bims-cesirm 2025-08-31 papers

bims-cesirm

Biomed News

on Cell Signaling mediated regulation of metabolism

Issue of 2025–08–31
thirteen papers selected by
Tigist Tamir, University of North Carolina

Multi-Omic Characterization of Epithelial-Mesenchymal Transition: Lipidomic and Metabolomic Profiles as Key Markers of TGF-β-Induced Transition in Huh7 Hepatocellular Carcinoma.
Kisspeptin Mitigates Hepatic De Novo Lipogenesis in Metabolic Dysfunction-Associated Steatotic Liver Disease.
Crotonylation of IDH1 alleviates MASLD progression by enhancing the TCA cycle.
GPT2 mediates glutamine metabolism-driven metabolic alterations in platinum-resistant ovarian cancer cells.
Inducible skeletal muscle-specific p53 deletion alleviates high-fat diet-induced insulin resistance by modulating mitochondria-associated membrane in obese mice.
Joint Metabolomics and Transcriptomics Reveal Rewired Glycerophospholipid and Arginine Metabolism as Components of BRCA1-Induced Metabolic Reprogramming in Breast Cancer Cells.
Targeted Quantitation of Phosphotyrosine-Containing Proteins in T-Cell Receptor Signaling Using a SureQuant-Based Mass Spectrometry Approach.
Fatty acid addiction in cancer: A high-fat diet directly promotes tumor growth through fatty acid oxidation.
High fat diet enhances catalase loading into adipose tissue derived extracellular vesicles with limited effect on oxidative stress.
Retinoic Acid-Induced Transglutaminase 2 Expression Reduces Sensitivity to Cisplatin in the Hormone-Positive MCF-7 Breast Cancer Cell Model.
Malonyl-CoA Promotes Prostate Cancer Progression and Castration Resistance by Enhancing Lipogenesis and Ran Activation.
Nucleoside diphosphate kinase A (NME1) catalyses its own oligophosphorylation.
Metabolite Functions Revealed by Mass Spectrometry-Based Target Engagement Proteomics Approaches.

Cells. 2025 Aug 10. pii: 1233. [Epub ahead of print]14(16):

Multi-Omic Characterization of Epithelial-Mesenchymal Transition: Lipidomic and Metabolomic Profiles as Key Markers of TGF-β-Induced Transition in Huh7 Hepatocellular Carcinoma.

Agnese Bertoldi, Gaia Cusumano, Eleonora Calzoni, Husam B R Alabed, Roberto Maria Pellegrino, Sandra Buratta, Lorena Urbanelli, Carla Emiliani.

  Epithelial-mesenchymal transition (EMT) is a key process in cancer progression and fibrogenesis. In this study, EMT was induced in Huh7 hepatocellular carcinoma cells via TGF-β1 treatment, and the resulting lipidomic and metabolomic alterations were characterized. Morphological changes and protein marker analyses confirmed the transition to a mesenchymal phenotype, with reduced E-cadherin and increased vimentin and N-cadherin expression. Lipidomic profiling revealed a dose-dependent reorganization of membrane lipids, with a pronounced increase in the levels of ceramides, cholesteryl esters, and lysophospholipids, consistent with alterations in membrane structure, potential cellular stress, and modulation of inflammatory pathways. Changes in the content of phospholipid classes, including phosphatidylethanolamines and phosphatidylserines, indicate possible variations in membrane dynamics and potentially point to modifications in mitochondrial function, cellular stress responses, and redox balance. Metabolomic analysis further indicates an alteration of choline and phosphatidylcholine metabolism, consistent with a shift from de novo membrane synthesis toward lipid turnover. Reduced glycolytic capacity and modified acylcarnitine levels indicated impaired metabolic flexibility and mitochondrial efficiency. The integration of phenotypic, lipidomic, and metabolomic data suggests that TGF-β1 induces EMT and drives a coordinated metabolic reprogramming. These findings highlight the involvement of lipid and energy metabolism in sustaining EMT and suggest that specific metabolic reprogramming events characterize the mesenchymal shift in hepatocellular carcinoma. By exploring this process in a tumor-specific context, we aim to deepen our understanding of EMT complexity and its implications for tumor progression and therapeutic vulnerability.

Keywords:  TGF-β1 signaling; epithelial–mesenchymal transition (EMT); hepatocellular carcinoma (HCC); lipidomic; membrane remodeling; metabolomic

DOI:  https://doi.org/10.3390/cells14161233
Cells. 2025 Aug 20. pii: 1289. [Epub ahead of print]14(16):

Kisspeptin Mitigates Hepatic De Novo Lipogenesis in Metabolic Dysfunction-Associated Steatotic Liver Disease.

Kimberly Izarraras, Ankit Shah, Kavita Prasad, Helena Tan, Zhongren Zhou, Moshmi Bhattacharya.

  The peptide hormone kisspeptin, signaling via its receptor, KISS1R, decreases hepatic steatosis and protects against metabolic dysfunction-associated steatotic liver disease (MASLD). Enhanced de novo lipogenesis (DNL) contributes to MASLD. Here, we investigated whether kisspeptin treatment in obese, diabetic mice directly attenuates DNL. DNL was assessed in kisspeptin-treated mouse livers, using a mouse model of MASLD, (DIAMOND mice), employing 2H2O-enriched water, mass spectrometry analysis, and transcriptomic profiling. Gene and protein expression were evaluated in primary hepatocytes and livers. Additionally, hepatic Kiss1r expression was increased in DIAMOND mice, following which various biochemical and metabolic assessments were employed. Metabolic tracing in kisspeptin-treated steatotic livers demonstrated a decrease in the DNL of free fatty acids (FFAs), known to be associated with diabetes, steatosis, and hepatocellular carcinoma. Transcriptomic profiling of kisspeptin-treated livers identified disruption of key metabolic pathways, the most prominent being a decrease in fatty acid metabolism, and downregulation of Cidea, a key regulator of lipid droplet formation. Kisspeptin treatment of FFA-loaded primary mouse hepatocytes significantly decreased Cidea expression. Mechanistically, we found that kisspeptin administration decreased levels of transcription factor SREBP-1c, a crucial regulator of DNL, and CIDEA. Thus, enhanced KISS1R signaling limits hepatic DNL, suggesting a crucial role in restricting MASLD.

Keywords:  CIDEA; KISS1R; MASLD; SREBP; de novo lipogenesis; kisspeptin; liver; steatosis

DOI:  https://doi.org/10.3390/cells14161289
Nat Commun. 2025 Aug 26. 16(1): 7961

Crotonylation of IDH1 alleviates MASLD progression by enhancing the TCA cycle.

Shanshan Liu, Yu Ji, Luyang Wei, Yiqiao Zhang, Linghang Zeng, Yiyang Min, Danyang Yin, Kun Liu, Chengjian Guan, Shumeng Liu, Huajing Yu, Zhongtao Zhang.

Metabolic dysfunction-associated steatotic liver disease (MASLD), potentially ameliorated by bariatric-metabolic surgery, remains a global health concern in the absence of approved drugs. Protein post-translational modifications (PTMs) are crucial for MASLD. However, the functional significance of lysine crotonylation (Kcr) remains unclear. We aimed to investigate the mechanisms by Kcr-regulated IDH1 in the tricarboxylic acid (TCA) cycle and MASLD development. Herein, we reported a quantitative proteomics analysis of global crotonylome upon MASLD and Post-bariatric. Specifically, decreases in K58cr, K151cr, K212cr and K345cr of IDH1 upon MASLD were observed. PCAF and SIRT7 dynamically regulated the IDH1 Kcr. Abolishment of IDH1 Kcr impaired TCA cycle by decreasing IDH1 enzymatic activity. Male mice with liver-specific expression of crotonylation-mimic mutants of IDH1 were resistant to HFD-induced obesity, insulin resistance, glucose intolerance and MASLD. Our findings unravel the mechanisms of IDH1 Kcr and indicate that targeting PCAF/SIRT7-IDH1 Kcr and metabolites may be a promising strategy for MASLD therapy.

DOI: https://doi.org/10.1038/s41467-025-62731-9
Sci Rep. 2025 Aug 20. 15(1): 30528

GPT2 mediates glutamine metabolism-driven metabolic alterations in platinum-resistant ovarian cancer cells.

Adriana Ponton-Almodovar, Mary P Udumula, Vrinda Khullar, Faraz Rashid, Ramandeep Rattan, Jamie J Bernard, Sachi Horibata.

  Metabolic reprogramming is recognized as a hallmark of cancer frequently associated with drug resistance in ovarian cancer. This is problematic as ovarian cancer is one of the deadliest gynecologic cancers with platinum resistance contributing to poor survival. However, the mechanism by which ovarian cancer cell metabolism contributes to platinum resistance is not well understood. Herein, metabolic signatures were determined in platinum-resistant ovarian cancer cell lines compared to the more platinum-sensitive parental lines. Chemoresistant ovarian cancer cells showed increased oxidative phosphorylation (OXPHOS) compared to chemosensitive cells. This was associated with elevated levels of glutaminolysis and tricarboxylic acid (TCA)-related metabolites supporting their dependence on OXPHOS. Key enzymes involved in glutaminolysis, specifically, glutamic-pyruvic transaminase 2 (GPT2), were upregulated in chemoresistant compared to chemosensitive cells. Interestingly, high GPT2 gene expression is associated with worse prognosis in ovarian cancer patients, adding translational relevance to the pre-clinical findings. GPT2 knockout in chemoresistant cells restored the metabolic phenotype to that of the sensitive cells and reversed drug resistance. These data suggest that GPT2 is a critical link between glutaminolysis, the TCA cycle, and OXPHOS and is a potential target to attenuate the increased metabolic activity associated with a chemoresistant phenotype.

Keywords:  GPT2; Glutamine; Metabolism; Ovarian cancer

DOI:  https://doi.org/10.1038/s41598-025-15707-0
Redox Biol. 2025 Aug 20. pii: S2213-2317(25)00341-6. [Epub ahead of print]86 103828

Inducible skeletal muscle-specific p53 deletion alleviates high-fat diet-induced insulin resistance by modulating mitochondria-associated membrane in obese mice.

Soyoung Park, Jin Ki Jung, Jung-Yoon Heo, Themis Thoudam, Su-Yeon Jeong, Seok-Hui Kang, Chang-Hoon Woo, Hyoung Chul Choi, In-Kyu Lee, Jinmyoung Dan, Jongsoon Lee, Jae-Ryong Kim, So-Young Park.

  p53 has been implicated in metabolic regulation, but its role in obesity-induced skeletal muscle insulin resistance remains incompletely understood. This study aimed to determine the functional contribution of skeletal muscle p53 to insulin resistance and mitochondrial dysfunction, particularly in the context of obesity. We demonstrate that inducible, skeletal muscle-specific deletion of p53 (iMp53 KO) significantly improves insulin sensitivity in high-fat diet (HFD)-induced obese mice, with no effect in chow-fed controls. This metabolic improvement was accompanied by enhanced mitochondrial respiration and membrane potential, as well as reduced mitochondrial calcium overload in palmitate-treated C2C12 myotubes. Electron microscopy and immunoblotting revealed a marked reduction in mitochondria-associated membrane (MAM) area and decreased levels of MAM components (IP3R, VDAC, GRP75) in iMp53 KO muscle. Co-immunoprecipitation assays demonstrated physical interactions between p53 and MAM proteins, supporting a role for p53 in promoting MAM formation under obese conditions. Consistently, skeletal muscle from patients with type 2 diabetes exhibited elevated expression of both p53 and MAM markers, with a positive correlation between them. These findings suggest that p53 plays an important role in modulating ER-mitochondrial contacts and mitochondrial homeostasis in skeletal muscle and suggest its contribution to obesity-induced insulin resistance. This study provides new mechanistic insight into the pathological role of p53 in muscle metabolism.

Keywords:  Insulin resistance; Mitochondria-associated membrane; Obesity; Skeletal muscle; p53

DOI:  https://doi.org/10.1016/j.redox.2025.103828
Metabolites. 2025 Aug 07. pii: 534. [Epub ahead of print]15(8):

Joint Metabolomics and Transcriptomics Reveal Rewired Glycerophospholipid and Arginine Metabolism as Components of BRCA1-Induced Metabolic Reprogramming in Breast Cancer Cells.

Thomas Lucaora, Daniel Morvan.

  Background/Objectives: The breast cancer susceptibility gene 1 (BRCA1) is a tumor suppressor gene whose mutations are associated with increased susceptibility to develop breast or ovarian cancer. BRCA1 mainly exerts its protective effects through DNA double-strand break repair. Although not itself a transcriptional factor, BRCA1, through its multiple protein interaction domains, exerts transcriptional coregulation. In addition, BRCA1 expression alters cellular metabolism including inhibition of de novo fatty acid synthesis, changes in cellular bioenergetics, and activation of antioxidant defenses. Some of these actions may contribute to its global oncosuppressive effects. However, the breadth of metabolic pathways reprogrammed by BRCA1 is not fully elucidated. Methods: Breast cancer cells expressing BRCA1 were investigated by multiplatform metabolomics, metabolism-related transcriptomics, and joint metabolomics/transcriptomics data processing techniques, namely two-way orthogonal partial least squares and pathway analysis. Results: Joint analyses revealed the most important metabolites, genes, and pathways of metabolic reprogramming in BRCA1-expressing breast cancer cells. The breadth of metabolic reprogramming included fatty acid synthesis, bioenergetics, HIF-1 signaling pathway, antioxidation, nucleic acid synthesis, and other pathways. Among them, rewiring of glycerophospholipid (including phosphatidylcholine, -serine and -inositol) metabolism and increased arginine metabolism have not been reported yet. Conclusions: Rewired glycerophospholipid and arginine metabolism were identified as components of BRCA1-induced metabolic reprogramming in breast cancer cells. The study helps to identify metabolites that are candidate biomarkers of the BRCA1 genotype and metabolic pathways that can be exploited in targeted therapies.

Keywords:  BRCA1; breast cancer; joint metabolomics/transcriptomics; metabolic reprogramming; pathway analysis; two-way orthogonal partial least squares

DOI:  https://doi.org/10.3390/metabo15080534
Proteomics. 2025 Aug;25(16): 40-47

Targeted Quantitation of Phosphotyrosine-Containing Proteins in T-Cell Receptor Signaling Using a SureQuant-Based Mass Spectrometry Approach.

Firdous A Bhat, Husheng Ding, Dong-Gi Mun, Jane A Peterson, Mary Cristine Charlesworth, Richard K Kandasamy, Akhilesh Pandey.

  T-cell receptor (TCR) signaling plays a crucial role in various biological processes and is usually studied using global mass spectrometry-based phosphoproteomic studies. Despite advancements in targeted mass spectrometry-based assays for protein quantification, their application in studying signaling processes, for example, reproducible measurements of post-translational modifications (PTMs) such as phosphorylation, remains limited. Tyrosine phosphorylation is critical for many signaling pathways but presents challenges due to the low abundance of phosphotyrosine-containing peptides. Conventional untargeted methods often encounter data gaps when analyzing large sample sets, particularly for low-abundance peptides. To address this issue, a targeted proteomics method called "SureQuant" was employed, which relies on triggered data acquisition with heavy isotope-labeled peptides. This method has been shown to provide sensitive and reproducible quantification of low-abundance peptides. Here we describe the development of a SureQuant-based method to quantify phosphotyrosine peptides that are involved in the TCR signaling pathway. To monitor the change in phosphotyrosine signals upon activation, the T-cells were stimulated with anti-CD3/CD28 antibodies. We successfully quantified changes in important phosphotyrosine peptides in primary T-cells upon stimulation with anti-CD3/CD28 antibodies. This study showcases the ability of the SureQuant approach to accurately quantify low-abundance phosphotyrosine peptides, highlighting its broader potential to study a diverse set of PTMs in physiological or clinical settings. SUMMARY: T-cell receptor (TCR) signaling plays a fundamental role in immune responses, regulating T-cell activation, differentiation, and function. While tyrosine phosphorylation is a key regulatory mechanism in this pathway, the low abundance of phosphotyrosine peptides presents a major challenge for their detection and quantification in complex biological samples. By employing the SureQuant targeted mass spectrometry approach, we achieved highly sensitive and reproducible quantification of key phosphotyrosine sites involved in T-cell activation. This study provides a systematic view of TCR signaling dynamics, revealing distinct phosphorylation patterns across different activation timepoints. Our findings demonstrate the effectiveness of SureQuant in quantifying low-abundance, post-translationally modified peptides, offering a valuable tool for studying signaling pathways with greater precision. Additionally, this methodological framework can be extended to investigate other signaling networks, immune cell functions, and disease-associated phosphotyrosine modifications.

Keywords:  Anti‐CD3/CD28 antibodies; T‐cell activation; immunoblotting; phosphotyrosine peptides; post‐translational modifications; targeted proteomics

DOI:  https://doi.org/10.1002/pmic.70023
Biochim Biophys Acta Rev Cancer. 2025 Aug 20. pii: S0304-419X(25)00170-2. [Epub ahead of print]1880(5): 189428

Fatty acid addiction in cancer: A high-fat diet directly promotes tumor growth through fatty acid oxidation.

Soo-Youl Kim.

  Tumor growth promoted by a high-fat diet (HFD) was completely reversed by inhibiting fatty acid oxidation (FAO). The promotion of tumors by an HFD is known to result from the indirect effects of sex hormones, leptin, and adipokines such as insulin-like growth factor-1 (IGF-1) on cancer cells. However, even though HFD notably increased blood levels of IGF-1, knocking down the carnitine-acylcarnitine carrier (CAC) to inhibit FAO completely reversed the tumor-promoting effects in pancreatic cancer cells, accompanied by a significant decrease in ATP production. When ATP levels dropped due to FAO inhibition in cancer cells, mTOR - a key regulator of survival - became inactive, leading to reduced cell viability and increased cell death. This shows that HFD promotes cancer cell growth by supplying more calories through FAO, indicating that cancer is addicted to fatty acids. This review emphasizes the crucial role of cancer-specific FAO in tumor growth and proposes potential new therapeutic strategies targeting various FAO enzymes as innovative anti-cancer treatments.

Keywords:  ATP production; Fatty acid oxidation; High-fat diet (HFD); Obesity; cancer

DOI:  https://doi.org/10.1016/j.bbcan.2025.189428
Sci Rep. 2025 Aug 23. 15(1): 31010

High fat diet enhances catalase loading into adipose tissue derived extracellular vesicles with limited effect on oxidative stress.

Inae Jeong, Juhwan Lee, Soo-Jeung Park, Ok-Kyung Kim.

  Obesity is closely related to liver disease. However, few studies have focused on the impact of adipose tissue-derived extracellular vesicles (EVs) in obesity on liver disease. Therefore, we aimed to investigate the effect of adipose tissue-derived EVs from high-fat diet (HFD)-fed obese mice (EV-HFD) on liver damage induced by oxidative stress. We investigated alterations in the expression of antioxidant enzymes in adipose tissue, and the loading of those enzymes into adipose tissue-derived EVs. Furthermore, we treated alpha mouse liver 12 (AML12) cells with adipose tissue-derived EVs and induced oxidative stress. We observed that the HFD did not exert an effect on the protein expressions of antioxidant enzymes in adipose tissue. Intriguingly, the EV-HFD exhibited an upregulation in the loading of catalase (CAT) when compared to the adipose tissue-derived EVs from normal chow-fed mice (EV-NC). Notably, both types of EVs exhibited a similar capacity to mitigate cell damage when exposed to oxidative stress. Our findings indicate that obesity-induced loading of more CAT into adipose tissue-derived EVs cannot improve their antioxidant capacity in AML12 cells. We suggest that adipose tissue-derived EVs can serve as a tool to maintain homeostasis and defend against oxidative stress, thereby supporting normal physiological functions.

Keywords:  Antioxidant enzymes; Catalase; Extracellular vesicles; Liver disease; Obesity; Oxidative stress

DOI:  https://doi.org/10.1038/s41598-025-15594-5
Int J Mol Sci. 2025 Aug 21. pii: 8101. [Epub ahead of print]26(16):

Retinoic Acid-Induced Transglutaminase 2 Expression Reduces Sensitivity to Cisplatin in the Hormone-Positive MCF-7 Breast Cancer Cell Model.

Ebidor U Lawani-Luwaji, Claire V S Pike, Peter J Coussons.

  Cisplatin is an effective chemotherapeutic drug, but is limited both by its toxicity and its tendency to induce drug resistance rapidly in some patients. Tissue transglutaminase 2 (TG2), which is overexpressed in various cancers, has two main isoforms: a long (TG2-L) and a short form (TG2-S). While TG2-L supports cell survival, conversely, TG2-S promotes cell death. Evidence increasingly suggests that TG2 may be a suitable target for combating chemoresistance in a variety of human cancers. Here, we show that cisplatin toxicity towards wild-type MCF-7 breast cancer cells is associated with reduced TG2-L and TG2-S expression, whereas approximately doubling the TG2-L expression through the retinoic acid pre-treatment of these cells induces survival in the presence of cisplatin at levels similar to those seen in long-term cisplatin-co-cultured cells, which have reduced sensitivity. The treatment of cisplatin-surviving cells with cisplatin alone did not significantly alter the levels of either TG2 isoform, whereas the cisplatin challenge of cisplatin-surviving MCF-7 cells following 20 µM retinoic acid pre-treatment resulted in increased levels of TG2-L, increased TG2 enzyme activity, and no significant change in TG2-S levels, with increased cell survival. These findings suggest a subtype-specific regulatory effect of RA in cisplatin-surviving MCF-7 cells, with TG2-L upregulated at higher RA concentrations, potentially contributing to altered cisplatin sensitivity. Anti-TG2 siRNA silencing reduced cisplatin IC50 to base levels in both wild-type and cisplatin-surviving MCF-7 cells, supporting the notion that the modulation of TG2 expression could offer a significant benefit to cisplatin efficacy. Preventing excessive retinoic acid exposure may also be a mechanism for maximising cisplatin efficacy, considering TG2 modulation.

Keywords:  MCF-7; breast cancer; cisplatin; dietary retinoids; transglutaminase 2

DOI:  https://doi.org/10.3390/ijms26168101
Cancer Res. 2025 Aug 27.

Malonyl-CoA Promotes Prostate Cancer Progression and Castration Resistance by Enhancing Lipogenesis and Ran Activation.

Yiheng Dai, Lilong Liu, Yongbo Luo, Cai Zhang, Sayu Xiao, Kaixuan Du, Yuanhao Liu, Youmiao Zeng, Zhengfeng Wang, Zhaohui Chen, Ke Chen, Lijie Zhou.

Malonyl-CoA, a key metabolite, is not only the building block for lipogenesis, but also a critical regulator of mitochondrial fatty acid (FA) β-oxidation. Given the altered metabolic state of many cancers, malonyl-CoA may play a role in tumor development and drug resistance, especially in malignancies characterized by abnormal lipid metabolism, such as prostate cancer (PCa). Here, we showed that the levels of malonyl-CoA were increased in PCa, especially in castration-resistant prostate cancer (CRPC). Abnormal accumulation of malonyl-CoA promoted lipogenesis and regulated metabolic processes, maintaining endoplasmic reticulum (ER) homeostasis and mitochondrial function and ultimately contributing to PCa progression. Restoration of malonyl-CoA decarboxylase (MLYCD) expression activated the unfolded protein response via the consumption of malonyl-CoA. Importantly, malonyl-CoA accumulation promoted lysine malonylation in PCa. Ran K141 malonylation increased Ran activity and enhanced androgen receptor nuclear translocation and transcriptional activity, ultimately contributing to PCa development and resistance to antiandrogens. These findings highlight the function of malonyl-CoA in PCa progression by regulating metabolic processes and malonylating Ran K141, revealing that the malonyl-CoA axis might be a reliable biomarker and a potential therapeutic target in PCa.

DOI: https://doi.org/10.1158/0008-5472.CAN-24-4247
Nat Chem. 2025 Aug 20.

Nucleoside diphosphate kinase A (NME1) catalyses its own oligophosphorylation.

Arif Celik, Felix Schöpf, Christian E Stieger, Sarah Lampe, Björn Hanf, Jeremy A M Morgan, Max Ruwolt, Fan Liu, Christian P R Hackenberger, Daniel Roderer, Dorothea Fiedler.

Protein phosphorylation is a central signalling mechanism in eukaryotic cells. The scope of this post-translational modification includes protein pyro- and polyphosphorylation. Here we report the discovery of another mode of phosphorylation: protein oligophosphorylation. Using site-specifically phosphorylated and pyrophosphorylated nucleoside diphosphate kinase A (NME1), the effects of these modifications on enzyme activity were investigated. Phosphorylation, and more so pyrophosphorylation, on Thr94 reduced the nucleoside diphosphate kinase activity. Nevertheless, both phosphoprotein and pyrophosphoprotein catalysed their own oligophosphorylation-up to the formation of a hexaphosphate chain-using ATP as a cofactor. Oligophosphorylation was critically dependent on the catalytic histidine residue His118, and cryogenic electron microscopy analysis of the modified proteins suggests an intramolecular phosphoryl transfer mechanism. Oligophosphorylation of NME1 in biochemical samples, and in cell lysates, was further confirmed using mass spectrometry, and was found to promote a new set of protein interactions. Our results highlight the complex nature of phosphoregulation, and the methods described here provide the opportunity to investigate the impact of this unusual modification in the future.

DOI: https://doi.org/10.1038/s41557-025-01915-8
J Proteome Res. 2025 Aug 20.

Metabolite Functions Revealed by Mass Spectrometry-Based Target Engagement Proteomics Approaches.

Nisha A Owens, Tayah B Sommer, Brenna G Ing, Mukhayyo Sultonova, J Patrick Murphy.

  In addition to their roles in energetics and biosynthesis, endogenous metabolites have functional roles performed in part through protein interactions that result in allosteric regulation, transcriptional regulation, and post-translational modifications. Novel bioactive roles for metabolites continue to emerge in cancer progression, immune response, and host-pathogen interactions. Defining metabolite-protein interactions will further reveal bioactive metabolite downstream effects and help to characterize the intersection between the metabolome and the proteome. Here, we summarize recently revealed secondary functions for metabolites that have been uncovered by mass spectrometry-based approaches for small molecule target engagement. We propose that further developments and application of these approaches will greatly advance our understanding of metabolite functions and may facilitate large-scale metabolome-proteome interaction networks that harbor new targets for diseases such as cancer.

Keywords:  mass spectrometry; metabolite-protein interactions; metabolome; proteome; target engagement techniques

DOI:  https://doi.org/10.1021/acs.jproteome.5c00341