bims-cesirm 2025-07-20 papers

bims-cesirm

Biomed News

on Cell Signaling mediated regulation of metabolism

Issue of 2025–07–20
eighteen papers selected by
Tigist Tamir, University of North Carolina

Metabolomic Profiling Reveals Key Metabolic Alterations in MCF7 Tamoxifen-Resistant Cells Following EPAS1 Inhibition.
Decoding protein phosphorylation during oocyte meiotic divisions using phosphoproteomics.
Muscle very long-chain ceramides associate with insulin resistance independently of obesity.
Identification of SRSF9 through pooled shRNA screening links BNIP3 splicing to autophagy and metabolic reprogramming in breast cancer.
Elevated BCRP Transporter and Altered NF-кB Pathway Mediate Zoledronic Acid Resistance in MCF-7 Cells.
Fibroblast growth factor receptor signaling modulates cholesterol storage in a SOAT1-dependent manner to promote mammary tumor cell invasion.
Role of d-serine in intestinal ROS accumulation after sleep deprivation.
AI-powered Deep Visual Proteomics reveals critical molecular transitions in pancreatic cancer precursors.
Mealtime alters daily rhythm in nuclear O-GlcNAc proteome to regulate hepatic gene expression.
Multi-omics characterization of acquired Olaparib resistance in BRCA1 and BRCA2 mutant breast cancer cell lines.
Transient AMPK activation by nutrient stress of high fat diet preserves cardiac electrophysiological stability and protects against arrhythmias.
Micromapping (µMap) of HER2 Across Human Breast Cancers: Photocatalytic Proximity Labeling Identifies Primary Resistance Mechanisms and Functional Interactors.
Multi-omics analysis reveals glutathione metabolism-related immune suppression and constructs a prognostic model in lung adenocarcinoma.
Cancer cells differentially modulate mitochondrial respiration to alter redox state and enable biomass synthesis in nutrient-limited environments.
CO2 and electrical stunning differentially affect energy metabolism in pigs.
Rosuvastatin ameliorates obesity-associated insulin resistance in high-fat diet-fed mice by modulating the gut microbiota and gut metabolites.
Metabolism of epigenetic ribonucleosides leads to nucleolar stress and cytotoxicity.
An Optimized SP3 Sample Processing Workflow for In-Depth and Reproducible Phosphoproteomics.

J Proteome Res. 2025 Jul 17.

Metabolomic Profiling Reveals Key Metabolic Alterations in MCF7 Tamoxifen-Resistant Cells Following EPAS1 Inhibition.

Enzhi Luo, Neeraj Manvi Agarwal, Junjeong Choi.

  Tamoxifen (TAM) is a frontline therapy for luminal A breast cancer, yet acquired resistance poses a significant clinical challenge. This study investigates the molecular and metabolic basis of TAM resistance in MCF7/Tam1 cells, focusing on EPAS1 (HIF-2α)-driven hypoxia-induced metabolic reprogramming and the potential of the EPAS1 inhibitor PT2977 to restore TAM sensitivity. Comparative transcriptomic analysis revealed upregulation of EPAS1 along with enrichment of hypoxia-associated pathways, including JAK-STAT, TGF-beta, and lipid metabolism in resistant cells. Untargeted LC-MS/MS metabolomics identified 1,039 significantly altered metabolites, with notable dysregulation in glutamate and glutathione metabolism, the Warburg effect, and fatty acid oxidation. Mechanistically, EPAS1 promoted fatty acid uptake via CD36 and enhanced glutamine metabolism through SLC1A5, contributing to redox balance and cell survival under TAM stress. Treatment with PT2977 disrupted these metabolic pathways, as evidenced by PCA and Venn analyses, leading to a dose-dependent normalization of metabolite profiles and selective reduction in cell viability. These findings highlight EPAS1-mediated metabolic reprogramming as a key driver of TAM resistance and support EPAS1 inhibition by PT2977 as a promising therapeutic strategy to overcome resistance in luminal A breast cancer.

Keywords:  EPAS1; PT2977; hypoxia; metabolomics.; tamoxifen resistance

DOI:  https://doi.org/10.1021/acs.jproteome.5c00170
Elife. 2025 Jul 17. pii: RP104255. [Epub ahead of print]13

Decoding protein phosphorylation during oocyte meiotic divisions using phosphoproteomics.

Leonid Peshkin, Enrico Maria Daldello, Elizabeth S Van Itallie, Matthew Sonnett, Johannes Kreuzer, Wilhelm Haas, Marc W Kirschner, Catherine Jessus.

  Oocyte meiotic divisions represent a critical process in sexual reproduction, as a diploid non-dividing oocyte is transformed into a haploid fertilizable egg, as a prelude for the subsequent embryonic divisions and differentiation. Although cell differentiation and proliferation are governed by transcription, oocyte maturation and early embryonic divisions depend entirely on changes in protein abundance and post-translational modifications. Here, we analyze the abundance and phosphorylation of proteins during Xenopus oocyte meiotic maturation. We reveal significant shifts in protein stability, related to spindle assembly, DNA replication, and RNA-binding. Our analysis pinpoints broad changes in phosphorylation correlating with key cytological meiotic milestones, noteworthy changes in membrane trafficking, nuclear envelope disassembly, and modifications in microtubule dynamics. Additionally, specific phosphorylation events target regulators of protein translation, Cdk1 and the Mos/MAPK pathway, thereby providing insight into the dynamics of Cdk1 activity, as related to the meiotic cell cycle. This study sheds light on the orchestration of protein dynamics and phosphorylation events during oocyte meiotic divisions, providing a rich resource for understanding the molecular pathways orchestrating meiotic progression in the frog, and most likely applicable to other vertebrate species.

Keywords:  biochemistry; cell biology; chemical biology; meiotic maturation; oocyte; phosphoproteome; xenopus

DOI:  https://doi.org/10.7554/eLife.104255
Mol Metab. 2025 Jul 11. pii: S2212-8778(25)00119-X. [Epub ahead of print] 102212

Muscle very long-chain ceramides associate with insulin resistance independently of obesity.

Søren Madsen, Harry B Cutler, Kristen C Cooke, Meg Potter, Jasmine Khor, Christoph D Rau, Stewart Wc Masson, Anna Howell, Zora Modrusan, Anthony S Don, Jacqueline Stöckli, Alexis Diaz Vegas, David E James.

Lipids, in particular ceramides and diacylglycerols (DAGs), are implicated in insulin resistance (IR), however their precise roles remain unclear. Here, we leverage natural genetic variation to examine muscle lipids and systemic IR in 399 Diversity Outbred Australia mice fed either chow or a high-fat diet. Adipose tissue mass was significantly associated with 55% of muscle lipid features and whole-body insulin sensitivity, with DAGs as the only lipid class enriched in this association. To disentangle the contribution of adiposity and muscle lipids to whole-body insulin sensitivity, we employed two independent approaches: (1) a linear model correcting muscle lipid features for adipose tissue mass to assess their relationship with insulin sensitivity, and (2) stratifying mice into insulin sensitivity quartiles within adiposity bins. Both revealed that very long-chain ceramides, but not DAGs, were linked to IR. RNA sequencing and proteomics from the same muscles further associated these very long-chain ceramides with cellular stress, mitochondrial dysfunction, and protein synthesis. Meanwhile, DAGs correlated with leptin gene expression in skeletal muscle, suggesting they originate from contaminating adipocytes rather than myocytes per se. We propose that many muscle lipids, including DAGs, associate with muscle and systemic IR due to accumulation of adipose tissue rather than directly influencing muscle insulin sensitivity. By addressing the relationship between adiposity and metabolic state, we identified very long-chain muscle ceramides as being highly associated with IR independently of adiposity.

DOI: https://doi.org/10.1016/j.molmet.2025.102212
J Biol Chem. 2025 Jul 15. pii: S0021-9258(25)02332-4. [Epub ahead of print] 110482

Identification of SRSF9 through pooled shRNA screening links BNIP3 splicing to autophagy and metabolic reprogramming in breast cancer.

Anchala Pandey, B Jithin, Srinivas Abhishek Mutnuru, Atul Samaiya, Sanjeev Shukla.

  Autophagy is a critical catabolic process that maintains cellular homeostasis, yet the role of alternative splicing in regulating hypoxia-induced autophagy remains largely unexplored. Here, through a pooled shRNA screen of RNA binding proteins (RBPs) in hypoxic breast cancer cells, we identified the splicing factor SRSF9 as a key regulator. We found that SRSF9 expression is significantly reduced under hypoxia, while its restoration diminishes autophagosome formation. SRSF9 directly controls the alternative splicing of BNIP3 by binding to its third exon, generating two functionally distinct isoforms. The full-length isoform, BNIP3-FL, promotes canonical autophagy by interacting with the BCL-2-BECN1 complex. In contrast, the truncated isoform, BNIP3-Δ3, lacks this function and instead promotes a metabolic shift to the Warburg effect. This metabolic reprogramming by BNIP3-Δ3 enhances breast cancer progression, including proliferation and invasion, and confers chemoresistance to paclitaxel. Collectively, our study identifies a previously unreported mechanism where SRSF9 governs the balance between autophagy and the Warburg effect via BNIP3 alternative splicing, thereby establishing a critical link between splicing regulation, metabolic adaptation, and therapeutic resistance in breast cancer.

Keywords:  BNIP3-FL; BNIP3-Δ3; High Content Screening; Hypoxia; Paclitaxel; SRSF9

DOI:  https://doi.org/10.1016/j.jbc.2025.110482
J Biochem Mol Toxicol. 2025 Jul;39(7): e70397

Elevated BCRP Transporter and Altered NF-кB Pathway Mediate Zoledronic Acid Resistance in MCF-7 Cells.

Öykü Irmak Dikkatli, Yunus Emre Cavlak, Yaprak Dönmez Çakıl, Sueda Atılkan, Erkan Yurtcu, Özlem Darcansoy İşeri.

  Zoledronic acid (ZA), a bisphosphonate derivate, became the standard for preserving bone structure in cancer. Using various intracellular signaling pathways, including NF-κB, ZA inhibits tumor cell proliferation, induces apoptosis, and has additive and synergistic effects with cytotoxic agents. However, it has been observed that resistance has developed against ZA. This study aims to explore the underlying mechanisms of ZA resistance in MCF-7 breast cancer cells by investigating the activity and localization of the human breast cancer resistance protein (BCRP), changes in the NF-κB pathway, and the markers of epithelial-mesenchymal transition (EMT). Previously, MCF-7 cells were stepwise selected in increasing concentrations of ZA and became resistant to 8 µM ZA (MCF-7/Zol). We determined that BCRP levels were elevated with altered intracellular localization in ZA resistant MCF-7 cells, and BCRP pump caused a decrease in the substrate accumulation in the MCF-7/Zol cells whereas no change in intercellular substrate accumulation was observed in parental cells. MCF-7/Zol cells have increased amount of phosphorylated IκB which is associated with increased nuclear translocation of NF-κB. Concordantly, BCRP upregulation may be associated with increased nuclear NF-κB in ZA resistant cells. MCF-7/Zol cells did not harbor EMT markers. Elucidation of molecular mechanisms of resistance developed against chemotherapeutic agents is important to target critical pathways and proteins to eliminate the resistant clones as well as for determining biomarkers for MDR.

Keywords:  ABCG2 transporter; EMT; NF‐κB pathway; Zoledronic acid; multidrug resistance

DOI:  https://doi.org/10.1002/jbt.70397
Breast Cancer Res. 2025 Jul 15. 27(1): 132

Fibroblast growth factor receptor signaling modulates cholesterol storage in a SOAT1-dependent manner to promote mammary tumor cell invasion.

Jennifer E Tuokkola, Lyndsay E Reese, Ying Wang, Christine H O'Connor, Jillian G VanTreeck, Annisa H Rumahorbo, Kathryn L Schwertfeger.

  Signaling by fibroblast growth factor receptors (FGFRs) is active in up to 85% of breast cancers and results in enhanced proliferation, migration, and invasion of tumor cells. Here, we show that FGFR signaling regulates cholesterol metabolism in breast cancer. Specifically, we demonstrate that FGFR activation promotes cellular cholesterol storage by upregulating expression of the enzyme sterol O-acyltransferase 1 (SOAT1). Moreover, we demonstrate that inhibition of SOAT1 attenuates FGFR-driven colony formation and invasion in tumor cells, which correlates with reduced expression of matrix metalloproteinase expression. Furthermore, genetic knockdown of SOAT1 decreases mammary tumor growth in vivo. Taken together, these findings suggest a largely undiscovered metabolic role for FGFR signaling in regulating cholesterol metabolism in breast cancer and present a therapeutic vulnerability that could be targeted in FGFR-driven cancers.

Keywords:  Cholesterol metabolism; Cholesterol storage; Fibroblast growth factor; Triple-negative breast cancer

DOI:  https://doi.org/10.1186/s13058-025-02084-9
Sci Adv. 2025 Jul 18. 11(29): eadr8592

Role of d-serine in intestinal ROS accumulation after sleep deprivation.

Feng Zheng, Shuai Liu, Tian Wei, Lei Wang, Yuanyuan Chang, Hao Qu, Lei Zheng.

Prolonged sleep deprivation (SD) results in increased accumulation of reactive oxygen species (ROS) in gut, although the underlying mechanisms remain to be elucidated. This study identifies d-serine as a crucial regulator of gut ROS during SD. Knockdown of serine racemase (SR), the enzyme responsible for d-serine production, prevents the enhanced ROS buildup during SD in Drosophila. Gut enterocytes (ECs) respond to γ-aminobutyric acid (GABA) signaling by producing d-serine, which influences downstream N-methyl-d-aspartate receptor (NMDAR) activity and modulates sleep pressure. However, the continuous demand for sleep disrupts this feedback loop. Prolonged SD leads to increased levels of d-serine in the gut, an elevated pyruvate pool in ECs, enhanced mitochondrial oxidative phosphorylation, impaired lipid metabolism in peroxisomes, and the accumulation of harmful ROS. In conclusion, our findings illuminate the metabolic alterations and brain-gut communication pathways that may contribute to the increase in gut d-serine and subsequent ROS accumulation induced by SD.

DOI: https://doi.org/10.1126/sciadv.adr8592
bioRxiv. 2025 Jul 07. pii: 2025.07.07.663528. [Epub ahead of print]

AI-powered Deep Visual Proteomics reveals critical molecular transitions in pancreatic cancer precursors.

Jimin Min, Lisa Schweizer, Gijs Zonderland, Benson Chellakkan Selvanesan, Lukas Oldenburg, Seong-Woo Bae, Bong Jun Kim, Benjamin J Swanson, Kelsey A Klute, Thomas C Caffrey, Paul M Grandgenett, Michael A Hollingsworth, Ishani Ummat, Maximilian T Strauss, Andreas Mund, Anirban Maitra.

Pancreatic ductal adenocarcinoma (PDAC) evolves through non-invasive precursor lesions, yet its earliest molecular events remain unclear. We established the first spatially resolved proteomic atlas of these lesions using Deep Visual Proteomics (DVP). AI-driven computational pathology classified normal ducts, acinar-ductal metaplasia (ADM), and pancreatic intraepithelial neoplasia (PanIN) from cancer-free organ donors (incidental, "iPanINs") and PDAC patients (cancer-associated, "cPanINs"). Laser microdissection of 96 discrete regions containing as few as 100 phenotypically matched cells and ultrasensitive mass spectrometry quantified a total of 8,512 proteins from formalin-fixed tissues. Distinct molecular signatures stratifying cPanINs from iPanINs, and remarkably, many cancer-associated proteins already marked histologically normal epithelium. Four core programs - stress adaptation, immune engagement, metabolic reprogramming, mitochondrial dysfunction - emerged early and intensified during progression. By integrating DVP with AI-guided tissue annotation, we demonstrate that molecular reprogramming precedes histological transformation, creating opportunities for earlier detection and interception of a near-uniformly lethal cancer.
Significance: Our spatially-resolved proteomics atlas uncovers distinct molecular signatures in pancreatic cancer adjacent precursor lesions, clearly diverging from those in incidental, cancer-free pancreatic lesions. Our deep proteomics dataset offers a valuable resource for identifying novel biomarkers and therapeutic targets, informed by the earliest cancer-associated molecular events in archival pancreatic tissues.

DOI: https://doi.org/10.1101/2025.07.07.663528
bioRxiv. 2025 Jun 19. pii: 2024.06.13.598946. [Epub ahead of print]

Mealtime alters daily rhythm in nuclear O-GlcNAc proteome to regulate hepatic gene expression.

Xianhui Liu, Yao D Cai, Chunyan Hou, Xu Liu, Youcheng Luo, Aron Judd P Mendiola, Xuehan Xu, Yige Luo, Haiyan Zheng, Caifeng Zhao, Ching-Hsuan Chen, Yong Zhang, Yang K Xiang, Junfeng Ma, Joanna C Chiu.

The liver circadian clock and hepatic transcriptome are highly responsive to metabolic signals generated from feeding-fasting rhythm. Previous studies have identified a number of nutrient-sensitive signaling pathways that could interpret metabolic input to regulate rhythmic hepatic biology. Here, we investigated the role of O-GlcNAcylation, a nutrient-sensitive post-translational modification (PTM) in mediating metabolic regulation of rhythmic biology in the liver. We observe daily oscillation of global nuclear protein O-GlcNAcylation in the liver of mice subjected to night-restricted feeding (NRF) using label-free global O-GlcNAc proteomics. Additional site-specific O-GlcNAc analysis by tandem mass tag mass spectrometry further supports temporal differences in O-GlcNAcylation by revealing day-night differences. Proteins involved in gene expression are enriched among rhythmically O-GlcNAcylated proteins, suggesting rhythmic O-GlcNAcylation may directly regulate the daily rhythmicity of the hepatic transcriptome. We show that rhythmic O-GlcNAcylation can also indirectly modulate the hepatic transcriptome by interacting with phosphorylation. Several proteins harboring O-GlcNAcylation-phosphorylation interplay motif exhibit rhythmic O-GlcNAcylation and phosphorylation. Specifically, we show that O-GlcNAcylation occurs at a phospho-degron of a key circadian transcriptional activator, circadian locomotor output cycles kaput (CLOCK), thus regulating its stability and transcriptional output. Finally, we report that day-restricted feeding (DRF) in the nocturnal mouse significantly alters O-GlcNAcylation rhythm. Whereas global O-GlcNAcylation analysis indicates dampening of global O-GlcNAcylation rhythm in mice fed under DRF, site-specific analysis reveals differential responses of O-GlcNAc sites when timing of food intake is altered. Notably, a substantial number of O-GlcNAcylation sites exhibit inverted day-night profiles when mice are subjected to DRF. This suggests the dysregulation of daily nuclear protein O-GlcNAcylation rhythm may contribute to the disruption in liver transcriptomic rhythm previously observed in DRF condition. In summary, our results provide new mechanistic insights into metabolic regulation of daily hepatic transcriptomic rhythm via interplay between O-GlcNAcylation and phosphorylation and shed light on the deleterious effects of improper mealtimes.

DOI: https://doi.org/10.1101/2024.06.13.598946
Mol Cell Proteomics. 2025 Jul 14. pii: S1535-9476(25)00133-1. [Epub ahead of print] 101034

Multi-omics characterization of acquired Olaparib resistance in BRCA1 and BRCA2 mutant breast cancer cell lines.

Holda A Anagho-Mattanovich, Meeli Mullari, Matthias Anagho-Mattanovich, Hayoung Cho, Anna-Kathrine Pedersen, Oana Palasca, Jesper V Olsen, Marie Locard-Paulet, Michael L Nielsen.

  Poly (ADP-ribose) polymerase inhibitors (PARPi) are widely used as targeted therapies against breast cancers with BRCA mutations. However, the development of resistance to PARPi poses a significant challenge for long-term efficacy of these therapies, warranting further understanding of mechanisms of PARPi resistance. Here, we generated and characterized Olaparib resistance (OR) in BRCA1/2 mutant breast cancer cell lines MDAMB436 and HCC1428 using a systems-level multi-omics approach, including transcriptome, proteome, phosphoproteome, and ADP-ribosylation analysis. Our analyses revealed that resistance development strongly correlated with protein expression changes, while modest effects on phosphorylation- and ADP-ribosylation-dependent signaling pathways were observed. We found that BRCA1 expression was reestablished in OR MDAMB436 cell lines, while PARP1 expression was decreased. In OR HCC1428 cell lines, the BRCA2 mutation was not reverted. However, we observed increased expression of Fanconi anemia group D2 (FANCD2), histone parylation factor 1 (HPF1), and Nicotinamide phosphoribosyltransferase (NAMPT) in various cell lines, suggesting increased replication fork protection, and changes in the ADPr pathway and adaptation of metabolic pathways as resistance mechanisms. Our findings provide valuable insights into the complex landscape of PARPi resistance, offering potential targets for further investigation and therapeutic intervention.

Keywords:  ADP-ribosylation; BRCA1/2 mutant; DNA damage; EThcD; LC-MSMS; Olaparib; Olaparib resistance; PARP inhibitors; Phosphoproteomics; Proteomics

DOI:  https://doi.org/10.1016/j.mcpro.2025.101034
bioRxiv. 2025 Jun 14. pii: 2025.06.11.658631. [Epub ahead of print]

Transient AMPK activation by nutrient stress of high fat diet preserves cardiac electrophysiological stability and protects against arrhythmias.

Michael W Rudokas, Margaret McKay, Xiaohong Wu, Jonathan Granger, Yancey Williams, Markus Bögner, Taekyung Kang, Anton Seyfried, Zeren Toksoy, Marine Cacheux, Lawrence H Young, Fadi G Akar.

Sudden cardiac death (SCD) is a major complication of obesity, yet it remains unclear whether early metabolic stress, prior to the onset of overt obesity or structural remodeling, can independently promote arrhythmias. In vitro studies suggest that fatty acids can allosterically stimulate AMP-activated protein kinase (AMPK), a key metabolic sensor known to preserve myocardial viability and mitochondrial function following ischemia-reperfusion (I/R) injury. We hypothesized that AMPK signaling critically modulates the electrophysiological (EP) response to high-fat diet (HFD)-induced metabolic stress.
Methods: To test this, wild-type (WT) and AMPK kinase-dead (AMPK-KD) mice were subjected to an 8-week HFD regimen beginning at 4 weeks of age. Controls remained on normal diet (ND) for the same duration. Arrhythmia susceptibility was assessed ex vivo using rapid pacing and I/R challenge protocols. Changes in the EP substrate were defined by high-resolution optical action potential mapping. Underlying mechanisms were probed using western blotting, confocal and transmission electron microscopy.
Results: HFD-fed wild-type (WT) hearts did not display increased arrhythmia susceptibility in response to either burst pacing or I/R challenge. On the contrary, they exhibited a paradoxical enhancement in post-ischemic EP recovery compared to ND-fed controls. This improvement was associated with increased phosphorylation of canonical AMPK targets, including acetyl-CoA carboxylase (ACC) and raptor, consistent with the activation of a cardioprotective metabolic program. In sharp contrast, AMPK-deficient (AMPK-KD) hearts demonstrated heightened vulnerability to inducible ventricular tachycardia (VT), irrespective of diet. Conduction slowing emerged as an early EP abnormality in these hearts and served as the initial substrate (or 'first hit') that promoted their increased incidence of non-sustained VT. Notably, this conduction impairment arose in conjunction with an increase (rather than decrease) in Cx43 and Nav1.5 protein expression. Mechanistically, defective conduction in AMPK-KD hearts was linked to impaired autophagic degradation of intercalated disc proteins resulting from reduced phosphorylation of ULK1, a downstream effector of AMPK. Consequently, unphosphorylated Cx43 accumulated at the intercalated disc, likely replacing phosphorylated isoforms (p-Cx43). In addition, AMPK-KD hearts exhibited swollen, fragmented mitochondria and reduced levels of mitochondrial fusion proteins. Upon HFD challenge, this vulnerable mitochondrial substrate generated excessive reactive oxygen species (ROS) coinciding with accelerated repolarization. Together, impaired conduction and action potential shortening promoted VT sustenance in HFD-fed AMPK-deficient hearts.
Conclusions: Our findings identify AMPK as a key metabolic regulator that integrates redox balance, mitochondrial integrity, and protein homeostasis to preserve cardiac excitability during early nutrient overload. Loss of AMPK signaling, as occurs with aging and advanced metabolic disease, may therefore represent a pivotal mechanism linking HFD to increased SCD risk.

DOI: https://doi.org/10.1101/2025.06.11.658631
bioRxiv. 2025 Jun 14. pii: 2025.06.10.658685. [Epub ahead of print]

Micromapping (µMap) of HER2 Across Human Breast Cancers: Photocatalytic Proximity Labeling Identifies Primary Resistance Mechanisms and Functional Interactors.

Steve D Knutson, Jacob A Boyer, Danielle C Morgan, Johannes Großkopf, Joshua D Rabinowitz, David W C MacMillan.

Interactions among receptor tyrosine kinases (RTKs), particularly HER2, are critical in driving the growth of certain breast cancer subtypes. However, the mechanisms of HER2 dependency and resistance to targeted therapies remain unclear. Using photocatalytic micromapping (µMap) proximity labeling, we profiled the HER2 interactome across human breast cancer lines. We identify galectin family proteins as uniquely enriched in trastuzumab-resistant models, and show that genetic and pharmacological inhibition of galectins restores trastuzumab sensitivity. Mechanistically, galectin inhibition destabilized HER2 and other RTKs and enhanced antibody-mediated receptor degradation. Galectin inhibition in combination with trastuzumab triggered mitochondrial and endoplasmic reticulum stress pathways, revealing new mechanisms underlying HER2 signaling, dependency, and resistance in breast cancer. We also identified protein tyrosine phosphatase F (PTPRF) as a pan-cancer HER2 interactor, which is broadly upregulated and whose knockdown suppresses proliferation in HER2-low cancers. This work provides an extensive new interactomic resource and underscores the utility of proximity labeling for mapping complex cancer networks and identifying new therapeutic targets.

DOI: https://doi.org/10.1101/2025.06.10.658685
Front Immunol. 2025 ;16 1608407

Multi-omics analysis reveals glutathione metabolism-related immune suppression and constructs a prognostic model in lung adenocarcinoma.

Yuxiang Chi, Guoyuan Ma, Qiang Liu, Yunzhi Xiang, Defeng Liu, Jiajun Du.

   Background: Metabolic reprogramming within the tumor microenvironment plays a pivotal role in tumor progression and therapeutic responses. Nevertheless, the relationship between aberrant glutathione (GSH) metabolism and the immune microenvironment in lung adenocarcinoma, as well as its clinical implications, remains unclear.
Methods: We leveraged genome-wide association study (GWAS) data and applied genetic causal analysis to evaluate the causal relationships among plasma 5-oxoproline levels, lung adenocarcinoma (LUAD) risk, and 731 immune phenotypes. We incorporated single-cell RNA sequencing data from LUAD to compare transcription factor activity, cell communication networks, and CD8+ T cell subset distributions across distinct GSH metabolic groups, followed by pseudotime analysis. Whole-transcriptome data from the TCGA database were analyzed for functional enrichment, immune infiltration, and immune functionality. Prognostic genes were identified using WGCNA and LASSO-Cox regression, and the expression was validated via qRT-PCR. Thereafter, immunotherapeutic efficacy and drug sensitivity were predicted using the TIDE platform and the oncoPredict package. A prognostic model was constructed to forecast patient survival, which was further validated in two independent GEO datasets.
Results: Genetic causal analysis indicated a positive correlation between plasma 5-oxoproline levels and LUAD risk. ScRNA-seq analysis revealed an increased proportion of exhausted CD8+ T cells in the high GSH metabolic group, accompanied by altered transcription factor activity and distinct cell communication patterns. Furthermore, whole-transcriptome data analysis demonstrated that patients with a high metabolic phenotype exhibited significantly diminished immune functionality and overall immune infiltration. Using WGCNA and LASSO-Cox regression, we ultimately identified three key genes (LCAL1, RHOV, and MARCHF4) and generated a gene risk score. This score effectively predicts both immunotherapy response and drug sensitivity. qRT-PCR confirmed the upregulation of MARCHF4 in LUAD cells. In addition, stratification by gene risk scores revealed significant differences in immune cell infiltration, immunotherapeutic response, and drug sensitivity. The nomogram model demonstrated strong predictive accuracy in both the TCGA cohort and two independent GEO validation datasets.
Conclusions: GSH metabolic reprogramming may suppress antitumor immunity by modulating transcription factor activity, remodeling cell communication networks, and regulating CD8+ T cells. The prognostic risk model developed herein effectively predicts immunotherapeutic response, drug sensitivity, and overall survival in patients with LUAD.

Keywords:  glutathione metabolism; immunotherapy; multi-omics; prognostic model; single-cell sequencing

DOI:  https://doi.org/10.3389/fimmu.2025.1608407
bioRxiv. 2025 May 10. pii: 2025.05.09.653205. [Epub ahead of print]

Cancer cells differentially modulate mitochondrial respiration to alter redox state and enable biomass synthesis in nutrient-limited environments.

Sarah M Chang, Muhammad Bin Munim, Sonia E Trojan, Anna Shevzov-Zebrun, Keene L Abbott, Matthew G Vander Heiden.

The cell NAD+/NADH ratio can constrain biomass synthesis and influence proliferation in nutrient-limited environments. However, which cell processes regulate the NAD+/NADH ratio is not known. Here, we find that some cancer cells elevate the NAD+/NADH ratio in response to serine deprivation by increasing mitochondrial respiration. Cancer cells that elevate mitochondrial respiration have higher serine production and proliferation in serine limiting conditions than cells with no mitochondrial respiration response, independent of serine synthesis enzyme expression. Increases in mitochondrial respiration and the NAD+/NADH ratio promote serine synthesis regardless of whether serine is environmentally limiting. Lipid deprivation can also increase the NAD+/NADH ratio via mitochondrial respiration in some cells, including cells that do not increase respiration following serine deprivation. Thus, in cancer cells where lipid depletion raises the NAD+/NADH ratio, proliferation in serine depleted environments improves when lipids are also depleted. Taken together, these data suggest that changes in mitochondrial respiration in response to nutrient deprivation can influence the NAD+/NADH ratio in a cell-specific manner to impact oxidative biomass synthesis and proliferation. Given the complexity of tumor microenvironments, this work provides a metabolic framework for understanding how levels of more than one environmental nutrient affects cancer cell proliferation.

DOI: https://doi.org/10.1101/2025.05.09.653205
Sci Rep. 2025 Jul 17. 15(1): 25979

CO2 and electrical stunning differentially affect energy metabolism in pigs.

Manuela Peukert, Sebastian Zimmermann, Björn Egert, Dagmar Adeline Brüggemann.

  The use of CO₂ or electrical stunning to render pigs unconscious and insensible before exsanguination is a common practice. Although both methods are widely implemented, they differ fundamentally in their underlying mechanisms, and studies have produced conflicting results regarding their influence on meat quality. In the case of CO₂ stunning, impaired pulmonary gas exchange causes a rapid onset of systemic hypoxia, accompanied by hypercapnia, which in turn lowers blood pH and triggers additional physiological stress responses. Electrical stunning, by contrast, induces a generalized epileptic seizure by depolarizing neuronal cell membranes, markedly increasing oxygen consumption in both the brain and peripheral muscles. Coupled with apnea-induced cessation of respiration, this leads to rapid systemic hypoxia and associated metabolic disturbances. With this study, we aim to generate comprehensive metabolic data as a foundation for deeper understanding of the animal's physiological responses depending on the stunning method used. We identified differences in metabolite pathways associated with the stunning method and evaluated potential influence on early post mortem processes relevant to meat quality development. After CO2 stunning, there was a marked increase in purine degradation into inosine (p < 0.0001) and hypoxanthine (p < 0.0001), along with increased levels of C4 intermediates (succinate, fumarate and malate, all p < 0.0001) in the tricarboxylic acid (TCA) cycle. In contrast, electrical stunning showed a higher rate of glycolysis, as indicated by reduced levels of C6 sugars (e.g. glucose p < 0.0001), and elevated levels of TCA cycle entry metabolites such as citrate (p = 0.0053) and aconitate (p = 0.0009). Our findings suggest that purinergic signaling acts as a rapid emergency response mechanism during gas stunning, reflected by pronounced purine catabolism. The distinct metabolite patterns likely result from different physiological stress responses, such as CO2-induced acidosis and variable oxygen availability. In addition, differences in cellular redox balance (NAD⁺/NADH) between stunning methods may further modulate glycolytic flux and TCA cycle activity. These divergent metabolic states at the time of death may, in turn, influence subsequent post mortem biochemical processes and ultimately influence meat quality development.

Keywords:  CO2 stunning; Electrical stunning; Energy metabolism; Hypoxia; Metabolomics

DOI:  https://doi.org/10.1038/s41598-025-10874-6
Front Cell Infect Microbiol. 2025 ;15 1593581

Rosuvastatin ameliorates obesity-associated insulin resistance in high-fat diet-fed mice by modulating the gut microbiota and gut metabolites.

Chao Yao, Xin Xue, Yunxi Jia, Min Li, Lu Zhang, Hong Yuan, Huiting Xue, Ruiping Hu.

   Introduction: Insulin resistance (IR) underlies metabolic diseases such as obesity and diabetes. Statins are lipid-lowering drugs that have also been studied to improve insulin resistance, but the mechanism is not well understood. Metagenomics and metabolomics were used to analyze the main species and metabolic pathways involved in intestinal microbes while improving insulin resistance in mice with rosuvastatin in this study.
Methods: C57BL/6J male mice fed a high-fat diet were used to establish the insulin resistance (IR) mouse model. Rosuvastatin (RSV) was then administered for 8 weeks. Metagenomics and metabolomics were utilized to analyze the microbial composition and short chain fatty acid metabolites in intestinal feces of mice.
Results: It was observed that insulin-resistant mice showed significant improvement in insulin resistance following treatment with RSV. In comparison to the HFD group, specific bacterial strains were significantly increased, and the levels of butyric acid, caproic acid, and isovaleric acid among the short-chain fatty acids were notably elevated in the RSV group. Through KEGG enrichment analysis, 19 dominant strains and 15 key enzymes involved in butyric acid metabolism were identified.
Conclusions: The results suggested that IR mice might enhance insulin sensitivity by promoting butyric acid synthesis via intestinal microbes following RSV treatment.

Keywords:  butyric acid; insulin resistance; metabolome; metagenome; rosuvastatin

DOI:  https://doi.org/10.3389/fcimb.2025.1593581
bioRxiv. 2025 Jun 13. pii: 2025.06.11.659152. [Epub ahead of print]

Metabolism of epigenetic ribonucleosides leads to nucleolar stress and cytotoxicity.

Xuemeng Sun, Anita Donlic, Jacob A Boyer, Neal Reddy, Clifford P Brangwynne, Joshua D Rabinowitz, Ralph E Kleiner.

Post-transcriptional RNA modifications are ubiquitous in biology, but the fate of epigenetic ribonucleotides after RNA turnover and the consequences of their metabolism and misincorporation into nucleic acids are largely unknown. Here we explore the metabolism of epigenetic ribonucleosides in human cells by studying effects on cell growth, quantifying misincorporation into cellular RNAs and identifying metabolic regulators, and exploring phenotypes associated with cytotoxicity. We find that bulky N 6 -modified adenosines (i.e. i 6 A) exhibit high levels of cytotoxicity and RNA misincorporation, whereas cells dramatically restrict the misincorporation of small N 6 -modified adenosines (i.e. m 6 A), partly through sanitization by enzymatic deamination. Epigenetic ribopyrimidines also exhibit cytotoxicity, mediated primarily by nucleoside kinase UCK2, but only at much higher concentrations than ribopurines. We further characterize the effects of cytotoxic ribonucleoside metabolism on nucleolar morphology and protein translation. Taken together, our work provides new insights into the metabolism of epigenetic ribonucleosides and mechanisms underlying their cytotoxicity to cells.

DOI: https://doi.org/10.1101/2025.06.11.659152
J Proteome Res. 2025 Jul 17.

An Optimized SP3 Sample Processing Workflow for In-Depth and Reproducible Phosphoproteomics.

Leonard A Daly, Christopher J Clarke, Sally O Oswald, Andris Jankevics, Philip J Brownridge, Richard A Scheltema, Claire E Eyers.

  Protein phosphorylation is a ubiquitous post-translational modification (PTM) found across the kingdoms of life and is critical for the regulation of protein function in health and disease. Advances in high-throughput mass spectrometry have transformed our ability to interrogate the phosphoproteome. However, sample preparation methodologies optimized for phosphoproteomics have not kept pace, compromising the ability to fully exploit these technological advances. In this study, we present an optimized phosphoproteomics workflow using carboxylated SP3 magnetic beads, which have simplified proteomics sample preparation. By employing a washing step with 8 M urea and omitting the conventional C18 SPE cleanup, we demonstrate a significant improvement in phosphopeptide identifications, with application of this refined protocol to HEK-293T cell extracts increasing the number nearly 2-fold compared to standard SP3 techniques (7908 cf. 4129). We also observed substantial improvement in the detection of multiply phosphorylated peptides. Our findings suggest that the complexity of PTM cross-talk using current peptide-based proteomics workflows is currently under-represented and underscores the necessity of methodological innovations to better capture the intricacies of the phosphoproteome landscape.

Keywords:  C18; PTM; SP3; TiO2; mass spectrometry; multiply phosphorylated; phosphoproteomics; phosphorylation; proteomics

DOI:  https://doi.org/10.1021/acs.jproteome.5c00220