bims-cesirm 2025-06-15 papers

bims-cesirm

Biomed News

on Cell Signaling mediated regulation of metabolism

Issue of 2025–06–15
twenty-six papers selected by
Tigist Tamir, University of North Carolina

PFKFB2 is Pivotal for Metabolic Flexibility and Differential Glucose Utilization.
Metabolic reprogramming in hepatocellular carcinoma: an integrated omics study of lipid pathways and their diagnostic potential.
Insulin- and exercise-induced phosphoproteomics of human skeletal muscle identify REPS1 as a regulator of muscle glucose uptake.
Differential Role of Phosphorylation in Glucagon Family Receptor Signaling Revealed by Mass Spectrometry.
Apatinib modulates sorafenib-resistant hepatocellular carcinoma through inhibiting the EGFR/JNK/ERK signaling pathway.
PBX3-HMGCR Axis Promotes Hepatocellular Carcinoma Progression Through Enhancing De Novo Cholesterol Biosynthesis.
Metabolic Reprogramming Triggered by Fluoride in U-87 Glioblastoma Cells: Implications for Tumor Progression?
Steatotic liver disease induces YAP/TAZ-driven cell competition that can suppress tumor initiation.
Pathway Analysis Utilizing Metabolomic and Proteomic Datasets.
A Chemical Mechanistic Path Leads the Way to Cellular Argpyrimidine.
Metabolic Pathway Tracing for NAD+ Synthesis and Consumption.
The intersection between metabolism and translation through a subcellular lens.
RNF213-Dependent EGFR and HER2 Activation Regulates Specific Downstream Signaling Pathways in Human Cancer Cells.
PTPN2 inhibits TG-induced ERS-initiated TNBC apoptosis through the mitochondrial pathway.
A Biological-Systems-Based Analyses Using Proteomic and Metabolic Network Inference Reveals Mechanistic Insights into Hepatic Lipid Accumulation: An IMI-DIRECT Study.
2,5-Dihydroxybenzoic Acid Ameliorates Metabolic Dysfunction-Associated Steatotic Liver Disease by Targeting the CCL2-CCR2 Axis to Reduce Lipid Accumulation.
Cold exposure stimulates cross-tissue metabolic rewiring to fuel glucose-dependent thermogenesis in brown adipose tissue.
Alleviation of metabolic dysfunction-associated steatotic liver disease by silymarin is associated with maintaining mitochondrial homeostasis via regulation of optic atrophy 1.
Endarachne binghamiae Ameliorates Hepatic Steatosis, Obesity, and Blood Glucose via Modulation of Metabolic Pathways and Oxidative Stress.
Targeting the leptin receptor promotes MDA-MB-231 cells' metabolic reprogramming and malignancy: the role of extracellular vesicles derived from obese adipose tissue.
Analysis of isobaric quantitative proteomic data using TMT-Integrator and FragPipe computational platform.
Histone and non-histone lactylation: molecular mechanisms, biological functions, diseases, and therapeutic targets.
Global Landscape of Human Kinase Motifs in Viral Proteomes.
Tumorous cholesterol biosynthesis curtails anti-tumor immunity by preventing MTOR-TFEB-mediated lysosomal degradation of CD274/PD-L1.
Elevation of hepatic de novo lipogenesis in mice with overnutrition is dependent on multiple substrates.
Cell death and cancer: Metabolic interconnections.

bioRxiv. 2025 May 27. pii: 2025.05.26.656235. [Epub ahead of print]

PFKFB2 is Pivotal for Metabolic Flexibility and Differential Glucose Utilization.

Kylene M Harold, Satoshi Matsuzaki, Atul Pranay, Jie Zhu, Anna Faakye, Kenneth M Humphries.

Background: The heart's constant energy demands make metabolic flexibility critical to its function as nutrient availability varies. The enzyme phosphofructokinase-2/fructose 2,6-bisphosphatase (PFKFB2) contributes to this flexibility by acting as a positive or negative regulator of cardiac glycolysis. We have previously shown that PFKFB2 is degraded in the diabetic heart and that a cardiac-specific PFKFB2 knockout (cKO) impacts ancillary glucose pathways and mitochondrial substrate preference. Therefore, defining PFKFB2's role in mitochondrial metabolic flexibility is paramount to understanding both metabolic homeostasis and metabolic syndromes. Further, it is unknown how PFKFB2 loss impacts the heart's response to acute stress. Here we examined how cardiac mitochondrial flexibility and the post-translational modification O-GlcNAcylation are affected in cKO mice in response to fasting or pharmacologic stimulation.
Methods: cKO and litter-matched controls (CON) were sacrificed in the fed or fasted (12 hours) states, with or without a 20 minute stimulant stress of caffeine and epinephrine.Mitochondrial respiration, metabolomics, and changes to systemic glucose homeostasis were evaluated.
Results: cKO mice had moderate impairment in mitochondrial metabolic flexibility, affecting downstream glucose oxidation, respiration, and CPT1 activity. O-GlcNAcylation, a product of ancillary glucose metabolism, was upregulated in cKO hearts in the fed state, but this was ameliorated in the fasted state. Furthermore, metabolic remodeling in response to PFKFB2 loss was sufficient to impact circulating glucose in fasted and stressed states.
Conclusions: PFKFB2 is essential for fed-to-fasted changes in cardiac metabolism and plays an important regulatory role in protein O-GlcNAcylation. Its loss also affects systemic glucose homeostasis under stressed conditions.
Graphic Abstract:
Research Perspective: This study raises and answers three key questions: how PFKFB2 contributes to cardiac mitochondrial metabolic flexibility, how post-prandial status regulates O-GlcNAcylation in a PFKFB2-dependent manner, and how altered cardiac glucose use impacts systemic glucose homeostasis under stress.These findings highlight a novel role for nutrient state in regulating cardiac metabolism, and especially O-GlcNAcylation, with PFKFB2 loss.Future studies should investigate whether reducing O-GlcNAcylation through fasting is sufficient to ameliorate pathological changes observed in the absence of PFKFB2.

DOI: https://doi.org/10.1101/2025.05.26.656235
J Transl Med. 2025 Jun 11. 23(1): 644

Metabolic reprogramming in hepatocellular carcinoma: an integrated omics study of lipid pathways and their diagnostic potential.

Peng Dai, Jing Feng, Yanyan Dong, Shujing Zhang, Jianghong Cao, Xiaopeng Cui, Xueliang Qin, Shiming Yang, Daguang Fan.

  Metabolic reprogramming is an important cancer hallmark. Recent studies have indicated that lipid metabolic reprogramming play a potential role in the development of hepatocellular carcinoma (HCC). However, the underlying mechanisms remain incompletely understood. In this study, we employed an integrated multi-omics approach, combining transcriptomic, proteomic, and metabolomic analyses, to explore the lipid metabolism pathways in HCC and evaluate their diagnostic potential.We collected ten pairs of HCC tissues (HCT) and adjacent non-tumor tissues (ANT) from patients undergoing surgical resection. Transcriptomic analysis identified 4,023 differentially expressed genes (DEGs) between HCT and ANT, with significant enrichment in lipid metabolism-related pathways, including fatty acid degradation and steroid hormone biosynthesis. Proteomic analysis revealed 2,531 differentially expressed proteins (DEPs), further highlighting lipid metabolism as a critical driver of HCC development. Metabolomic profiling identified 88 differentially expressed metabolites (DEMs), with notable alterations in lipid-related metabolites. Integrated analysis of transcriptomic, proteomic, and metabolomic data identified six key genes (LCAT, PEMT, ACSL1, GPD1, ACSL4, and LPCAT1) involved in lipid metabolism, which exhibited significant changes at both mRNA and protein levels and correlated strongly with lipid-related metabolites in HCT. Additionally, nine lipid-related metabolites were identified as potential diagnostic biomarkers for HCC, with six metabolites demonstrating high discriminative ability (AUC > 0.8) between HCT and ANT.Our findings provide new insights into the molecular mechanisms of lipid metabolism reprogramming in HCC, emphasize the critical role of lipid metabolism in its pathogenesis. The identification of lipid-related metabolites as potential diagnostic biomarkers holds significant promise for early detection and improved clinical management of HCC. The integrated multi-omics approach as a powerful tool for identifying novel biomarkers and therapeutic targets.

Keywords:  Diagnostic biomarkers; Hepatocellular carcinoma (HCC); Lipid metabolism; Metabolic reprogramming; Multi-omics analysis

DOI:  https://doi.org/10.1186/s12967-025-06698-7
Cell Rep Med. 2025 May 29. pii: S2666-3791(25)00236-8. [Epub ahead of print] 102163

Insulin- and exercise-induced phosphoproteomics of human skeletal muscle identify REPS1 as a regulator of muscle glucose uptake.

Jeppe Kjærgaard, Cecilie B Lindqvist, Júlia Prats Quesada, Søren Jessen, Farina Schlabs, Amy M Ehrlich, Caio Y Yonamine, Mario García-Ureña, Johann H Schmalbruch, Lewin Small, Martin Thomassen, Anders Krogh Lemminger, Kasper Eibye, Alba Gonzalez-Franquesa, Jacob V Stidsen, Kurt Højlund, Juleen R Zierath, Tuomas O Kilpeläinen, Jens Bangsbo, Jonas T Treebak, Morten Hostrup, Atul S Deshmukh.

  Skeletal muscle glucose uptake, essential for metabolic health, is regulated by both insulin and exercise. Using phosphoproteomics, we analyze skeletal muscle from healthy individuals following acute exercise or insulin stimulation, generating a valuable dataset. We identify 71 phosphosites on 55 proteins regulated by both stimuli in the same direction, suggesting a convergence of exercise and insulin signaling pathways. Among these, the vesicle-associated protein, REPS1, is highly phosphorylated at Ser709 in response to both stimuli. We identify p90 ribosomal S6 kinase (RSK) to be a key upstream kinase of REPS1 S709 phosphorylation and that the RSK-REPS1 signaling axis is involved in insulin-stimulated glucose uptake. Insulin-induced REPS1 Ser709 phosphorylation is closely linked to muscle and whole-body insulin sensitivity and is impaired in insulin-resistant mice and humans. These findings highlight REPS1 as a convergence point for insulin and exercise signaling, presenting a potential therapeutic target for treating individuals with insulin resistance.

Keywords:  REPS1; RSK; exercise; glucose metabolism; insulin; phosphoproteomics; skeletal muscle signaling

DOI:  https://doi.org/10.1016/j.xcrm.2025.102163
J Proteome Res. 2025 Jun 12.

Differential Role of Phosphorylation in Glucagon Family Receptor Signaling Revealed by Mass Spectrometry.

Ian M Lamb, Alex D White, Francis S Willard, Michael J Chalmers, Junpeng Xiao.

  In response to extracellular ligands, G protein-coupled receptors (GPCRs) undergo conformational changes that induce coupling to intracellular effectors such as heterotrimeric G proteins that trigger various downstream signaling pathways. These events have been shown to be highly regulated by concerted effects of post-translational modifications (PTMs) that occur in a ligand-dependent manner. Most notably, phosphorylation of residues in the C-terminal cytoplasmic tail of GPCRs has been strongly implicated in promoting receptor interactions with β-arrestins (βarrs), which are cytosolic adaptor proteins that modulate G protein coupling, receptor internalization, and perhaps also serve as signaling modules in their own right. Here, we use proteomic methods to identify C-tail residues that are phosphorylated in the glucagon family of class B1 GPCRs (GLP-1R, GCGR, and GIPR) upon agonist addition. We demonstrate that the phosphorylation of GLP-1R and GIPR is a critical determinant in the formation of GPCR-βarr complexes. However, our results suggest that ligand-induced βarr recruitment to GCGR proceeds in a phosphorylation-independent manner. These findings highlight the importance of recognizing phosphorylation as a component in the regulation of class B1 GPCR signaling but also the need to consider how such phenomena may not necessarily yield identical effects on intracellular signaling cascades.

Keywords:  GPCRs; bottom-up proteomics; cell signaling; cyclic AMP; glucagon; mass spectrometry; middle-down proteomics; phosphorylation; β-arrestin

DOI:  https://doi.org/10.1021/acs.jproteome.5c00079
Oncol Res. 2025 ;33(6): 1459-1472

Apatinib modulates sorafenib-resistant hepatocellular carcinoma through inhibiting the EGFR/JNK/ERK signaling pathway.

Dexue Fan, Wei Su, Zhaowen Bi, Xinxing Wang, Xianwen Xu, Mingze Ma, Lichao Zhu, Zhenhai Zhang, Junlin Gao.

   Objectives: Apatinib has been reported to be a promising treatment for sorafenib-resistant hepatocellular carcinoma (HCC) patients. However, the underlying mechanism remains ambiguous. The study aimed to explore the efficacy of apatinib in sorafenib-resistant HCC and the underlying mechanism both in vitro and in vivo.
Methods: After observing epithelial-mesenchymal transformation (EMT) changes in HepG2 and HepG2/Sorafenib cells, we treated them with varying concentrations of apatinib to assess its impact on sorafenib-resistant HCC. Subsequently, specific inhibitors of c-Jun N-terminal kinase (JNK, SP600125) and extracellular signal-regulated kinase (ERK, PD98059) were introduced to investigate whether apatinib influenced sorafenib-resistant HCC via modulation of the epidermal growth factor receptor (EGFR)/JNK/ERK signaling pathway in vitro and in vivo. Biological behavior changes were assessed through cell counting kit-8 (CCK-8), colony formation, transwell, and immunofluorescence tests. Simultaneously, Western blot analysis was conducted to elucidate the expression of proteins associated with EMT and the EGFR/JNK/ERK signaling pathway.
Results: The HepG2/Sorafenib cells exhibited greater resistance to sorafenib compared to HepG2 cells, and sorafenib-resistant HCC was characterized by EMT changes. Apatinib demonstrated concentration-dependent inhibition of biological behaviors in HepG2/Sorafenib cells, with minimal impact on HepG2 cells. Additionally, apatinib had a pronounced effect on the expression of EMT-related proteins in sorafenib-resistant cells similar to that in sorafenib-sensitive cells. Furthermore, there was a dose-dependent reduction in the expression of proteins associated with the EGFR/JNK/ERK pathway in apatinib-treated groups. Notably, SP600125 and PD98059 contributed to the inhibition of EMT and EGFR/JNK/ERK pathway-related proteins by apatinib in sorafenib-resistant HCC.
Conclusion: Apatinib potentially hindered the progression of sorafenib-resistant HCC by suppressing both EMT and the EGFR/JNK/ERK pathway.

Keywords:  Apatinib; EGFR/JNK/ERK; Epithelial mesenchymal transformation; Hepatocellular carcinoma (HCC); Sorafenib resistance

DOI:  https://doi.org/10.32604/or.2025.060407
Int J Mol Sci. 2025 May 29. pii: 5210. [Epub ahead of print]26(11):

PBX3-HMGCR Axis Promotes Hepatocellular Carcinoma Progression Through Enhancing De Novo Cholesterol Biosynthesis.

Xia Zhang, Li Qiu, Lei Zhang, Wenfang Li, Debing Xiang, Jian Wang, Shourong Wu, Vivi Kasim.

  Tumor cells alter lipid metabolic pathways to meet their demands for energy and membrane biosynthesis. Despite its crucial role in tumor cell growth, survival, and metastasis, the mechanisms underlying tumor cell lipid metabolic reprogramming remain poorly understood. Pre-B-cell leukemia transcription factor 3 (PBX3), a member of the PBX family, could promote tumorigenesis; however, whether it is involved in tumor lipid metabolic reprogramming remains unknown. Herein, we found that PBX3 significantly promotes tumor growth by enhancing lipid accumulation in HCC cells. By assessing the effect of PBX3 on the expression levels of lipid metabolism-related genes, we found that PBX3 could positively regulate the expression of 3-hydroxy-3-methylglutaryl CoA reductase (HMGCR), a rate-limiting enzyme in the cholesterol biosynthesis pathway. Mechanistically, we revealed that PBX3 could directly bind to the -167/-151 region of HMGCR promoter, thereby increasing its transcriptional activity and, subsequently, its expression level. This leads to the increase of HCC cell cholesterol biosynthesis and, eventually, to the increase of the in vivo tumorigenic potential. Collectively, our research revealed an unprecedented regulatory mechanism of cholesterol metabolism in HCC cells through PBX3 positive regulation on HMGCR expression levels. These findings provide novel insights into tumor metabolic reprogramming and uncover a previously unknown physiological function for PBX3. Moreover, these results suggest the potential of targeting PBX3 as an anti-tumor therapeutic strategy.

Keywords:  HMGCR; PBX3; cholesterol biosynthesis; lipid metabolism; tumor metabolic reprogramming

DOI:  https://doi.org/10.3390/ijms26115210
Cells. 2025 May 29. pii: 800. [Epub ahead of print]14(11):

Metabolic Reprogramming Triggered by Fluoride in U-87 Glioblastoma Cells: Implications for Tumor Progression?

Wojciech Żwierełło, Agnieszka Maruszewska, Marta Skórka-Majewicz, Agata Wszołek, Izabela Gutowska.

  Chronic inflammation is a hallmark of brain tumors, especially gliomas, which exhibit elevated levels of pro-inflammatory mediators within the tumor and its microenvironment. Metabolic disturbances triggered by fluoride as a pro-oxidative agent in glioma cells, known for their high aggressiveness and resistance to therapy-remain poorly understood. Therefore, investigating the impact of physiologically elevated fluoride concentrations on oxidative stress and pro-inflammatory responses in glioma cells represents a relevant and timely research objective.
METHODS: U-87 human glioblastoma cells were subjected to short-term and long-term exposure to physiologically high concentrations of NaF (0.1-10 µM). Both the cells and the culture medium were analyzed. We assessed levels of reactive oxygen species (ROS), antioxidant defenses, and a panel of cytokines and chemokines.
RESULTS: Our results demonstrated that oxidative stress and inflammatory conditions in U-87 cells varied with fluoride concentration and exposure time. This led to an increase in ROS levels and key pro-inflammatory cytokines, including IL-6 and TNF-α.
CONCLUSIONS: Fluoride compounds can generate ROS and disrupt the antioxidant defense system in U-87 human glioblastoma cells, leading to the initiation and progression of inflammatory states. Furthermore, prolonged exposure to NaF may induce adaptive mechanisms in U-87 cells.

Keywords:  fluorides; gliomas; inflammation; oxidative stress; tumor microenvironment

DOI:  https://doi.org/10.3390/cells14110800
J Hepatol. 2025 Jun 06. pii: S0168-8278(25)02263-9. [Epub ahead of print]

Steatotic liver disease induces YAP/TAZ-driven cell competition that can suppress tumor initiation.

Ana Algueró-Nadal, Hasse Mol, Elena Zoppolato, Weronika Kowalczyk, Leticia Sansores-García, Soheil Soheily, Hanne Hillen, Leen van Huffel, Matthias Van Haele, Marina Corral-Ibáñez, Dorothea Katharina Hoffelner, Leo A van Grunsven, Tania Roskams, Olivier Govaere, Iván M Moya, Georg Halder.

   BACKGROUND & AIMS: Metabolic dysfunction-associated steatotic liver disease (MASLD) and its progressive form, metabolic dysfunction-associated steatohepatitis (MASH), are leading risk factors for liver cancer. While inflammation and fibrosis are known to promote tumorigenesis in advanced MASH, it remains unclear how earlier stages of MASLD contribute to cancer initiation. Here, we investigated how steatosis alone, in the absence of significant fibrosis and inflammation, influences liver cancer development in mouse models.
METHODS: We fed mice a Western diet to induce early-stage MASLD, characterized by steatosis and mild hepatitis without fibrosis. We triggered liver tumorigenesis by hydrodynamic tail vein injection of plasmids encoding oncogenes. We combined this with genetic manipulation of Hippo signaling and assessed tumor development by histology and single-nucleus RNA-sequencing.
RESULTS: Western diet suppressed liver tumor development by promoting the elimination of tumor-initiating cells. This effect was not due to a direct impact on oncogene-expressing cells, but rather to increased competitiveness of the surrounding hepatocytes. Mechanistically, the Western diet activated the Hippo pathway effectors Yap and Taz in steatotic hepatocytes, enhancing their cellular fitness and enabling them to outcompete tumor-initiating cells. The progression to advanced MASH abrogated this tumor-suppressing mechanism thus allowing tumor development.
CONCLUSIONS: These findings reveal that steatotic hepatocytes in early MASLD can activate endogenous cell competition programs to suppress tumor initiation, a process that depends on Yap/Taz activity. This adds a new layer to our understanding of how fitness landscapes and cell-to-cell interactions within the tissue microenvironment shape cancer risk. It also shows that progression of chronic liver disease not only promotes tumorigenesis through effects of inflammation and fibrosis on tumor cells but also by disrupting the competitive defenses of normal surrounding cells.
IMPACT AND IMPLICATIONS: We found that early stages of steatotic liver disease (MASLD) can suppress tumor initiation in mouse models of liver cancer by triggering Yap/Taz-mediated cell competition. This reveals an unexpected tumor-suppressive role for early MASLD and highlights the importance of non-cell autonomous mechanisms during tumor initiation. Since Hippo-YAP/TAZ signaling is deregulated in many cancers, similar cell competition-based mechanisms may operate in other tissues.

Keywords:  HCC; Hippo pathway; MASH; MASLD; cell competition; fibrosis; steatosis; tumorigenesis

DOI:  https://doi.org/10.1016/j.jhep.2025.06.002
Methods Mol Biol. 2025 ;2925 121-131

Pathway Analysis Utilizing Metabolomic and Proteomic Datasets.

Guoqiang Zhu, Molly Kennedy, Sanjoy K Bhattacharya.

  Pathway analysis of metabolomic and proteomic data is critical for understanding the intricacies of biological processes and disease mechanisms. The challenging process of pathway analysis has become less burdensome thanks to online tools and databases that enable the comparison of pathways in intricate biological systems. Data analysis tools, like MetaboAnalyst 6.0, evaluate complex interactions and metabolic networks in biological pathways. Metabolomic and proteomic data integration is performed by utilizing databases, like KEGG, to analyze pathways and determine the interplay of proteins, metabolites, and other molecules in common pathways. Molecular interactions and similarities between pathways are explored to promote hypothesis generation and guide further research. This comprehensive chapter will enhance the understanding of utilizing pathway analysis of metabolic and proteomic data of various conditions, biomarkers, organisms, and therapeutic molecular targets, paving the way for future investigations and clinical applications, especially in pharmacology. Drugs like Metformin can be studied more extensively with pathway analysis, as demonstrated in this chapter, to enhance our understanding of how drugs affect patients.

Keywords:  Compound discoverer; MetaboAnalyst; Metabolomics; Pathway analysis; Proteome discoverer; Proteomics

DOI:  https://doi.org/10.1007/978-1-0716-4534-5_8
bioRxiv. 2025 May 30. pii: 2025.05.30.657038. [Epub ahead of print]

A Chemical Mechanistic Path Leads the Way to Cellular Argpyrimidine.

Vo Tri Tin Pham, Suprama Datta, Amy C Sterling, Stefan M Hansel, Rebecca A Scheck.

Argpyrimidine (APY) is a methylglyoxal-derived advanced glycation end-product (AGE) that has been associated with multiple diseases. As APY formation occurs without an enzyme, it remains exceptionally difficult to pinpoint where APY is likely to be found, both on individual proteins and in cells. In this study, we used a peptide model system and mass spectrometry analysis to investigate the chemical mechanism through which APY forms from methylglyoxal (MGO), a biologically relevant glycating agent. Consistent with other proposed APY formation mechanisms, our results show that that another AGE, tetrahydropyrimidine (THP) is a direct precursor to APY. However, our results rule out previously proposed reductone or oxidative decarboxylation mechanisms. Instead, we show that a formal oxidation step is not required, and that formate, not CO 2 is released. We further show the potential for a nearby residue such as Tyr to assist in the APY formation mechanism by acting as a general base. These experiments revealed that phosphorylated Tyr or Ser residues could also promote equivalent levels of APY formation, despite introducing additional negative charges that we previously showed to impede glycation. Guided by these mechanistic insights and newly defined role for phosphorylated residues on glycation substrates, we performed quantitative bottom-up proteomics analysis for MGO-treated cells. Gene ontology analysis for AGE-modified proteins revealed significant enrichment of phosphorylation-related terms (e.g. kinase activity or protein phosphorylation) for APY, while other Arg post-translational modifications did not. Collectively, these data define a chemical mechanistic path to APY and suggest significant crosstalk between cellular phosphorylation and glycation events including APY formation.

DOI: https://doi.org/10.1101/2025.05.30.657038
Methods Mol Biol. 2025 ;2925 203-222

Metabolic Pathway Tracing for NAD+ Synthesis and Consumption.

Tumpa Dutta, Stephen J Gardell.

  NAD+ is an abundant cellular metabolite which plays vital roles in central metabolism while serving as a cofactor for oxidoreductases and cosubstrate for sirtuins and poly(ADP-ribose)polymerases (PARPs). Decreased tissue NAD+ levels have been linked to aging-associated metabolic decline and a host of chronic diseases. Cellular steady-state NAD+ levels are governed by contemporaneous synthetic and consumptive processes. Hence, lower NAD+ levels in aged tissues can arise from decreased synthesis or increased consumption. A static snapshot of the tissue levels of NAD+ is inadequate for assessing the highly dynamic pathway network which mediates NAD+ synthesis and consumption. Metabolic pathway tracing with stable isotope-labeled NAD+ precursors (e.g., nicotinamide (NAM), nicotinic acid (NA), tryptophan) and high-resolution mass spectrometry (HRMS) can unveil the individual contributions of synthesis and consumption to the steady-state NAD+ concentration. The metabolic fate of the NAD+ precursor can also be traced to metabolic products of NAD+ including NADH, NADP, and NADPH as well as intermediates in the various NAD+ biosynthetic pathways. Metabolic tracing of NAD+ synthesis and degradation as well as conversion of NAD+ to its downstream products is a highly versatile technique. It can be used to interrogate isolated cells, tissues slices, or specimens collected from preclinical or clinical in vivo studies (e.g., blood, urine, tissues). Bold claims about the pivotal role of NAD+ in human health and disease are typically fraught with uncertainty due to an incomplete understanding of NAD+ metabolism. Insight gleaned from metabolic pathway tracing can shed important new light on NAD+ metabolism and help to critically evaluate the intriguing link between cellular NAD+ levels and healthy aging.

Keywords:  Mass isotopomer distribution profiling; Mass spectrometry; NAD+ consumption; NAD+ flux; NAD+ metabolism; NAD+ synthesis; Stable isotope tracing

DOI:  https://doi.org/10.1007/978-1-0716-4534-5_14
Trends Cell Biol. 2025 Jun 09. pii: S0962-8924(25)00113-8. [Epub ahead of print]

The intersection between metabolism and translation through a subcellular lens.

Massimo M Santoro.

  The crosstalk between metabolism and mRNA translation (protein synthesis) is crucial for modulating cellular physiology. Signals from metabolic pathways or various metabolic states can influence multiple aspects of RNA biology and translation machinery. In turn, cells can reprogram their metabolism by controlling mRNA translation. Current studies have revealed that localized mRNA translation is specifically regulated by distinct metabolic states, suggesting the existence of specialized subcellular machinery that coordinates this interplay. This review aims to explore recent discoveries and provide an overview of the specialized methodologies developed in recent years on novel modes of translation-metabolism cross-regulation by subcellular localized cues. Spatial compartmentalization, especially in the context of metabolism and mRNA translation, offers a unique advantage, providing a novel mechanism for cellular regulation and function.

Keywords:  RNA condensate; glycolysis; mRNA translation; mTOR signaling; metabolism; organelles; stress granules

DOI:  https://doi.org/10.1016/j.tcb.2025.05.003
Genes Cells. 2025 Jul;30(4): e70033

RNF213-Dependent EGFR and HER2 Activation Regulates Specific Downstream Signaling Pathways in Human Cancer Cells.

Intisar M Fouad, Jungmi Choi, Qianying Huang, Minsoo Kim, Seiji Masuda, James A Hejna, Yohei Mineharu, Akio Koizumi, Tohru Tezuka, Shohab Youssefian.

  In this study, we reveal a novel relationship between RNF213, an E3 ubiquitin ligase associated with Moyamoya disease (MMD) and the ubiquitination of both endogenous and pathogenic substrates, and EGFR, the epithelial growth factor receptor involved in cell growth, angiogenesis, and cancer. RNF213 knockdown or knockout in HeLa and A549 cells markedly reduces EGFR phosphorylation at key tyrosine sites following EGF and TGFα stimulation. In RNF213 knockout cells, HER2 phosphorylation, typically activated through heterodimerization with EGFR, and Src recruitment and/or phosphorylation are also diminished. Mutations in the RNF213 RING, RZ finger, or AAA+ domains, including the prevalent R4810K mutation in MMD, consistently reduce EGFR phosphorylation. In vivo, EGF injections increase EGFR and HER2 phosphorylation in WT but not in RNF213 knockout mice. Despite the reduced phosphorylation levels of these tyrosine kinases in knockout cells, the activation of downstream signals such as AKT, ERK1/2, and STAT3 remains unaffected, although phosphorylation of PLCγ, a key mediator of Ca2+ release, is selectively reduced by RNF213 knockout. These findings demonstrate that RNF213 modulates EGFR-related pathways and specific downstream signal pathways, possibly affecting physiologic and pathogenic angiogenesis, and may have implications for unraveling the etiology of MMD and for developing cancer therapies that target RNF213.

Keywords:  EGFR; HER2; Moyamoya disease; PLCγ; RNF213; Src; angiogenesis; cancer; phosphorylation; vasculopathy

DOI:  https://doi.org/10.1111/gtc.70033
Sci Rep. 2025 Jun 06. 15(1): 19896

PTPN2 inhibits TG-induced ERS-initiated TNBC apoptosis through the mitochondrial pathway.

Yanhe An, Jinxin Lan, Jiaping Tang, Na Luo.

  Triple negative breast cancer (TNBC) is the most malignant subtype of breast cancer that portends a poor prognosis and limited treatment. PTPN2 is a member of the non-receptor protein tyrosine phosphatase family that regulates biological processes by dephosphorylating various signaling molecules. Endoplasmic reticulum stress (ERS) plays a dual regulatory role by promoting both survival and apoptosis. This study aims to elucidate the role of PTPN2 in mediating the pro-apoptotic effects of ERS induced by Thapsigargin (TG), and its influence on the fate of TNBC cells, utilizing both loss-of-function and gain-of-function methodologies. Our findings indicate that PTPN2 modulates TG-induced ERS via the IRE1-XBP1 and PERK/EIF2α/ATF-4 signaling pathways. Furthermore, PTPN2 mitigates the TG-induced reduction in cell proliferation and the concomitant increase in apoptosis. Specifically, PTPN2 appears to inhibit several facets of TG-induced apoptosis, including: (1) Ca2+ elevation in mitochondria, (2) the production of reactive oxygen species (ROS), and (3) Bax/Bcl-2 augmentation which dictates mitochondria-mediated apoptosis. Additionally, we observed that the knockdown of PTPN2 enhances TG-induced autophagy; however, our results suggest that autophagy may serve a protective role against TG-induced apoptosis. Consequently, targeting PTPN2 in conjunction with ERS-inducing agents may represent a promising therapeutic strategy for the treatment of TNBC.

Keywords:  Apoptosis; ERS; PTPN2; TNBC; The mitochondrial pathway

DOI:  https://doi.org/10.1038/s41598-025-04312-w
medRxiv. 2025 Jun 02. pii: 2025.06.02.25328773. [Epub ahead of print]

A Biological-Systems-Based Analyses Using Proteomic and Metabolic Network Inference Reveals Mechanistic Insights into Hepatic Lipid Accumulation: An IMI-DIRECT Study.

Natalie N Atabaki, Daniel E Coral, Hugo Pomares-Millan, Kieran Smith, Harry H Behjat, Robert W Koivula, Andrea Tura, Hamish Miller, Katherine Pinnick, Leandro Agudelo, Kristine H Allin, Andrew A Brown, Elizaveta Chabanova, Piotr J Chmura, Ulrik P Jacobsen, Adem Y Dawed, Petra J M Elders, Juan J Fernandez-Tajes, Ian M Forgie, Mark Haid, Tue H Hansen, Elizaveta L Hansen, Angus G Jones, Tarja Kokkola, Sebastian Kalamajski, Anubha Mahajan, Timothy J McDonald, Donna McEvoy, Mirthe Muilwijk, Konstantinos D Tsirigos, Jagadish Vangipurapu, Sabine van Oort, Henrik Vestergaard, Jerzy Adamski, Joline W Beulens, Søren Brunak, Emmanouil T Dermitzakis, Giuseppe N Giordano, Ramneek Gupta, Torben Hansen, Leen T Hart, Andrew T Hattersley, Leanne Hodson, Markku Laakso, Ruth J F Loos, Jordi Merino, Mattias Ohlsson, Oluf Pedersen, Martin Ridderstråle, Hartmut Ruetten, Femke Rutters, Jochen M Schwenk, Jeremy Tomlinson, Mark Walker, Hanieh Yaghootkar, Fredrik Karpe, Mark I McCarthy, Elizabeth Louise Thomas, Jimmy D Bell, Andrea Mari, Imre Pavo, Ewan R Pearson, Ana Viñuela, Paul W Franks.

Objective: To delineate organ-specific and systemic drivers of metabolic dysfunction-associated steatotic liver disease (MASLD), we applied integrative causal inference across clinical, imaging, and proteomic domains in individuals with and without type 2 diabetes (T2D).
Research Design and Methods: We used Bayesian network analyses to quantify causal pathways linking adipose distribution, glycemia, and insulin dynamics with fatty liver using data from the IMI-DIRECT prospective cohort study. Measurements were made of glucose and insulin dynamics (using frequently-sampled metabolic challenge tests), MRI-derived abdominal and liver fat content, serological biomarkers, and Olink plasma proteomics from 331 adults with new-onset T2D and 964 adults free from diabetes at enrolment. The common protocols used in these two cohorts provided the opportunity for replication analyses to be performed. When the direction of the effect could not be determined with high probability through Bayesian networks, complementary two-sample Mendelian randomization (MR) was employed.
Results: High basal insulin secretion rate (BasalISR) was identified as the primary causal driver of liver fat accumulation in both diabetes and non-diabetes. Excess visceral adipose tissue (VAT) was bidirectionally associated with liver fat, indicating a self-reinforcing metabolic loop. Basal insulin clearance (Clinsb) worsened as a consequence of liver fat accumulation to a greater degree before the onset of T2D. Out of 446 analysed proteins, 34 mapped to these metabolic networks and 27 were identified in the non-diabetes network, 18 in the diabetes network, and 11 were common between the two networks. Key proteins directly associated with liver fat included GUSB, ALDH1A1, LPL, IGFBP1/2, CTSD, HMOX1, FGF21, AGRP, and ACE2. Sex-stratified analyses revealed distinct proteomic drivers: GUSB and LEP were most predictive of liver fat in females and males, respectively.
Conclusions: Basal insulin hypersecretion is a modifiable, causal driver of MASLD, particularly prior to glycaemic decompensation. Our findings highlight a multifactorial, sex-and disease-stage-specific proteo-metabolic architecture of hepatic steatosis. Proteins such as GUSB, ALDH1A1, LPL, and IGFBPs warrant further investigation as potential biomarkers or therapeutic targets for MASLD prevention and treatment.

DOI: https://doi.org/10.1101/2025.06.02.25328773
Nutrients. 2025 May 28. pii: 1835. [Epub ahead of print]17(11):

2,5-Dihydroxybenzoic Acid Ameliorates Metabolic Dysfunction-Associated Steatotic Liver Disease by Targeting the CCL2-CCR2 Axis to Reduce Lipid Accumulation.

Chien-Yun Hsiang, Kuang-Ting Hsu, Hsin-Yi Lo, Yun-Jhu Hou, Tin-Yun Ho.

  Background/Objectives: Metabolic dysfunction-associated steatotic liver disease (MASLD) is the most prevalent chronic liver disease worldwide, contributing to metabolic dysfunction and increased healthcare costs. The green Mediterranean diet reduces intrahepatic fat and elevates the plasma levels of 2,5-dihydroxybenzoic acid (2,5-DHBA), suggesting a mechanistic role for 2,5-DHBA in hepatic lipid metabolism. This study aimed to evaluate the therapeutic potential of 2,5-DHBA in MASLD and elucidate its molecular mechanism. Methods: Lipid accumulation was assessed in oleic acid-treated HepG2 cells and a high-fat diet (HFD)-induced MASLD mouse model. RNA sequencing, molecular docking, and immunohistochemical staining were performed to investigate the molecular mechanisms, focusing on the chemokine (C-C motif) ligand 2 (CCL2)-CCL2 receptor (CCR2) axis. Results: 2,5-DHBA significantly reduced hepatic lipid accumulation in both HepG2 cells and HFD-fed mice in a dose-dependent manner. RNA sequencing revealed the marked downregulation of CCL2, a key proinflammatory mediator in MASLD pathogenesis. Molecular docking predicted that 2,5-DHBA competed with CCL2 for binding at the CCR2 axis. Immunohistochemistry further confirmed that 2,5-DHBA treatment lowered hepatic CCL2 expression, suppressed nuclear factor-κB activation, and reduced inflammatory cell infiltration. These findings suggest that 2,5-DHBA exerted anti-steatotic effects by modulating the CCL2-CCR2 signaling pathway. Conclusions: This is the first study to demonstrate that 2,5-DHBA attenuates hepatic steatosis via targeting the CCL2-CCR2 axis. These findings highlight its potential as a novel nutraceutical strategy for MASLD treatment.

Keywords:  2,5-dihydroxybenzoic acid; chemokine (C-C motif) ligand 2; chemokine (C-C motif) receptor 2; metabolic dysfunction-associated steatotic liver disease

DOI:  https://doi.org/10.3390/nu17111835
Sci Adv. 2025 Jun 13. 11(24): eadt7369

Cold exposure stimulates cross-tissue metabolic rewiring to fuel glucose-dependent thermogenesis in brown adipose tissue.

Harry B Cutler, Sigrid Jall-Rogg, Senthil Thillainadesan, Kristen C Cooke, Stewart W C Masson, James M Sligar, Jonathan G Crowston, Luke Carroll, Jacqueline Stöckli, David E James, Søren Madsen.

To gain insight into the root causes of metabolic dysfunction, it is essential to understand how tissues communicate and coordinate their metabolic functions. Here, we sought to address this in the context of cold exposure, a well-studied metabolic perturbation. We performed proteomics across six metabolic tissues and plasma, quantifying 11,394 proteins. Beginning our investigation in brown adipose tissue (BAT), we identified a mechanism to explain enhanced glucose utilization in cold-adapted BAT. This was characterized by select remodeling of upper glycolysis and pentose cycling to increase oxygen consumption, likely by increasing uncoupling protein 1 activity through the production of reactive oxygen species. Cold-induced remodeling of the plasma proteome appeared to underpin the ability of BAT to modify its fuel preference, stimulating lipolysis in white adipose tissue and glucose production in the liver. These findings emphasize the importance of considering metabolic adaptations in the context of the whole body and suggest overlap between the mechanisms of cold adaptation and obesity.

DOI: https://doi.org/10.1126/sciadv.adt7369
J Pharmacol Exp Ther. 2025 May 19. pii: S0022-3565(25)39824-1. [Epub ahead of print]392(7): 103611

Alleviation of metabolic dysfunction-associated steatotic liver disease by silymarin is associated with maintaining mitochondrial homeostasis via regulation of optic atrophy 1.

Ming-Qiang Liu, Yuan Wu, Ye Li, Yan-Bo Wei, Ling-Yue Dong, Wei An.

  Silibinin (silybin) is the major active compound of silymarin used to treat several chronic liver diseases including metabolic dysfunction-associated steatotic liver disease (MASLD). However, the molecular mechanism of hepatic protection offered by silibinin remains still incompletely understood. In this study, we aimed to investigate whether silibinin could ameliorate hepatic steatosis by regulating mitochondrial function in Western diet (WD)-fed MASLD mice and free fatty acid-treated HepG2 cells. WD-fed mice and oleic acid/palmitic acid (OA/PA; 2:1)-treated HepG2 cells were established to evaluate the protection of silibinin against hepatocyte steatosis. Mitochondrial quality was detected using transmission electron microscope, confocal microscope, and cell analyzer for energy metabolism. Silibinin effectively attenuated WD-fed steatotic liver in mice and decreased lipid accumulation in hepatocytes, proved to be associated with stabilization of mitochondrial networked areas and inhibition of mitochondrial swelling. Functionally, silibinin at concentrations of 100 ng/μL was found to enhance mitochondrial respiratory capacity in the OA/PA-treated cells. RNA transcriptome analysis showed that, following silibinin administration, the expressions of numerous mitochondria-associated signaling molecules including AMP-activated protein kinase and mitophagy were upregulated. Among them, optic atrophy (OPA)1 expression increased prominently, which coincided with not only elevated mitochondrial fusion but also declined mitochondrial fragmentation in mouse steatotic livers and OA/PA-treated hepatocytes. In contrast, knockdown OPA1 abolished the protective effect offered by silibinin against lipid accumulation and deteriorated hepatocyte steatosis. Our findings suggest that silibinin attenuating hepatic steatosis is potentially attributed to stabilizing mitochondrial homeostasis via upregulation of OPA1. SIGNIFICANCE STATEMENT: The study results revealed that silibinin maintains mitochondrial homeostasis by upregulating optic atrophy 1 expression in hepatocytes to attenuate lipid accumulation and oxidative stress. Therefore, silibinin is a potential therapeutic candidate for the treatment of metabolic dysfunction-associated steatotic liver disease.

Keywords:  Metabolic dysfunction–associated steatotic liver disease; Mitochondrial fusion; Mitochondrial respiration; Reactive oxygen species; Silibinin

DOI:  https://doi.org/10.1016/j.jpet.2025.103611
Int J Mol Sci. 2025 May 26. pii: 5103. [Epub ahead of print]26(11):

Endarachne binghamiae Ameliorates Hepatic Steatosis, Obesity, and Blood Glucose via Modulation of Metabolic Pathways and Oxidative Stress.

Sang-Seop Lee, Sang-Hoon Lee, So-Yeon Kim, Ga-Young Lee, Seung-Yun Han, Bong-Ho Lee, Yung-Choon Yoo.

  Obesity and metabolic dysfunction-associated steatotic liver disease (MASLD) are major contributors to the rise in metabolic disorders, particularly in developed countries. Despite the need for effective therapies, natural product-based interventions remain underexplored. This study investigated the therapeutic effects of Endarachne binghamiae, a type of brown algae, hot water extract (EB-WE) in ameliorating obesity and MASLD using high-fat diet (HFD)-induced ICR mice for an acute obesity model (4-week HFD feeding) and C57BL/6 mice for a long-term MASLD model (12-week HFD feeding). EB-WE administration significantly reduced body and organ weights and improved serum lipid markers, such as triglycerides (TG), total cholesterol (T-CHO), HDL (high-density lipoprotein), LDL (low-density lipoprotein), adiponectin, and apolipoprotein A1 (ApoA1). mRNA expression analysis of liver and skeletal muscle tissues revealed that EB-WE upregulated Ampkα and Cpt1 while downregulating Cebpα and Srebp1, suppressing lipogenic signaling. Additionally, EB-WE activated brown adipose tissue through Pgc1α and Ucp1, contributing to fatty liver alleviation. Western blot analysis of liver tissues demonstrated that EB-WE enhanced AMPK phosphorylation and modulated lipid metabolism by upregulating PGC-1α and UCP-1 and downregulating PPAR-γ, C/EBP-α, and FABP4 proteins. It also reduced oxidation markers, such as OxLDL (oxidized low-density lipoprotein) and ApoB (apolipoprotein B), while increasing ApoA1 levels. EB-WE suppressed lipid peroxidation by modulating oxidative stress markers, such as SOD (superoxide dismutase), CAT (catalase), GSH (glutathione), and MDA (malondialdehyde), in liver tissues. Furthermore, EB-WE regulated the glucose regulatory pathway in the liver and muscle by inhibiting the expression of Sirt1, Sirt4, Glut2, and Glut4 while increasing the expression of Nrf2 and Ho1. Tentative liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis for EB-WE identified bioactive compounds, such as pyropheophorbide A and digiprolactone, which are known to have antioxidant or metabolic regulatory activities. These findings suggest that EB-WE improves obesity and MASLD through regulation of metabolic pathways, glucose homeostasis, and antioxidant activity, making it a promising candidate for natural product-based functional foods and pharmaceuticals targeting metabolic diseases.

Keywords:  AMPK; Endarachne binghamiae; MASLD; obesity; steatosis

DOI:  https://doi.org/10.3390/ijms26115103
Front Oncol. 2025 ;15 1568524

Targeting the leptin receptor promotes MDA-MB-231 cells' metabolic reprogramming and malignancy: the role of extracellular vesicles derived from obese adipose tissue.

Carol Costa Encarnação, Carolinne Souza Amorim, Victor Aguiar Franco, Luiz Gabriel Xavier Botelho, Ronan Christian Machado Dos Santos, Isadora Ramos-Andrade, Luiz Guilherme Kraemer-Aguiar, Christina Barja-Fidalgo, João Alfredo Moraes, Mariana Renovato-Martins.

   Introduction: Leptin, a key adipokine secreted by adipose tissue (AT), has emerged as a critical mediator linking obesity and breast cancer, both of which are major global health concerns. Elevated leptin levels are detected in the circulation and in extracellular vesicles (EVs) released by adipose tissue, particularly in cases of obesity. These leptin-enriched EVs have been implicated in various stages of tumor progression. In this study, we investigated the effects of leptin within extracellular vesicles (EVs) secreted by obese adipose tissue on the functional properties and metabolism of MDA-MB-231 breast cancer cells, a model for triple-negative breast cancer (TNBC).
Method: MDA-MB-231 cells were treated with EVs derived from the subcutaneous adipose tissue of eutrophic (EUT EVs) and obese (OB EVs) individuals.
Results: Our findings revealed that OB EVs induced significant phosphorylation of STAT3, a key signaling molecule in cancer progression, and promoted increased cell migration, dependent on fatty acid oxidation (FAO). This effect was reversed in the presence of a leptin receptor antagonist, highlighting leptin's pivotal role in these processes. Additionally, OB EVs caused metabolic changes, including reduced lactate levels and decreased pyruvate kinase (PK) activity, while increasing glucose-6-phosphate dehydrogenase (G6PDH) activity, suggesting metabolic reprogramming that supports tumor cell survival and proliferation. In addition to metabolic alterations, OB EVs also impacted mitochondrial dynamics. We observed an upregulation of fusion and fission markers and a redistribution of mitochondria toward the cell periphery, which supports migration. Moreover, OB EVs increased the invasive capacity of MDA-MB-231 cells, an effect mediated by matrix metalloproteinase-9 (MMP-9).
Discussion: Overall, our results highlight how obese adipose tissue modulates breast cancer cell behavior, with leptin-enriched EVs playing a central role in driving migration, metabolic reprogramming, and invasiveness, thereby promoting tumor malignancy. This study underscores the importance of EVs in the obesity-cancer link and offers new insights for therapeutic strategies targeting leptin signaling and EV-mediated communication in breast cancer.

Keywords:  adipose tissue; breast cancer; extracellular vesicles; leptin; obesity

DOI:  https://doi.org/10.3389/fonc.2025.1568524
bioRxiv. 2025 May 31. pii: 2025.05.27.656447. [Epub ahead of print]

Analysis of isobaric quantitative proteomic data using TMT-Integrator and FragPipe computational platform.

Hui-Yin Chang, Yamei Deng, Ruohong Li, Dmitry Avtonomov, Bo Wen, Sarah E Haynes, Felipe da Veiga Leprevost, Bing Zhang, Fengchao Yu, Alexey I Nesvizhskii.

Isobaric mass tags, such as iTRAQ and TMT, are widely utilized for peptide and protein quantification in multiplex quantitative proteomics. We present TMT-Integrator, a bioinformatics tool for processing quantitation results from TMT and iTRAQ experiments, offering integrative reports at the gene, protein, peptide, and post-translational modification site levels. We demonstrate the versatility of TMT-Integrator using five publicly available TMT datasets: an E. coli dataset with 13 spike-in proteins, the clear cell renal cell carcinoma (ccRCC) whole proteome and phosphopeptide-enriched datasets from the Clinical Proteomic Tumor Analysis Consortium, and two human cell lysate datasets showcasing the latest advances with the Astral instrument and TMT 35-plex reagents. Integrated into the widely used FragPipe computational platform ( https://fragpipe.nesvilab.org/ ), TMT-Integrator is a core component of TMT and iTRAQ data analysis workflows. We evaluate the FragPipe/TMT-Integrator analysis pipeline's performance against MaxQuant and Proteome Discoverer with multiple benchmarks, facilitated by the bioinformatics tool OmicsEV. Our results show that FragPipe/TMT-Integrator quantifies more proteins in the E. coli and ccRCC whole proteome datasets, identifies more phosphorylated sites in the ccRCC phosphoproteome dataset, and delivers overall more robust quantification performance compared to other tools.

DOI: https://doi.org/10.1101/2025.05.27.656447
Mol Biomed. 2025 Jun 09. 6(1): 38

Histone and non-histone lactylation: molecular mechanisms, biological functions, diseases, and therapeutic targets.

Xia Peng, Juan Du.

  Lysine lactylation (Kla) is a recently discovered post‑translational modification in which a lactyl moiety is transferred onto the ε‑amino group of lysine residues, linking cellular metabolism to epigenetic and signaling pathways. This process is regulated by a range of enzymes and metabolites, including lactate, "lactyltransferases (writers)", "Delactylases (erasers)", and "readers" involved in the modification. Histone lactylation has been observed in H2A, H2B, H3, and H4, with H3K18la and H4K12la being the most extensively studied sites, linked to numerous biological functions. Beyond chromatin, Kla has also been identified in a growing number of non-histone proteins, further expanding its functional significance. For instance, non-histone proteins such as AARS1-K120la, ACSS2-Kla, MRE11-K673la, NBS1-K388la and GNAT13-Kla has illuminated novel regulatory mechanisms and reinforced the potential of non-histone Kla as a promising avenue for research. Importantly, aberrant Kla patterns have been linked to various disease states, including cancer, inflammation, and metabolic disorders, highlighting its emerging potential as a biomarker and therapeutic target. In this review, we systematically summarize the molecular mechanisms, biological functions, disease associations, and therapeutic implications of both histone and non-histone Kla. By integrating current findings and discussing existing challenges, we aim to provide a comprehensive overview that will deepen understanding of Kla biology and inspire future research into its diagnostic and therapeutic potential.

Keywords:  Histone; Lactylation (Kla); Non-Histone; Post-Translational Modification

DOI:  https://doi.org/10.1186/s43556-025-00275-6
bioRxiv. 2025 Jun 03. pii: 2025.06.02.657064. [Epub ahead of print]

Global Landscape of Human Kinase Motifs in Viral Proteomes.

Kareem Alba, Declan M Winters, Sara K Makanani, Prashant Kaushal, Yennifer Delgado, Immy A Ashley, Shipra Sharma, Sophie F Blanc, Erin Kim, Tomer Yaron, Jared L Johnson, Justin Selby, Min Hur, Jocelyn Ni, Jasmine Nguyen, Marc H Brent, Elaine Yip, Ahmad Kassem, James Wohlschlegel, Oliver I Fregoso, Ting-Ting Wu, Melody Mh Li, Mehdi Bouhaddou.

The successful establishment of infection relies on an ability to sense and adapt to the host signaling state. One key mechanism of virus-host sensing is host-mediated post-translational modifications of viral proteins. While viral protein phosphorylation by host kinases is known to modulate viral functions, the global prevalence of kinase motifs across diverse viruses, and the signaling pathways they reflect, remains to be systematically explored. Here, we annotated human kinase motifs in 1,505 viral proteomes and uncovered enriched motifs in viral proteins that diverged from patterns observed in human proteins. Integration of our findings with 21,606 viral protein structures and deep mass spectrometry phosphoproteomics of infected human cells revealed that surface-accessible residues were preferentially phosphorylated and exhibited greater kinase specificity compared to buried sites. Virus-enriched motifs mapped predominantly to stress, inflammation, and cell cycle pathways-key signaling hubs dysregulated during infection that are central to the virus-host arms race-most strikingly for Flaviviridae , Togaviridae , Herpesviridae, and Retroviridae families. Temporal phosphoproteomic profiling of host kinase activity during alphavirus infection revealed dynamic patterns of stress kinase activation and viral protein phosphorylation, and the inhibition of MAP kinases reduced viral replication and phosphorylation at viral motifs with specificity for ERK and JNK kinases. Our findings suggest that viruses have evolved as biosensors of the host signaling state to optimize their life cycles, revealing new antiviral opportunities aimed at disrupting virus decision-making by manipulating host signaling cues.

DOI: https://doi.org/10.1101/2025.06.02.657064
Autophagy. 2025 Jun 12.

Tumorous cholesterol biosynthesis curtails anti-tumor immunity by preventing MTOR-TFEB-mediated lysosomal degradation of CD274/PD-L1.

Huina Wang, Xiuli Yi, Di Qu, Xiangxu Wang, Hao Wang, Hengxiang Zhang, Yuqi Yang, Tianwen Gao, Weinan Guo, Chunying Li.

  Enhanced cholesterol biosynthesis is a hallmark metabolic characteristic of cancer, exerting an oncogenic role by supplying intermediate metabolites that regulate intracellular signaling pathways. The pharmacological blockade of cholesterol biosynthesis has been well documented as a promising therapeutic approach in cancer. Particularly, cholesterol biosynthesis is linked to macroautophagy/autophagy and lysosome metabolism, with the engagement of the critical autophagy regulators like MTOR to be fully activated by lysosomal cholesterol trafficking and accumulation. Previous studies have primarily focused on the role of cholesterol biosynthesis in tumor cell-intrinsic biological processes, whereas its involvement in tumor immune evasion and the underlying mechanisms related to autophagy or lysosome metabolism remain elusive. Herein, through bioinformatics analysis we discovered a negative correlation between cholesterol biosynthesis and the score of tumor-infiltrating lymphocytes in cancers. Inhibition of tumor cell cholesterol biosynthesis leads to increased infiltration and activation of CD8+ T cells in the tumor microenvironment, which is largely responsible for the impairment of tumor growth. Mechanistically, cholesterol biosynthesis inhibition impairs the activation of MTOR at lysosomes, thereby promoting the nuclear translocation of TFEB and downstream lysosome biosynthesis, facilitating the degradation of CD274/PD-L1 within lysosomes in tumor cells. Ultimately, the HMGCR-MTOR-LAMP1 axis that connects cholesterol, lysosome and tumor immunology, predicts poor response to immunotherapy and worse prognosis of patients with melanoma. These findings unveil an immunomodulatory role of tumorous cholesterol biosynthesis via the regulation of CD274 lysosomal degradation. Targeting cholesterol biosynthesis holds promise as a potential therapeutic strategy in cancer, particularly when combined with immune checkpoint blockade.

Keywords:  Cholesterol; PD-L1; TFEB; immune evasion; lysosome; protein degradation

DOI:  https://doi.org/10.1080/15548627.2025.2519066
J Lipid Res. 2025 Jun 09. pii: S0022-2275(25)00098-7. [Epub ahead of print] 100838

Elevation of hepatic de novo lipogenesis in mice with overnutrition is dependent on multiple substrates.

Jordan W Strober, Stephan Siebel, Susan F Murray, Manuel González Rodríguez, Carlos Rodriguez-Navas Gonzalez, Daniel F Vatner.

  Increased de novo lipogenesis (DNL) contributes to hyperlipidemia, MASLD, and ASCVD in insulin resistant subjects. However, multiple pathways support lipogenesis and few have sought to quantify the contributions of the discrete metabolic pathways that contribute to lipogenesis. In this study, antisense oligonucleotides (ASOs) targeting glucokinase (Gck), lactate dehydrogenase A (Ldha), and glutamic-pyruvic transaminase 2 (Gpt2) were utilized to restrict substrate flux from lipogenic precursors in C57BL6/J mice, comparing controls (CO) and chronic overnutrition (ON). In CO mice, ASO treatments did not significantly alter lipogenesis; however, there was a trend toward decreased hepatic triglyceride content and DNL, especially with the GPT2 ASO (TG=-46.8%; DNL=-53.7%). Expectedly, increased hepatic TG content and DNL (ON vs CO: TG=+187.9%; DNL=+41.8%) was observed in mice with chronic overnutrition. Gas chromatography-mass spectrometry analyses demonstrated increased hepatic TCA cycle metabolites (ON vs CO: fumarate +74.2%; malate +54.0%; and citrate +43.2) and decreased hepatic concentrations of multiple amino acids (ON vs CO: Leu -41.7%; Ile -45.0%; Val -56.3%; Ser -22.6%). With ON, TG content and DNL were reduced by restricting lipogenic carbon entry from alanine (GPT2: TG=-45.5%; DNL=-48.1%), lactate (LDHA: TG=-25.8%; DNL=-33.1%), or glucose (GCK: TG=-59.2%; DNL=-69.2%). Amino acids appear to be a consistent carbon source for DNL in mice; however, carbon entry from all sources is required to maintain the significantly elevated rates of hepatic DNL in chronically overfed mice. These findings may inform the development of novel therapies and underscore the importance of peripheral substrate storage and oxidation in the prevention of dyslipidemia in the metabolic syndrome.

Keywords:  Antisense oligonucleotide; De Novo Lipogenesis; Insulin Resistance; Lipolysis and fatty acid metabolism; Liver; Mitochondria; TCA cycle; Triglyceride

DOI:  https://doi.org/10.1016/j.jlr.2025.100838
Cell Rep. 2025 Jun 07. pii: S2211-1247(25)00575-3. [Epub ahead of print]44(6): 115804

Cell death and cancer: Metabolic interconnections.

Destiny Dalseno, Nikolai Gajic, Lyndsey Flanagan, Stephen W G Tait.

  Recent findings in the cell death field have transformed our understanding of the interplay between metabolism and cell death in the context of cancer. In this review, we discuss the relationships between metabolism and the cell death pathways of apoptosis, necroptosis, pyroptosis, and ferroptosis, with a particular focus on recent advancements. We will also explore the regulation of metabolism by the BCL-2 family and the participation of oncometabolites in the regulation of cell death. Finally, we examine the emerging links between cell death signaling and cellular persistence. As we highlight in this review, the intersection of metabolic and cell death pathways has implications for cancer cell survival, treatment resistance, and the tumor microenvironment.

Keywords:  BCL-2; CP: Cancer; CP: Metabolism; apoptosis; cancer; cell death; ferroptosis; metabolism; necroptosis

DOI:  https://doi.org/10.1016/j.celrep.2025.115804