bims-cesirm 2026-04-12 papers

bims-cesirm

Biomed News

on Cell Signaling mediated regulation of metabolism

Issue of 2026–04–12
twenty-two papers selected by
Tigist Tamir, University of North Carolina

PHGDH is a targetable driver of PDAC progression.
Fatty acid scavenging enables cancer escape from KRAS inhibition.
Discovery and Enzymatic Regulation of Lysine Fumarylation, a Post-Translational Modification in Bacteria.
Mitochondrial ACSS1 Links Acetate Metabolism to Pyrimidine Biosynthesis in Nutrient-Stressed B-Cell Lymphomas.
Intracellular enzymatic reducing systems control receptor tyrosine kinase signaling via PTP1B.
A Modular Platform for Effector Discovery in Induced-Proximity Lysine Acetylation.
Live-cell decoding of labile post-translational modifications in APE1 with a rationally engineered nano-catcher.
Metabolic profiling reveals pyrimidine synthesis enzyme CAD as a central carbon metabolism signaling node in cancer cell proliferation.
A feedback loop between cell proliferation and ROS regulates ferroptosis sensitivity.
SLC13A2-transported citrate remodels transcriptional regulation through protein acetylation to suppress tumor growth.
Secretory autophagy mediates SLC16A3/MCT4-dependent lactate secretion to drive metastatic progression in triple-negative breast cancer.
Mapping the mammalian dark metabolome by in vivo isotope tracing.
Expanding the Global Map of Protein Post Translational Modifications with Immunoaffinity Enrichment and nDIA Analysis on the Orbitrap Astral Mass Spectrometer.
Integrative multi-omics suggests core gene dysregulation of histidine metabolism in diabetic kidney disease.
Chemical Proteomic Profiling of the Histaminylation Proteome in Cancer Cells Unveils Uncharted Epigenetic Marks on Core Histones.
Glutathione-deficiency promotes basal hyperinsulinemia in the insulin secreting cell line INS-1 (832/13).
Excess cysteine drives conjugate formation and impairs proliferation of NRF2-activated cancer cells.
CD276 promotes CD36-mediated lipid metabolism and confers resistance to tyrosine kinase inhibitors.
Reconstruction of human metabolic models with large language models.
Expanding the Chemoproteomic Toolkit to Asparagine and Glutamine.
Remote regulation of hepatic lipid secretion in the intestine by metabolic interaction of dietary arginine with ornithine.
Metabolomics across scales: from single cells to population studies.

bioRxiv. 2026 Mar 14. pii: 2026.03.11.711147. [Epub ahead of print]

PHGDH is a targetable driver of PDAC progression.

Yumi Kim, Le Jin Sun, Meredith Long, Samantha Caldwell, H Carlo Maurer, Kenneth P Olive, Florian Karreth, Gina M DeNicola.

Pancreatic ductal adenocarcinoma (PDAC) arises in a nutrient-deprived microenvironment through progressive stages from pancreatic intraepithelial neoplasia (PanIN) to invasive carcinoma. While serine metabolism supports tumor growth across multiple cancer types, the stage-specific role of de novo serine synthesis in PDAC evolution remains undefined. Here, we show that expression of phosphoglycerate dehydrogenase (PHGDH), the rate-limiting enzyme of serine biosynthesis, increases progressively from PanIN to invasive PDAC in human and mouse specimens. Using genetically engineered mouse models with inducible PHGDH knockdown, we found that PHGDH loss delayed PDAC development. Unexpectedly, PHGDH-deficient tumors did not increase reliance on exogenous serine, and dietary serine/glycine manipulation had no effect on tumor development. Instead, stable isotope tracing and metabolomic profiling revealed that PHGDH loss suppressed mTOR signaling, reduced expression of the glutamine transporter ASCT2, and impaired glutamine uptake and utilization. Leveraging this metabolic liability, we demonstrated that PHGDH-deficient tumors exhibited selective sensitivity to the glutamine antagonist DRP-104, whereas PHGDH-intact tumors were resistant. These findings reveal an unanticipated connection between serine biosynthesis and glutamine metabolism in PDAC and identify a therapeutic vulnerability that may be exploited through combined metabolic targeting.
Statement of significance: PHGDH supports PDAC progression not primarily through serine provision, but by maintaining glutamine metabolism and mTOR signaling. This unanticipated metabolic crosstalk creates a synthetic lethal vulnerability to glutamine antagonism in PHGDH-deficient tumors, providing a rationale for combining serine synthesis pathway inhibitors with glutamine-targeting therapies in pancreatic cancer.

DOI: https://doi.org/10.64898/2026.03.11.711147
bioRxiv. 2026 Apr 03. pii: 2026.04.01.715565. [Epub ahead of print]

Fatty acid scavenging enables cancer escape from KRAS inhibition.

Zihang Yuan, Bo Lin, Chunlan Wang, Yingying Miao, Da Zhang, Ziru Meng, Gangqi Wang, Andrew M Lowy, Michael Karin, Fei Yang, Beicheng Sun, Hua Su.

Although inhibitors of oncogenic KRAS have shown clinical efficacy 1 , resistance to KRAS inhibition is common 2 , and its molecular basis remains unclear. Here we show that KRASi-resistant cancer cells sustain mitochondrial bioenergetics through enhanced fatty acid (FA) metabolism, despite suppression of canonical KRAS signaling. Specifically, KRASi-resistant pancreatic cancer cells exploit macropinocytosis to scavenge FA released from adipose tissue, fueling beta-oxidation independently of KRAS-PI3Kα signaling. This adaptive metabolic program is driven by the adhesion G protein-coupled receptor ADGRB1, which activates non-canonical PI3Kγ-PAK1 signaling to stimulate macropinocytosis and maintain metabolic homeostasis under KRASi. Disruption of ADGRB1-PI3Kγ signaling dismantles this metabolic program and restores KRASi sensitivity. This pathway operates across multiple KRAS-mutated cancers and is associated with poor therapeutic response and outcome. These findings offer a promising strategy for overcoming KRASi resistance.

DOI: https://doi.org/10.64898/2026.04.01.715565
J Am Chem Soc. 2026 Apr 09.

Discovery and Enzymatic Regulation of Lysine Fumarylation, a Post-Translational Modification in Bacteria.

Chen Chen, Xinyun Zhang, Xue Bai, Yong Zang, Zilong Fan, Jianji Zhang, Jia-Nan Wang, Yanpu Han, Kai Zhang.

Protein post-translational modifications (PTMs) derived from primary metabolites have emerged as fundamental mechanisms linking cellular metabolism to physiological regulation. Here, we report the discovery and characterization of lysine fumarylation (Kfu), a previously unrecognized PTM originating from the tricarboxylic acid (TCA) cycle intermediate fumarate. Utilizing an open-search mass spectrometry approach, we identified a mass shift of +98.0002 Da on lysine residues in Escherichia coli, corresponding to the addition of a fumaryl group. By enrichment with a pan-succinyl-lysine antibody followed by mass spectrometry analysis, we demonstrated that fumarate significantly elevates global Kfu levels and mapped 857 endogenous Kfu sites. The occurrence and structural identity of Kfu were confirmed through chromatographic retention and MS/MS fragmentation comparisons with heavy isotope-labeled synthetic peptides, as well as metabolic tracing using deuterated fumarate. We further elucidate the enzymatic pathway regulating this modification: The SucC-SucD complex functions as a bona fide fumaryl-CoA synthetase, converting fumarate to fumaryl-CoA; SpeG catalyzes fumaryl group transfer to lysine substrates; and CobB acts as an NAD+-dependent defumarylase. Integrated transcriptomic and proteomic analyses suggest that Kfu regulates genes involved in stress responses, including temperature and oxidative stress pathways. This work shows lysine fumarylation as a distinct metabolic signaling mechanism, expands the repertoire of protein acylations, and provides a molecular framework for understanding how fumarate exerts its regulatory functions through covalent protein modification.

DOI: https://doi.org/10.1021/jacs.6c04986
Cancer Lett. 2026 Apr 07. pii: S0304-3835(26)00251-X. [Epub ahead of print] 218488

Mitochondrial ACSS1 Links Acetate Metabolism to Pyrimidine Biosynthesis in Nutrient-Stressed B-Cell Lymphomas.

Johnvesly Basappa, Aaron R Goldman, Cosimo Lobello, Shengchun Wang, David Rushmore, Olga Melnikov, Neil V Sen, Vinay S Mallikarjuna, Priyanka Jain, Masoud Edalati, David S Nelson, Kathy Q Cai, Pin Lu, Reza Nejati, Hossein Borghaei, Pradeep K Gupta, Kavindra Nath, Kathryn E Wellen, Mariusz A Wasik.

  Acetate serves as an alternative carbon source in nutrient-limited tumors, yet its role in supporting nucleotide biosynthesis remains poorly understood. Here, we identify the mitochondrial enzyme ACSS1 as a key metabolic driver in mantle cell lymphoma (MCL), diffuse large B-cell lymphoma (DLBCL), and chronic lymphocytic leukemia (CLL). ACSS1 is frequently overexpressed and catalyzes the conversion of acetate to mitochondrial acetyl-CoA, sustaining oxidative metabolism and biosynthesis under nutrient stress. Genetic silencing of ACSS1 impairs mitochondrial respiration and disrupts acetate incorporation into acetyl-CoA, TCA cycle intermediates, glutamate, and aspartate, while markedly reducing 13C-acetate labeling of dihydroorotate and orotate, intermediates in de novo pyrimidine synthesis. Untargeted metabolomics reveal enrichment of pyrimidine biosynthesis pathways in ACSS1-high cells. Notably, acetate or uridine supplementation rescues the growth of ACSS1-deficient cells, confirming a functional link between acetate metabolism and nucleotide synthesis. Importantly, in vivo studies using two different MCL xenografts demonstrate that ACSS1 knockdown profoundly suppresses tumor growth, indicating that ACSS1 is required not only for metabolic adaptation of lymphoma cells in vitro but also in vivo. Collectively, our results uncover an ACSS1-dependent mitochondrial acetate-pyrimidine axis that sustains lymphoma growth and represents a previously unrecognized therapeutic vulnerability.

Keywords:  ACLY; ACSS1; ACSS2; CAD; DHODH; acetate metabolism; cancer metabolism; oncometabolite

DOI:  https://doi.org/10.1016/j.canlet.2026.218488
Sci Adv. 2026 Apr 10. 12(15): eadv5362

Intracellular enzymatic reducing systems control receptor tyrosine kinase signaling via PTP1B.

Lucia Coppo, Wenchao Zhao, Qing Cheng, Axel Tobias Scholz, Elias S J Arnér, Markus Dagnell.

Protein tyrosine phosphatases (PTPs) counteract receptor tyrosine kinase (RTK) signaling. Inhibition of PTPs by oxidation can be reversed by cytosolic thioredoxin (TXN), but less is known about regulation of PTPs by glutathione (GSH)-driven glutaredoxins (GLRXs). Here, we thus assessed GLRX1, GLRX2, and/or TXN1 in regulation of CO2/bicarbonate- and H2O2-mediated oxidation of the physiologically important PTP1B. GLRXs and TXN1 synergistically maintained PTP1B activity, and modulating cellular levels of either GLRX1, GLRX2, or TXN1 gave strong effects on phosphorylation cascades triggered by epidermal growth factor (EGF) or platelet-derived growth factor (PDGF). Furthermore, transient intracellular interactions of PTP1B with GLRX1, GLRX2, and TXN1 were discovered within minutes after stimuli with either PDGF or EGF, coinciding with control of the corresponding RTK-driven phosphorylation cascades. We conclude that TXN1 and GLRXs are key regulators of PTP1B activity and thus control cellular responses to RTK stimulation.

DOI: https://doi.org/10.1126/sciadv.adv5362
bioRxiv. 2026 Mar 13. pii: 2026.03.11.711209. [Epub ahead of print]

A Modular Platform for Effector Discovery in Induced-Proximity Lysine Acetylation.

Brianna Hill-Payne, Mohd Younis Bhat, George M Burslem.

The regulation of post-translational modifications (PTMs) is central to cellular biology and disease. Induced-proximity strategies enable manipulation of PTMs by recruiting modifying enzymes to proteins of interest, but identifying effective effector enzymes typically requires extensive heterobifunctional molecule synthesis before biological validation. Here we report a modular platform that enables rapid evaluation of PTM editing enzymes against defined protein substrates in living cells using compound-dependent or nanobody-mediated induced proximity. Using lysine acetylation as a model system, we demonstrate programmable acetylation of GFP, histone H3, and p53 through recruitment of diverse acetyltransferases. Effector identity dictates site-specific acetylation patterns, enabling selective PTM deposition across substrates and cellular compartments. This platform enables rapid identification of productive effector-substrate relationships prior to heterobifunctional molecule development, accelerating the design of induced-proximity chemical probes for targeted PTM editing.

DOI: https://doi.org/10.64898/2026.03.11.711209
Nucleic Acids Res. 2026 Mar 19. pii: gkag323. [Epub ahead of print]54(6):

Live-cell decoding of labile post-translational modifications in APE1 with a rationally engineered nano-catcher.

Ruilan Zhang, Huaisyuan Xie, Chenxu Zhu, Ying Sun, Kexuan Li, Hongwei Li, Xiaogang Niu, Changwen Jin, Meiping Zhao.

Human apurinic/apyrimidinic endonuclease 1/redox effector factor 1 (APE1) is a multifunctional protein central to DNA repair and redox regulation, yet its dynamic post-translational modifications (PTMs) remain poorly understood. Here, we report a biotin-regulated avidin-based nano-catcher (bMIPAPE1) capable of capturing active APE1 in living cells. By leveraging biotin-saturated avidin assembled onto magnetic nanoparticles and surface-imprinted with polydopamine, we engineered highly specific binding cavities for APE1 that enable retention of labile PTMs. This platform revealed 25 previously unreported PTMs across 18 residues of APE1, encompassing acetylation, phosphorylation, ubiquitination, methylation, S-nitrosylation, palmitoylation, and succinylation, and highlighting several PTM hotspots. Representative modifications include phosphorylation at Y264 and Y269, and acetylation at K63, with several PTMs associated with APE1 nuclear export. In addition to high specificity and intracellular compatibility, bMIPAPE1 attenuated both the DNA repair and redox-related functions of APE1. Our findings demonstrate the utility of artificial nanocomposites as tools for live-cell PTM profiling and functional modulation of target proteins, offering a powerful approach to decode protein regulation in living systems and identify potential therapeutic targets in cancer.

DOI: https://doi.org/10.1093/nar/gkag323
Mol Cell. 2026 Apr 07. pii: S1097-2765(26)00192-9. [Epub ahead of print]

Metabolic profiling reveals pyrimidine synthesis enzyme CAD as a central carbon metabolism signaling node in cancer cell proliferation.

Chao Qin, Zhenhao An, Shu Feng, Wen Fu, Xinchi Xie, Ali Can Savas, Taolin Xie, Charles Brenner, Takeshi Saito, Pinghui Feng.

  Rapid cancer cell proliferation requires extensive macromolecular biosynthesis, yet how distinct anabolic pathways are coordinated remains incompletely understood. Here, we report that the trifunctional carbamoyl-phosphate synthase, aspartate transcarbamoylase, and dihydroorotase (CAD) activates key glycolytic enzymes to support biosynthesis and cancer cell proliferation. When cancer proteomics datasets were queried, a CAD activation signature was identified in diverse tumors. Metabolomics analysis revealed that CAD fuels central carbon metabolism, specifically the pentose phosphate pathway (PPP) and serine synthesis pathway (SSP). Mechanistically, CAD deamidates and activates glucose-6-phosphate dehydrogenase (G6PD) and phosphoglycerate dehydrogenase (PHGDH), rate-limiting enzymes of the PPP and SSP, respectively, which are fully recapitulated by the glutaminase domain of CAD. Functional interrogation of cancer-associated CAD mutations and human hepatocellular carcinoma tumors predicts the metabolic signature endowed by G6PD and PHGDH deamidation. Simultaneous inhibition of G6PD and PHGDH effectively impeded tumor formation. This work identifies CAD as a central carbon metabolism signaling node and a potential therapeutic target.

Keywords:  CAD; Cancer metabolism; G6PD; PHGDH; central carbon metabolism; deamidation; pyrimidine synthesis; the pentose phosphate pathway; the serine synthesis pathway

DOI:  https://doi.org/10.1016/j.molcel.2026.03.016
Front Cell Dev Biol. 2026 ;14 1756238

A feedback loop between cell proliferation and ROS regulates ferroptosis sensitivity.

Eric Seidel, E Yaren Itak, Fabienne Müller, F Isil Yapici, Johannes Brägelmann, Johannes Berg, Silvia von Karstedt.

   Background: Ferroptosis is a form of regulated cell death characterized by iron-dependent lipid peroxidation and membrane rupture. While cellular populations reaching confluence are known to have limited sensitivity to ferroptosis, an understanding of the interplay between growth dynamics, reactive oxygen species (ROS) levels, metabolism and ferroptosis is currently lacking. This study aimed to establish a regulatory framework for the systemic interplay of these biological processes.
Results: Here we use live-cell imaging coupled to ROS tracing to reveal a feedback loop between population growth and ferroptotic cell death. Starting out from the observation that the cellular proliferation rate declines with increased cellular density, we find that ROS levels also decline with increasing cellular density. In turn, low ROS levels make cells insensitive to ferroptosis, which enables population growth. Conversely, keeping cell numbers and drug concentration/cell constant while restricting growth space led to reduced proliferation, reduced ROS and decreased ferroptotic cell death. We find that this feedback between population growth and ferroptotic cell death leads to two steady states: (i) a ferroptosis-insensitive state characterized by slow growth, low levels of ROS and low rates of cell death and (ii) a ferroptosis-sensitive state characterized by rapid growth, ROS accumulation, and high rates of ferroptosis. A mathematical model of the feedback mechanism predicts the long-term fate of populations as well as their ferroptosis sensitivity when external conditions impacting cell proliferation rates, ROS, or both are changed. We tested the proposed feedback mechanism experimentally by interfering with lipid hydroperoxide clearance and by increasing cellular and lipid ROS production through a galactose-promoted OXPHOS switch.
Conclusion: We find a feedback loop between population growth and ferroptotic cell death that dictates cellular fate (growth or cell death via ferroptosis) and is mechanistically determined by the levels of metabolic ROS. These results provide a unifying framework that dynamically links population growth and metabolic ROS regulation with ferroptosis sensitivity.

Keywords:  ROS; feeedback loop; ferroptosis; lipid ROS; modelling

DOI:  https://doi.org/10.3389/fcell.2026.1756238
Sci Adv. 2026 Apr 10. 12(15): eaec4368

SLC13A2-transported citrate remodels transcriptional regulation through protein acetylation to suppress tumor growth.

Mengyao Qin, Longcheng Shang, Hao Chen, Li Shi, Chan Liu, Ming Ding, Dandan He, Chang Shao, Shengtao Yuan, Hong Yu, Haiping Hao, Yong Ma, Jing Xiong.

Metabolic reprogramming is a hallmark of cancer, while tricarboxylic acid cycle is increasingly recognized as a multifaceted hub driving tumor metabolism and progression. Integrated analysis of solute carrier (SLC) transporters revealed consistent down-regulation of SLC13A2 in hepatocellular carcinoma (HCC) cells and liver tissues from human patients and mouse models. Adeno-associated virus-mediated liver-specific knockout or overexpression of SLC13A2 (SLC13A2-OE) promoted or ameliorated HCC progression, indicating its protective role. SLC13A2 inhibited HCC proliferation by decreasing mitochondrial function via suppressed glycolysis, respiration, and adenosine 5'-triphosphate production. Flux analysis showed that SLC13A2 imported citrate to generate acetyl-coenzyme A for pyruvate kinase isozyme type M2 acetylation, triggering its degradation. Reduced pyruvate kinase activity limited pyruvate supply, impairing amino acid synthesis and nucleotide metabolism. Moreover, SLC13A2-imported citrate induced intracellular protein acetylation, particularly histone proteins, which provided an epigenetic basis for transcriptional regulation and contributed to tumor suppression. Thus, SLC13A2 perturbs metabolic and transcriptional programs to suppress tumor growth, highlighting potential drug targets for HCC therapy.

DOI: https://doi.org/10.1126/sciadv.aec4368
Autophagy. 2026 Apr 08.

Secretory autophagy mediates SLC16A3/MCT4-dependent lactate secretion to drive metastatic progression in triple-negative breast cancer.

Shan-Ying Wu, Hung-Ju Lin, Kai-Ying Lan, Hong-Chen Chen, Chao-Hsiung Lin, Chih-Yi Hsu, Yi-Jang Lee, Yen-Yu Chou, Yeh-Shiu Chu, Wei-Chung Chiang, Hsiao-Sheng Liu, Yuan-Chieh Yeh, Sheng-Hui Lan.

  Triple-negative breast cancer (TNBC) exhibits hyperactive EGF (epidermal growth factor) signaling that drives metabolic plasticity and metastasis. Here, we identify secretory macroautophagy/autophagy as a key downstream effector linking EGF signaling to metabolic reprogramming that fuels TNBC metastatic progression. In TNBC cells, EGF stimulation redirected autophagosomes toward the plasma membrane through a SEC22B-dependent route, signifying activation of secretory autophagy. Proteomic profiling of purified autophagosomes revealed enrichment of the lactate transporter SLC16A3/MCT4 and its chaperone BSG/CD147 on autophagosomal membranes. Mechanistically, EGF promoted MAP1LC3/LC3-SLC16A3 interaction, facilitating SLC16A3 trafficking to the plasma membrane and enhancing lactate efflux. Genetic or pharmacological blockade of autophagy abrogated SLC16A3 surface localization, reduced extracellular lactate accumulation, and markedly suppressed lung metastasis originating from orthotopic TNBC tumors in mice. Although pharmacological inhibition of SLC16A3 effectively blocks its transporter activity and reduces lactate secretion, targeting autophagy provides a more precise approach to suppress EGF-driven SLC16A3 expression and the consequent rise in lactate secretion. Clinically, multiplex immunofluorescence of patient tumors demonstrated strong co-expression of EGFR, LC3, and SLC16A3, which correlated with poor disease-free survival. Our study reveals a previously unrecognized EGF-secretory autophagy axis that orchestrates metabolic remodeling in TNBC and highlights the therapeutic potential of targeting the secretory autophagy- SLC16A3-lactate pathway to restrain metastasis.

Keywords:  Lactate secretion; SLC16A3/MCT4; TNBC; metastasis; secretory autophagy; tumor microenvironment

DOI:  https://doi.org/10.1080/15548627.2026.2656780
bioRxiv. 2026 Apr 02. pii: 2026.03.31.713900. [Epub ahead of print]

Mapping the mammalian dark metabolome by in vivo isotope tracing.

Michael R MacArthur, Justine Raeber, Wenyun Lu, Hantao Qiang, Amelia V Schueppert, Lucas B Ayres, Ricardo A Cordova, Michael D Neinast, Edmundo Leiva, Vanha N Pham, Jenna E AbuSalim, Connor S R Jankowski, Laith Z Samarah, Asael Roichman, Christian G Peace, Daniil G Ivanov, Gianna L Renzo, Anna M Oschmann, Julien F Ayroles, Sarah J Mitchell, Xi Xing, Kellen Olszewski, Hahn Kim, Joshua D Rabinowitz, Michael A Skinnider.

Despite decades of biochemical study, a comprehensive map of the mammalian metabolome remains elusive. Mass spectrometry-based metabolomics detects thousands of small molecule-associated signals in mammalian tissues, but it is currently unclear how many of these reflect products of endogenous metabolism. Here, we leverage systematic in vivo isotope tracing to infer the biosynthetic origins of unidentified metabolites. We administered 26 different isotopically labelled nutrients to mice, measured circulating and tissue metabolite labelling by mass spectrometry, and developed a statistical framework to infer the number of carbon atoms incorporated from each of these precursors into more than 4,000 putative metabolites. We show this information can be harnessed for biosynthesis-aware structure elucidation using a multimodal AI model that co-embeds isotopic labelling patterns with chemical structures. This approach revealed several previously unrecognized families of mammalian metabolites, including cysteine-derived alkylthiazolidines, dithioacetal mercapturic acid derivatives, short-chain N-acyltaurines, acylglycyltaurines, and N-oxidized taurines. It further uncovered a family of mevalonate-derived isoprenoid metabolites that includes 2,3-dihydrofarnesoic acid, which is markedly depleted in both mouse and human aging. Age-related depletion of these isoprenoids is driven by impaired coenzyme A synthesis. Our work establishes the biosynthetic precursors for thousands of unidentified metabolites and reveals multiple previously unrecognized branches of mammalian metabolism.

DOI: https://doi.org/10.64898/2026.03.31.713900
Mol Cell Proteomics. 2026 Apr 06. pii: S1535-9476(26)00058-7. [Epub ahead of print] 101562

Expanding the Global Map of Protein Post Translational Modifications with Immunoaffinity Enrichment and nDIA Analysis on the Orbitrap Astral Mass Spectrometer.

Mukesh Kumar, Anthony P Possemato, Barry M Zee, Srikanth Subramanian, Jian Min Ren, Alissa J Nelson, Bin Zhang, Sean Landry, Jeffrey C Silva, Brett Larsen, Tonya Pekar Hart, Matthew P Stokes, Sean A Beausoleil.

Post-translational modifications (PTMs) contribute greatly to the diversity of the human proteome by affecting protein structure, function, interactions, stability, localization, and more. The study of PTMs is essential to understand various cellular functions, disease mechanisms, and aid in the development of biomarkers and design of therapeutic targets. Owing to their diversity, dynamic nature, and low stoichiometry compared to unmodified proteome counterparts, the analysis of PTMs remains challenging. In this study, immunoaffinity enrichment of PTM peptides was combined with analysis using Data Dependent Acquisition (DDA) and narrow window Data Independent Acquisition (nDIA) on the Orbitrap Astral mass spectrometer (MS) as well as comparative analysis using the Orbitrap Fusion Lumos MS for Ubiquitination, Phosphorylation, Acetylation, Succinylation, and Methylation. Human cell line and mouse tissue samples at various input peptide amounts were immuno-enriched and mass spectrometry data was acquired on both instruments to assess depth of coverage and number of novel sites identified. The study identified a total of 106,152 unique ubiquitin sites, 64,397 phosphorylation sites (43,721 phosphoserine, 8,414 phosphothreonine and 12,262 phosphotyrosine), 14,245 acetylation, 5,272 succinylation and 1,461 mono-methylation sites. In half the acquisition time, nDIA analysis of immuno-enriched samples on Orbitrap Astral MS provided much greater depth of coverage for all PTMs compared to DDA analysis on Orbitrap Fusion Lumos MS, with up to 33-fold more PTM peptides identified and quantified. Overall, the data presented in this study demonstrates the need for enrichment for PTM detection and the utility of combining antibody-based peptide capture and nDIA on the Orbitrap Astral MS as powerful tools for discovery and profiling of protein post-translational modifications in cells and tissues.

DOI: https://doi.org/10.1016/j.mcpro.2026.101562
Diabet Med. 2026 Apr 07. e70238

Integrative multi-omics suggests core gene dysregulation of histidine metabolism in diabetic kidney disease.

Jiang Tan, Yuqin Chen, Fengning Chuan, Youyuan Gao, Mingjun Wu, Jiliang Hu.

   AIMS: To investigate the role of histidine metabolism in diabetic kidney disease (DKD), we analysed histidine metabolism-related genes using an integrative multi-omics approach.
METHODS: Untargeted metabolomics was performed on serum from DKD persons and healthy controls, as well as on high glucose-treated and normal glucose-treated HK-2 cells, to assess metabolic alterations. We also analysed publicly available datasets, including GEO transcriptomes, Kidney Precision Medicine Project (KPMP), Kidney Interactive Transcriptomics single-cell data, the Human Protein Atlas (HPA) and Nephroseq, to examine the expression and function of histidine metabolism-related genes.
RESULTS: Serum metabolomics confirmed alterations in histidine metabolism. Single-cell analysis revealed that five histidine metabolism-related genes were expressed in proximal tubular epithelial cells and significantly downregulated in DKD. Immunohistochemistry data from the HPA further demonstrated that the corresponding proteins are localized in the proximal tubule (PT). High-glucose treatment suppressed histidine metabolism in HK-2 cells, supporting specific metabolic reprogramming. Clinical correlation analyses using Nephroseq linked the decreased expression of these genes to renal function decline. Collectively, these findings indicate that histidine metabolic disruption is associated with tubular cell dysfunction, suggesting a mechanistic contribution to DKD progression.
CONCLUSION: By integrating multi-omics analyses, we suggest that histidine metabolic reprogramming represents a PT pathological event in DKD, providing novel mechanistic insights and potential therapeutic targets.

Keywords:  diabetic kidney disease; histidine metabolism; metabolic reprogramming; proximal tubular cells

DOI:  https://doi.org/10.1111/dme.70238
bioRxiv. 2026 Mar 10. pii: 2026.03.07.710331. [Epub ahead of print]

Chemical Proteomic Profiling of the Histaminylation Proteome in Cancer Cells Unveils Uncharted Epigenetic Marks on Core Histones.

Xingyu Ma, Anne A Leaman, Zeng Lin, Huapeng Li, Zhengjun Cai, Kaiwaan Dalal, Md Shahadat Hossain, Venkatesh P Thirumalaikumar, Zhihong Wang, Valerie P O'Brien, W Andy Tao, Qingfei Zheng.

Histamine is a key signaling molecule in pathophysiology that can exhibit significant regulatory roles in diverse health and disease status. Besides the well-studied noncovalent interactions between histamine and its receptors, protein histaminylation is a recently discovered mode of action, through which histamine regulates cellular signaling pathways in a covalent-interaction manner. Histaminylation is an emerging protein post-translational modification, where an isopeptide bond is formed between the histamine primary amine and γ-carboxyl group of glutamine through a transamidation reaction catalyzed by transglutaminase 2 (TGM2). However, due to the lack of efficient pan-specific antibodies targeting histaminylated glutamine, the histaminylation proteome in cells remains poorly explored. Here, we report the design and development of a novel N τ -propargylated histamine probe as well as its successful application in chemical proteomic profiling of the histaminylation proteome in cancer cells. Notably, new TGM2-catalyzed epigenetic marks on core histones, e . g ., H2AXQ84 and Q104 histaminylation, have been identified from cancer cells and verified in this study.

DOI: https://doi.org/10.64898/2026.03.07.710331
Chem Biol Interact. 2026 Apr 08. pii: S0009-2797(26)00188-2. [Epub ahead of print] 112080

Glutathione-deficiency promotes basal hyperinsulinemia in the insulin secreting cell line INS-1 (832/13).

E A Davidson, Y Chen, R L Cardone, B Thompson, R Aalizadeh, G Charkoftaki, R G Kibbey, V Vasiliou.

  Glutathione (GSH) is an abundant antioxidant which maintains intracellular redox homeostasis by scavenging excess reactive oxygen species to abate oxidative stress. Previous studies have reported lowered GSH synthesis enzyme expression and GSH content in type 2 diabetic (T2D) islets. However, whether impairment to endogenous GSH synthesis and subsequent lowering of GSH content can be implicated in the progressive loss of β cell function in type 2 diabetes, independent of glucolipotoxicity remains unclear. This study sought to determine the impact of endogenous GSH synthesis on β cell function. Glutamate-cysteine ligase catalytic subunit (GCLC) is essential for GSH synthesis. To induce GSH deficiency, GCLC was inhibited in INS-1 (832/13) cells using buthionine sulfoximine (BSO). The 24-hour treatment of INS-1 cells with BSO (250 μM) reduced GSH content to 33% of untreated, however, GSIS was unchanged. INS-1 cells require culture medium which contains 2-Mercaptoethanol (BME) to artificially bolster the cellular redox state. We removed BME from the cell culture medium to determine if further lowering of GSH content altered insulin secretion. The 24-hour treatment of INS-1 cells with BME-free medium containing BSO further reduced GSH levels to 9% of untreated and elicited significantly higher basal insulin secretion. As expected, the concentration of reduced GSH, concentration of oxidized GSH (GSSG), the total GSH pool, redox state of the GSH/GSSG redox couple, and relative redox potential were significantly lower. We find that >90% GSH-deficiency induced basal hyperinsulinemia, independent of significant transcriptomic or metabolomic alteration. These results suggest endogenous GSH synthesis is directly related to β cell function. Additionally, basal hyperinsulinemia is a poorly-understood early change to β cell function in T2D, we provide a useful model for further investigation regarding the control that cellular redox state has over basal hyperinsulinemia.

Keywords:  Insulin secretion; beta cell; glutathione biosynthesis; hyperinsulinemia

DOI:  https://doi.org/10.1016/j.cbi.2026.112080
Nat Metab. 2026 Apr 07.

Excess cysteine drives conjugate formation and impairs proliferation of NRF2-activated cancer cells.

Jennifer A Brain, Anna-Lena B G Vigil, Kristian Davidsen, Ayaha Itokawa, Abby C Jurasin, Hannah J Kerbyson, Maximilian Kobiesa, Madeleine L Hart, Sang Jun Yoon, Peter Bellotti, Juan Pablo Maianti, Gina M DeNicola, Lucas B Sullivan.

Cancer cells with constitutive NRF2 activation take up excess cystine beyond the cysteine demands of conventional pathways, implying unknown metabolic fates. Here, we develop an unbiased approach for the identification of cysteine metabolic fates and find that both known and previously uncharacterized cysteine-derived metabolites accumulate in NRF2-activated cancer cells. We identify many of these unknown metabolites as conjugates formed between cysteine and endogenous sugar metabolites, which can also be generated in vitro. We confirm the presence of these cysteine-derived conjugates in murine lung cancer models and primary human lung cancer samples, and their enrichment in NRF2-activated tumours in each context. Mechanistically, NRF2 promotes cystine uptake by driving SLC7A11 expression, which increases intracellular cysteine levels to promote these cysteine fates in a panel of cancer cell lines. Finally, we show that NRF2 activation creates a sensitivity to high environmental cystine, which impairs cell proliferation through excess free cysteine, and can be mitigated by sequestration into cysteine-derived conjugates. Overall, these findings reveal a cancer-associated metabolic vulnerability to excess cysteine stress, and reveal unrecognized routes of cysteine metabolism.

DOI: https://doi.org/10.1038/s42255-026-01499-8
Cancer Lett. 2026 Apr 07. pii: S0304-3835(26)00255-7. [Epub ahead of print] 218492

CD276 promotes CD36-mediated lipid metabolism and confers resistance to tyrosine kinase inhibitors.

Xiaojuan Huang, Leina Ma, Yangyang Lu, Jinfeng Cui, Weiwei Qi, Jialin Song, Jing Guo, Shasha Wang, Jing Fang, Zhimin Lu, Wensheng Qiu.

  The efficacy of tyrosine kinase inhibitor (TKI)-based systemic therapy in advanced hepatocellular carcinoma (HCC) is often limited by drug resistance, the mechanisms of which remain incompletely understood. Here, we demonstrate that CD276, an immune checkpoint protein, promotes TKI resistance in HCC by reprogramming lipid metabolism. Upon TKI treatment, CD276 binds pSTAT3 and undergoes importin α/β-dependent nuclear translocation. In the nucleus, CD276 cooperates with STAT3 to promote CD36 transcription, thereby potentiating fatty acid uptake, lipid droplet accumulation, and mitochondrial fatty acid β-oxidation. This metabolic rewiring drives HCC proliferation and confers TKI resistance. Importantly, pharmacological inhibition of CD36 with sulfosuccinimidyl oleate sodium suppresses fatty acid uptake and tumor lipid metabolism, resensitizing resistant HCC cells to TKIs. Our findings reveal the CD276-STAT3-CD36 axis as a key regulator of lipid metabolic reprogramming in TKI resistance, providing a promising therapeutic target to overcome treatment resistance in HCC.

Keywords:  CD276; CD36; hepatocellular carcinoma; lipid metabolism; tyrosine kinase inhibitor resistance

DOI:  https://doi.org/10.1016/j.canlet.2026.218492
Proc Natl Acad Sci U S A. 2026 Apr 14. 123(15): e2516511123

Reconstruction of human metabolic models with large language models.

Jiahao Luo, Hao Wang, Devlin Moyer, Zhetao Guo, Jonathan L Robinson, Johan Gustafsson, Mihail Anton, Yu Chen, Eduard J Kerkhoven, Jens Nielsen, Feiran Li.

  Genome-scale metabolic models (GEMs) have become essential tools for understanding human metabolism. Here, we introduce Human2, a consensus human GEM with enhanced precision and biological relevance, which leverages large language models (LLMs) and GitHub Action checks to streamline automated, efficient, and collaborative curation. Human2 supports the reconstruction of tissue- and organ-specific models tailored to sex- and age-specific human groups. By integrating transcriptomic, proteomic, and kinetic data, we reveal distinct metabolic features across these groups, such as significant differences in arachidonic acid and leukotriene metabolism. The specific models were integrated into a dynamic whole-body framework, marking an enzyme-constrained dynamic model that simulates interorgan metabolite exchanges under varying nutritional states, from feeding to fasting. Our work highlights the transformative role of LLMs in GEM reconstruction and introduces a whole-body dynamic simulation that integrates kinetic data, offering a powerful resource for multiscale human metabolism modeling.

Keywords:  genome-scale metabolic model; large language model; organ-specific model; whole-body model

DOI:  https://doi.org/10.1073/pnas.2516511123
ACS Chem Biol. 2026 Apr 09.

Expanding the Chemoproteomic Toolkit to Asparagine and Glutamine.

Benjamin Emenike, John M Talbott, Zachary E Paikin, Christian M Beusch, Sohail Khoshnevis, David E Gordon, Monika Raj.

Chemoproteomic strategies have revolutionized proteome annotation by targeting nucleophilic and redox-active side chains. However, the primary amides of asparagine (Asn) and glutamine (Gln) have long lacked robust chemical tools for proteome-wide interrogation. We report a chemoselective palladium-mediated dehydration that converts Asn/Gln amides to nitriles under mild aqueous conditions. This transformation enables the first proteome-wide mapping of chemically addressable Asn/Gln sites in lysates and living cells. Leveraging this reactivity, we establish an inverse chemoproteomic framework in which reduced nitrile formation reports PTM-mediated protection of Asn/Gln sites, including those impacted by deamidation and N-glycosylation. This approach reveals sites masked by post-translational modifications (PTMs), specifically those associated with deamidation and N-glycosylation. In yeast, this framework expanded the known N-glycoproteome, identifying numerous candidates missed by traditional glycopeptide enrichment due to low abundance or noncanonical motifs. Furthermore, comparative profiling in Candida albicans captured the dynamic remodeling of glycosylation patterns during morphogenesis. This dehydration-to-nitrile platform establishes a scalable handle on the amide proteome to map residue accessibility and PTM-linked site dynamics across biological states.

DOI: https://doi.org/10.1021/acschembio.6c00173
Sci Rep. 2026 Apr 09.

Remote regulation of hepatic lipid secretion in the intestine by metabolic interaction of dietary arginine with ornithine.

Hiroki Nishi, Sena Nakanishi, Lin Xie, Masayuki Fujinaga, Yiding Zhang, Daisuke Yamanaka, Suguru Fujita, Junji Saruwatari, Kentaro Oniki, Ming-Rong Zhang, Fumihiko Hakuno.

  The quantity and quality of dietary protein profoundly influence satiety, body growth, and systemic metabolism. Among the 20 major proteinogenic amino acids, arginine (Arg) is considerably associated with hepatic steatosis; when animals fed an Arg-deficient diet (ΔArg), triacylglyceride (TAG) dramatically accumulates in the liver. To explore the underlying mechanism, we first investigated the role of ornithine (Orn), as Orn is the primary metabolite of Arg and it is reportedly involved in the regulation of liver metabolism. While male Wistar rats fed a ΔArg diet exhibited a significant increase in liver TAG levels due to an attenuated TAG secretion, and consistently marked reduction of TAG-rich lipoproteins in the circulation, Orn addition to the diet completely abolished all these metabolic changes. Orn was only effective when taken orally, but not through intraperitoneal administration, suggesting that the intestine plays an essential role for Orn to regulate liver metabolism. The metabolic features similar to those of our rat model was also observed in the analyses of clinical samples, implying the common mechanism in humans. Conclusively, dietary Arg deficiency lowers local Arg-to-Orn conversion in the intestine, which in turn inhibits hepatic lipid secretion remotely via gut-liver axis.

Keywords:  Arginine; Dyslipidemia; Fatty liver; Ornithine; Very-low-density lipoprotein

DOI:  https://doi.org/10.1038/s41598-026-47841-8
Nature. 2026 04;652(8109): 313-320

Metabolomics across scales: from single cells to population studies.

Theodore Alexandrov, Nicola Zamboni.

Metabolomics has matured into a powerful approach for probing metabolism, offering readouts that closely reflect cellular and organismal function in health and disease. Here we highlight two rapidly advancing frontiers: single-cell metabolomics and population-scale metabolomics. Single-cell metabolomics resolves the metabolic states of individual cells, uncovering cell-to-cell heterogeneity and spatial organization within tissues. Population-scale profiling profiles metabolites across large cohorts, enabling the discovery of markers of disease, environmental exposures and genetic variation. Although these approaches operate at different scales, they face shared challenges-including metabolite identification, quantification and multimodal data integration-and offer common advantages, such as the ability to capture non-genetic influences on phenotype and to scale to high throughput. We propose that continued advances in scalability will bring these domains together, enabling the construction of comprehensive metabolic atlases that chart cellular and interindividual variation and provide training data for foundation models of metabolism. By integrating cellular and population-level insights, single-cell and population-scale metabolomics promise to advance our understanding of metabolism across biology, medicine and pharmacology.

DOI: https://doi.org/10.1038/s41586-026-10277-1