bims-cesirm 2026-03-29 papers

bims-cesirm

Biomed News

on Cell Signaling mediated regulation of metabolism

Issue of 2026–03–29
24 papers selected by
Tigist Tamir, University of North Carolina

Integrative Analysis of Post-Translational Modifications Identifies a PTM-Enriched Regulatory Core in Human Metabolic Enzymes.
UFMylation of Pyruvate Dehydrogenase Regulates Mitochondrial Metabolism.
Rational design of a protein-protein interaction inhibitor that activates Protein Tyrosine Phosphatase 1B.
Tyrosine phosphoproteome profiling identifies cell-intrinsic signals limiting the efficacy of tyrosine kinase inhibitor therapies.
The pyruvate branch point controls lymphoid cancer cell dissemination.
Midgestation metabolic constraint in purine metabolism drives distinct strategies for placenta and fetal growth.
Reactive Metabolite Post-Translational Modifications: Linking Metabolism and Cellular Homeostasis.
PHGDH phosphorylation mediated by WNK1 serves as a dual marker of metabolic vulnerability and responsiveness to oxaliplatin treatment.
Phosphatidylserine Decarboxylase Promotes Ferroptosis Through STAT3/GPX4 Signaling in Gastric Cancer.
Navigating Challenges in Mass Spectrometry Analysis of Endogenous and Synthetic Protein Modifications.
A novel subset of hepatocytes is simultaneously gluconeogenic and de novo lipogenic in the fed state and is naturally insulin resistant.
An ATP-associated membrane interface integrating methionine flux with redox-regulated signaling in cancer.
A Mathematical Model of Cysteine-Driven Metabolic Adaptation to Hypoxia in Ovarian Cancer.
Degradomics for large-scale mechanistic insights on proteases and proteolysis in human health.
Enhanced Untargeted Metabolomics Based on High-Resolution Mass Spectrometry Reveals Global Rewiring Due to Mitochondrial Dysfunction in Yeast.
Integration of alternative fragmentation techniques into standard LC-MS workflows using a single deep learning model enhances proteome coverage.
Integrative Insights Into Mitochondrial Dysfunction and Organelle Crosstalk in Diabetic Kidney Disease.
Metabolomic Profiling of Tyrosine Kinase Inhibitor-Induced Endothelial Dysfunction and Cardiovascular Toxicity.
Association of statin use with pathological complete response in postmenopausal patients with hormone receptor-positive breast cancer.
Methionine metabolism is linked with phospholipid and glutamine metabolism to drive ferroptosis.
Atlas of one-carbon metabolism in conventional and germ-free mice reveals folate as a key determinant of biochemical pathways.
Quantitative analysis of S-acylation.
Photocatalytic Depletion of GSH/NADH and O2-Adaptive Pathway Switching in Producing ROS: Overcoming Treatment Resistances of Cancer Cells to Photodynamic Therapy and Inducing Ferroptotic Cell Death.
What Does Next-Generation Mass Spectrometry Offer for Proteomics? A Comprehensive Platform Comparison.

Metabolites. 2026 Feb 28. pii: 163. [Epub ahead of print]16(3):

Integrative Analysis of Post-Translational Modifications Identifies a PTM-Enriched Regulatory Core in Human Metabolic Enzymes.

Susmi Varghese, Sreelakshmi Pathappillil Soman, Mukhtar Ahmed, Levin John, Poornima Ramesh, Sowmya Soman, Vinitha Ramanath Pai, Rajesh Raju.

  Background: Metabolic enzymes catalyze biochemical pathways that sustain cellular metabolism. Their activity, stability, and molecular interactions are extensively regulated by post-translational modifications (PTMs). However, an integrated systems-level understanding of how diverse PTMs are organized across the human metabolic network remains poorly defined. Methods: We integrated experimentally reported PTM annotations from PhosphoSitePlus, dbPTM, and the quantitative PTM database (qPTM), and identified 29 distinct PTM types present across the 771 human metabolic enzymes. PTM features were quantitatively characterized at multiple levels, including sequence- and composition-based metrics (modification density and PTM potentiality rate), recurrence- and co-occurrence-based features (predominant sites, hotspot regions and PTM crosstalk), and functional-context annotations (protein-region localization and mutation overlap). These integrated features were subsequently used for unsupervised clustering to evaluate higher-order organizational patterns. Results: The analysis revealed that PTMs are unevenly distributed across metabolic enzymes, with phosphorylation, acetylation, ubiquitination, and methylation representing the most prevalent and recurrent regulatory modifications. Clustering segregated enzymes into two regulatory groups: (i) a PTM-enriched regulatory group characterized by high PTM density, frequent hotspot and crosstalk regions, and enrichment of rate-limiting enzymes, and (ii) a broad metabolic group with comparatively sparse PTM regulation. This non-uniform organization reflects the preferential accumulation of multiple regulatory PTMs on enzymes occupying key control points in central metabolic pathways, thereby forming a discrete regulatory subnetwork within metabolism. Conclusions: This study presents a systems-level, multi-PTM atlas of human metabolic enzymes and provides a quantitative framework for prioritizing PTM-regulated enzymes and pathways relevant to signaling-metabolism integration and disease-associated metabolic regulation.

Keywords:  metabolic enzymes; metabolic pathways; metabolic signaling pathway integration; multi-omic regulation; multiple-post-translational modifications; rate-limiting metabolic enzymes; unsupervised clustering

DOI:  https://doi.org/10.3390/metabo16030163
bioRxiv. 2026 Mar 18. pii: 2026.03.18.712693. [Epub ahead of print]

UFMylation of Pyruvate Dehydrogenase Regulates Mitochondrial Metabolism.

Phong T Nguyen, Zheng Wu, Dohun Kim, Tamaratare Ogu, Siyu Yin, Varun Sondhi, Feng Cai, Trevor S Tippetts, Annie Jen, Evgenia Shishkova, Ling Cai, Dennis Dumesnil, Margaret Cervantes, Hongli Chen, Prashant Mishra, Joshua J Coon, Gerta Hoxhaj, Min Ni, Ralph J DeBerardinis.

The ubiquitin-fold modifier 1 (UFM1) post-translational modification (PTM), or UFMylation, regulates protein homeostasis and is essential for human development. Yet the roles of the de-UFMylase, UFM1-specific peptidase 2 (UFSP2), which removes UFM1 from UFMylated proteins, remain poorly characterized. Here, we demonstrate that UFMylation and UFSP2 regulate mitochondrial metabolism. Quantitative proteomics in UFSP2-deficient cells revealed the accumulation of many proteins previously unknown to be impacted by UFMylation. These included components of the mitochondrial ribosome, electron transport chain (ETC), and pyruvate dehydrogenase (PDH) complex. Functional analyses demonstrated that excessive UFMylation in UFSP2-deficient cells increases mitochondrial respiration, glucose oxidation in the tricarboxylic acid (TCA) cycle, and PDH enzymatic activity. We identified dihydrolipoamide S-acetyltransferase (DLAT), the E2 component of PDH, as a direct UFMylation substrate, with lysine 118 (K118) as the primary conjugation site. Mutating K118 to arginine (K118R) abolished DLAT UFMylation and reduced pyruvate oxidation, identifying this modification as an activator of PDH. These findings reveal a UFMylation-based regulatory mechanism that controls mitochondrial function by inducing utilization of pyruvate as a TCA cycle fuel.

DOI: https://doi.org/10.64898/2026.03.18.712693
bioRxiv. 2026 Mar 21. pii: 2026.03.19.712938. [Epub ahead of print]

Rational design of a protein-protein interaction inhibitor that activates Protein Tyrosine Phosphatase 1B.

Avinash D Londhe, Sophie Rizzo, Syed M Rizvi, Alexandre Bergeron, R Sudheer Sagabala, Nilesh K Banavali, Damien Thévenin, Benoit Boivin.

Reversible inactivation of protein tyrosine phosphatases by reactive oxygen species (ROS) is essential to the phosphorylation of growth factor receptors. An important outcome of the inactivation of protein tyrosine phosphatase 1B (PTP1B) by ROS involves the conformational change of its phosphotyrosine binding loop which adopts a solvent exposed position in its oxidized form. We previously demonstrated that 14-3-3ζ binds to the phosphotyrosine binding loop of the oxidized form of PTP1B. Using a rational approach, we developed a unique protein-protein interaction (PPI) inhibitor peptide derived from the phosphotyrosine binding loop of PTP1B designed to disrupt the interaction between PTP1B and the 14-3-3ζ-complex. Exploiting this cell-permeable peptide, we showed decreased association between PTP1B and the 14-3-3ζ-complex in cells treated with epidermal growth factor (EGF). We also demonstrated that preventing the association of this 14-3-3ζ-complex to PTP1B deterred oxidation and inactivation of PTP1B following EGF receptor (EGFR) activation and generation of ROS. Treating cells with our PPI inhibitor decreased EGFR phosphorylation on PTP1B-specific sites. Furthermore, treating EGFR-driven epidermal cancer cells with our PPI inhibitor also significantly inhibited colony formation and cell viability, consitent with increased activation of PTP1B. These data highlight the ability of PTP1B to downregulate critical signaling pathways in cancer when activated using peptide drugs such as our protein-protein interaction inhibitor. We anticipate that preventing or destabilizing the reversible oxidation of other members of the protein tyrosine phosphatase superfamily using PPI inhibitors may offer a foundation for a broad therapeutic approach to rectify dysregulated signaling pathways in vivo .
Significance Statement: Limited understanding of redox mechanisms regulating PTP catalytic activity is a major knowledge gap that has hampered our efforts to develop activation strategies. In its reversibly oxidized and inactivated form, conformational changes of PTP1B influence its association with regulatory proteins. We demonstrate that designing a cell-permeable peptide based on a loop of PTP1B that becomes exposed during oxidation can block its interaction with the 14-3-3ζ-multiprotein complex and activate the phosphatase. Moreover, activating PTP1B using our protein-protein interaction inhibitor peptide decreases the phosphorylation of its substrate EGFR and decreases the effectiveness of cancer cells to form colonies. This study provides important insights into the therapeutic potential of protein-protein interaction inhibitors that regulate the redox cycle of PTPs to reestablish physiological signaling.

DOI: https://doi.org/10.64898/2026.03.19.712938
Proc Natl Acad Sci U S A. 2026 Mar 31. 123(13): e2522090123

Tyrosine phosphoproteome profiling identifies cell-intrinsic signals limiting the efficacy of tyrosine kinase inhibitor therapies.

Cameron T Flower, Forest M White.

  Tyrosine kinases (TKs) are frequently mutated or overexpressed in cancer, and TK inhibitors (TKIs) are an important therapeutic modality against TK-driven cancers, but many patients show an underwhelming response to TKIs prescribed on the basis of tumor genotype. To find cell-intrinsic TK signaling patterns which might be predictive of poor response to TKI therapies, we used high-sensitivity multiplexed mass spectrometry to quantify endogenous levels of 1,222 phosphotyrosine (pY) sites across the proteomes of TK-driven human cancer cell lines with variable response to genotype-matched TKIs. In direct comparisons between TKI-tolerant and TKI-sensitive lines with a common driver TK, we found that TKI treatment was equally effective at blocking driver TK signaling, and higher basal activity of the driver TK did not always predict higher sensitivity to TKI. All tolerant lines showed a dampened proteome-wide pY response to TKI exposure compared to sensitive lines, suggesting that tumor cells with more robust TK signaling are less vulnerable to driver TK blockade. We found that each tolerant line depends on a unique set of compensatory TKs and signaling axes but are unified by hyperactivity of at least one of the SRC family kinases (SFKs) or the related ABL1/2 kinases, both at rest and under TKI treatment, despite the absence of SFK or ABL genetic mutations. In time- and dose-resolved drug combination experiments, SFK/ABL inhibitors were potently synergistic with all TKIs tested, demonstrating that elevated SFK/ABL signaling is a conserved bottleneck for maximal TKI efficacy which could be exploited therapeutically.

Keywords:  drug synergy; phosphoproteomics; precision oncology; targeted therapy; tyrosine kinase signaling

DOI:  https://doi.org/10.1073/pnas.2522090123
bioRxiv. 2026 Mar 18. pii: 2026.03.16.712182. [Epub ahead of print]

The pyruvate branch point controls lymphoid cancer cell dissemination.

Hamidullah Khan, Steven John, Sushmita Roy, Mohd Farhan, Nguyet Minh Hoang, Patrick Buethe, Aman Prasad, Aman Nihal, David T Yang, Lixin Rui, Jing Fan, Stefan M Schieke.

Cancer cell dissemination critically determines clinical prognosis, yet metabolic dependencies and corresponding therapeutic targets during spread of lymphoid malignancies remain poorly understood. Here we show that the pyruvate branch point operates as a metabolic checkpoint for lymphoid cancer cell migration and disease dissemination through mitochondrial ROS (mROS)/HIF-1a signaling. Isolation of highly migratory mROS hi cells led us to identify selective metabolic requirements of malignant lymphocyte migration and disease dissemination. Highly migratory cells show a reprogrammed metabolic profile characterized by increased glucose uptake and reduced glucose-carbon entry into the TCA cycle. Reprogramming of the TCA cycle with downregulation of citrate synthase provide the mechanistic basis for decreased pyruvate oxidation leading to increased migration and disease dissemination through mROS/HIF-1a signaling. Our findings connect central carbon metabolism and migratory capacity of lymphoid cancer cells and identify the pyruvate branch point as a metabolic switch and potential therapeutic target in lymphoid cancer cell dissemination.

DOI: https://doi.org/10.64898/2026.03.16.712182
bioRxiv. 2026 Mar 18. pii: 2026.03.18.712680. [Epub ahead of print]

Midgestation metabolic constraint in purine metabolism drives distinct strategies for placenta and fetal growth.

Weizhi Xu, Nancy De La Cruz, Andrea Woods, Dmitry Lokshtanov, Shihong Gao, Nawal Khan, Sylvia Wright, Maria E Florian-Rodriguez, Donald D McIntire, Elaine L Duryea, David B Nelson, Catherine Y Spong, Christina L Herrera, Jacob H Hanna, Sanjay Srivatsan, Alejandro Aguilera-Castrejon, Ashley Solmonson.

Purine nucleotides are essential for mammalian development 1,2 . Purine monophosphates support cell signaling and proliferation and are synthesized by cells through either de novo synthesis or a salvage pathway 3 . We previously identified a midgestational metabolic transition in mice (gestational days gd10.5-11.5) characterized by changes in purine metabolism 4 . Midgestation is a period of rapid growth for placenta and embryo, yet it remains unclear how the placental tissues expand without directly competing with the embryo for biosynthetic resources. Here, we show that this midgestational metabolic transition is associated with a marked reduction in embryonic expression of purine salvage enzymes, which constrains embryonic metabolism and leads to different strategies for purine synthesis between the placenta and embryo. Midgestation embryos are unable to engage the purine salvage pathway even when de novo purine synthesis is blocked either in vivo or in ex utero embryo culture, whereas placental tissue and trophoblasts retain the capacity to use either pathway. Disruption of de novo purine synthesis in mice causes reduced embryonic growth, impaired axial elongation, and abnormal brain and placental development, which are only partially rescued by supplementation with purine salvage precursors. In human placenta, trophoblast stem cells readily switch between the de novo and salvage pathways based on nutrient availability, and syncytiotrophoblasts (STB) preferentially rely on the salvage pathway. We identified guanosine monophosphate (GMP) as a metabolic checkpoint regulating STB differentiation, with insufficient GMP levels causing degradation of the small GTPase Rheb and failure of mTOR activation. Supplementation of purine salvage substrates restored GMP synthesis and STB differentiation in humans, but not mice. Further, in vivo measurements in humans revealed that maternal circulating hypoxanthine decreases during pregnancy and is further reduced in women with clinically small placentas, highlighting the role of hypoxanthine in supporting placental growth. These results uncover compartmentalized purine salvage between the embryo and placenta as a mechanism that limits competition for biosynthetic resources and enables coordinated growth during mammalian development.

DOI: https://doi.org/10.64898/2026.03.18.712680
Chem Res Toxicol. 2026 Mar 23.

Reactive Metabolite Post-Translational Modifications: Linking Metabolism and Cellular Homeostasis.

Krishna C Gurajala, Reinner O Omondi.

Post-translational modifications (PTMs) include the addition of functional chemical groups, representing a crucial biochemical process that occurs after or during the synthesis of proteins, considerably impacting protein function, stability, localization, and interaction. In this ToxWatch, we review reactive metabolite PTMs as presented at the Fall 2025 American Chemical Society Meeting as part of the symposium entitled: Reactive Metabolite Post-Translational Modifications and Their Analysis.

DOI: https://doi.org/10.1021/acs.chemrestox.5c00465
Proc Natl Acad Sci U S A. 2026 Mar 31. 123(13): e2525213123

PHGDH phosphorylation mediated by WNK1 serves as a dual marker of metabolic vulnerability and responsiveness to oxaliplatin treatment.

Shaobo Fang, Guoguo Jin, Mingyang Yan, Yanming Song, Simin Zhao, Chengjuan Zhang, Yang Shao, Kexin Zhao, Meng Liu, Zhenwei Wang, Xinyang Jia, Qinxin Guo, Manman Guo, Meiyun Wang, Zhiping Guo, Zigang Dong.

  Metabolic reprogramming is a fundamental hallmark of cancer progression. However, the oncogenic mechanisms underlying serine metabolism and its impact on chemotherapeutic sensitivity in gastric cancer (GC) remain poorly defined. Here, through integrated metabolomics and 13C-labeled metabolic flux analysis, we identify marked dysregulation of serine metabolism in GC, primarily driven by increased expression of phosphoglycerate dehydrogenase (PHGDH). Mechanistically, we show that with no lysine kinase 1 (WNK1) phosphorylates PHGDH at Ser349 and Ser371, enhancing its enzymatic activity and protein stability by preventing ubiquitin-mediated degradation. In vivo, WNK1 knockout mice exhibit significantly reduced gastric tumor burden, accompanied by decreased serine levels and disrupted redox balance, supporting the protumorigenic role of the WNK1-PHGDH axis. Clinically, enhanced PHGDH activity, elevated serine levels, and increased glutathione abundance are strongly associated with poor oxaliplatin response in GC patient cohorts, suggesting PHGDH as a potential predictive biomarker for chemotherapy resistance. Together, these findings delineate a WNK1-PHGDH-driven serine metabolic reprogramming axis that promotes redox adaptation and chemoresistance in GC, highlighting its dual value as a mechanistic driver and a therapeutic vulnerability in cancer treatment.

Keywords:  PHGDH; WNK1; oxaliplatin treatment; serine metabolism; therapeutic vulnerability

DOI:  https://doi.org/10.1073/pnas.2525213123
Curr Issues Mol Biol. 2026 Mar 11. pii: 300. [Epub ahead of print]48(3):

Phosphatidylserine Decarboxylase Promotes Ferroptosis Through STAT3/GPX4 Signaling in Gastric Cancer.

Li Wang, Yaoxing Wang, Mingkai Shao, Tao Wang, Wanbao Zheng, Jun Cao, Renwen Luo, Youyan Tu, Yiting Xia, Yiming Wei, Ning Liu, Wenjie Lu, Youzhi Xu.

  Gastric cancer (GC) remains a major global health burden, and increasing evidence suggests that ferroptosis plays an important role in regulating tumor cell survival. Phosphatidylserine decarboxylase (PISD) is a key mitochondrial enzyme responsible for phosphatidylethanolamine (PE) synthesis; however, its molecular function in GC remains poorly understood. In this study, we suggest that downregulation of PISD is associated with enhanced ferroptosis in GC cells by disrupting mitochondrial PE homeostasis and impairing mitochondrial function. Mechanistically, PISD depletion reduces PE levels, is accompanied by a reduction in signal transducer and activator of transcription 3 (STAT3) phosphorylation, and decreases GPX4 expression, leading to enhanced lipid peroxidation, iron accumulation, and redox imbalance. Pharmacological inhibition of ferroptosis using Ferrostatin-1 (Fer-1), activation of STAT3 by ML115, or supplementation with lysophosphatidylethanolamine (LPE) partially rescues PISD knockdown-induced ferroptosis. In vivo, PISD downregulation is significantly accompanied by a reduction in tumor growth in GC xenograft models. Collectively, our findings reveal a previously unrecognized role of PISD in linking mitochondrial phospholipid metabolism to STAT3/GPX4-dependent ferroptosis, providing mechanistic insights into the regulation of ferroptosis in gastric cancer.

Keywords:  GPX4; STAT3; ferroptosis; gastric cancer; mitochondria; phosphatidylethanolamine; phosphatidylserine decarboxylase

DOI:  https://doi.org/10.3390/cimb48030300
Biomolecules. 2026 Feb 28. pii: 367. [Epub ahead of print]16(3):

Navigating Challenges in Mass Spectrometry Analysis of Endogenous and Synthetic Protein Modifications.

Caroline M Hanson, Dina L Bai, Jarrod A Marto.

  Mass spectrometry-based analysis of post-translational modifications (PTMs) is a key strategy for characterizing protein regulation and identifying disease-associated targets, with endogenous PTMs serving as biomarkers for disease diagnosis and therapeutic response. More recently, chemical proteomic strategies have adapted PTM-focused workflows to measure engagement of covalent and photoactivatable small-molecule probes, expanding the scope of ligand discovery for these disease-associated targets. This review provides an overview of mass spectrometry-based PTM analysis workflows, including LC-MS/MS acquisition and post-acquisition data processing, with an emphasis on how modification-specific physicochemical properties influence PTM detection and identification. Common analytical challenges that limit PTM identification, including variable MS/MS fragmentation behavior and modification site localization, are discussed using modifications such as phosphorylation and photoaffinity labeling probe adducts as representative examples. Recent advances in acquisition strategies and computational tools that improve spectral quality and confidence in PTM assignment are also summarized. Additionally, approaches for the analytical validation of modification events, such as metabolic labeling strategies, are described. Together, this review outlines key considerations, capabilities, and limitations of MS-based PTM profiling and provides a framework for interpreting PTM datasets to support their effective integration into downstream biochemical and disease target validation studies.

Keywords:  chimeric spectra; collision induced dissociation (CID); database search; diagnostic ion; dynamic exclusion; electron capture dissociation (ECD); electron transfer dissociation (ETD); error-tolerant search; fragment remnant; immonium ion; isobaric; labeling profile; open search; parallel reaction monitoring (PRM); peptide-spectrum match (PSM); positional isomer; precursor ion scanning; site-determining ion; synthetic modification

DOI:  https://doi.org/10.3390/biom16030367
bioRxiv. 2026 Mar 16. pii: 2026.03.09.710526. [Epub ahead of print]

A novel subset of hepatocytes is simultaneously gluconeogenic and de novo lipogenic in the fed state and is naturally insulin resistant.

Junichi Okada, Austin Landgraf, Maxwell Horton, Yunping Qiu, Alus M Xiaoli, Roberto Ribas, Li Liu, Sofia V Krylova, Hernando J Olivos, Victor L Schuster, Fajun Yang, Takeshi Saito, Ramon C Sun, Meredith Hawkins, Gary J Schwartz, Carolina Eliscovich, Kosaku Shinoda, Irwin J Kurland, Jeffrey E Pessin.

It is generally accepted that hepatic gluconeogenesis, the synthesis of glucose from non-carbohydrate substrates is active in the fasted state and inactive in the fed state. In contrast, de novo lipogenesis is active in the fed state and is inactive in the fasted state. Here, we used targeted single cell RNA-seq, HCR RNA-FISH, and PrimeFlow in normal physiological mouse liver, and identified a subpopulation of periportal hepatocytes that simultaneously co-express both gluconeogenic and lipogenic genes in the fed state. Euglycemic-hyperinsulinemic clamps further demonstrated that this novel hepatocyte subpopulation is naturally insulin resistant. Spatial metabolic imaging coupled with stable isotope tracing analyses revealed individual hepatocytes that simultaneously undergo both gluconeogenesis and de novo lipogenesis. These dual-positive hepatocytes were also present in human hepatocytes from humanized mouse livers. Moreover, the number of dual-positive hepatocytes increased in high-fat diet-fed mice, suggesting a paradigm shift in our understanding of how the liver becomes insulin resistant.

DOI: https://doi.org/10.64898/2026.03.09.710526
Front Oncol. 2026 ;16 1779365

An ATP-associated membrane interface integrating methionine flux with redox-regulated signaling in cancer.

Maximo A Benavides.

  Methionine dependence and redox-regulated post-translational modifications (PTMs) represent well-characterized and therapeutically relevant features of cancer cell metabolism. Although established amino acid transporters and one-carbon pathways account for methionine uptake and utilization, current models do not fully explain how methionine influx is dynamically integrated with ATP-dependent membrane energetics and redox-sensitive signaling networks in malignant cells. Here, we propose a testable conceptual framework in which a thiol- and methyl-responsive, ATP-associated membrane interface operates at the membrane-metabolism boundary, coupling methionine availability with redox-regulated PTM networks. Rather than postulating a novel transporter, this model introduces a regulatory layer linking sulfur and methyl-group flux to membrane energetics and signaling adaptability. By positioning membrane energetics as an active component of metabolic-redox coordination, this framework advances a systems-level perspective in which methionine dependence emerges from coordinated energetic, metabolic, and signaling processes rather than isolated transporter activity. The hypothesis generates experimentally tractable predictions: perturbation of thiol redox balance, methyl-group flux, ion gradients, or ATP-dependent membrane processes should produce coordinated alterations in methionine uptake dynamics and PTM signaling states. This model provides a foundation for mechanistic investigation and rational therapeutic exploration.

Keywords:  ATP-dependent membrane processes; cancer metabolism; membrane energetics; methionine metabolism; one-carbon metabolism; post-translational modifications; redox signaling

DOI:  https://doi.org/10.3389/fonc.2026.1779365
Bioengineering (Basel). 2026 Mar 04. pii: 300. [Epub ahead of print]13(3):

A Mathematical Model of Cysteine-Driven Metabolic Adaptation to Hypoxia in Ovarian Cancer.

José A Rodrigues, Sofia C Nunes, Cristiano Ramos, Luis G Gonçalves, Jacinta Serpa.

  Ovarian cancer progression is strongly influenced by tumour hypoxia and associated oxidative stress. Experimental evidence indicates that cysteine availability supports ovarian cancer cell fitness under hypoxic conditions, yet the quantitative integration of cysteine metabolism, redox control, and energetic maintenance remains incompletely understood. We present a reduced mechanistic mathematical model describing intracellular cysteine allocation between glutathione (GSH) synthesis and hydrogen sulfide production under experimentally imposed hypoxia. The model integrates extracellular cysteine uptake, GSH-dependent reactive oxygen species (ROS) detoxification, hypoxia-amplified ROS generation, and redox-modulated ATP maintenance. Parameter estimation was performed using experimentally derived extracellular metabolite fluxes measured over a 24 h interval. Uncertainty was assessed via bootstrap resampling, and variance-based sensitivity analysis was conducted within (patho)physiologically constrained parameter domains. The calibrated model reproduces extracellular fluxes with relative deviations below 7% and identifies GSH synthesis capacity as the dominant determinant of ATP maintenance within experimentally supported ranges. Hydrogen sulfide (H2S) production exerts a secondary stabilising influence, whereas hypoxia-driven ROS amplification negatively impacts energetic state. Numerical continuation across hypoxia levels reveals distinct qualitative response regions but does not imply a formal bifurcation structure. Importantly, intracellular metabolite dynamics are inferred as latent variables consistent with extracellular constraints and established biochemical knowledge; the model does not uniquely identify intracellular pool sizes or enzyme kinetics. The framework therefore provides flux-consistent mechanistic plausibility rather than direct intracellular validation. This systems-level analysis supports cysteine allocation as a quantitatively influential control point in hypoxic adaptation and establishes a constrained modelling framework for subsequent metabolic network expansions and experimental validation.

Keywords:  cysteine metabolism; hypoxia; mathematical modelling; metabolic adaptation; metabolic network dynamics; model calibration; nonlinear dynamics; ovarian cancer; quantitative redox modelling; redox homeostasis; systems biology modelling

DOI:  https://doi.org/10.3390/bioengineering13030300
FEBS J. 2026 Mar 23.

Degradomics for large-scale mechanistic insights on proteases and proteolysis in human health.

Daniel R Martin, Sumit Bhutada, Suneel S Apte.

  Tissue breakdown, especially extracellular matrix or secretome breakdown is a significant aspect of physiological remodeling and disease processes in solid organs, with profound structural and regulatory impact. Tissue and circulating proteins undergo breakdown through a chemical process mediated by proteases, that is, hydrolysis of peptide bonds. Proteolysis has immense biological impact because it is irreversible, results in protein inactivation or activation, and can generate fragments with new functions to expand the functional genome. The traditional focus on a few proteases of interest against candidate substrates provided limited insights into the proteolytic landscape of human diseases. In contrast, innovations in protein terminomics workflows, tandem mass spectrometry and data handling now routinely permit identification of proteolytic events and proteases on the proteome scale, the degradome. The unbiased, de novo elucidation of disease degradomes, termed forward degradomics, has increased the number of known in vivo proteolytic events, despite only limited application to human disease to date. In reverse degradomics, activities of proteases are elucidated individually, but also at the proteome scale by digesting protein libraries sourced from tissues and cell secretomes, or by comparing the degradomes of protease-deficient/overexpressing and parental cells. Integration of forward and reverse degradomes precisely defines protease primary mechanisms in disease. Cross-disease degradome analysis can define disease-relevant, protease-specific biomarkers, identify proteases as appropriate therapeutic targets, and predict cross-organ impact of protease inhibitors. A systematic effort to map disease degradomes, that is, a prospective human degradome project would generate a comprehensive proteolysis knowledgebase for diagnostics and therapeutics.

Keywords:  mass spectrometry; protease; proteolysis; proteomics; terminomics

DOI:  https://doi.org/10.1111/febs.70504
Int J Mol Sci. 2026 Mar 13. pii: 2624. [Epub ahead of print]27(6):

Enhanced Untargeted Metabolomics Based on High-Resolution Mass Spectrometry Reveals Global Rewiring Due to Mitochondrial Dysfunction in Yeast.

Fabrizio Mastrorocco, Luca De Martino, Igor Fochi, Graziano Pesole, Ernesto Picardi, Clara Musicco, Sergio Giannattasio.

  Mitochondrial dysfunction profoundly alters cellular metabolism, yet its systems-level consequences remain incompletely characterized. Here, we present a comprehensive untargeted metabolomics analysis of respiratory-deficient (ρ0) and competent (ρ+) Saccharomyces cerevisiae prototrophic cells using ultra-high-performance liquid chromatography coupled to Orbitrap Fusion™ Tribrid™ high-resolution mass spectrometry. By integrating hydrophilic interaction and reversed-phase chromatography in both ionization modes, we detected ~7000 features per chromatographic condition, of which ~12% were structurally annotated through MSn fragmentation and in silico spectral matching. Principal component analysis revealed distinct metabolic signatures between ρ0 and ρ+ cells, with ~73% of total variance explained by the first two components. Volcano plot and hierarchical clustering analyses identified a marked accumulation of phosphate-containing metabolites, sphingolipids, ceramides, and fatty acid residues in ρ0 cells, whereas amino acids, excluding arginine, cysteine, and aromatics, were enriched in ρ+ cells. Notably, branched-chain amino acid depletion in ρ0 cells correlated with impaired growth and mitochondrial stress. Pathway enrichment analysis, supported by transcriptomic integration, prompted us to further investigate reprogramming of polyamine biosynthesis and aromatic amino acid metabolism. Calibration curves constructed from certified standards validated the accuracy of the LC-MS platform and reinforced annotation confidence. Our findings demonstrate that advanced untargeted metabolomics, coupled with MS3 fragmentation and multi-omics integration, enables high-resolution mapping of metabolic reconfiguration under mitochondrial dysfunction, offering mechanistic insights into mitochondrial retrograde signaling and adaptation.

Keywords:  mass spectrometry; metabolite annotation; mitochondrial dysfunction; mitochondrial retrograde pathway; untargeted metabolomics; yeast

DOI:  https://doi.org/10.3390/ijms27062624
Nat Methods. 2026 Mar 23.

Integration of alternative fragmentation techniques into standard LC-MS workflows using a single deep learning model enhances proteome coverage.

Nikita Levin, Cemil Can Saylan, Joel Lapin, Yana Demyanenko, Kevin L Yang, John Sidda, Alexey I Nesvizhskii, Mathias Wilhelm, Shabaz Mohammed.

Bottom-up proteomics relies predominantly on collision-induced dissociation (CID) for peptide sequencing, which has achieved remarkable sensitivity and efficiency now enabling single-cell analysis. However, CID shows limitations in characterizing post-translational modifications and complex proteoforms. Here we have developed an integrated mass spectrometry platform enabling automated collision-, electron- and photon-based fragmentation techniques. Using multi-enzyme deep proteomics workflows, we generated comprehensive datasets to train a unified Prosit deep learning model predicting spectra across all dissociation methods. This publicly available model, now integrated into FragPipe's MSBooster module, increased protein identifications by >10% on average for both data-dependent and data-independent acquisition across all fragmentation techniques. We demonstrate that alternative approaches, particularly electron-induced and ultraviolet photodissociation, which generate richer, more informative spectra, achieve identification efficiency competitive with CID while providing superior sequence coverage. This work establishes a framework enabling routine application of advanced fragmentation techniques in standard proteomics pipelines.

DOI: https://doi.org/10.1038/s41592-026-03042-9
FASEB J. 2026 Mar 31. 40(6): e71692

Integrative Insights Into Mitochondrial Dysfunction and Organelle Crosstalk in Diabetic Kidney Disease.

Wanyu Cao, Guoding Cao, Qingtai Meng, Dingfei Li, Jie Zhang, Tianhui Wu, Fengmin Zhang.

  Diabetic kidney disease (DKD) is the leading cause of end-stage kidney disease and is driven in large part by early, sustained mitochondrial dysfunction, which promotes metabolic reprogramming, oxidative stress and inflammation that accelerate glomerular and tubular injury. We review recent mechanistic and translational advances linking mitochondrial dysfunction and organelle crosstalk to DKD progression. We synthesize evidence across four interrelated mitochondrial axes-metabolic reprogramming, altered fission-fusion dynamics, defective mitophagy, and mtDNA release-and highlight mitochondria-ER contacts (MAMs) as a nexus integrating redox signaling and calcium homeostasis. Preclinical studies indicate that interventions restoring mitochondrial biogenesis, rebalancing dynamics, enhancing selective mitophagy and preserving mtDNA attenuate glomerular and tubular injury. Clinically, several approved agents (metformin, SGLT2 inhibitors, finerenone, GLP-1RAs) exert renoprotective effects involving mitochondrial pathways; deconvolution of multi-component formulations, targeted antioxidants, metabolic activators and fission inhibitors expand therapeutic options, while organelle-level approaches such as mitochondrial transplantation are emergent. We propose a translational framework that links redox-centered mitochondrial mechanisms to actionable therapeutic strategies for DKD.

Keywords:  diabetic kidney disease; metabolism reprogramming; mitochondrial dynamics; mitochondria‐associated membranes; mitophagy; mtDNA

DOI:  https://doi.org/10.1096/fj.202504735R
Metabolites. 2026 Mar 17. pii: 200. [Epub ahead of print]16(3):

Metabolomic Profiling of Tyrosine Kinase Inhibitor-Induced Endothelial Dysfunction and Cardiovascular Toxicity.

Gurkaranvir Singh, Inderjeet Bharaj, Joey Bettencourt, Amarjit Kaur Sekhon, Gurparvesh Singh, Aaron Sidhu, Emanuel Zayas Diaz, Sulaiman Paika, Ariel De Leon, Ajit Brar, Gursimran Brar, Inderbir Padda, Ambar Andrade.

   BACKGROUND: Tyrosine kinase inhibitors (TKIs) have transformed cancer therapy; however, they are associated with cardiovascular toxicity. Metabolomics provides a comprehensive framework for identifying early biochemical disruptions that precede clinical manifestations and for formulating mechanism-based intervention strategies.
METHODS: We conducted a narrative synthesis of published preclinical and translational studies on TKI cardiotoxicity, focusing on untargeted and targeted metabolomic findings and complementary proteomic and transcriptomic data. Functional validation was performed using rodent and cellular models. Mechanistic themes were identified, and implications for biomarker panels, multi-omic integration, and metabolomics-guided interventions were proposed.
CONCLUSIONS: Metabolomic analyses of various TKIs identified convergent signatures along three interconnected axes: (1) mitochondrial bioenergetic dysfunction characterized by impaired long-chain fatty acid oxidation and adenylate depletion; (2) disruption of endothelial nitric oxide signaling with redox imbalance, including increased nitrotyrosine, Nox activation, and eNOS uncoupling; and (3) an inflammatory metabolic profile marked by elevated branched-chain and aromatic amino acids, creatine, and osmolytes. Rodent models of sunitinib and sorafenib replicate these signatures and demonstrate histological injury, contractile dysfunction, and fibrosis. Preclinical intervention data, particularly restoration of myocardial carnitine, AMPK signaling, and fatty acid oxidation by L-carnitine, provide proof of concept for metabolomics-guided cardioprotection. Metabolomics can identify mechanistic biomarkers that facilitate the early detection, risk stratification, and targeted prevention of TKI-induced cardiovascular injury. Translation into precision cardio-oncology requires prospective validation, standardized assays, and biomarker-driven interventional trials.

Keywords:  L-carnitine; cardiotoxicity; endothelial dysfunction; metabolomics; tyrosine kinase inhibitors

DOI:  https://doi.org/10.3390/metabo16030200
Sci Rep. 2026 Mar 22.

Association of statin use with pathological complete response in postmenopausal patients with hormone receptor-positive breast cancer.

Mustafa Ersoy.

  Hormone receptor-positive, HER2-negative breast cancer represents a significant subset of patients who often exhibit suboptimal responses to neoadjuvant chemotherapy (NACT). Identifying strategies to enhance chemosensitivity in this population is a clinical priority. In this study, we investigated the potential contribution of statin therapy to the efficacy of NACT. We retrospectively analyzed 60 patients treated between 2014 and 2025, comprising 22 statin users and 38 non-users. While the overall cohort analysis did not demonstrate a statistically significant difference in pCR rates, an exploratory postmenopausal subgroup analysis (performed because all statin users were postmenopausal) showed a higher pCR rate among statin users; this finding is hypothesis-generating and should be interpreted cautiously (31.8 vs. 5.0%, p = 0.047). In an exploratory multivariable logistic regression analysis limited by sparse events in the postmenopausal subgroup, statin use was associated with pCR after adjustment for Ki-67 proliferation index and clinical T stage; however, the estimate was imprecise and should be interpreted cautiously. Although pCR is not a validated surrogate for long-term survival in this specific subtype, our findings suggest that statins may biologically enhance short-term chemosensitivity, potentially through mevalonate pathway inhibition and modulation of the tumor microenvironment. These preliminary results support the need for larger prospective studies to further elucidate the role of statins as adjunctive agents in breast cancer management.

Keywords:  Breast cancer; Neoadjuvant chemotherapy; Statin

DOI:  https://doi.org/10.1038/s41598-026-45629-4
Cell Rep. 2026 Mar 26. pii: S2211-1247(26)00235-4. [Epub ahead of print]45(4): 117157

Methionine metabolism is linked with phospholipid and glutamine metabolism to drive ferroptosis.

Jong Woo Kim, Seo Young Jang, Yeon Jin Roh, Yeajin Ju, Ju-Bin Kang, Byung-Sun Park, Ji-Yoon Lee, Min Wook Kim, Byung Jun Jeong, Woosung Jung, Kyoung-Jin Oh, Won Kon Kim, Baek-Soo Han, Kwang-Hee Bae, Tackhoon Kim, Yun Pyo Kang, Hee Min Yoo, Chuna Kim, Scott J Dixon, Dong Wook Choi, Geum-Sook Hwang, Eun-Woo Lee.

  Ferroptosis is a lipid peroxidation-induced cell death mechanism that is regulated by amino acid metabolism. Cystine deprivation induces ferroptosis, but ferroptosis execution requires other amino acids. While methionine contributes to several metabolic pathways, including transsulfuration (TS), its role in ferroptosis remains controversial. Here, we report that methionine is required for ferroptosis triggered by cysteine deprivation. Notably, the TS pathway and methionine cycle in lung cancer cells are largely inactive, and methionine is instead funneled into polyamine synthesis via the methionine salvage route. Methionine depletion provokes metabolic shifts that dampen glutamine catabolism via the glutamine-methionine bi-cycle. Furthermore, methionine depletion alters phospholipid metabolism by promoting ACSL4 degradation, limiting polyunsaturated fatty acid (PUFA) incorporation into phospholipids. The methionine cycle intermediate S-adenosylmethionine (SAM) supplementation is sufficient to restore the perturbed metabolic state and ferroptosis sensitivity. Taken together, the results of this study highlight methionine as a key coordinator of ferroptosis through dynamic metabolic remodeling.

Keywords:  ACSL4; CP: metabolism; CP: molecular biology; ferroptosis; glutaminolysis; methionine; methionine salvage pathway; phospholipid metabolism; transsulfuration pathway

DOI:  https://doi.org/10.1016/j.celrep.2026.117157
Nat Metab. 2026 Mar 26.

Atlas of one-carbon metabolism in conventional and germ-free mice reveals folate as a key determinant of biochemical pathways.

Jonathan Williams, Woo Sung Kim, Rebecca Danner, Juyeong Cho, Bianca F Silva, David A Harris, Federico E Rey, Snehal N Chaudhari.

Folates participate in the one-carbon metabolism (OCM) cycle, supporting many biochemical pathways. Existing methods to profile folate are limited in the diversity of vitamers they measure and the samples they profile. Here we present a metabolomics workflow for stable extraction, separation and measurement of folates, along with precursors and products of OCM-associated pathways. We profile these metabolites in 37 mouse tissues to chart an interactive 'OCM atlas' ( https://chaudharilab.com/folate-atlas/ ), revealing vast heterogeneity across organs and an uncharacterized folate derivative. We discover that, in adult mice, the gut microbiota is a consumer of folate and folate polyglutamylation in the host is not regulated by folate availability. Germ-free mice show tissue-specific shifts in methyl donor abundances relative to conventionally raised mice, indicative of altered DNA methylation. Correlation analyses uncover the central roles of folates in potentially modulating other biochemical pathways in tissues, thus linking microbial folate consumption directly to its global impacts on host metabolism.

DOI: https://doi.org/10.1038/s42255-026-01489-w
Methods Enzymol. 2026 ;pii: S0076-6879(25)00528-2. [Epub ahead of print]728 117-128

Quantitative analysis of S-acylation.

Carla Busquets Hernández, Alexandra Tsiotsia, Gemma Triola.

  S-acylation is a protein post-translational modification that relies on the attachment of a hydrophobic fatty acid chain to a cysteine residue through the formation of a thioester bond. This reversible modification is controlled by the counteraction of protein acyltransferases and acyl protein thioesterases. The bonded lipid moiety can modulate the physicochemical properties of the substrate proteins, their membrane-binding affinity, subcellular localization, protein stability, or interactions with other proteins or cell components, thereby playing a key role in several cell processes such as protein trafficking, signal transduction, or cell proliferation. Moreover, increasing evidence has associated S-acylation malfunction with several pathological processes, including various types of cancers or neurodegenerative disorders, making S-acylation and its controlling enzymes an ideal target for therapeutic strategies. S-acylation has been commonly known as S-palmitoylation because palmitic acid was considered the predominant fatty acid attached to proteins. However, recent advances, especially in the mass spectrometry field, have suggested a diversity in the identity of the attached lipids greater than that previously considered. Moreover, since variations in the length and saturation degree of the fatty acyl chains may alter the intracellular localization and biological function of proteins, its potential role in the regulation of protein function is just being explored. However, this heterogeneous lipid composition could not be systematically studied, mainly due to the lack of suitable methods. In order to address these challenges, this protocol reports a method to identify and quantify the fatty acids attached to S-acylated proteins.

Keywords:  Fatty acids; Heterogeneous; Hydroxylamine; Palmitoylation; Protein lipidation; S-acylation

DOI:  https://doi.org/10.1016/bs.mie.2025.12.001
ACS Appl Bio Mater. 2026 Mar 26.

Photocatalytic Depletion of GSH/NADH and O2-Adaptive Pathway Switching in Producing ROS: Overcoming Treatment Resistances of Cancer Cells to Photodynamic Therapy and Inducing Ferroptotic Cell Death.

Peiwen Fan, Jianzhi Chen, Jing Liu, Hongxing Zhang, Yuanqiang Sun, Wei Guo.

  Photosensitizers (PSs), capable of overcoming the treatment resistances caused by the elevated levels of glutathione (GSH) and nicotinamide adenine dinucleotide (NADH) within cancer cells as well as the hypoxic microenvironment of solid tumors, are highly desirable for photodynamic therapy (PDT) of tumors. Herein, leveraging the redox activity and heavy atom effect of selenium (Se), we develop a cancer-cell-targetable, enzyme/light dual-activatable PS based on a Se-rhodamine platform. Upon encountering cancer cells, the dual-activatable PS can be enzymatically cleaved by aminopeptidase N (APN, overexpressed on the outer membrane of cancer cells) to release a cytomembrane-permeable prodrug PS, which, after being internalized by cancer cells, can be further activated by light to produce an active PS. The resulting active PS features not only dual photocatalytic activities in depleting GSH and NADH but also O2-adaptive type-II (under normoxia) → type-I (under hypoxia) pathway switching in producing reactive oxygen species (ROS), thereby effectively potentiating the sensitivity of cancer cells to PDT and overcoming the treatment resistances. Due to interrupting the GSH/NADH-dependent antioxidant systems, the active PS almost exclusively induces cancer cell ferroptosis. The study provides an all-in-one strategy in overcoming the treatment resistances of tumors to PDT, paving the way for developing high-performance PSs in the future.

Keywords:  glutathione; nicotinamide adenine dinucleotide; photodynamic therapy; photoredox catalysis; photosensitizer

DOI:  https://doi.org/10.1021/acsabm.5c02454
J Proteome Res. 2026 Mar 25.

What Does Next-Generation Mass Spectrometry Offer for Proteomics? A Comprehensive Platform Comparison.

Filipa Blasco Tavares Pereira Lopes, Daniela Schlatzer, Tara Sudhadevi, Anantha Harijith, Marzieh Ayati, Mehmet Koyutürk, Mark R Chance.

  Next-generation mass spectrometry platforms (Orbitrap Astral, timsTOF Ultra) are reshaping proteomics by enhancing analytical depth and sensitivity. We compared these platforms against Orbitrap Exploris 480 using neonatal mouse lung tissues from a bronchopulmonary dysplasia model (n = 12), employing four acquisition strategies: Exploris 480 DDA/DIA, Astral HR-DIA, and timsTOF Ultra DIA-PASEF. All platforms identified ∼4000 proteins in common, with 98% proteome coverage of data-dependent acquisition (DDA) identifications using data-independent (DIA) methods and 92% concordance between next-generation systems. Orbitrap Astral and timsTOF Ultra quantified >225,000 peptides and 13,000 proteins, representing ∼800% and ∼300% greater depth than Exploris 480 DDA, respectively. Furthermore, new-generation platforms cut recommended sample size by ∼66%. Enhanced proteome depth improved subcellular compartment annotations from 30% (DDA) to 66% (next-generation platforms) and reactome pathway coverage from 58% (DDA) to 90% (next-generation platforms). Differential expression analysis identified up to four times more phenotype-associated proteins in DIA data sets, enriched in mitochondrial, ribosomal, and extracellular components, with up to 44 enriched pathways. Importantly, proteins uniquely detected showed no functional annotation bias. These findings demonstrate that DIA acquisition on multivendor next-generation platforms provides superior proteome coverage and more complete systems biology assessment without introducing bias, enabling enhanced understanding of complex biological systems.

Keywords:  DDA; DIA; Orbitrap Astral; bronchopulmonary dysplasia; data-dependent acquisition; data-independent acquisition; proteomics; timsTOF Ultra

DOI:  https://doi.org/10.1021/acs.jproteome.5c01007