bims-cesirm 2025-12-07 papers

bims-cesirm

Biomed News

on Cell Signaling mediated regulation of metabolism

Issue of 2025–12–07
twenty papers selected by
Tigist Tamir, University of North Carolina

Recurrent Breast Cancer Cells Depend on De novo Pyrimidine Biosynthesis to Suppress Ferroptosis.
The interplay between extracellular matrix remodeling and cellular lipid metabolic reprogramming in cancer: a review.
Renal and hepatic function is preserved following inducible knockout of kynurenine pathway enzymes KMO or QPRT in adult mice.
De Novo Hepatic Pyrimidine Synthesis Regulates Systemic Energy Homeostasis.
Pathway coessentiality mapping reveals complex II is required for de novo purine biosynthesis in acute myeloid leukaemia.
Atom-level enzyme active site scaffolding using RFdiffusion2.
Aberrant sialic acid metabolism promotes metabolic reprogramming and metastasis in breast cancer.
High-Fat Diet Induces Senescence in ADSCs via CDK4 Ubiquitination-Mediated Cell Cycle Disruption, Contributing to Impaired Glucose Tolerance.
Adaptability of lung and liver metastatic breast cancer cells to glucose.
Mitochondrial Metabolic Reprogramming along with NRF2/KEAP1-Mediated Antioxidant Mechanisms Drive Temozolomide Resistance in Glioblastoma Multiforme.
Computational enzyme design by catalytic motif scaffolding.
ProteoformDB: A Built-In Application to Generate Proteoform Database.
Exploiting metabolic adaptations to overcome dabrafenib treatment resistance in melanoma cells.
Ei24 deficiency in brown adipocytes induces severe hypothermia under cold stress independent of UCP1 activity.
Computational approaches to enzymatic reaction assignment: a review of methods, validations, and future directions.
Acylation modification-mediated metabolism reprogramming in cancer.
Quantitative comparison of PI(3,5)P 2 biosensors reveals SnxA is the most sensitive and unbiased.
Ubiquitination of glucose and lipid metabolic proteins is altered in diabetic rat livers.
Spatiotemporal profiling of modification-specific proteome secretion uncovers an itaconation-activated tyrosine kinase.
Progesterone receptors drive advanced breast cancer phenotypes including circulating tumor-and stem-like cell expansion in the context of ESR1 mutation.

bioRxiv. 2025 Nov 17. pii: 2025.11.17.688927. [Epub ahead of print]

Recurrent Breast Cancer Cells Depend on De novo Pyrimidine Biosynthesis to Suppress Ferroptosis.

Kelley R McCutcheon, Josh Wu, Yasemin Ceyhan Ozdemir, Brock J McKinney, Sharan Srinivasan, Ayaha Itokawa, Oliver J Newsom, Anna Vigil, Douglas B Fox, Lucas B Sullivan, James V Alvarez.

Breast cancer recurrence remains a major clinical challenge, often associated with therapy resistance and altered metabolic states. To define metabolic vulnerabilities of recurrent disease, we performed a CRISPR knockout screen targeting 421 metabolic genes in paired primary and recurrent HER2-driven breast cancer cell lines. While both primary and recurrent tumors shared dependencies on core metabolic pathways, recurrent tumors exhibited selective essentiality for the de novo pyrimidine synthesis pathway, including Cad , Dhodh , and Ctps . Pharmacologic inhibition of the rate-limiting enzyme DHODH with BAY-2402234 selectively impaired the growth of recurrent tumor cells, while primary tumor cells were relatively resistant. BAY treatment robustly inhibited pyrimidine synthesis in all lines, but only recurrent cells underwent iron-dependent lipid peroxidation and ferroptotic cell death. Lipidomic profiling revealed enrichment of polyunsaturated ether phospholipids in recurrent cells, which may predispose them to ferroptosis. A sensitizer CRISPR screen in primary cells further identified nucleotide salvage and lipid metabolic pathways as modifiers of DHODH inhibitor sensitivity. Stable isotope tracing and nutrient depletion experiments showed that primary cells can compensate for DHODH inhibition through nucleotide salvage, whereas recurrent cells exhibit impaired salvage capacity, likely due to reduced expression of Slc28 / Slc29 nucleoside transporters. Together, these findings reveal that breast cancer recurrence is associated with increased dependence on de novo pyrimidine synthesis to suppress ferroptosis, highlighting a therapeutically actionable metabolic vulnerability in recurrent disease.

DOI: https://doi.org/10.1101/2025.11.17.688927
Mol Biol Rep. 2025 Dec 01. 53(1): 145

The interplay between extracellular matrix remodeling and cellular lipid metabolic reprogramming in cancer: a review.

Minyue Yin, Xue Li, Shutian Zhang, Si-An Xie.

  Tumor-associated extracellular matrix (ECM) remodeling provides a supportive microenvironment for aberrant cellular behaviors and fate, resulting in tumor progression. Concurrently, reprogrammed lipid metabolism, characterized by dysregulated de novo lipogenesis, fatty acid oxidation (FAO), and lipid peroxidation, serves as a metabolic hallmark of cancer. Emerging evidence reveals a bidirectional crosstalk between ECM remodeling and lipid metabolic rewiring, which collectively drive tumorigenesis, survival, metastasis, and drug resistance. However, the mechanistic links connecting ECM dynamics to cellular lipid metabolism remain incompletely elucidated. In this review, we dissect the mechanistic underpinnings of ECM-lipid metabolism crosstalk, focusing on biochemical and biophysical modulation. In general, ECM-lipid metabolism axis form a self-amplifying feedback circuit, wherein ECM remodeling regulates lipid anabolism and catabolism to fuel energy production, membrane biosynthesis, and signaling molecules generation, while lipid metabolites reciprocally promote ECM degradation or deposition. Targeting critical nodes within this circuit-such as ECM-derived cues (e.g., collagen) or intracellular lipid metabolism pathway (e.g., FAO)-represents a promising strategy to disrupt tumor-stroma coevolution and enhance therapeutic efficacy. Notably, this crosstalk is not static but highly dynamic, exhibiting context-dependent dual roles influenced by variables such as cell state, cancer type, tumor site, and disease stage.

Keywords:  Biochemical signaling; Biophysical signaling; Extracellular matrix remodeling; Lipid metabolic reprogramming; Mechanical-metabolic axis

DOI:  https://doi.org/10.1007/s11033-025-11283-8
PLoS One. 2025 ;20(12): e0335906

Renal and hepatic function is preserved following inducible knockout of kynurenine pathway enzymes KMO or QPRT in adult mice.

Benjamin S Summers, Luke Milham, Sonia Bustamante, Krishan Gondal, Peggy Rentsch, Gayathri Sundaram, Michael D Lovelace, Bryce Vissel, Bruce J Brew.

The kynurenine pathway (KP) is the canonical route by which tryptophan is metabolised, almost all of which occurs in the liver, with significant expression of its enzymes also known in the kidney. We generated two novel mouse models for inducible global knockout of midpoint KP enzyme kynurenine-3-monooxygenase (KMO) and endpoint enzyme quinolinate phosphoribosyltransferase (QPRT; converts known neurotoxic KP metabolite Quinolinic acid to nicotinamide adenine dinucleotide (NAD) precursor via the de novo synthesis pathway). The KP is dysregulated in many renal and hepatic disorders, but as an essential step prior to use in disease studies, we set out to characterise their basal KP metabolome and investigate any changes to their overall phenotype in the liver and kidney, free of exogenous inflammatory stimuli. Both enzyme knockouts caused rapid alterations in accumulation of blood metabolite levels upstream of the affected enzyme, although downstream metabolite concentrations were surprisingly unaffected. KMO knockout elevated kynurenine, kynurenic acid and anthranilic acid, while QPRT knockout elevated quinolinic acid. Regardless of these significant metabolic alterations, histological examination of liver and kidney tissues, standard clinical blood chemistry and gross animal observations indicated no evidence of pathological changes in both the renal and hepatic systems. Our findings suggest that in a timeframe of 1-5 weeks and without evoked inflammation, robust homeostatic mechanisms can accommodate substantial fluctuations in KP metabolite concentrations in knockout mice without affecting renal or hepatic structure or function.

DOI: https://doi.org/10.1371/journal.pone.0335906
bioRxiv. 2025 Nov 18. pii: 2025.11.18.689117. [Epub ahead of print]

De Novo Hepatic Pyrimidine Synthesis Regulates Systemic Energy Homeostasis.

Ling Fu, Pradnya H Patil, Pengfei Zhang, Ignacio Norambuena-Soto, Qiutang Xiong, Yin Wang, Chelsea Jang, Kevin Wang, Yunqian Peng, Lu Ding, Patrick Fueger, Lihua Jin, Wendong Huang, Philip L Lorenzi, Lin Tan, Markus Kalkum, Philipp E Scherer, Zhao V Wang, Yingfeng Deng.

Fasting blood uridine is increased in obesity and type 2 diabetes (T2D), but the significance of hepatic uridine biosynthesis to the etiology of both remains elusive. We found that de novo pyrimidine synthesis in the liver is reduced by fasting and diet-induced obesity, while suppression of hepatic pyrimidine synthesis promotes obesity and insulin resistance. The metabolic sequalae of hepatic pyrimidine synthesis suppression, however, is not associated with altered plasma uridine concentration. Instead, it is associated with an increased hepatic glucose production and a decreased hepatic insulin clearance, two key functions of hepatocytes in regulating systemic energy homeostasis. We found that enhanced gluconeogenesis is the primary reason for increased hepatic glucose production. Moreover, uridine, which was maintained stable in the circulation by adipose tissue and the liver, preferentially shut down pyrimidine synthesis in hepatocytes but not adipocytes at blood concentrations that occur with fasting. Remarkably, uridine, at fasting levels, increases gluconeogenesis further in hepatocytes when de novo pyrimidine synthesis is suppressed, indicating a synergistical action of uridine and its biosynthesis pathway in promoting hepatic glucose production, a mechanism highly relevant to the pathophysiology of insulin resistance in obesity. Theologically, maintenance of blood uridine within the narrow range protects mammals from high-rate spontaneous tumorigenesis. Since obesity promotes an increase in blood uridine from adipocytes, suppressing uridine synthesis in hepatocytes becomes a critical response to lower spontaneous tumorigenesis. Pyrimidine synthesis suppression in hepatocytes, however, promotes gluconeogenesis and ultimately triggers obesity and T2D. These findings suggest a new paradigm for the etiology of metabolic deterioration in diet-induced obesity, in which perturbations in uridine promotes obesity and T2D.

DOI: https://doi.org/10.1101/2025.11.18.689117
Nat Metab. 2025 Dec 05.

Pathway coessentiality mapping reveals complex II is required for de novo purine biosynthesis in acute myeloid leukaemia.

Amy E Stewart, Derek K Zachman, Pol Castellano-Escuder, Lois M Kelly, Ben Zolyomi, Michael D I Aiduk, Christopher D Delaney, Ian C Lock, Claudie Bosc, John Bradley, Shane T Killarney, J Darren Stuart, Paul A Grimsrud, Olga R Ilkayeva, Christopher B Newgard, Navdeep S Chandel, Alexandre Puissant, Kris C Wood, Matthew D Hirschey.

Understanding how cellular pathways interact is crucial for treating complex diseases like cancer. Individual gene-gene interaction studies have provided valuable insights, but may miss pathways working together. Here we develop a multi-gene approach to pathway mapping which reveals that acute myeloid leukaemia (AML) depends on an unexpected link between complex II and purine metabolism. Through stable-isotope metabolomic tracing, we show that complex II directly supports de novo purine biosynthesis and that exogenous purines rescue AML cells from complex II inhibition. The mechanism involves a metabolic circuit where glutamine provides nitrogen to build the purine ring, producing glutamate that complex II metabolizes to sustain purine synthesis. This connection translates into a metabolic vulnerability whereby increasing intracellular glutamate levels suppresses purine production and sensitizes AML cells to complex II inhibition. In a syngeneic AML mouse model, targeting complex II leads to rapid disease regression and extends survival. In individuals with AML, higher complex II gene expression correlates with resistance to BCL-2 inhibition and worse survival. These findings establish complex II as a central regulator of de novo purine biosynthesis and a promising therapeutic target in AML.

DOI: https://doi.org/10.1038/s42255-025-01410-x
Nat Methods. 2025 Dec 03.

Atom-level enzyme active site scaffolding using RFdiffusion2.

Woody Ahern, Jason Yim, Doug Tischer, Saman Salike, Seth M Woodbury, Donghyo Kim, Indrek Kalvet, Yakov Kipnis, Brian Coventry, Han Raut Altae-Tran, Magnus S Bauer, Regina Barzilay, Tommi S Jaakkola, Rohith Krishna, David Baker.

Designing new enzymes typically begins with idealized arrangements of catalytic functional groups around a reaction transition state, then attempts to generate protein structures that precisely position these groups. Current AI-based methods can create active enzymes but require predefined residue positions and rely on reverse-building residue backbones from side-chain placements, which limits design flexibility. Here we show that a new deep generative model, RoseTTAFold diffusion 2 (RFdiffusion2), overcomes these constraints by designing enzymes directly from functional group geometries without specifying residue order or performing inverse rotamer generation. RFdiffusion2 successfully generates scaffolds for all 41 active sites in a diverse benchmark, compared to 16 using previous methods. We further design enzymes for three distinct catalytic mechanisms and identify active candidates after experimentally testing fewer than 96 sequences in each case. These results highlight the potential of atomic-level generative modeling to create de novo enzymes directly from reaction mechanisms.

DOI: https://doi.org/10.1038/s41592-025-02975-x
Front Oncol. 2025 ;15 1698087

Aberrant sialic acid metabolism promotes metabolic reprogramming and metastasis in breast cancer.

Longyu Yang, Zhenhua Li, Meijin Wang, Xing Xiong, Shilin Zhang, Zhi Man, Chunyan Dong, Li Fu.

   Background: Dysregulated tumour metabolism is increasingly recognised as a central driver of malignant phenotypes. Against this background, the aberrant metabolism of N-acetylneuraminic acid (Neu5Ac), a core constituent of the sialic acid family, and its impact on breast cancer progression is now receiving significant research attention.
Methods: The purpose of this study is to employ metabolomic approaches to analyze and interpret differences in metabolite profiles connected to breast cancer. Following this, a comprehensive multi-omics analysis will be employed to reveal the differences at transcriptional and metabolic levels in cells after the addition of external sialic acid. Finally, modification proteomics will be applied to recognize and characterize proteins that have different sialylation patterns.
Results: Cells treated with sialic acid showed improved motility, underwent metabolic reprogramming, and experienced a significant rise in the sialylation levels of key proteins.
Conclusion: This study collectively elucidates the role of Neu5Ac metabolism in promoting breast cancer invasion and metastasis through the remodeling of lipid metabolic pathways and alterations in protein sialylation. The findings present novel evidence supporting the targeting of sialic acid metabolism and its modifications as potential therapeutic strategies for inhibiting tumor progression.

Keywords:  Neu5Ac; breast cancer; metabolic reprogramming; metastasis; sialylation

DOI:  https://doi.org/10.3389/fonc.2025.1698087
Mol Metab. 2025 Nov 28. pii: S2212-8778(25)00200-5. [Epub ahead of print] 102293

High-Fat Diet Induces Senescence in ADSCs via CDK4 Ubiquitination-Mediated Cell Cycle Disruption, Contributing to Impaired Glucose Tolerance.

Zheng Ge, Zitian Liu, Shuohui Dong, Xiang Zhao, Guangwei Yang, Ao Yu, Wei Guo, Xiang Zhang, Qunzheng Wu, Kexin Wang.

  High-fat diet (HFD) promotes adipose tissue senescence, which in turn disrupts insulin-mediated glycemic homeostasis. The underlying mechanisms remain unclear. Through clinical survey data, animal models, and primary adipose-derived mesenchymal stem cells (ADSC), we investigated how dietary patterns influence adipocyte senescence. We found that elevated fatty acid levels enhance the interaction between the E3 ubiquitin ligase TRIP12 and Cyclin-dependent kinase 4 (CDK4) in ADSCs, triggering CDK4 ubiquitination and degradation. As a process associated with this disruption in cell cycle progression, cellular senescence may represent a key outcome. Consequently, senescent ADSC-derived mature adipocytes (ADSC-MA) exhibit impaired insulin-stimulated GLUT4 membrane translocation and reduced glucose uptake. In contrast, within an HFD setting, dietary fiber supplementation is associated with the reversal of cellular senescence. The gut microbiota-short-chain fatty acids (SCFAs) axis may be involved in the restoration of cell cycle progression and the amelioration of ADSC senescence, correlating with a partial recovery of glucose uptake capacity in ADSC-MAs. Our study highlights potential strategies to reverse cellular senescence and identifies promising therapeutic targets for impaired glucose tolerance.

Keywords:  Adipocyte; Cell cycle; Cellular senescence; Glucose tolerance; Stem cell; Ubiquitination

DOI:  https://doi.org/10.1016/j.molmet.2025.102293
Cancer Cell Int. 2025 Oct 24. 25(1): 374

Adaptability of lung and liver metastatic breast cancer cells to glucose.

Marjorie Anne Layosa, Madeline P Sheeley, Alekya Raghavan, Chaylen Andolino, Michael K Wendt, Stephen D Hursting, Dorothy Teegarden.

   BACKGROUND: Breast cancer is the most common cancer among women, and metastasis is the leading cause of mortality. It is still unknown how breast cancer cells metabolically adapt to successfully metastasize to different organs to survive adverse conditions, including varying nutrient availability. The purpose of this study is to elucidate the metabolic characteristics and glucose adaptation mechanisms of breast cancer cells that preferentially metastasize to the lungs or the liver.
METHODS: Using a Wnt-driven breast cancer model with preferential metastasis to lung (metM-WntLung) or liver (metM-WntLiver), we measured 14C-glucose uptake, 13C6-glucose metabolic flux, metabolic enzyme levels, and cell viability under normal (5 mM), high (25 mM), and low (1 or 0 mM) glucose conditions.
RESULTS: Under normal glucose conditions, metM-WntLung cells were more glycolytic, exhibiting greater flux of 13C6-glucose-derived carbons into glycolytic intermediates, such as pyruvate and lactate. In contrast, metM-WntLiver cells favored oxidative phosphorylation, with higher levels of 13C6-glucose-derived carbons in tricarboxylic acid (TCA) cycle metabolites such as oxaloacetate indicative of higher pyruvate carboxylase (PC) activity. Exposure to high glucose reduced metM-WntLiver cell viability, with no effect on metM-WntLung cells, suggesting better adaptability of metM-WntLung cells to glucose excess. This was accompanied by increased PC activity and oxidative phosphorylation in metM-WntLung cells, whereas metM-WntLiver cells shifted to a more glycolytic phenotype. Under glucose deprivation, metM-WntLung cells were more viable than metM-WntLiver cells, suggesting that metM-WntLung cells have better adaptability to glucose deprivation. Inhibiting phosphoenolpyruvate carboxykinase, a key enzyme in gluconeogenesis, reduced metM-WntLung cell viability compared to metM-WntLiver cells. Similarly, inhibiting catabolism of glutamine, a gluconeogenic substrate, decreased metM-WntLung cell viability compared to metM-WntLiver cells, indicating that metM-WntLung cells rely on more on gluconeogenesis and glutamine metabolism under glucose deprivation.
CONCLUSION: Our findings reveal that metM-WntLung cells exhibit greater metabolic flexibility to glucose than metM-WntLiver cells by shifting from glycolysis to oxidative phosphorylation under high glucose conditions while utilizing gluconeogenesis and glutamine under glucose deprivation conditions.

Keywords:  Breast cancer; Glucose; Metabolic adaptation; Metastasis

DOI:  https://doi.org/10.1186/s12935-025-04006-3
J Proteome Res. 2025 Dec 05.

Mitochondrial Metabolic Reprogramming along with NRF2/KEAP1-Mediated Antioxidant Mechanisms Drive Temozolomide Resistance in Glioblastoma Multiforme.

Manendra Singh Tomar, Chirag Kulkarni, Kaveri R Washimkar, Shobhit Verma, Amita Bhadkaria, Fabrizio Araniti, Madhav Nilakanth Mugale, Naibedya Chattopadhyay, Ashutosh Shrivastava.

  Temozolomide (TMZ) is a frontline chemotherapeutic agent for glioblastoma multiforme (GBM); however, approximately half of patients develop resistance to therapy. This study investigates the role of altered cellular bioenergetics and metabolism in the acquired TMZ resistance. Using untargeted metabolomics, we explored the metabolic rewiring in TMZ-resistant GBM cells and identified key alterations in glycolysis, the tricarboxylic acid (TCA) cycle, fatty acid metabolism, and amino acid metabolism, all might be linked to cellular proliferation. Our findings suggest that while glycolysis remains important, increased TCA cycle activity contributes to the drug resistance, supported by increased levels of mitochondrial mass and mitochondrial membrane potential. We observed significantly elevated glutamine levels, which may enhance mitochondrial activity, thereby supporting increased energy production. Furthermore, resistant cells exhibited enhanced NRF2 level in parallel with higher levels of antioxidants, including glutathione and catalase enzyme, and a concomitant decrease in the level of its negative regulator, KEAP1. These factors collectively may contribute to drug resistance by mitigating oxidative stress. These findings indicate that mitochondrial metabolic reprogramming and NRF2/KEAP1-mediated antioxidant defense mechanisms play a crucial role in TMZ resistance, and targeting these pathways may offer a novel strategy to overcome resistance in GBM therapy.

Keywords:  drug resistance; glioblastoma multiforme; mitochondria metabolism; oxidative stress; temozolomide

DOI:  https://doi.org/10.1021/acs.jproteome.5c00734
Nature. 2025 Dec 03.

Computational enzyme design by catalytic motif scaffolding.

Markus Braun, Adrian Tripp, Morakot Chakatok, Sigrid Kaltenbrunner, Celina Fischer, David Stoll, Aleksandar Bijelic, Wael Elaily, Massimo G Totaro, Melanie Moser, Shlomo Y Hoch, Horst Lechner, Federico Rossi, Matteo Aleotti, Mélanie Hall, Gustav Oberdorfer.

Enzymes find broad use as biocatalysts in industry and medicine owing to their exquisite selectivity, efficiency and mild reaction conditions. Custom-designed enzymes can produce tailor-made biocatalysts with potential applications that extend beyond natural reactions. However, current design methods require testing a large number of designs and mostly produce de novo enzymes with low catalytic activities1-3. As a result, they require costly experimental optimization and high-throughput screening to be industrially viable4,5. Here we present rotamer inverted fragment finder-diffusion (Riff-Diff), a hybrid machine learning and atomistic modelling strategy for scaffolding catalytic arrays in de novo proteins. We highlight the general applicability of Riff-Diff by designing enzymes for two mechanistically distinct chemical transformations, the retro-aldol reaction and the Morita-Baylis-Hillman reaction. We show that in both cases, it is possible to generate catalysts that exhibit activities rivalling those optimized by in vitro evolution, along with exquisite stereoselectivity. High-resolution structures of six of the designs revealed near-atomic active site design precision. The design strategy can, in principle, be applied to any catalytically competent amino acid array. These findings lay the basis for practical applicability of de novo protein catalysts in synthesis and describe fundamental principles of protein design and enzyme catalysis.

DOI: https://doi.org/10.1038/s41586-025-09747-9
J Proteome Res. 2025 Dec 03.

ProteoformDB: A Built-In Application to Generate Proteoform Database.

Trung Hoàng, Yingwei Hu, Hui Zhang.

  Proteins play essential functions through their complex regulations on cell-type-specific expression, localization, and molecular complexes. Protein complexity is further enhanced by proteoforms, which are the diverse molecular forms that each gene can produce through genomic alterations, transcriptional variations, translational regulations, and protein modifications. Profiling of proteoforms is a promising method for gaining a deeper understanding of the role of proteins in biological pathways and disease mechanisms. Here, we developed ProteoformDB, an application tool for generating proteoform databases, and we cataloged a total of over one million unique single-site human proteoforms. We showed that ProteoformDB can serve as a valuable resource to document the experimentally identified proteoforms in a database, supporting protein characterization in quantitative proteomics for both total protein abundances and modified protein forms.

Keywords:  MS database search strategies; combinatorial PTMs; joint quantification; mass spectrometry-based proteomics; multisite proteoforms; proteoform annotation; proteoform biology; proteoform characterization; proteoformDB; quantitative proteomics

DOI:  https://doi.org/10.1021/acs.jproteome.5c00461
Mol Oncol. 2025 Dec 02.

Exploiting metabolic adaptations to overcome dabrafenib treatment resistance in melanoma cells.

Silvia Eller, Susanne Ebner, Carmen Haselrieder, Julia K Günther, Astrid Drasche, Sophie Strich, Chiara Volani, Andrea Medici, Aleksandar Nikolajevic, Alex Deltedesco, Johannes E Sigmund, Michael J Blumer, Martin Hermann, Johanna Vanacker, Gerald Brandacher, Eduard Stefan, Omar Torres-Quesada, Jakob Troppmair.

  The emergence of resistance to mutant BRAF-specific inhibitors (BRAFi) requires novel strategies for melanoma treatment. The progression of these tumors involves metabolic adaptations, which also affect the cellular redox status. Previous studies have linked RAF kinase signaling, a key component of the MAPK/ERK pathway involved in cell division and survival, to the suppression of mitochondrial reactive oxygen species (ROS) production, resulting in protection against cell death. In BRAF-transformed cells, we have identified impaired JNK1/2-dependent activation of the mitochondrial prooxidant protein p66Shc as a potential cause. In the present study, we dissected signaling and mitochondrial alterations that characterize the transition from BRAFi responsiveness to resistance in A375 melanoma cells. Insensitivity to BRAFi dabrafenib exposure was associated with reactivation of ERK1/2 phosphorylation, increased JNK1/2 kinase activity, p66ShcS36 phosphorylation, and elevated ROS production. Utilizing high-resolution respirometry (HRR) and transmission electron microscopy (TEM), we show that dabrafenib-resistant cells displayed mitochondrial damage, compensated by increased respiration, leading to high ROS levels. Moreover, dabrafenib-resistant cells (A375D) have more efficient antioxidant systems, which may explain why despite ongoing cell death, net cell growth was observed. Treatment of both parental and resistant cells with phenethyl isothiocyanate (PEITC) increased ROS production but caused substantial cell death only in A375D melanoma cells. This PEITC effect could be demonstrated in two further dabrafenib-resistant cell lines, WM164D and 451LuP. These results suggest that the altered redox status is linked to compromised mitochondria and is associated with the development of BRAFi resistance, rendering cells exquisitely sensitive to the actions of selective ROS-inducing therapeutics.

Keywords:  BRAFV600E; dabrafenib resistance; high‐resolution respirometry; melanoma; mitochondria; p66Shc

DOI:  https://doi.org/10.1002/1878-0261.70169
Nat Commun. 2025 Dec 01. 16(1): 10426

Ei24 deficiency in brown adipocytes induces severe hypothermia under cold stress independent of UCP1 activity.

Su Bin Lee, Bui Thanh Thu, Tae Wook Nam, Yaechan Song, Jae Hoon Lee, Yangsik Jeong, Han-Woong Lee.

Brown adipocytes facilitate non-shivering thermogenesis, which is critical for maintaining energy balance and heat production in response to environmental stimuli. Here, we delineate the physiological and biochemical role of etoposide-induced 2.4 (Ei24) in adenosine triphosphate (ATP) production and thermogenesis in brown adipocytes. We generated Ei24 adipocyte-specific knockout (EiaKO) mice that exhibited brown adipose tissue hypertrophy, lipid accumulation, and various mitochondrial abnormalities. Despite mitochondrial defects, uncoupling protein 1 (UCP1) expression and activity remained unchanged. However, those impairments caused lethal hypothermia in mice subjected to cold challenge, underscoring the key role of Ei24 in mitochondrial functions. Mechanistically, Ei24 deficiency disrupted cristae structure, dissipated mitochondrial membrane potential, and reduced matrix pH, leading to severe ATP depletion. We further identify the C-terminal region of Ei24 as essential for supporting ATP synthase function. Those bioenergetic defects not only destabilized the mitochondrial environment necessary for efficient UCP1-mediated thermogenesis, but also impaired ATP-dependent futile cycles such as SERCA-mediated calcium cycling and creatine substrate cycling. Together, our findings indicate that Ei24 functions as a thermogenic regulator that ensures mitochondrial ATP synthesis and structural integrity, enabling both coupled and uncoupled respiration in brown adipose tissue.

DOI: https://doi.org/10.1038/s41467-025-66460-x
Brief Bioinform. 2025 Nov 01. pii: bbaf635. [Epub ahead of print]26(6):

Computational approaches to enzymatic reaction assignment: a review of methods, validations, and future directions.

Luke Kennedy, Mary-Ellen Harper, Miroslava Cuperlovic-Culf.

  Characterizing the proteins and molecules that underpin cellular metabolism is fundamental to advancing our understanding of biological processes. However, the rapidly expanding repertoire of newly identified proteins and metabolites presents significant challenges for experimental characterization and functional analysis. Computational approaches can be used to identify and elucidate catalytic relationships between enzymes and their substrates and provide powerful tools that support biological research and applications in biochemical engineering, and drug discovery. In this review, we describe the problem of reaction assignment for predicting enzymatic reactions leveraging structural, network, and high-throughput experimental data. Also considered are theoretical perspectives motivating the design of computational methods, available resources, and validation techniques. Current and future computational approaches for enzymatic reaction assignment are expected to advance in tandem with technologies for experimental analysis of metabolism, such as metabolomics, and flux-based methods, to expand our understanding of metabolism.

Keywords:  enzyme discovery; enzyme retrieval; metabolic networks; metabolomics; multiomics; protein function annotation

DOI:  https://doi.org/10.1093/bib/bbaf635
iScience. 2025 Dec 19. 28(12): 113883

Acylation modification-mediated metabolism reprogramming in cancer.

Kaiwei Huang, Yunshan Wang, Bohao Li, Yuchen Xiu, Hanxiang Zhan, Guangwei Wei, Yangmiao Duan.

  With the development of high-resolution liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS), various modifications resulting from the reactivity of acyl-CoA intermediates with protein residues have been identified. Acylation modifications, a diverse type of post-translational modifications (PTMs), play pivotal roles in regulating protein functions and are critically involved in tumor metabolic reprogramming. These modifications exhibit significant regulatory effects in various cancers, and their dysregulation is closely associated with malignant tumor progression. In this review, we summarize existing evidence and describe how different types of acylation modifications, including succinylation, crotonylation, lactylation, palmitoylation, and β-hydroxybutyrylation, regulate protein functions and signaling pathways, thereby influencing tumor metabolism reprogramming. Future research into the regulatory functions of acylation modifications and their roles in tumor metabolism will help elucidate the molecular mechanisms of metabolic reprogramming and provide potential targets for developing novel diagnostic and therapeutic strategies for cancer.

Keywords:  Cancer; Molecular physiology

DOI:  https://doi.org/10.1016/j.isci.2025.113883
bioRxiv. 2025 Nov 17. pii: 2025.11.10.687688. [Epub ahead of print]

Quantitative comparison of PI(3,5)P 2 biosensors reveals SnxA is the most sensitive and unbiased.

Tiernan Swayhoover, Claire C Weckerly, Gerald R V Hammond.

PI(3,5)P 2 is an endosomal lipid whose depletion is associated with a variety of pathologies such as neurodegenerative diseases. However, studying this lipid in physiological and disease models has been difficult due to the scarcity of the lipid and the lack of live-cell imaging tools. That is until recently, when a novel PI(3,5)P 2 biosensor, SnxA, was characterized. Despite the exciting promise of this new sensor, it was still unclear if SnxA unbiasedly reported on PI(3,5)P 2 levels and how its sensitivity compared to other PI(3,5)P 2 biosensors. In this work, we addressed these gaps by using a recruitable PIKfyve construct to demonstrate that ectopically generated PI(3,5)P 2 at mitochondria was sufficient to recruit SnxA. Further, we co-expressed putative PI(3,5)P 2 biosensors to definitively show that SnxA is more sensitive to PI(3,5)P 2 . We also validated previous results by showing that SnxA depends on PI(3,5)P 2 for membrane binding, SnxA responds to PI(3,5)P 2 production at endosomes, and that PI(3,5)P 2 levels decline quickly when its production is inhibited. Thus, we conclude that SnxA is a robust and sensitive PI(3,5)P 2 biosensor that facilitates real-time analysis of this key lipid.

DOI: https://doi.org/10.1101/2025.11.10.687688
Life Sci. 2025 Nov 27. pii: S0024-3205(25)00756-8. [Epub ahead of print]385 124120

Ubiquitination of glucose and lipid metabolic proteins is altered in diabetic rat livers.

Ehab M Abo-Ali, Divya K Shetty, Rhema Khairnar, Sunil Kumar, Vikas V Dukhande.

   AIM: Post-translational modifications in the form of phosphorylation of key insulin signaling proteins are known to contribute to insulin resistance by regulating the activity and function of proteins such as IR, IRS, and Akt. However, little is known about the ubiquitination code in an insulin-resistant state. Several studies have connected the ubiquitin-proteasome system to dysfunctional insulin signaling. We aimed to investigate how reduced sensitivity to insulin affects hepatic ubiquitination in vivo.
MATERIALS AND METHODS: We studied hepatic ubiquitination patterns in a high-fat diet and low-dose (40 mg/kg) streptozotocin (HF-STZ) animal model of diabetes. Affinity pull-down and proteomics techniques were employed to explore differential ubiquitination as well as lysine-48 (K48)- and lysine-63 (K63)-linkage-specific differences between control and diabetic animals. Bioinformatic tools such as gene ontology, KEGG pathway, and STRING analysis were used to categorize the ubiquitinated proteins. Western blotting and immunoprecipitation were used to validate the proteomics results of selected hits. Lipid metabolism was further investigated using triglyceride content assay and expression of lipid metabolic proteins.
KEY FINDINGS: Proteomics data showed that both the overall and linkage-specific ubiquitination were higher in diabetic rat livers. Bioinformatic analysis of the top 150 protein hits in each ubiquitination category revealed enrichment in metabolic processes involving glucose and lipid metabolism. Glycogen synthase 2 (GYS2) levels were moderately elevated with reduced total and K48-polyubiquitination in HF-STZ rat livers.
SIGNIFICANCE: Our study provides insight into hepatic ubiquitination in an animal model of insulin resistance; further studies could tease out potential targets for the pharmacotherapy of metabolic disorders.

Keywords:  Diabetes; Glucose metabolism; Glycogen synthase; Insulin resistance; Lipid metabolism; Liver ubiquitination

DOI:  https://doi.org/10.1016/j.lfs.2025.124120
Nat Commun. 2025 Dec 04.

Spatiotemporal profiling of modification-specific proteome secretion uncovers an itaconation-activated tyrosine kinase.

Wenjie Lu, Yanling Zhang, Xinrui Ni, Pian Wang, Shentian Zhuang, Wei Qin.

Macrophages secrete diverse signaling proteins critical for intercellular communication and immune responses, processes tightly regulated by post-translational modifications (PTMs). Itaconate, an immunoregulatory metabolite produced in macrophages, induces widespread intracellular protein modification (itaconation), affecting pathways like the KEAP1-NRF2 axis and glycolysis. However, the impact of itaconation on the extracellular proteome and signaling remains poorly characterized. Herein, we introduce PTM-based secretome profiling (PBSP), a novel approach to identify secreted proteins bearing specific PTMs. The method employs a bioorthogonal probe to label modified proteins in live cells, followed by enrichment of labeled proteins from the culture medium upon secretion. We established a streamlined chemoproteomic workflow integrating spintip-based affinity purification (FISAP) with data-independent acquisition (DIA) mass spectrometry for enhanced sensitivity and coverage. This identified 818 macrophage-secreted itaconated proteins, among which 447 are exosome-dependent. Further biochemical analysis revealed that itaconation of Cys239 on FYN (a tyrosine kinase) enhances its kinase activity in macrophages. We finally demonstrate PBSP's versatility by profiling secreted proteins with other PTMs, including fumarate-induced succination. PBSP provides a powerful platform to explore PTM roles in protein secretion, offering insights into PTMs' regulatory functions in cell-cell communication.

DOI: https://doi.org/10.1038/s41467-025-66508-y
bioRxiv. 2025 Nov 21. pii: 2025.11.20.689560. [Epub ahead of print]

Progesterone receptors drive advanced breast cancer phenotypes including circulating tumor-and stem-like cell expansion in the context of ESR1 mutation.

Thu H Truong, Noelle E Gillis, Amy R Dwyer, Rosemary J Huggins, Kyla M Hagen, Sai Harshita Posani, Nuri A Temiz, Carlos Perez Kerkvliet, Ellie M Piepgras, Julie H Ostrander, Geoffrey L Greene, Carol A Lange.

Endocrine therapy resistance remains a major challenge in the treatment of advanced estrogen receptor positive (ER+) breast cancer. This can be driven by acquired mutations in the estrogen receptor gene ( ESR1 ), such as Y537S or D538G, that primarily emerge in patients with prior aromatase inhibitor therapy and results in constitutive estrogen-independent ER activity. Progesterone receptors (PR) are important modifiers of ER activity, in part via direct binding. We previously showed that PR mediates expansion of cancer stem-like cell (CSC) populations and promotes tamoxifen resistance in nuclear ER/PR transcriptional complexes. In this study, we sought to define whether PR function changes in the context of ESR1 mutations. PR readily interacted with wild type (WT), but not Y537S or D538G ERs. RNA-seq and ChIP-seq studies demonstrated that ER+ breast cancer models expressing Y537S ER exhibited a distinct response to progesterone. CSC populations were enhanced in Y537S ER+ cells compared to WT ER+ cells. PR knockdown demonstrated that this property required PR expression but was unresponsive to antiprogestins. Moreover, we identified PR-dependent transcriptional programs such as the unfolded protein response (UPR) that can be leveraged to target CSC populations in Y537S ESR1 -mutant breast cancer. The UPR activator ErSO, but not UPR inhibitors, blocked expansion of CSCs in WT as well as Y537S ER + models. Together, our findings demonstrate a critical interplay between PR and mutant ER function and provide insight into PR-driven pathways including hyperactivation of the stress-sensing UPR that can be exploited as potential therapeutic avenues in advanced ER+ breast cancer.

DOI: https://doi.org/10.1101/2025.11.20.689560