bims-cesirm Biomed News
on Cell Signaling mediated regulation of metabolism
Issue of 2025–10–05
eleven papers selected by
Tigist Tamir, University of North Carolina



  1. Sci Rep. 2025 Sep 30. 15(1): 34004
      Breast cancer is a heterogeneous disease with a high incidence, but its proteomes have not yet been thoroughly characterized. To construct a comprehensive dynamic network of breast cancer-related proteins, we integrated the whole-cell proteome (WCP), phospho-proteome, malonyl-proteome of breast cancer tumor tissues and adjacent healthy tissues. We identified 2,417 differentially expressed proteins (DEPs), 646 differentially phosphorylated proteins (DPPs), and 107 differentially malonylated proteins (DMPs). Functional enrichment analysis revealed that these differentially expressed proteins are involved in extracellular matrix (ECM) interactions and immune-related pathways. Protein‒protein interaction (PPI) analysis revealed posttranslational modification (PTM) crosstalk between proteins involved in phosphorylation and malonylation. The acetyltransferase EP300 and deacetylase HDAC1 are involved in the DPP network, whereas the phosphatase PKM is a hub protein in the DMP network. Kinase-substrate enrichment analysis (KSEA) revealed the activation of the kinases CSNK1D, ROCK1, ROCK2, and CDK2. Overall, this study provides a foundation for understanding the functions of phosphorylation and malonylation in breast cancer. It systematically reveals critical features of breast cancer, providing a resource for exploring PTM crosstalk within and across proteins involved in the disease.
    Keywords:  Breast cancer; Malonylation; Phosphorylation; Posttranslational modification
    DOI:  https://doi.org/10.1038/s41598-025-11573-y
  2. bioRxiv. 2025 Sep 28. pii: 2025.09.25.678523. [Epub ahead of print]
      Lactate has emerged as a key metabolite involved in multiple physiological processes, including memory formation, immune response regulation, and muscle biogenesis. However, its role in aging and cellular protection remains unclear. Here, we show that lactate promotes longevity in C. elegans through a mechanism that requires early-life intervention, indicating a hormetic priming effect. This pro-longevity action depends on its metabolic conversion via LDH-1 and NADH, which drives redox-dependent metabolic reprogramming. Multi-omics approaches revealed that lactate induces early-stage metabolic adaptations, with a strong modulation of lipid metabolism, followed by late-life transcriptional remodeling. These shifts are characterized by enhanced stress response pathways and suppression of energy- associated metabolic processes. Our genetic screening identified sir-2.1 /SIRT1 and rict- 1/ RICTOR as essential for lactate-mediated lifespan extension. Our findings establish lactate as a pro-longevity metabolite that couples redox signaling with lipid remodeling and nutrient- sensing pathways. This work advances our understanding of lactate's dual role as a metabolic intermediary and geroprotector signaling molecule, offering insights into therapeutic strategies for age-related metabolic disorders.
    DOI:  https://doi.org/10.1101/2025.09.25.678523
  3. J Proteomics. 2025 Sep 29. pii: S1874-3919(25)00167-8. [Epub ahead of print] 105540
      Visceral obesity is closely related to insulin resistance (IR), a key process in developing metabolic diseases. Adipocyte-derived extracellular vesicles (AdEVs) have emerged as mediators of intercellular communication, carrying signals reflecting adipose tissue's functional state. This study aimed to perform a comparative proteomic analysis of AdEVs to propose a molecular fingerprint of specific biomarker candidates for IR in early-onset obesity. AdEVs were isolated from epididymal adipocytes of 16-week-old male Wistar rats on a high-fat diet (HFD) and controls and analyzed by mass spectrometry coupled to a multi-software protein identification bioinformatics strategy. For relative quantification using the label-free method, more than 1200 proteins were identified, with 431 being overrepresented and unique to HFD, associated explicitly with energy metabolism, cellular stress, and insulin signaling. Based on biological plausibility, and/or the best log2FC and p-value scores, six proteins were proposed as part of the IR molecular fingerprint: Atp5f1b, Anxa6, Myo1c, GLUT4, Anxa5, and Aoc3. Phosphoproteomic analysis revealed key modifications in phosphorylated proteins such as CaATPase (S663), PLIN (S130), and PPM1H (S260,265). The results suggest that AdEVs reflect early mitochondrial alterations related to IR, which could be employed as potential non-invasive biomarker candidates for metabolic dysfunction and follow-up in early overweight or obesity. Significance In this study, we demonstrate that adipocyte-derived extracellular vesicles (AdEVs) encapsulate a stage-resolved molecular signature that reflects key pathophysiological events underlying the early development of insulin resistance in obesity. These vesicles carry proteins linked to lipotoxicity, mitochondrial and endoplasmic reticulum stress, and impaired vesicular trafficking, offering mechanistic insight into how local adipocyte dysfunction may trigger systemic metabolic impairment. This EV-based proteomic fingerprint advances our understanding of insulin resistance pathogenesis and identifies potential biomarker candidates for early metabolic risk stratification.
    Keywords:  Early-onset obesity; Extracellular vesicles; Insulin resistance; Mitochondrial dysfunction; Phosphoproteomics; Proteomics
    DOI:  https://doi.org/10.1016/j.jprot.2025.105540
  4. J Chem Inf Model. 2025 Oct 03.
      We developed an advanced computational framework to accelerate the study of the impact of post-translational modifications on protein structures and interactions (PTM-Psi) using asynchronous, loosely coupled workflows on the Azure Quantum Elements Cloud platform. We seamlessly integrate emerging cloud computing assets that further expand the scope and capability of PTM-Psi Python package by refactoring it into a cloud-compatible library. We employed a "workflow of workflows" approach, wherein a parent workflow spawns one or more child workflows, managing them, and acting on their results. This approach enabled us to optimize resource allocation according to each workflow's needs and allowed us to use the cloud heterogeneous architecture for the computational investigation of a combinatorial explosion of thiol protein PTMs on an exemplary protein megacomplex critical to the Calvin-Benson cycle of light-dependent sugar production in cyanobacteria. With PTM-Psi on the cloud, we transformed the pipeline for the thiol PTM analysis to achieve high throughput by leveraging the strengths of the cloud service. PTM-Psi on the cloud reduces operational complexity and lowers entry barriers to data interpretation with structural modeling for a redox proteomics mass spectrometry specialist.
    DOI:  https://doi.org/10.1021/acs.jcim.5c01661
  5. Cancer Res. 2025 Oct 01. OF1-OF3
      Metabolic changes are a major hallmark of cancer with the mitochondrial tricarboxylic acid (TCA) cycle playing a central role in this process. Remodeling of the TCA cycle occurs in cancer cells to sustain the increased anabolic and energetic demands required to grow, proliferate, and metastasize. Alternative splicing (AS) is increasingly recognized as a key regulator of cancer metabolism, yet its specific impact on TCA cycle enzymes remains unclear. In this issue of Cancer Research, Cheung and colleagues describe a novel splicing isoform of citrate synthase (CS), termed CS-ΔEx4, which is highly expressed in colorectal cancer. This CS-ΔEx4 isoform forms heterocomplexes with full-length CS, enhancing CS activity and promoting the metabolic reprogramming characteristic of malignancy. Overexpression of CS-ΔEx4 increases mitochondrial respiration and drives glycolytic carbon flux toward TCA intermediates, resulting in elevated levels of the metabolite 2-hydroxyglutarate. Mechanistically, this increase in 2-hydroxyglutarate, facilitated by increased activity of phosphoglycerate dehydrogenase, leads to epigenetic alterations that support oncogenic gene expression and tumor progression. Suppression of CS-ΔEx4 or pharmacologic inhibition of its activity reverts these metabolic and epigenetic changes, reducing cancer cell survival and metastatic potential. These findings establish a direct link between AS of a core metabolic enzyme and the emergence of cancer hallmarks, suggesting that targeting AS-derived variants like CS-ΔEx4 may represent a promising therapeutic strategy for colorectal cancer and potentially other malignancies in which such isoforms are expressed. See related article by Cheung et al., p. XX.
    DOI:  https://doi.org/10.1158/0008-5472.CAN-25-3356
  6. Mol Cell. 2025 Oct 02. pii: S1097-2765(25)00746-4. [Epub ahead of print]85(19): 3694-3710.e8
      As the antigen receptor, the T cell receptor (TCR)-CD3 complex contains a panel of immunoreceptor tyrosine-based activation motifs (ITAMs) in the CD3 subunits to transduce diverse antigen signals, but the mechanism underlying TCR signaling versatility remains poorly understood. Here, we unraveled the structural and functional heterogeneity of the major CD3ζ signaling component. Using nuclear magnetic resonance spectroscopy, we characterized the membrane-bound structure of the dynamic CD3ζ cytoplasmic domain. ITAM 1 to 3 displayed a gradual increase of membrane insertion, leading to a sequential phosphorylation order from N to C terminus and the generation of partial- and full-phosphorylation species upon physiological triggering. Under chronic TCR stimulation, a scenario relevant to cancer and chronic infection, the C-terminal ITAM displayed faster decay kinetics of phosphorylation than the N-terminal one, causing insufficient TCR signaling. Our study thus reveals a new mechanism of ITAM heterogeneity in TCR signaling that is relevant to physiological and pathological contexts.
    Keywords:  CD3ζ; T cell receptor; immunoreceptor tyrosine-based activation motif; ionic protein-lipid interaction; membrane insertion; nuclear magnetic resonance spectroscopy; quantitative mass spectrometry; sequential phosphorylation; structural heterogeneity
    DOI:  https://doi.org/10.1016/j.molcel.2025.09.005
  7. Sci Rep. 2025 Oct 03. 15(1): 34513
      Glutamine plays a vital role in cellular biomass synthesis, serving as a key nutrient. Cancer profoundly impacts cellular size, promoting rapid proliferation and enhanced survival. Understanding the molecular mechanisms that regulate cell size in cancer is essential for designing interventions that can disrupt these processes and inhibit tumor progression. Polyploid giant cancer cells (PGCCs) represent a distinct subpopulation of tumor cells that are implicated in tumor initiation, immortality, invasion, metastasis, and resistance to chemotherapy and radiotherapy. These cells are characterized by their markedly increased size and polyploidy, underscoring the significance of cell size regulation in cancer biology. Although glutamine is known to influence cell growth, its role in regulating cell size remains poorly understood. Wee1, a key cell cycle regulator, controls the timing of mitotic entry, and is known to modulate cell size by preventing premature division. However, the potential link between glutamine, Wee1, and cell size has not been previously explored. In the present study, we investigated the role of glutamine in regulating cellular size. We found that glutamine depletion results in a significant reduction in cell size, along with decreased Wee1 expression at both mRNA and protein levels. Additionally, transient knockdown of Wee1 also led to a reduction in cellular size, reinforcing its role as a regulator of cell size. Moreover, we observed that cytochalasin-B-induced polyploidy was diminished under glutamine-deprived conditions, further affirming the importance of glutamine in maintaining polyploidy and cell size. Overall, our findings clearly indicate that glutamine is a key mediator of cellular size, and that glutamine regulates cell size at least in part through its influence on Wee1. These insights contribute to a better understanding of metabolic control of cell size in cancer and may offer novel therapeutic opportunities.
    Keywords:  And cancer; Cellular size; Glutamine; Polyploidy; Wee1
    DOI:  https://doi.org/10.1038/s41598-025-17687-7
  8. bioRxiv. 2025 Sep 26. pii: 2025.09.25.678565. [Epub ahead of print]
      Reactive oxygen species (ROS) are central players in redox signaling, controlling all biological processes in human health. Many reports demonstrated that ROS play essential roles in regulating cell migration and invasion, while contributing to cancer progression and metastasis, potentially via inducing protein cysteine oxidations. Nevertheless, specific redox players involved in cell migration and invasion remain ill-defined. In this report, we found that Nischarin (NISCH), established as a tumor suppressor, is susceptible to S-glutathionylation, selectively at Cys185 located near its leucine-rich repeat (LRR) domains, which are implicated in protein-protein interactions with Rac1 and PAK1. We demonstrated that epithelial breast cancer cell lines, MCF7 and MDA-MB-231, expressing NISCH wild-type (WT), compared to its cysteine mutant (C185S), exhibit increased migration and invasion in response to oxidative stress, such as limited glucose. Mechanistically, NISCH S-glutathionylation reduced its binding to Rac1 and PAK1, without altering its binding to integrin α5. The dissociation of NISCH led to the activation of Rac1 and PAK1, resulting in the localization of Rac1 to the cell periphery, which facilitates lamellipodia formation. The activated PAK1 increased the phosphorylation of the LIMK1-cofilin axis, thereby further enhancing actin filament dynamics that promote cell migration. Based on the mechanistic analysis, we produced an engineered NISCH construct, composed of the N-terminal PX and LRR domains. We demonstrated that the engineered NISCH PX-LRR constructs, particularly one lacking the S-glutathionylation site (i.e., C185S), can suppress the migration, invasion, and colony formation of MDA-MB-231 cells, regardless of the presence of oxidative stress. Our data reports a new redox player in cell migration and invasion, while supporting the potential application of NISCH-derived protein-based therapeutics for breast cancer.
    DOI:  https://doi.org/10.1101/2025.09.25.678565
  9. Sci Rep. 2025 Sep 30. 15(1): 34015
      Cancer cells exhibit metabolic reprogramming to fulfill their increased demands for abnormal growth and proliferation. We studied metabolic profiles of squamous cell lung carcinoma (LUSC).Elevated arginine levels and reduced acylcarnitine C18:2, along with decreased phosphatidylcholine (PC) with acyl-alkyl residues C38:0 were associated with the diagnosis and prognosis of LUSC. Most of the PCs demonstrated a decrease, while lysophosphatidylcholines (LPC) exhibited an increase in LUSC patients. Network analysis unveiled that LPCs mediated PC and amino acids subgroup in LUSC compared to the control group. Analysis of public LUSC data confirmed associations between the expression levels of genes encoding enzymes involved in the biosynthesis pathways of arginine, proline (ASL, OTC, PYCR2), PC (CEPT1, CHPT1, LPCAT1) and LPC (LCAT, PLA2G16, PLB1) with a 5-yr survival outcome. The observed metabolic reprogramming in LUSC patients suggested the potential utility of metabolites as a supportive biomarkers for LUSC diagnosis.
    Keywords:  Feature selection; LASSO; Lung squamous cell carcinoma; Mass spectormetry; Metabolic profiles
    DOI:  https://doi.org/10.1038/s41598-025-12412-w
  10. Sci Rep. 2025 Oct 02. 15(1): 34355
      This study identified biomarkers that could be leveraged to classify the state of healing in diabetic wounds. Firstly, by collecting wound samples from diabetic mice at different time points and generating their protein profiles using standard techniques, we set to interrogate whether a small number of biomarkers could serve as sensors to monitor the healing stage. Least absolute shrinkage and selection operator (LASSO) was applied. Large-scale analysis of wound tissue proteins integrated with the respective wound sizes allowed to establish a correlation between the observed protein profile and wound closure. We further evaluated human subjects' systemic serum proteomics for biomarkers. An additional wound healing model in diabetic mice was employed for microRNA quantitation at the same time points and similarly analyzed. Our analysis highlighted markers MMP-2, HGF, miR-1b and miR-107-3p in mice and Fractalkine and FGF-2 in humans that could correctly identify the extent of healing. By using proteomics from mice and human patients and complementary microRNA mouse data with computer regression models we can better predict molecular and protein deficits associated with impaired diabetic wound repair.
    DOI:  https://doi.org/10.1038/s41598-025-16914-5
  11. Sci Rep. 2025 Oct 02. 15(1): 34430
      Cardiac abnormalities resulting from the consumption of diets rich in fats have been attributed to their saturation level. Despite reductions in saturated fats, cardiac abnormalities still seem to increase. We compared the effects of two dietary fat sources (with animal-fat-fed having higher saturation levels than plant-fat-fed) on the fatty acid and lipid profiles of the cardiac tissues and its possible impact on metabolic phenotype in male Wistar rats after 17weeks of feeding. Serum and cardiac tissue lipid profiles were higher in plant-fat-fed than animal-fat-fed. The Saturated-fatty-acid (Stearic acid) concentration was reduced in plant-fat-fed cardiac tissues compared to animal-fat-fed. Unsaturated-fatty-acid (Palmitoleic acid, Oleic acid and Euricic acid) contents were higher while Linoleic acid, Eicosatrienoic acid and Docasapentanoic acid were lower in plant-fat-fed diet than animal-fat-fed. The plant-fat-fed diet also showed higher total saturated-fatty-acid, saturated-fatty-acid/poly-unsaturated-fatty-acid and omega-6/omega-3 fatty acid content, but lower total poly-unsaturated-fatty-acid and Palmitic acid/Palmitoleic acid in cardiac tissues compared with animal-fat-fed diet. Finally, plant-fat-fed had higher expression levels of FATP4 and CD36 proteins than animal-fat-fed. Although the level of saturation is a factor, the quantity of fat consumed has a higher tendency to predispose cardiac tissues to greater metabolic risk and is an important determinant of fatty acid metabolism in the cardiac tissues.
    Keywords:  Cluster of differentiation 36; Fatty acid transport protein 4; Fatty acids; High-fat diets; Lipids; Obesity
    DOI:  https://doi.org/10.1038/s41598-025-17493-1