bims-cesirm 2025-12-21 papers

bims-cesirm

Biomed News

on Cell Signaling mediated regulation of metabolism

Issue of 2025–12–21
23 papers selected by
Tigist Tamir, University of North Carolina

Splicing factor SF3B4 promotes mitochondrial glutamine metabolism in hepatocellular carcinoma by regulating GLS1 isoform switching.
Depletion of individual dietary amino acids induce distinct metabolic and chromatin states.
Palmitic acid fuels triple-negative breast cancer through metadherin-dependent fatty acid β-oxidation: Relevance to high fat diet-induced breast cancer progression.
Compression-induced NF-κB activation sustains tumor cell survival in confinement by detoxifying aldehydes and promotes metastasis.
Redox-dependent protein S-glutathionylation governs azacitidine sensitivity and resistance in AML.
Chemical proteomics reveals regulation of bile salt hydrolases via oxidative post-translational modifications.
Doxorubicin Resistance Reprograms Triple-Negative Breast Cancer Cell Metabolism via the Fatty Acid β-Oxidation (FAO)-CD36 Regulatory Circuit: Relevance of Enhanced FAO on Tumor Cell Invasiveness.
Mechanistically informed machine learning links non-canonical TCA cycle activity to Warburg metabolism and hallmarks of malignancy.
Reprogramming of the kynurenine pathway impairs NAD+ homeostasis and mediates doxorubicin-induced cardiotoxicity in mice.
Lactate mitochondrial oxidation drives stemness potential in metastatic breast cancer.
Metabolic profiling of therapy-induced senescent cancer cells via TPEF, MALDI-MS, and RNA-sequencing.
Reductive death is averted by an ancient metabolic switch.
Multi-gradient permutation survival analysis identifies mitosis and immune signatures steadily associated with cancer patient prognosis.
ALDH3A2 targets arachidonic acid to promote cell metastasis in TNBC via AMPK/m-TOR signaling pathway.
A covalent allosteric molecular glue suppresses NRF2-dependent cancer growth.
Comprehensive discovery of m6A sites in the human transcriptome at single-molecule resolution.
Citrate trafficking supports rewiring of mitochondrial metabolism via RTG signaling in yeast osmoadaptation.
Fructose uptake by brown adipose tissue is independent of carbohydrate response element-binding protein and does not cause elevated de novo lipogenesis.
Missense3D-PTMdb: a web tool for visualising and exploring human genetic variants and post-translational modification sites using AlphaFold models.
A High-Resolution Subcellular Map of Proteins in Cells with Motile Cilia.
Targeting PRDX6-dependent localization and function of GPX4 enhances ferroptosis-mediated tumor suppression.
Rapid quantitation of NAD+/NADH and NADPH/NADP+ with mass spectrometry by using calibration constants.
Serotonin modulates lineage plasticity in neuroendocrine prostate cancer via epigenetic reprogramming.

Biochem Biophys Res Commun. 2025 Dec 15. pii: S0006-291X(25)01850-9. [Epub ahead of print]796 153134

Splicing factor SF3B4 promotes mitochondrial glutamine metabolism in hepatocellular carcinoma by regulating GLS1 isoform switching.

Seungyeon Yang, Minbeom Ko, Wei Zhang, Seung Min Jeong.

  Metabolic reprogramming is a hallmark of cancer, enabling tumor cells to adapt to nutrient stress and sustain uncontrolled proliferation. In hepatocellular carcinoma (HCC), glutamine metabolism is markedly upregulated and plays a pivotal role in supporting tumor growth and survival. However, the molecular mechanisms underlying this metabolic shift remain poorly understood. Here, we identify the splicing factor SF3B4 as a key regulator of glutamine metabolism in HCC through its control of glutaminase 1 (GLS1) alternative splicing. SF3B4 is highly expressed HCC and is essential for tumor cell proliferation, migration and colony formation. Mechanistically, SF3B4 preferentially promotes the production of the GAC isoform of GLS1, which exhibits higher catalytic activity, while repressing the KGA isoform. Genetic or pharmacological inhibition of SF3B4 leads to reduced GAC expression, decreased GLS enzymatic activity, impaired glutaminolysis, and suppression of glutamine-driven mitochondrial respiration. Moreover, SF3B4 is required for tumor cell survival under glucose-deprived conditions, highlighting its role in supporting metabolic flexibility under nutrient stress. Collectively, these findings uncover a previously unrecognized function of SF3B4 in promoting mitochondrial glutamine metabolism in HCC and suggest that the SF3B4-GAC axis may represent a potential therapeutic target for glutamine-addicted liver cancers.

Keywords:  GLS1; Glutamine metabolism; HCC; SF3B4

DOI:  https://doi.org/10.1016/j.bbrc.2025.153134
J Biol Chem. 2025 Dec 17. pii: S0021-9258(25)02926-6. [Epub ahead of print] 111074

Depletion of individual dietary amino acids induce distinct metabolic and chromatin states.

Spencer A Haws, Yang Liu, Cara L Green, Krittisak Chaiyakul, Pragyan Mishra, Reji Babygirija, Eric A Armstrong, Anusha T Mehendale, Irene M Ong, Dudley W Lamming, John M Denu.

  Reducing dietary levels of protein or specific essential amino acids (EAAs) promotes favorable metabolic reprogramming, including improved glucose tolerance, increased insulin sensitivity and reduced fat mass. However, the extent to which shared or EAA-specific mechanisms facilitate diet-associated phenotypes remains unclear. Here, we compared the physiological and molecular responses to dietary levels of methionine, leucine, and isoleucine by feeding C57BL/6J mice diets in which each of these specific AAs is depleted. Dietary depletion of Met, Leu, or Ile (Met-D, Leu-D, or Ile-D) elicited distinct, AA-specific physiological and hepatic molecular (transcriptome, metabolome, histone proteome) responses that were not phenocopied by mTORC1 inhibition via rapamycin treatment. Ile-D yielded the most distinct and dramatic responses, highlighted by expression of select chromatin modifying and metabolic enzymes that led to a prominent epigenetic state of histone H2A/H4 hypoacetylation and maintained hepatic acetyl-CoA levels despite downregulated β-oxidation. Multi-Omics Factor Analysis of 14,139 data points objectively affirmed Ile-D phenotypes are distinct from Met-D or Leu-D and identified metabolic and chromatin features as primary discriminators. We further demonstrated the metabolic and epigenetic responses to Ile-D can be recapitulated in vitro, suggesting that these responses are cell intrinsic. Together, these results demonstrate that dietary depletion of EAAs induce unique phenotypes and highlight distinct molecular mechanisms by which individual EAAs may control metabolic health.

Keywords:  epigenetics; isoleucine; leucine; methionine; post-translational modification; protein depletion

DOI:  https://doi.org/10.1016/j.jbc.2025.111074
Cell Signal. 2025 Dec 12. pii: S0898-6568(25)00735-1. [Epub ahead of print]139 112320

Palmitic acid fuels triple-negative breast cancer through metadherin-dependent fatty acid β-oxidation: Relevance to high fat diet-induced breast cancer progression.

Sunita Kumari, Shashikanta Sahoo, Sriravali Pulipaka, Annatta Thomas, Madhusudana Kuncha, Srigiridhar Kotamraju.

  Diets rich in saturated fats, specifically palmitic acid (PA), are associated with increased breast cancer risk. However, the exact mechanisms linking dietary fat and cancer progression remain unclear. Herein, we show that PA increases the levels of metadherin (MTDH), an oncogene, and its spliced isoform MTDHΔ7 in triple-negative breast cancer (TNBC) cells. PA significantly increased TNBC cell proliferation and invasiveness in an MTDH-Wt/Δ7-dependent way. Intriguingly, while PA alone promoted mitochondrial fatty acid β-oxidation (FAO), the addition of PA to TNBC cells stably expressing MTDH-Wt/MTDHΔ7 further potentiated FAO and ATP production. Conversely, PA failed to increase FAO in TNBC cells stably depleted of MTDH-Wt/MTDHΔ7. Also, etomoxir, a carnitine palmitoyl transferase (CPT)1 inhibitor, decreased PA- and MTDH-Wt/Δ7-induced TNBC cell invasive potential. Mechanistically, MTDH-Wt/MTDHΔ7-mediated increase in SIRT3 activity led to the activation of CPT1 via its deacetylation, promoting FAO and raising acetyl-CoA levels. Moreover, overexpression of MTDH-Wt/MTDHΔ7 notably increased free fatty acids uptake and subsequent consumption by boosting CD36 levels. Accordingly, depletion of either SIRT3 or CD36 significantly abrogated MTDH-Wt/MTDHΔ7-induced fatty acids uptake and subsequent FAO. Thus, MTDH-Wt/MTDHΔ7 plays a crucial role in utilizing fatty acids to fuel mitochondrial metabolism in TNBC cells. Further, SCID mice bearing sh.MTDH-Wt or sh.MTDHΔ7-MDA-MB-231cells fed a high-fat diet (HFD) showed significant resistance to tumor growth and metastatic spread compared to mice bearing parental MDA-MB-231 cells fed either HFD or chow diet. In conclusion, this study highlights a novel mechanism by which PA or HFD can promote TNBC aggressiveness through MTDH-mediated upregulation of mitochondrial FAO.

Keywords:  Breast cancer; FAO; HFD; MTDH; Palmitic acid

DOI:  https://doi.org/10.1016/j.cellsig.2025.112320
Nat Commun. 2025 Dec 14.

Compression-induced NF-κB activation sustains tumor cell survival in confinement by detoxifying aldehydes and promotes metastasis.

Bing Liu, Min Liu, Yajuan Zhang, Yifei Zhu, Dingpei Zhou, Hong Gao, Fan Yang, Dong Gao, Yun Zhao, BangBao Tao, Feng Yao, Weiwei Yang.

Metastasis remains the primary cause of cancer-related mortality. During dissemination, cancer cells must navigate spatially confined microenvironments, yet the underlying metabolic adaptations that facilitate this process remain unclear. Here, through an in vivo CRISPR screen targeting metabolic enzymes, we identify aldehyde dehydrogenase 1 family member B1 (ALDH1B1) as essential for tumor cell survival in confining capillaries. Mechanistically, compressive force induces casein kinase 2 alpha 3 (CSK23) to phosphorylate kappa-B kinase subunit beta (IKKβ) at Ser177/181, which activates the nuclear factor kappa B (NF-κB) pathway and upregulates ALDH1B1. The upregulation of ALDH1B1 enhances aldehyde detoxification, which suppresses ferroptosis and promotes tumor cell survival during migration through the capillaries, thereby facilitating metastasis. Importantly, genetic or pharmacological inhibition of CSK23 or ALDH1B1 effectively impairs metastasis. In lung cancer patients, confined tumor cells exhibit higher levels of ALDH1B1 and NF-κB activation, which correlates with metastatic recurrence. Our findings reveal a mechano-metabolic pathway that promotes metastasis and suggest CSK23 and ALDH1B1 as potential therapeutic targets.

DOI: https://doi.org/10.1038/s41467-025-67452-7
Redox Biol. 2025 Dec 04. pii: S2213-2317(25)00471-9. [Epub ahead of print]89 103958

Redox-dependent protein S-glutathionylation governs azacitidine sensitivity and resistance in AML.

Dušan Nemes, Michaela Myšáková, Lubomír Minařík, Anna Jonášová, Tomáš Stopka, Kristýna Gloc Pimková.

  Disruption of redox metabolism is a hallmark of drug-resistant cancer cells, representing a major obstacle to the effective treatment of acute myeloid leukemia (AML). While recent studies have highlighted the importance of redox balance in AML therapy, the specific contribution of protein redox signaling to resistance remains poorly understood. Defining these mechanisms could uncover therapeutic vulnerabilities of resistant AML cells and guide the development of novel combination strategies. Here, we performed comprehensive mass spectrometry-based redox and quantitative proteomic profiling of AML cell lines and patient samples sensitive or resistant to the hypomethylating agent azacitidine (AZA). We demonstrate that AZA disrupts redox homeostasis, which inactivates the glyoxalase system and DNA damage response, and thereby induces cell death. In contrast, AZA resistance is associated with a redox reset characterized by elevated glutathione levels and diminished protein S-glutathionylation. Importantly, AZA failed to induce oxidation of proteins in these pathways in resistant cells and patient-derived AML samples. Pharmacological inhibition of glutathione synthesis restored protein S-glutathionylation and resensitized resistant AML cells to AZA.

Keywords:  Acute myeloid leukemia; Azacitidine; Cysteine oxidation; DNA damage; Drug resistance; Glyoxalase system; Hypomethylation therapy; Redox proteomics; S-glutathionylation

DOI:  https://doi.org/10.1016/j.redox.2025.103958
bioRxiv. 2025 Dec 14. pii: 2025.12.11.693737. [Epub ahead of print]

Chemical proteomics reveals regulation of bile salt hydrolases via oxidative post-translational modifications.

Amy K Bracken, Kien P Malarney, Pamela V Chang.

The gut microbiome is the vast, diverse ecosystem of microorganisms that inhabits the human intestines and provides numerous essential functions for the host. One such key role is the metabolism of primary bile acids that are biosynthesized in the host liver into a plethora of secondary bile acids produced by gut bacteria. These metabolites serve as both antimicrobial and chemical signaling agents within the host. The critical microbial enzyme that plays a gatekeeping role in secondary bile acid metabolism is bile salt hydrolase (BSH), a cysteine hydrolase that is primarily known for its deconjugating and reconjugating activities on bile acid substrates. Despite the crucial nature of these biotransformations, regulation of BSH activity is not well understood. Here, we found that the catalytic cysteine 2 (Cys2) within the BSH active site exists in multiple sulfur oxidation states including sulfenic acid (Cys-SOH). Importantly, we show this reversible oxidative post-translational modification (oxPTM) ablates BSH catalytic activity. We have leveraged this discovery to develop a chemoproteomic platform featuring a sulfenic acid-reactive bile acid probe to profile BSH Cys2 oxPTMs throughout the gut microbiome. Our results reveal that though most gut microbiota-associated BSHs exist in the active Cys2-SH state, some are preferentially and reversibly inactivated in the Cys2-SOH state. This reversible oxidation of Cys2 may serve as a general mechanism to regulate BSH activity in vivo in response to a changing physiological environment.

DOI: https://doi.org/10.64898/2025.12.11.693737
Mol Carcinog. 2025 Dec 15.

Doxorubicin Resistance Reprograms Triple-Negative Breast Cancer Cell Metabolism via the Fatty Acid β-Oxidation (FAO)-CD36 Regulatory Circuit: Relevance of Enhanced FAO on Tumor Cell Invasiveness.

Sunita Kumari, Shashikanta Sahoo, Annatta Thomas, Srigiridhar Kotamraju.

  Chemotherapy remains the frontline treatment strategy for triple-negative breast cancer (TNBC). However, the aggressive nature of TNBC, due to metabolic reprogramming, is often associated with chemoresistance, which limits treatment efficacy. Herein, we investigated the impact of altered lipid homeostasis, in particular, the fatty acid β-oxidation (FAO) pathway, during doxorubicin (Dox)-induced chemoresistance and its effect on drug retention and efficacy in TNBC cells. Results indicate that Dox-induced chemoresistance in MDA-MB-231 cells and an in vivo Dox-resistance breast cancer model in SCID mice are associated with a marked upregulation of FAO. Intriguingly, the basal levels of carnitine palmitoyltransferase 1 (CPT1; a rate-limiting enzyme of FAO), CD36, (a fatty acid translocase), FAO-related gene transcript levels, and acetyl-CoA production were significantly elevated with increased degree of Dox resistance. These changes were paralleled by enhanced uptake of fatty acids and their oxidation. Dox-resistance in TNBC cells was associated with enhanced mitochondrial respiration, possibly due to increased activities of complex I and IV. Conversely, inhibition of CPT1 by etomoxir caused increased intracellular Dox retention, leading to Dox-induced cytotoxicity and attenuating the invasiveness of TNBC cells. Importantly, FAO-derived ATP levels, compared to glucose-derived ATP, seem to enhance the invasiveness of Dox-resistant cells. Mechanistically, Dox-resistance potentiated FAO via CREB activation, which in turn led to the enhancement of the PGC1α/PPARα/CD36-CPT1 axis. Taken together, Dox-resistance reprograms cellular metabolism towards FAO regulatory circuit sustaining the mitochondrial bioenergetics, promoting drug efflux, and accentuating breast cancer progression. Based on these findings, it is possible that FAO inhibitors effectively combat drug-induced TNBC chemoresistance.

Keywords:  CD36; CPT1; FAO; breast cancer; chemoresistance; doxorubicin

DOI:  https://doi.org/10.1002/mc.70072
PLoS Comput Biol. 2025 Dec 18. 21(12): e1013384

Mechanistically informed machine learning links non-canonical TCA cycle activity to Warburg metabolism and hallmarks of malignancy.

Lihao Lin, Francesco Lapi, Bruno Giovanni Galuzzi, Marco Vanoni, Lilia Alberghina, Chiara Damiani.

Cancer cells undergo extensive metabolic rewiring to support growth, survival, and phenotypic plasticity. A non-canonical variant of the tricarboxylic acid (TCA) cycle, characterized by mitochondrial-to-cytosolic citrate export, has emerged as critical for embryonic stem cell differentiation. However, its role in cancer remains poorly understood. Here, we present a two-step computational framework to systematically analyze the activity of this non-canonical TCA cycle across over 500 cancer cell lines and investigate its role in shaping hallmarks of malignancy. First, we applied constraint-based modeling to infer cycle activity, defining two complementary metrics: Cycle Propensity, measuring the likelihood of its engagement in each cell line, and Cycle Flux Intensity, quantifying average flux through the reaction identified as rate-limiting. We identified distinct tumor-specific patterns of pathway utilization. Notably, cells with high Cycle Propensity preferentially reroute cytosolic citrate via aconitase 1 (ACO1) and isocitrate dehydrogenase 1 (IDH1), promoting [Formula: see text]-ketoglutarate ([Formula: see text]KG) and NADPH production. Elevated engagement of this cycle strongly correlated with Warburg-like metabolic shifts, including decreased oxygen consumption and increased lactate secretion. In the second step, to uncover non-metabolic transcriptional signatures associated with non-canonical TCA cycle activity, we performed machine learning-based feature selection using ElasticNet and XGBoost, identifying robust gene signatures predictive of cycle activity. Over-representation analysis revealed enrichment in genes involved in metastatic behavior, angiogenesis, stemness, and key oncogenic signaling. SHapley Additive exPlanations (SHAP) further prioritized genes with the strongest predictive contributions, highlighting candidates for experimental validation. Correlation analysis of DepMap gene-dependency profiles revealed distinct vulnerability patterns associated with non-canonical TCA cycle activity, outlining a characteristic landscape of genetic dependencies. Together, our integrative framework uniting constraint-based metabolic modeling and machine learning systematically reveals how non-canonical TCA cycle dynamics underpin metabolic plasticity and promote malignant traits.

DOI: https://doi.org/10.1371/journal.pcbi.1013384
Redox Biol. 2025 Dec 06. pii: S2213-2317(25)00470-7. [Epub ahead of print]89 103957

Reprogramming of the kynurenine pathway impairs NAD+ homeostasis and mediates doxorubicin-induced cardiotoxicity in mice.

Danlei Li, Yang Zhang, Yuanyuan Kuang, Zhong Lin, Ping Wang, Jianjun Jiang, Wenhu Pi, Qilin Ma.

  Imbalance of Nicotinamide adenine dinucleotide (NAD+) homeostasis is a key contributor to various cardiac pathologies, including doxorubicin (DOX)-induced cardiomyopathy (DIC). The kynurenine pathway (KP), initiated by indoleamine 2,3-dioxygenase 1 (IDO1), serves as the primary route for de novo NAD + biosynthesis. While this pathway regulates critical biological processes such as cellular metabolism, inflammatory responses, oxidative stress, and aging, its specific role in DIC remains poorly understood. Here, we reveal a protective function of the KP in DIC by facilitating NAD+ synthesis. Genetic ablation of IDO1 exacerbates DOX-induced cardiac injury and structural damage in mice. In cardiomyocytes, DOX treatment upregulates α-amino-β-carboxy-muconate-semialdehyde decarboxylase (ACMSD) while downregulating quinolinate phosphoribosyl-transferase (QPRT), thereby reducing levels of the intermediate metabolite quinolinic acid (QA) and NAD+ levels. These effects can be pharmacologically reversed by TES-1025, an ACMSD inhibitor that enhances QPRT activity and potentiates the cardioprotective effects of the KP pathway against DIC. Mechanistically, we show that DOX modulates the STING/interferon γ/5'-AMP-activated protein kinase (p-AMPK) signaling axis to elevate ACMSD and suppress QPRT. Our findings establish a novel therapeutic potential that targets the metabolic switch ACMSD to QPRT, restoring NAD+ redox homeostasis and conferring protection against DIC in murine models.

Keywords:  ACMSD; Cardiotoxicity; DOX; Kynurenine pathway; NAD(+); ROS

DOI:  https://doi.org/10.1016/j.redox.2025.103957
Nat Commun. 2025 Dec 18.

Lactate mitochondrial oxidation drives stemness potential in metastatic breast cancer.

Jia-Jia Zhang, Ruo-Fei Tian, Chang-Geng Song, Rui Liu, Duo He, Gai-Qin Zhang, Xin-Yu Fan, Zi-Chuan Duan, Kun Zhang, Tian-Jiao Zhang, Ya-Tong Chen, Jian Zhang, Ke Wang, Ju-Mei Zhao, Xiang-Min Yang, Zhi-Nan Chen, Ling Li.

Metastatic cancer cells, originating from cancer stem cells with metastatic capacity, utilize nutrient flexibility to navigate the challenges of the metastatic cascade. However, the nutrient required to maintain the stemness potentials of metastatic cancer cells remains unclear. Here, we reveal that metastatic breast cancer cells sustain stemness and initiate metastasis upon detachment by taking up and oxidizing lactate. In detached metastasizing breast cancer cells, lactate is incorporated into the tricarboxylic acid cycle, boosting oxidative phosphorylation, and promoting the stemness potentials via α-KG-DNMT3B-mediated SOX2 hypomethylation. Moreover, lactate is taken up and oxidized in mitochondria by the CD147/MCT1/LDHB complex, which correlates with stemness potentials and tumor metastasis in patients with breast cancer. An intracellularly expressed single-chain variable fragment targeting mitochondrial CD147 (mito-CD147 scFv) effectively disrupts the mitochondrial CD147/MCT1/LDHB complex, inhibits lactate-induced stemness potential, depletes circulating breast cancer cells, and reduces metastatic burden, suggesting promising clinical applications in reducing lactate-fueled metastasis.

DOI: https://doi.org/10.1038/s41467-025-67091-y
Sci Rep. 2025 Dec 17.

Metabolic profiling of therapy-induced senescent cancer cells via TPEF, MALDI-MS, and RNA-sequencing.

Silvia Ghislanzoni, Federica Padelli, Matteo Niero, Alessia Bertolotti, Antonino Belfiore, Simone Torelli, Arianna Bresci, Andrea Masella, Silvia Betti, Dario Polli, Luca Agnelli, Italia Bongarzone.

  Despite advances in cancer therapies, treatment failure from resistance and recurrence remains a major clinical challenge. Therapy-induced senescence (TIS), a state of stable cell cycle arrest with sustained metabolic activity, has emerged as a driver of inflammation, tumor persistence, and relapse. However, the heterogeneity of TIS complicates its detection and targeting. Here, we applied a multi-modal strategy to characterize metabolic alterations in senescent cancer cells induced by doxorubicin or γ-irradiation across three tumor cell lines: MCF7, HeLa, and TPC-1. Mitochondrial dysfunction was assessed using MitoTracker and JC-1 staining, while two-photon excitation fluorescence (TPEF) microscopy enabled label-free visualization of intracellular NAD(P)H and FAD distribution. Lipid remodeling was evaluated by MALDI mass spectrometry imaging, and RNA sequencing was performed on control, senescent, and engulfing-senescent MCF7 cells to identify differentially expressed genes and enriched pathways. Senescent cells displayed mitochondrial dysfunction, with altered NAD(P)H/FAD distribution and decreased membrane potential. TPEF confirmed redistribution of coenzymes, reflecting redox changes. Lipidomics revealed consistent remodeling, notably involving cardiolipin precursors. Transcriptomic profiling showed engulfing-senescent MCF7 cells possess a distinct signature marked by increased lipid metabolism, endocrine signaling, and cell-cell communication. Overall, our findings reveal conserved and cell type-specific metabolic traits of TIS, highlighting metabolic vulnerabilities for senolytic intervention.

Keywords:  Breast cancer; Engulfing; Senescence

DOI:  https://doi.org/10.1038/s41598-025-32573-y
bioRxiv. 2025 Nov 25. pii: 2025.11.24.690166. [Epub ahead of print]

Reductive death is averted by an ancient metabolic switch.

Fasih M Ahsan, Jen F Rotti, Armen I Yerevanian, Sinclair W Emans, Nicole L Stuhr, Jose A Aceves-Salvador, Wei Wang, Daniel J Baker, Dimitra Pouli, Owen S Skinner, Michael D Blower, Alexander A Soukas.

Biguanides, including metformin, the world's most prescribed oral hypoglycemic, extend health-span and lifespan in vertebrates and invertebrates. Given the widespread use and apparent safety of metformin, it is assumed that its effects are not associated with toxicity, except when in marked excess. Here we determine that accumulation of damaging reducing equivalents is an unanticipated toxicity associated with biguanides, the defense against which requires post-transcriptional protection of de novo fatty acid biosynthesis. We demonstrate that biguanide treatment during impaired fatty acid biosynthesis drives NADPH toxicity, leading to catastrophic elevation of NADH/GSH reducing equivalents and accelerated death across metazoans. Multiple NADPH-generating interventions require fatty acid biosynthesis to prevent markedly shortened survival, indicating that this defense mechanism is broadly leveraged. We propose that fatty acid biosynthesis is a tunable rheostat which can minimize biguanide-induced reductive stress whilst maximizing its pro-longevity outcomes and serve as an exploitable vulnerability in reductive stress sensitive cancers.
HIGHLIGHTS: Biguanides inhibit cytosolic mRNA translation to extend lifespan in C. elegans . Fatty acid synthesis is translationally protected by eIF3 complex subunits. pod-2 / fasn-1 inactivation amplifies biguanide-induced reductive stress and death. NADPH-generating insults require fatty acid synthesis to buffer reductive stress.

DOI: https://doi.org/10.1101/2025.11.24.690166
Elife. 2025 Dec 17. pii: RP101619. [Epub ahead of print]13

Multi-gradient permutation survival analysis identifies mitosis and immune signatures steadily associated with cancer patient prognosis.

Xinlei Cai, Yi Ye, Xiaoping Liu, Zhaoyuan Fang, Luonan Chen, Fei Li, Hongbin Ji.

  The inconsistency of the association between genes and cancer prognosis is often attributed to many variables that contribute to patient survival. Whether there exist the Genes Steadily Associated with Prognosis (GEARs) and functions remains largely elusive. Here, we developed a novel method named 'Multi-gradient Permutation Survival Analysis' (MEMORY) to screen the GEARs by using RNA-seq data from the TCGA database. We employed a network construction approach to identify hub genes from GEARs and utilized them for cancer classification. In the case of lung adenocarcinoma (LUAD), the GEARs were found to be related to mitosis. Our analysis suggested that LUAD cell lines carrying PIK3CA mutations exhibit increased drug resistance. For breast invasive carcinoma (BRCA), the GEARs were related to immunity. Further analysis revealed that CDH1 mutation might regulate immune infiltration through the EMT process. Moreover, we explored the prognostic relevance of mitosis and immunity through their respective scores and demonstrated it as valuable biomarkers for predicting patient prognosis. In summary, our study offered significant biological insights into GEARs and highlights their potentials as robust prognostic indicators across diverse cancer types.

Keywords:  GEAR; Gene Steadily Associated with Prognosis; MEMORY; Multi-gradient Permutation Survival Analysis; cancer biology; hub genes; human; immune; mitosis

DOI:  https://doi.org/10.7554/eLife.101619
Breast Cancer Res. 2025 Dec 18. 27(1): 217

ALDH3A2 targets arachidonic acid to promote cell metastasis in TNBC via AMPK/m-TOR signaling pathway.

Ding Wang, Shulei Luo, Rongji Yu, Doudou Wen, Hao Jiang, Keli Xu, Xiaotang Di, Shubing Zhang.

   BACKGROUND: Triple negative breast cancer (TNBC), characterized by its aggressive clinical behavior and propensity for distant metastasis, presents critical challenges in therapeutic management. Emerging evidence implicates lipid metabolic reprogramming as a key facilitator of tumor progression and metastatic dissemination. However, the precise molecular mechanisms underlying lipid metabolic dysregulation in TNBC metastasis remain poorly characterized. Our work systematically elucidates the mechanistic role of ALDH3A2 in orchestrating lipid metabolic adaptations that drive breast cancer metastasis.
METHODS: Transcriptomic analysis of clinical datasets identified metastasis-related metabolic regulators. Cellular migration/invasion assays and murine metastasis models were utilized to assess metastatic effects of ALDH3A2. Lipidomic profiling coupled with pathway analysis characterized metabolic alterations. Mechanistic studies integrated western blot analysis with lipid droplet quantification. Computational approaches including structure-based virtual screening and molecular docking simulations were employed for inhibitor discovery.
RESULTS: ALDH3A2 was significantly upregulated in TNBC clinical specimens and showed significant association with adverse clinical outcomes. Functional validation confirmed that ALDH3A2 potentiates TNBC cell migration/invasion through epithelial-mesenchymal transition (EMT) activation. Metabolic profiling revealed ALDH3A2-driven lipid accumulation, evidenced by increased lipid droplet formation and elevated triglyceride levels. Specifically, arachidonic acid (AA) enrichment was observed in ALDH3A2-overexpressing cells, corresponding to enhanced glycerophospholipid metabolism. Mechanistic studies demonstrated that ALDH3A2-mediated AMP/ATP imbalance suppresses AMPK phosphorylation while activating mTOR/SREBP1 signaling. mTOR inhibition effectively attenuated ALDH3A2-induced lipid metabolic alterations. Importantly, oxaliplatin was identified as a potential therapeutic agent targeting ALDH3A2-mediated AA metabolism to suppress metastasis.
CONCLUSIONS: Our work establishes ALDH3A2 as a pivotal regulator of lipid metabolic reprogramming in TNBC metastasis, providing mechanistic insights into AA-mediated tumor progression. These findings position ALDH3A2 as a promising therapeutic target and prognostic biomarker for TNBC management.

Keywords:  ALDH3A2; Arachidonic acid; Lipid metabolic reprogramming; Metastasis; Oxaliplatin; Triple negative breast cancer

DOI:  https://doi.org/10.1186/s13058-025-02135-1
Cancer Discov. 2025 Dec 19.

A covalent allosteric molecular glue suppresses NRF2-dependent cancer growth.

Nilotpal Roy, Tine Wyseure, I-Chung Lo, Justine Lu, Christie L Eissler, Steffen M Bernard, Ilah Bok, Aaron N Snead, Albert Parker, U-Ging Lo, Jason C Green, Jordon Inloes, Sarah R Jacinto, Brent Kuenzi, Marie Pariollaud, Kathleen Negri, Khoi Le, Benjamin D Horning, Noah Ibrahim, Stephanie Grabow, Harit Panda, Dhaval P Bhatt, Emily M Wilkerson, Soma Saeidi, Paul Zolkind, Zoe Rush, Heather N Williams, Eric Walton, Martha K Pastuszka, John J Sigler, Eileen Tran, Kenneth Hee, Joseph McLaughlin, Géza Ambrus-Aikelin, Jonathan Pollock, Robert T Abraham, Todd M Kinsella, Gabriel M Simon, Michael B Major, David S Weinstein, Matthew P Patricelli.

The NRF2 transcription factor is constitutively active in cancer where it functions to maintain oxidative homeostasis and reprogram cellular metabolism. NRF2-active tumors exhibit NRF2-dependency and resistance to chemo/radiotherapy. Here we characterize VVD-065, a first-in-class NRF2 inhibitor that acts via an unprecedented allosteric molecular glue mechanism. In the absence of stress or mutation, NRF2 is rapidly degraded by the KEAP1-CUL3 ubiquitin-ligase complex. VVD-065 specifically and covalently engages Cys151 on KEAP1, which in turn promotes KEAP1-CUL3 complex formation, leading to enhancement of NRF2 degradation. Previously reported Cys151-directed compounds decrease KEAP1-CUL3 interactions and stabilize NRF2, thus establishing KEAP1_Cys151 as a tunable regulator of the KEAP1-CUL3 complex and NRF2 stability. VVD-065 inhibited NRF2-dependent tumor growth and sensitized cancers to chemo/radiotherapy, supporting an open Phase I clinical trial (NCT05954312).

DOI: https://doi.org/10.1158/2159-8290.CD-25-1187
Nat Commun. 2025 Dec 15.

Comprehensive discovery of m6A sites in the human transcriptome at single-molecule resolution.

Gihyeon Kang, Hyeonseo Hwang, Hyeonseong Jeon, Heejin Choi, Hee Ryung Chang, Nagyeong Yeo, Junehee Park, Narae Son, Eunkyeong Jeon, Jungmin Lim, Jaeung Yun, Wook Choi, Jae-Yoon Jo, Jong-Seo Kim, Sangho Park, Yoon Ki Kim, Daehyun Baek.

RNA modifications (RMs) are critical for diverse biological processes, but the lack of accurate, quantitative detection methods has limited their study. A large-scale and high-quality training dataset is an essential component for accurate deep learning, but such dataset has been absent for RM detection, resulting in low accuracies. We developed DeepRM (Deep learning for RNA Modification), a sophisticated deep learning framework powered by Nanopore sequencing. DeepRM dataset is a massive-scale, three orders of magnitude larger than the comparable previous ones, and unprecedentedly high-quality dataset that closely mirrors endogenous transcript environments. Accordingly, DeepRM detects RM sites and measures their modification stoichiometries with a near-perfect accuracy. Using DeepRM, we constructed a comprehensive, human m6A atlas at single-molecule resolution that reveals a large number of previously underappreciated non-canonical m6A sites and differentially modified transcripts, highlighting the complexity and dynamic nature of the human epitranscriptome. DeepRM is freely available, providing a unique, powerful opportunity for understanding the biological functions of RMs. DeepRM can also be expanded to various other RMs and organisms, potentially becoming a future standard for investigating the epitranscriptome.

DOI: https://doi.org/10.1038/s41467-025-67417-w
Biochem J. 2025 Dec 16. pii: BCJ20253414. [Epub ahead of print]482(24):

Citrate trafficking supports rewiring of mitochondrial metabolism via RTG signaling in yeast osmoadaptation.

Angela Primavera, Luna Laera, Alessandra Castegna, Pasquale Scarcia, Luigi Palmieri, Maria Antonietta Di Noia, Nicoletta Guaragnella.

  Inter-organellar cross-talk is an important component of cellular stress response enabling adaptation and survival. We have demonstrated the activation of RTG retrograde signaling to sustain the peroxisomesmitochondria- nucleus axis in a model of osmostressed Saccharomyces cerevisiae yeast cells. In this work, we aimed to gain insight into the molecular mechanisms regulating the communication between these organelles upon NaCl treatment. A metabolomic analysis revealed that the homeostasis of citrate is a pivotal factor in the osmoadaptive response. Gene expression analysis and citrate synthase activity showed that the synthesis of citrate mainly derives from peroxisomes, as indicated by the up-regulation of CIT2, and not CIT1 and CIT3, under the control of the RTG pathway. Furthermore, the involvement of the mitochondrial citrate transporter, encoded by YHM2, in the osmoadaptive response, as judged by gene and protein expression analysis together with growth assay, is demonstrated. In the absence of YHM2, alternative pathways relying on ODC2 and ACO1 are activated, indicating possible compensatory mechanisms for osmoadaptation. We propose a model in which peroxisome-derived citrate is converted to cytosolic 2-oxoglutarate to replenish TCA cycle and promote its rewiring. This work reveals a new layer of metabolic co-ordination among organelles and identifies citrate shuttling as a crucial adaptive mechanism to osmotic stress.

Keywords:   YHM2 ; RTG pathway; citrate; mitochondrial carriers; osmoadaptation; yeast

DOI:  https://doi.org/10.1042/BCJ20253414
Acta Biochim Biophys Sin (Shanghai). 2025 Dec 18.

Fructose uptake by brown adipose tissue is independent of carbohydrate response element-binding protein and does not cause elevated de novo lipogenesis.

Janina Behrens, Marceline Manka Fuh, Daniel T Haas, Michelle Y Jaeckstein, Markus Heine, Bente Siebels, Anna Worthmann, Natalie Krahmer, Joerg Heeren, Ludger Scheja.

  Brown adipose tissue (BAT) is a heat-generating organ burning significant amounts of calories from fatty acids and glucose. The importance of glucose metabolism in the context of thermogenic function has been underlined by several studies. However, fructose metabolism and consequences of fructose overfeeding are poorly studied in BAT. Here we provide evidence that brown adipocytes use fructose as a substrate, however to a lesser extent than glucose. Furthermore, our data suggest that carbohydrate response element binding protein (ChREBP) and its target glucose transporter 5 (GLUT5) are not essential for fructose uptake and metabolism in BAT. Notably, we report that high fructose feeding has no effect on ChREBP activity and thus de novo fatty acid synthesis in BAT as opposed to liver and intestine. Instead, excessive carbohydrate loading of brown adipocytes induced by both, high-fructose feeding and impairment of ChREBP-dependent glucose metabolism, causes a massive accumulation of hexosylceramide species, as revealed by mass spectrometry-based lipidomics. Based on our data we hypothesize a reprogramming of fructose utilization upon impaired carbohydrate metabolism from canonical glycolysis and pentose phosphate pathway towards glycosphingolipid synthesis.

Keywords:  ChREBP; brown adipose tissue; ceramides; fructose; lipogenesis

DOI:  https://doi.org/10.3724/abbs.2025229
J Mol Biol. 2025 Dec 16. pii: S0022-2836(25)00661-8. [Epub ahead of print] 169595

Missense3D-PTMdb: a web tool for visualising and exploring human genetic variants and post-translational modification sites using AlphaFold models.

Haotian Zhao, Ryan Pye, Grace Walker, Wendy Tran, Olivia Simmonds, Ifigenia Tsitsa, Suhail Islam, Gordon Hanna, Alessia David.

  Only a fraction of the >11 million missense variants identified in humans has a known clinical significance. Post-translational modifications (PTMs), such as phosphorylation, glycosylation and ubiquitination, are key regulators of protein function and structure. PTMs depend on correct protein folding and the recognition and binding of enzymes to specific amino acid motifs near modification sites. AlphaFold models provide an unprecedented opportunity to explore variants on 3D structures, enabling systematic identification of amino acid substitutions that could affect PTMs and should be further investigated experimentally. We present Missense3D-PTMdb, a "one-stop-shop" interactive web tool that provides a user-friendly sequence-structure mapping of 20,235 human proteins, 11,5 million naturally occurring human missense variants, >60 PTM types and 203,775 PTM residues and their neighbours in sequence and 3D structure space using AlphaFold models of the human proteome. The resource also supports visualization of novel variants not in the database. Missense3D-PTMdb is freely available at https://missense3d.bc.ic.ac.uk/ptmdb.

Keywords:  3D structures; AlphaFold; PTMs; missense variants

DOI:  https://doi.org/10.1016/j.jmb.2025.169595
J Proteome Res. 2025 Dec 18.

A High-Resolution Subcellular Map of Proteins in Cells with Motile Cilia.

Filippa Bertilsson, Feria Hikmet, Jan N Hansen, Mathias Uhlén, Loren Méar, Cecilia Lindskog.

  Motile cilia are complex structures regulated by thousands of genes, essential for various physiological functions like respiration and reproduction. Their dysfunction can result in severe conditions like primary ciliary dyskinesia (PCD), highlighting the need for a deeper molecular understanding of their specific ciliary compartments. Interestingly, ciliated cells harbor multiple proteins with limited evidence on biological function, as defined by Functional Evidence (FE) scores, a grading system developed by the Human Proteome Project (HPP). Building upon the stringent antibody validation pipeline of the Human Protein Atlas (HPA) project, we developed a high-throughput workflow that combines a novel multiplex immunohistochemistry protocol with image analysis to investigate protein expression and subcellular localization in motile ciliated cells across five human tissues: nasopharynx, bronchus, fallopian tube, endometrium, and cervix. We spatially mapped >180 proteins, out of which 73% have FE scores 2-5, suggesting that further evidence is needed to establish these proteins' biological function. Notably, expression patterns varied between tissues, suggesting that motile cilia proteins are not universally expressed across the different epithelia. Our pipeline constitutes a promising resource for comprehensive mapping of the motile cilia proteome, and a first step toward identifying cilia proteins for functional studies to understand the molecular mechanisms underlying ciliopathies.

Keywords:  antibody-based proteomics; ciliated cells; human protein atlas; image analysis; motile cilia; multiplex immunohistochemistry; protein mapping

DOI:  https://doi.org/10.1021/acs.jproteome.5c00686
Mol Cell. 2025 Dec 18. pii: S1097-2765(25)00940-2. [Epub ahead of print]85(24): 4602-4620.e9

Targeting PRDX6-dependent localization and function of GPX4 enhances ferroptosis-mediated tumor suppression.

Yameng Hu, Ziwen Li, Man Li, Xingui Wu, Shuxia Zhang, Miaoling Tang, Ruyuan Yu, Meisongzhu Yang, Xin Chen, Libing Song, Guido Kroemer, Valerian E Kagan, Hülya Bayir, Rui Kang, Jinbao Liu, Daolin Tang, Jun Li.

  Inducing lipid peroxidation-dependent ferroptosis is a promising anticancer strategy; however, the development of resistance poses a considerable challenge. This study identifies peroxiredoxin 6 (PRDX6) as a crucial modulator of glutathione peroxidase 4 (GPX4), affecting its localization and functional roles, thus contributing to ferroptosis resistance. PRDX6, endowed with phospholipase A2 activity, catalyzes the conversion of peroxy-phospholipids to lysophospholipids and oxidized fatty acids. Through targeted structural mutations and biochemical analyses, we demonstrate that PRDX6 binds to GPX4 via a C47 disulfide bond, facilitating GPX4's membrane translocation and enhanced production of hydroxy fatty acids. Combining the inhibition of PRDX6 with ferroptosis inducers increases lipid peroxidation, effectively suppressing tumor growth in liver and ovarian cancer mouse models, including patient-derived models. Furthermore, high PRDX6 expression correlates with shorter progression-free survival across multiple human cancer types. Collectively, our findings delineate a PRDX6-dependent mechanism in ferroptosis defense, offering new perspectives for targeted cancer therapy.

Keywords:  PRDX6; cancer therapy; lysophospholipids; membrane translocation of GPX4

DOI:  https://doi.org/10.1016/j.molcel.2025.11.023
Redox Biol. 2025 Nov 29. pii: S2213-2317(25)00466-5. [Epub ahead of print]89 103953

Rapid quantitation of NAD+/NADH and NADPH/NADP+ with mass spectrometry by using calibration constants.

Qiuyuan Guo, Mike Lingjue Wang, Michaela Schwaiger-Haber, Xiangfeng Niu, Shanshan Zhang, Leah P Shriver, Gary J Patti.

  NAD+/NADH and NADPH/NADP+ are important indicators of cellular redox status, but they cannot be reliably calculated from the relative intensities of mass spectrometry signals alone. Establishing accurate redox ratios by mass spectrometry has historically required converting relative signal intensities into absolute concentrations, which is a time-consuming process that limits rapid analysis. Here, we describe a simpler strategy to determine NAD+/NADH and NADPH/NADP+ by using mass spectrometry. While ionization is strongly influenced by factors such as instrument drift and sample type, we discovered that the relative signal intensities of oxidized and reduced cofactors change at the same rate across experiments performed on the same mass spectrometer. That rate can be experimentally determined and expressed as a calibration constant. Using calibration constants, relative intensities of mass spectrometry signals can be rapidly transformed into accurate redox ratios without the use of authentic standards or isotopically labeled internal standards. We present a metabolomics workflow to measure NAD+/NADH and NADPH/NADP+ by using calibration constants and compare the results to other methods, including commercial colorimetric assays. Although colorimetric assays are the most widely used, we demonstrate that mass spectrometry quantitation with calibration constants provides more accurate results.

Keywords:  Calibration constants; LC/MS; Metabolomics; NAD(+)/NADH; NADPH/NADP(+); Nicotinamide adenine dinucleotide; Nicotinamide adenine dinucleotide phosphate

DOI:  https://doi.org/10.1016/j.redox.2025.103953
Cancer Discov. 2025 Dec 19.

Serotonin modulates lineage plasticity in neuroendocrine prostate cancer via epigenetic reprogramming.

Yiyi Ji, Cheng-Wei Ju, Lei Chen, Kai Shen, Ruopeng Su, Ang Li, Xinyu Liu, Bo Liu, Xinran Zhang, Ruitu Lyu, Peng Xia, Han Li, Yiqian Pan, Yunzheng Liu, Man Hin Tse, Yizheng Xue, Hongyang Qian, Na Jing, Helen He Zhu, Liangliang Wang, Li-Sheng Zhang, Shu-Heng Jiang, Weiwei Zhang, Liang Dong, Zejun Yan, Jiahua Pan, Yinjie Zhu, Jiangbo Wei, Qi Wang, Wei Xue.

Neuroendocrine prostate cancer (NEPC) is an aggressive, therapy-resistant subtype of prostate cancer characterized by lineage plasticity. While metabolic and signaling molecules are increasingly recognized as modulators of tumor progression, their role in cell fate transition remains unclear. NE tumors produce and accumulate serotonin, a neurotransmitter that regulates diverse physiological processes. Here, we identify a tumor-intrinsic serotonin axis as key driver of NEPC lineage commitment and progression. NEPC endogenously synthesize serotonin via aromatic L-amino acid decarboxylase (DDC) and reuptake through the transporter SLC6A4. Mechanistically, high level of intracellular serotonin promotes histone serotonylation at H3K4me3Q5, reconfiguring the H3K4me3 chromatin landscape and downstream gene expression, which drives induced NE differentiation and is associated with suppressed androgen receptor signaling. Pharmacological inhibition of 5-HT synthesis using the FDA-approved DDC inhibitor carbidopa significantly impairs tumor growth and prolongs survival in both genetically engineered and patient-derived xenograft models, highlighting histone serotonylation as a druggable vulnerability in NEPC.

DOI: https://doi.org/10.1158/2159-8290.CD-25-0974