6.
Palmitate impairs autophagic degradation via oxidative stress-perilysosomal Ca2+ overload-mTORC1 activation in pancreatic β-cells.
A preserved TGFβ cytostatic response through DLD-mediated metabolic modulation undermines anti-TGFβ therapy in gastric cancer.
Protocol for in vivo assessment of glucose metabolism in mouse models.
Alterations in peroxisome-mitochondria interplay in skeletal muscle accelerate muscle dysfunction.
Structural basis of glucose-6-phosphate transport by human SLC37A2.
Functional profiling and visualization of the sphingolipid metabolic network in vivo.

Annu Rev Physiol. 2025 Nov 10.

Calcium Regulation of Mitochondrial Metabolism.

Carmen A Mannella, Pawel Swietach, Liron Boyman.

Mitochondrial ATP production dynamically adapts to cellular energy demands, with calcium (Ca2+) playing a crucial regulatory role. In this review, we critically evaluate the evidence for intramitochondrial Ca2+ ([Ca2+]m) sensitivity in key energy metabolic pathways, highlighting the [Ca2+]m dependence of specific mitochondrial systems. We also address the metabolic consequences of [Ca2+]m-sensitive ATP production, particularly its effects on the utilization of specific macronutrients that fuel ATP production. Next, we discuss the primary Ca2+ entry pathway into the matrix, the mitochondrial Ca2+ uniporter (MCU), its macromolecular complex structure (MCUcx), and allosteric regulation by Ca2+. Key to this regulation are specific auxiliary subunits, along with the influence of mitochondrial inner membrane architecture. While the Ca2+ signaling plays an important role, it does not fully explain the scope for regulating ATP production. Emerging evidence suggests that additional signaling systems operating alongside the Ca2+ signaling contribute to the control of mitochondrial ATP production, a topic requiring further investigation.

DOI: https://doi.org/10.1146/annurev-physiol-052424-082740
Nat Commun. 2025 Nov 14. 16(1): 10012

The SLC1A1/EAAT3 dicarboxylic amino acid transporter is an epigenetically dysregulated nutrient carrier that sustains oncogenic metabolic programs.

Treg Grubb, Pooneh Koochaki, Sayed Matar, Fatme Ghandour, Marc Machaalani, Eddy Saad, Cerise Tang, Eduard Reznik, Jesminara Khatun, Carleigh Salem, Noah Dubasik, David A Orlando, Matthew G Guenther, Gyanu Parajuli, Raghvendra M Srivastava, Steven R Martinez, Jesse A Coker, Ritesh R Kotecha, A Ari Hakimi, John M Asara, Timothy A Chan, Sakari Vanharanta, Shaun R Stauffer, William G Kaelin, Sabina Signoretti, Toni K Choueiri, Abhishek A Chakraborty.

Epigenetic dysregulation, including accumulation of Histone H3 lysine 27 acetylation (H3K27ac), is a hallmark of pVHL-deficient clear cell Renal Cell Carcinomas (ccRCCs). Using an in vivo positive selection ORF screen in poorly tumorigenic pVHL-proficient cells and mechanistic studies in pVHL-deficient cells, we discovered that the aspartate (Asp) and glutamate (Glu) transporter, SLC1A1/EAAT3, is a metabolic dependency in ccRCC. pVHL loss promotes Hypoxia Inducible Factor (HIF)-independent SLC1A1 expression via H3K27ac dysregulation. SLC1A1 inactivation, genetically or pharmacologically, depletes Asp/Glu-derived metabolites (e.g., Tricarboxylic acid cycle and nucleotide intermediates), impedes ccRCC growth, and sensitizes ccRCCs to anti-metabolite drugs (e.g., glutaminase blockers). In human tumors, higher SLC1A1 expression is associated with reduced immune infiltration, oncogenic metabolic programs, and advanced stage/metastatic disease. Finally, in ccRCC animal models, SLC1A1 inactivation diminishes lung metastasis and the outgrowth of established renal tumors. Altogether, our studies credential SLC1A1 as an actionable, HIF-independent, metabolic dependency in pVHL-deficient ccRCCs.

DOI: https://doi.org/10.1038/s41467-025-64983-x
Elife. 2025 Nov 12. pii: RP101894. [Epub ahead of print]13

Calcium transfer from the ER to other organelles for optimal signaling in Toxoplasma gondii.

Zhu-Hong Li, Beejan Asady, Le Chang, Myriam Andrea Hortua Triana, Catherine Li, Isabelle Coppens, Silvia N J Moreno.

  Ca2+ signaling in cells begins with the opening of Ca2+ channels in either the plasma membrane (PM) or endoplasmic reticulum (ER), leading to a sharp increase in the physiologically low (<100 nM) cytosolic Ca2+ level. The temporal and spatial regulation of Ca²+ is crucial for the precise activation of key biological processes. In the apicomplexan parasite Toxoplasma gondii, which infects approximately one-third of the global population, Ca²+ signaling governs essential aspects of the parasite's infection cycle. T. gondii relies on Ca²+ signals to regulate pathogenic traits, with several Ca²+-signaling components playing critical roles. Ca2+ entry from the extracellular environment has been demonstrated in T. gondii for both, extracellular parasites, exposed to high Ca2+, and intracellular parasites, which acquire Ca²+ from host cells during host Ca²+ signaling events. Active egress, an essential step of the parasite's infection cycle, is preceded by a large increase in cytosolic Ca2+, most likely initiated by release from intracellular stores. However, extracellular Ca2+ is also necessary to reach a cytosolic Ca2+ threshold required for timely egress. In this study, we investigated the mechanism of intracellular Ca²+ store replenishment and identified a central role for the SERCA-Ca2+-ATPase in maintaining Ca²+ homeostasis within the ER and in other organelles. We demonstrate mitochondrial Ca2+ uptake, which occurs by transfer of Ca2+ from the ER, likely through membrane contact sites. Our findings suggest that the T. gondii ER plays a key role in sequestering and redistributing Ca²+ to intracellular organelles following Ca²+ influx at the PM.

Keywords:  SERCA; Toxoplasma gondii; calcium signaling; cell biology; endoplasmic reticulum; membrane contact sites; mitochondria; toxoplasma gondii

DOI:  https://doi.org/10.7554/eLife.101894
Nat Commun. 2025 Nov 10. 16(1): 9896

Tumour sampling conditions perturb the metabolic landscape of clear cell renal cell carcinoma.

Cissy Yong, Christina Schmidt, Ming Yang, Alexander Von Kriegsheim, Anne Y Warren, Shubha Anand, James N Armitage, Antony C P Riddick, Thomas J Mitchell, Vishal Patil, Kourosh Saeb-Parsy, Sakari Vanharanta, Grant D Stewart, Christian Frezza.

Human isotopic tracer studies are key for in vivo studies of cancer metabolism. Yet, the effects of sampling conditions on the tissue metabolome remain understudied. Here, we perform a 13C-glucose study coupled with metabolomic, transcriptomic, and proteomic profiling in patients with clear cell renal cell carcinoma (ccRCC) to assess the impact of ischaemia on tissues sampled intraoperatively and post-surgical resection, where tissues are exposed to varying degrees of warm ischaemia. Although several metabolic features were preserved, including suppressed TCA cycle activity, ischaemia masked other metabolic phenotypes of ccRCC, such as suppressed gluconeogenesis. Notably, normal kidneys were more metabolically susceptible to ischaemia than the ccRCC tumours. Despite their overall stability, ischaemia caused subtle changes in the proteome and transcriptome. Using orthotopic ccRCC-derived xenografts, we evidenced that prolonged ischaemia disrupted the tissue metabolome stability. Overall, minimising tissue ischaemia is pivotal in accurately profiling cancer metabolism in patient studies.

DOI: https://doi.org/10.1038/s41467-025-65676-1
Trends Endocrinol Metab. 2025 Nov 10. pii: S1043-2760(25)00224-3. [Epub ahead of print]

Single-cell imaging of liver metabolic dynamics using fluorescent biosensors.

Israel Pérez-Chávez, Eduardo H Gilglioni, Daria Ezeriņa, Joris Messens, Esteban N Gurzov.

  Traditional metabolic studies rely on bulk tissue analyses, masking the cellular heterogeneity that underlies disease progression. Genetically encoded fluorescent biosensors now enable real-time, single-cell imaging of dynamic metabolic processes in the liver. These tools provide insights into the metabolic reprogramming in conditions such as chronic obesity, metabolic dysfunction-associated steatotic liver disease (MASLD), and hepatocellular carcinoma (HCC). By tracking specific metabolites involved in glycolysis, lipid oxidation, and the tricarboxylic acid (TCA) cycle, biosensors can reveal how these pathways respond to diverse stimuli. In this review we outline the core principles of fluorescent biosensors, provide specific recommendations for their usage, suggest possible applications in liver metabolism research, and discuss current technical challenges as well as emerging opportunities in this rapidly advancing field.

Keywords:  HCC; MASLD; fluorescent genetically encoded biosensors; liver metabolism; microscopy; single-cell resolution

DOI:  https://doi.org/10.1016/j.tem.2025.10.003
Sci Rep. 2025 Nov 10. 15(1): 39347

Endosomal microautophagy is activated by specific cellular stresses in trout hepatocytes.

Emilio J Vélez, Vincent Véron, Jeanne Gouis, Steffi Reji, Karine Dias, Amaury Herpin, Florian Beaumatin, Iban Seiliez.

Endosomal microautophagy (eMI) is a recently discovered autophagic process where cytosolic proteins are selectively captured in late endosome/multivesicular bodies (LE/MVB). This pathway, similar to chaperone-mediated autophagy (CMA), involves the recognition of KFERQ-like motif containing proteins by HSC70. While CMA targets substrates to lysosomes via the receptor LAMP2A, eMI involves internalization into intraluminal vesicles within LE/MVB through interactions with ESCRT machinery. Although the same proteins could be targeted by either pathway, eMI's role in cellular homeostasis is less understood. Our research identified an eMI-like process in rainbow trout hepatocytes, triggered by oxidative stress, high-glucose, DNA damage, and nutrient deprivation, but not serum deprivation. This finding suggests eMI's stimulus-specific induction and its potential compensatory role when CMA is impaired. Our study provides new insights into eMI and offers novel model organisms for exploring its interactions with CMA, enhancing our understanding of cellular stress responses.

DOI: https://doi.org/10.1038/s41598-025-23022-x
Proc Natl Acad Sci U S A. 2025 Nov 18. 122(46): e2513844122

The function of Mak16 in ribosome biogenesis depends on its [4Fe-4S] cluster.

Nadine Duppe, Lukas Knauer, Marc Hagebölling, Lena Langner, Martin Stümpfig, Volker Schünemann, Antonio J Pierik, Daili J Netz.

  Mak16 and its interacting partner Rpf1 play a critical role at an early step in the maturation of the ribosomal 60S subunit of eukaryotes, as revealed by cryoelectron microscopy structures. While these studies suggested no metal participation or the presence of a Zn2+ ion in Mak16, we identify a previously unexplored iron-sulfur (Fe/S) cluster in yeast Mak16 through both in vivo and in vitro methods. We demonstrate a functional link between mitochondrial and cytosolic Fe/S protein biogenesis and ribosome assembly, highlighting an overlooked aspect of 60S ribosomal biogenesis. Characterization of human and yeast Mak16 revealed a redox-active [4Fe-4S]2+/1+ cluster with a midpoint potential below -500 mV. Oxidative stress destabilizes Mak16 and disrupts its interaction with Rpf1 in vivo, while in vitro H2O2 causes [3Fe-4S]1+ cluster formation. Our findings also reveal that upon binding to rRNA expansion segment 7 the redox properties of the nearby Fe/S cluster largely remain unchanged. However, disruption of Fe/S cluster coordination destabilized Mak16, impaired the Mak16-Rpf1 complex formation and decreased the 25S rRNA level. The critical role of Fe/S proteins in eukaryotic DNA replication and repair, mitoribosomal function, and maturation has now been extended to nuclear ribosomal assembly. Relying on a vulnerable cofactor comes at a cost, as cluster loss can severely disrupt essential cellular processes. The inherent biosynthetic complexity and instability of the Fe/S cluster of Mak16 allows it to function as sensor for redox imbalance, creating the possibility to regulate cellular homeostasis under stress.

Keywords:  iron–sulfur; metallocofactor; ribosome biogenesis

DOI:  https://doi.org/10.1073/pnas.2513844122
Sci Adv. 2025 Nov 14. 11(46): eadx7809

The tumor suppressor LACTB remodels mitochondria to promote cytochrome c release and apoptosis.

Sukrut C Kamerkar, Taewook Kang, Radu V Stan, Edward J Usherwood, Henry N Higgs.

Mitochondria are pivotal regulators of cellular homeostasis, integrating energy metabolism, biosynthesis, and programmed cell death (apoptosis). During apoptosis, mitochondrial outer membrane permeabilization by BCL-2-associated X protein/BCL-2 Homolog Antagonist Killer (BAX/BAK) pores facilitates release of apoptotic factors, while the role of inner mitochondrial membrane (IMM) remodeling remains less understood. Here, we identify serine beta-lactamase-like protein (LACTB), a filament-forming serine protease and tumor suppressor, as a regulator of IMM dynamics during apoptosis. LACTB suppression reduces cytochrome c release and apoptosis, whereas its overexpression promotes these effects. LACTB does not affect BAX or Drp1 recruitment to mitochondria. Rather, LACTB is required for apoptosis-induced mitochondrial remodeling, independent of OPA1 processing. Intriguingly, LACTB knockdown does not affect mitochondrial shape changes induced by CCCP treatment, suggesting that LACTB action is apoptosis-specific. Purified LACTB binds and remodels cardiolipin-enriched membrane nanotubes preferentially over planar lipid membranes, suggesting a direct effect in apoptotic membrane remodeling. Collectively, our findings suggest LACTB to be a mediator of apoptosis-induced IMM remodeling, a possible mechanism for tumor suppression in cancer.

DOI: https://doi.org/10.1126/sciadv.adx7809
Sci Adv. 2025 Nov 14. 11(46): eadz2217

Ist2 promotes lipid transfer by Osh6 via its membrane tethering and lipid scramblase activities.

Alicia Fabbre, Camille Syska, Heitor Gobbi Sebinelli, Anna Cardinal, Maud Magdeleine, Noha Al-Qatabi, Juan Martín D'Ambrosio, Cédric Montigny, Guillaume Lenoir, Alenka Čopič, Guillaume Drin.

Lipid transfer proteins unevenly distribute lipids within the cell, which is crucial for its functioning. In yeast, Osh6 transfers phosphatidylserine (PS) from the endoplasmic reticulum (ER) to the plasma membrane (PM) by exchange with phosphatidylinositol 4-phosphate. We investigated why its activity depends on Ist2, an ER-resident lipid scramblase that connects the ER to the PM via an intrinsically disordered region (IDR). We found that Osh6, in a lipid-loaded state, binds the Ist2 IDR with micromolar affinity and functions at ER-PM contact sites only if its binding site within the IDR is sufficiently distant from the ER membrane. We determined, in reconstituted contact sites, that the association of Osh6 with the Ist2 IDR enables rapid, directed PS transfer. We identified the Ist2-binding site in Osh6 by molecular modeling and functional analyses. Last, we established that Ist2's scramblase activity sustains Osh6-mediated PS transfer between membranes. Identifying these functional partnerships highlights why lipid transport processes are organized in membrane contact sites.

DOI: https://doi.org/10.1126/sciadv.adz2217
Sci Adv. 2025 Nov 14. 11(46): eadz3889

iGlucoSnFR2: A genetically encoded fluorescent sensor for measuring intracellular or extracellular glucose in vivo in mouse brain.

Jonathan S Marvin, Philipp Mächler, Chengbo Meng, Tayfun Ates, Ronak H Patel, Raghabendra Adhikari, Monika A Makurath, Zaneta Ku, Daniel Feliciano, Deniz Atasoy, Guohong Cui, David Kleinfeld, Timothy A Brown.

Continuous glucose monitors have proven invaluable for monitoring blood glucose levels for diabetics, but they are of limited use for observing glucose dynamics at the cellular (or subcellular) level. We have developed a second generation, genetically encoded intensity-based glucose sensing fluorescent reporter (iGlucoSnFR2). We show that when it is targeted to the cytosol, it reports intracellular glucose consumption and gluconeogenesis in cell culture, along with efflux from the endoplasmic reticulum. It outperforms the original iGlucoSnFR in vivo when observed by fiber photometry in mouse brain and reports transient increase in glucose concentration when stimulated by noradrenaline or electrical stimulation. Last, we demonstrate that membrane localized iGlucoSnFR2 can be calibrated in vivo to indicate absolute changes in extracellular glucose concentration in awake mice. We anticipate iGlucoSnFR2 facilitating previously unobservable measurements of glucose dynamics with high spatial and temporal resolution in living mammals and other experimental organisms.

DOI: https://doi.org/10.1126/sciadv.adz3889
Nat Commun. 2025 Nov 13. 16(1): 9972

qMaLioffG: a genetically encoded green fluorescence lifetime-based indicator enabling quantitative imaging of intracellular ATP.

Satoshi Arai, Hideki Itoh, Cong Quang Vu, Loan Thi Ngoc Nguyen, Mizuho Nakayama, Masanobu Oshima, Atsuya Morita, Kazuko Okamoto, Satoru Okuda, Aki Teranishi, Madori Osawa, Yoshiteru Tamura, Shigeaki Nonoyama, Megumi Takuma, Toshinori Fujie, Satya Ranjan Sarker, Thankiah Sudhaharan, Akihiro Furube, Tetsuro Katayama, Taketoshi Kiya, E Birgitte Lane, Tetsuya Kitaguchi.

Genetically encoded indicators that can detect concentrations of metabolites and signalling molecules through fluorescence lifetime changes are gaining attention, because they expand the potential for quantitative imaging. These indicators offer advantages over conventional fluorescence intensity-based indicators by minimizing artifacts such as variations in indicator concentration, cellular morphological changes, and focus drift. However, the availability of fluorescence lifetime-based genetically encoded indicators remains limited, particularly those compatible with the widely used conventional 488 nm laser in microscopy. Here, we introduce qMaLioffG, a single green fluorescent protein-based ATP indicator that exhibits a substantial fluorescence lifetime shift (1.1 ns) within physiologically relevant ATP concentrations. This enables quantitative imaging of ATP levels in the cytoplasm and mitochondria under steady-state conditions across various cell types, providing insights into ATP distribution. We demonstrate that qMaLioffG can be used in multicellular systems, applying it to Drosophila brain and HeLa cell spheroids to reveal spatially heterogeneous ATP levels.

DOI: https://doi.org/10.1038/s41467-025-64946-2
Cell Biosci. 2025 Nov 14. 15(1): 156

Neuronal differentiation regulator CEND1 coordinately suppresses tumor growth and energetics via AMPK signaling in brain glioma.

Yuting Shu, Yunbo Yuan, Yuze He, Linzi Ji, Qiuyun Yuan, Jingwen Gong, Siliang Chen, Yanhui Liu, Wanchun Yang, Mina Chen.

  The aggressive proliferation and metabolic adaptability of glioma contribute to poor clinical prognosis, necessitating novel targets concurrently reprogram glioma cells toward a neuron-like, less proliferative, and metabolically suppressed state. Here, we identified neuronal differentiation factor CEND1 as a candidate and explored its impact on glioma growth and metabolism. We demonstrated that CEND1 was significantly reduced in high-grade gliomas and inversely correlated with patient survival. Elevated CEND1 in glioma cells induced a neuron-like morphology, accompanied with attenuated proliferation and migration. CEND1 overexpression suppressed tumor growth and prolonged the survival of animal models of intracranial orthotopic tumor formation. Metabolomics and biochemical assays revealed that CEND1 inhibited PDH activity and mitochondrial oxidative phosphorylation, ultimately reducing ATP levels. Mechanistically, CEND1 activated AMPK to induce cell proliferation arrest and enhance metformin sensitivity. Altogether, our findings reveal that CEND1 coordinates neuronal differentiation with mitochondrial energetic metabolic suppression to exert anti-proliferative function in glioma, supporting its role as a potential target for glioma therapy.

Keywords:  AMPK; CEND1; Cell proliferation; Glioma; Metabolism

DOI:  https://doi.org/10.1186/s13578-025-01500-z
J Transl Med. 2025 Nov 13. 23(1): 1277

Glutamine metabolism reprogramming promotes bladder cancer progression via PYCR1: a multi-omics and functional validation study.

Xinjia Ding, Enkui Zhang, Zhou Huang, Xiaohui Li, Zhigao Wang, Yanping Wu, Chao Liu, Shikai Wu.

   BACKGROUND: Bladder cancer (BLCA) is a prevalent malignancy worldwide, with advanced stages linked to poor prognosis. Although immune checkpoint inhibitors (ICIs) show clinical promise in treating both operable and advanced BLCA, predicting patient responses remains a major challenge. Glutamine metabolism, a key aspect of metabolic reprogramming, has been implicated in tumor progression and immune modulation. However, the exact role of glutamine metabolism in BLCA remains poorly understood. This study aims to explore its association with clinical outcomes and immunotherapy response while functionally validating key regulatory genes.
METHODS: An integrated approach combining targeted metabolomics, single-cell RNA sequencing, and bulk transcriptomic data was used to profile glutamine metabolism in BLCA comprehensively and identify potential metabolic biomarkers. A prognostic model, termed GMscore, based on glutamine metabolism, was constructed using principal component analysis (PCA). Key regulatory genes were identified through random forest analysis. Functional assays, including in vitro proliferation, migration, and metabolic assays, as well as in vivo xenograft models, were employed to validate the findings.
RESULTS: Targeted metabolomics revealed increased glutamine metabolism in BLCA cell lines. The GMscore model, developed and validated across multiple cohorts, accurately predicted patient survival. In two immunotherapy cohorts (IMvigor210 and GSE91061), a lower GMscore correlated with improved therapeutic response, suggesting its potential as a predictive biomarker for immunotherapy efficacy. PYCR1 was identified as a key regulatory gene, exhibiting high expression in epithelial cells and cancer-associated fibroblasts (CAFs). Functional assays demonstrated that PYCR1 knockdown inhibited cell proliferation and migration and suppressed tumor growth in vivo. Mechanistically, PYCR1 facilitated proline synthesis through P5CS and activated the PI3K/AKT/mTOR signaling pathway, which modulated glutamine utilization and metabolic reprogramming in BLCA.
CONCLUSIONS: This study provides a comprehensive analysis of glutamine metabolism in BLCA and introduces a clinically relevant prognostic model. PYCR1 was identified as a central metabolic regulator, underscoring its critical role in tumor development and progression.

Keywords:  Bladder cancer; Glutamine metabolism; Metabolic reprogramming; PYCR1; Prognostic model; Tumor microenvironment

DOI:  https://doi.org/10.1186/s12967-025-07386-2
Nat Commun. 2025 Nov 13. 16(1): 9979

A glucose kinase-independent HK2 activity prevents TNF-induced cell death by phosphorylating RIPK1.

Tianhao Zou, Ran Liu, Gengqiao Wang, Guoliang Wang, Zhengting Jiang, Chuanzheng Wang, Weimin Wang, Mao Cai, Shuhua Zhang, Huan Cao, Di Zhang, Xueling Wang, Shenghe Deng, Tongxi Li, Jinyang Gu.

Tumor necrosis factor (TNF)-induced RIPK1-mediated cell death is implicated in various human diseases. However, the mechanisms RIPK1-mediated cell death is regulated by metabolic processes remain unclear. Here, we identify hexokinase 2 (HK2), a critical regulator of glycolysis, as a suppressor of TNF-induced RIPK1 kinase-dependent cell death through its non-metabolic function. HK2 inhibits RIPK1 kinase activity through constitutively phosphorylation at serine 32 of RIPK1. Inhibition of RIPK1 S32-phosphorylation results in RIPK1 kinase activation and subsequent cell death in response to TNFα stimulation. We further show that HK2 is elevated under pathological conditions including liver ischemia-reperfusion (IR) injury and hepatocellular carcinoma (HCC) via the transcriptional factor HMGA1. Moreover, the upregulation of HK2 in the liver confers protection against liver IR injury mediated by RIPK1 kinase, while depleting HK2 in HCC cells enhances TNFα-induced cell death and synergistically improves the efficacy of anti-PD1 therapy in an HCC model. Thus, the findings reveal a potential therapeutic avenue for RIPK1-related diseases through manipulating HK2 non-metabolic function.

DOI: https://doi.org/10.1038/s41467-025-64939-1
Cell Rep. 2025 Nov 08. pii: S2211-1247(25)01314-2. [Epub ahead of print]44(11): 116543

Inducing ferroptosis to impede metastasis by inhibiting the calcium channel TRPC6.

Boris S Dimitrov, Dimpi Mukhopadhyay, Hira Lal Goel, Emmet R Karner, Christi A Silva, Ayush Kumar, Cornelia Peterson, Mengdie Wang, Arthur M Mercurio.

  We investigated a potential function of transient receptor potential cation channel 6 (TRPC6) in enabling breast cancer cells to resist stimuli that induce ferroptosis. A minority population of quiescent cells was isolated from triple-negative breast cancer (TNBC) cell lines that exhibit increased TRPC6 expression and resistance to ferroptosis compared to proliferating cells. These quiescent cells are also more metastatic than the proliferating cells, supporting the hypothesis that metastasis requires the ability of cells to evade ferroptosis. In pursuit of the mechanism, we discovered that the ability of TRPC6 to repress c-Myc is essential because its repression sustains levels of glutathione that are sufficient to impede ferroptosis. Importantly, treatment of TNBC cells with a TRPC6 inhibitor reduces metastasis significantly, an effect that is mitigated by a ferroptosis inhibitor. These results indicate that a sub-population of TNBC cells characterized by TRPC6 expression has the potential to form metastases by evading ferroptosis.

Keywords:  CP: cancer; TRPC6; breast cancer; cancer; ferroptosis; glutathione; metastasis

DOI:  https://doi.org/10.1016/j.celrep.2025.116543
JCI Insight. 2025 Nov 11. pii: e192827. [Epub ahead of print]

Palmitate impairs autophagic degradation via oxidative stress-perilysosomal Ca2+ overload-mTORC1 activation in pancreatic β-cells.

Ha Thu Nguyen, Luong Dai Ly, Thuy Thi Thanh Ngo, Soo Kyung Lee, Carlos Noriega Polo, Subo Lee, Taesic Lee, Seung-Kuy Cha, Xaviera Riani Yasasilka, Kae Won Cho, Myung-Shik Lee, Andreas Wiederkehr, Claes B Wollheim, Kyu-Sang Park.

  Saturated fatty acids impose lipotoxic stress on pancreatic β-cells, leading to β-cell failure and diabetes. In this study, we investigate the critical role of organellar Ca2+ disturbance on defective autophagy and β-cell lipotoxicity. Palmitate, a saturated fatty acid, induced perilysosomal Ca2+ elevation, sustained mTORC1 activation on the lysosomal membrane, suppression of the lysosomal transient receptor potential mucolipin 1 (TRPML1) channel, and accumulation of undigested autophagosomes in β-cells. These Ca2+ aberrations with autophagy defects by palmitate were prevented by an mTORC1 inhibitor or a mitochondrial superoxide scavenger. To alleviate perilysosomal Ca2+ overload, strategies such as lowering extracellular Ca2+, employing voltage-gated Ca2+ channel blocker or ATP-sensitive K+ channel opener effectively abrogated mTORC1 activation and preserved autophagy. Furthermore, redirecting perilysosomal Ca2+ into the endoplasmic reticulum (ER) with an ER Ca2+ ATPase activator, restores TRPML1 activity, promotes autophagic flux, and improves survival of β-cells exposed to palmitate-induced lipotoxicity. Our findings suggest oxidative stress-Ca2+ overload-mTORC1 pathway involvement in TRPML1 suppression and defective autophagy during β-cell lipotoxicity. Restoring perilysosomal Ca2+ homeostasis emerges as a promising therapeutic strategy for metabolic diseases.

Keywords:  Aging; Autophagy; Calcium signaling; Diabetes; Endocrinology

DOI:  https://doi.org/10.1172/jci.insight.192827
Nat Commun. 2025 Nov 14. 16(1): 10016

A preserved TGFβ cytostatic response through DLD-mediated metabolic modulation undermines anti-TGFβ therapy in gastric cancer.

Yi-Qian Pan, Yi Han, Zheng-Yu Qian, Xin-Yao Zhang, Ting-Ting Wang, Ze-Rong Cai, Huan Chen, Yun Li, Kun Liao, Yong-Qiang Zheng, Yan-Yu Zhang, Qi-Nian Wu, Hao-Xiang Wu, Tian Tian, Wenqi Chen, Yue Chen, Zhao-Lei Zeng, Ze-Xian Liu, Hai-Long Piao, Xin-Yuan Guan, Rui-Hua Xu, Huai-Qiang Ju.

Despite the well-known role of the transforming growth factor-β (TGFβ) pathway in cancer progression, therapies targeting it have largely failed in the clinic. This suggests our understanding of TGFβ's function is incomplete. Here we show that this therapeutic failure is rooted in a fundamental paradox: while TGFβ promotes malignant traits in gastric cancer, many cancer cells remain sensitive to its potent tumor-suppressive effects. We uncover that this suppression works by impairing the cell's energy metabolism through modulating dihydrolipoamide dehydrogenase (DLD). Therefore, broadly blocking the TGFβ pathway can inadvertently release a natural brake on tumor growth. Based on this insight, we demonstrate that co-targeting this metabolic vulnerability with an inhibitor (devimistat) alongside an anti-TGFβ agent significantly enhances therapeutic efficacy in gastric cancer models. This combination approach presents a promising strategy to overcome the limitations of current therapies.

DOI: https://doi.org/10.1038/s41467-025-64997-5
STAR Protoc. 2025 Nov 07. pii: S2666-1667(25)00598-2. [Epub ahead of print]6(4): 104192

Protocol for in vivo assessment of glucose metabolism in mouse models.

Titaya Lerskiatiphanich, Cedric S Cui, John D Lee.

  Metabolic disturbances are common in motor neuron disease (MND), and elucidating their mechanisms may reveal therapies. Here, we present a protocol to assess glucose homeostasis in mice, including glucose tolerance, insulin tolerance, and glucagon challenge tests. We describe steps for fasting, intraperitoneal injections, and serial blood glucose measurements. The protocol also includes plasma collection for catecholamine analysis using matrix-assisted laser desorption ionization (MALDI) mass spectrometry imaging and immunofluorescence of pancreatic hormones, enabling comprehensive metabolic profiling in aged and neurodegenerative mouse models. For complete details on the use and execution of this protocol, please refer to McDonald et al.1 and McDonald et al.2.

Keywords:  Metabolism; Metabolomics; Neuroscience

DOI:  https://doi.org/10.1016/j.xpro.2025.104192
Nat Commun. 2025 Nov 10. 16(1): 9868

Alterations in peroxisome-mitochondria interplay in skeletal muscle accelerate muscle dysfunction.

Marco Scalabrin, Eloisa Turco, Ilaria Davigo, Riccardo Filadi, Leonardo Nogara, Gaia Gherardi, Lucia Barazzuol, Andrea Armani, Giulia Trani, Samuele Negro, Anais Franco-Romero, Yorrick Jaspers, Elisa Baschiera, Rossella De Cegli, Eugenio Del Prete, Tito Cali, Bert Blaauw, Leonardo Salviati, Michela Rigoni, Cristina Mammucari, Sylvie Caspar-Bauguil, Cedric Moro, Paola Pizzo, Marco Sandri, Stephan Kemp, Vanina Romanello.

Skeletal muscles, which constitute 40-50% of body mass, regulate whole-body energy expenditure and glucose and lipid metabolism. Peroxisomes are dynamic organelles that play a crucial role in lipid metabolism and clearance of reactive oxygen species, however their role in skeletal muscle remains poorly understood. To clarify this issue, we generated a muscle-specific transgenic mouse line with peroxisome import deficiency through the deletion of peroxisomal biogenesis factor 5 (Pex5). Here, we show that Pex5 inhibition results in impaired lipid metabolism, reduced muscle force and exercise performance. Moreover, mitochondrial structure, content, and function are also altered, accelerating the onset of age-related structural defects, neuromuscular junction degeneration, and muscle atrophy. Consistent with these observations, we observe a decline in peroxisomal content in the muscles of control mice undergoing natural aging. Altogether, our findings show the importance of preserving peroxisomal function and their interplay with mitochondria to maintain muscle health during aging.

DOI: https://doi.org/10.1038/s41467-025-64833-w
Nat Struct Mol Biol. 2025 Nov 12.

Structural basis of glucose-6-phosphate transport by human SLC37A2.

Qinxuan Lai, Mengzhen Xu, Yongxiang Gao, Zhisen Yang, Linfeng Sun, Xin Liu.

Glucose-6-phosphate (G6P) transporters are crucial for glucose metabolism by mediating G6P transport from the cytoplasm to endoplasmic reticulum (ER). However, their transport mechanisms remain poorly understood. Here, we elucidate the structural and functional basis of human solute carrier family 37 member 2 (SLC37A2), a G6P transporter implicated in metabolic regulation and macrophage inflammation. We show that SLC37A2 functions as a uniporter, facilitating G6P transport independent of inorganic phosphate gradients. Structures of SLC37A2 in the apo and G6P-bound states reveal a dimeric architecture. Both the ER luminal-open and cytosolic-open structures are captured, showing the structural dynamics during G6P transport. G6P is coordinated by SLC37A2 through interactions with its phosphate and hydroxyl groups. Furthermore, mapping mutations associated with glycogen storage disease type Ib onto SLC37A2 highlights residues essential for transport activity. Together, this work provides structural insights into G6P transport and establishes a framework for understanding related metabolic disorders.

DOI: https://doi.org/10.1038/s41594-025-01712-4
EMBO Rep. 2025 Nov 10.

Functional profiling and visualization of the sphingolipid metabolic network in vivo.

Fei-Yang Tzou, Cheng-Li Hong, Kai-Hung Chen, John P Vaughen, Wan-Syuan Lin, Chia-Heng Hsu, Irma Magaly Rivas-Serna, Kai-Yi Hsu, Shuk-Man Ho, Michael Raphael Panganiban, Hsin-Ti Hsieh, Yi-Jhan Li, Yi Hsiao, Hsin-Chun Yeh, Cheng-Yu Yu, Hong-Wen Tang, Ya-Hui Chou, Chia-Lin Wu, Chung-Chuan Lo, Vera C Mazurak, M Thomas Clandinin, Shu-Yi Huang, Chih-Chiang Chan.

  Sphingolipids govern diverse cellular processes; their dysregulation underlies numerous diseases. Despite extensive characterizations, understanding the orchestration of the sphingolipid network within living organisms remains challenging. We established a versatile genetic platform of CRISPR-engineered reporters of 52 sphingolipid regulators, recapitulating endogenous gene activity and protein distribution. This platform further allows conditional protein degradation for functional characterization. In addition, we developed the biosensor OlyAw to detect ceramide phosphoethanolamine and visualize membrane raft dynamics in vivo. Using this platform, we established comprehensive profiles of the sphingolipid metabolic network in the brain at the transcriptional and translational levels. The highly heterogeneous patterns indicate extensive coordination between distinct cell types and regions, suggesting the brain functions as a coherent unit to execute specific steps of sphingolipid metabolism. As a proof-of-concept application, we showed cell type-specific requirements of sphingomyelinases, including CG6962/dSMPD4 and CG3376/aSMase, degrading distinct subcellular pools of ceramide phosphoethanolamine to maintain brain function. These findings establish a foundation for future studies on brain sphingolipid metabolism and showcase the utilization of this genetic platform in elucidating in vivo mechanisms of sphingolipid metabolism.

Keywords:  Brain; Cell-type Specificity; Spatial Heterogeneity; Sphingolipids; Systemic Profiling

DOI:  https://doi.org/10.1038/s44319-025-00632-0