bims-cesirm Biomed News
on Cell Signaling mediated regulation of metabolism
Issue of 2026–01–18
27 papers selected by
Tigist Tamir, University of North Carolina



  1. Angew Chem Int Ed Engl. 2026 Jan 16. e19830
      All the studies of ketogenesis-dependent post-translational modifications (PTMs), notably those mediated by ketone bodies, β-hydroxybutyrate (Bhb) and acetoacetate (Acac), have focused on lysine acylations. However, given the chemically diverse and reactive nature of metabolites generated, it remains unclear whether non-lysine modifications can also happen. Here, we develop an acetoacetate-alkyne (Acac-alkyne) chemical probe that enables efficient metabolic labeling, robust fluorescent visualization, and site-specific identification of Acac-modified proteins. By combining chemical proteomics with open-search strategy, we showed that Acac induces previously uncharacterized cysteine modifications in mammalian cells. Notably, cysteine crotonation (Ccr) is validated by employing both probe-based and standard peptide-based co-elution assays. Metabolic pathway tracing further identifies BDH1 and ECHS1 as key enzymes that generate Ccr formation. We further demonstrate that Ccr at PRDX3 C229 site impairs dimerization and redox activity, linking this newly discovered modification to the regulation of cellular reactive oxygen species. Together, these findings establish ketone metabolism as a novel source of cysteine modifications and provide an alternative mechanistic pathway to explain the profound biological effects of ketone bodies.
    Keywords:  Cysteine modifications; Ketone body; Protein modifications; Proteomics; Redox regulation
    DOI:  https://doi.org/10.1002/anie.202519830
  2. Nat Commun. 2026 Jan 10.
      Designing proteins that bind with high affinity to hydrophilic protein target sites remains a challenging problem. Here we show that RFdiffusion can be conditioned to generate protein scaffolds that form geometrically matched extended β-sheets with target protein edge β-strands in which polar groups on the target are complemented with hydrogen bonding groups on the design. We use this approach to design binders against edge-strand target sites on KIT, PDGFRɑ, ALK-2, ALK-3, FCRL5, NRP1, and α-CTX, and obtain higher (pM to mid nM) affinities and success rates than unconditioned RFdiffusion. Despite sharing β-strand interactions, designs have high specificity, reflecting the precise customization of interacting β-strand geometry and additional designed binder-target interactions. A binder-KIT co-crystal structure is nearly identical to the design model, confirming the accuracy of the design approach. The ability to robustly generate binders to the hydrophilic interaction surfaces of exposed β-strands considerably increases the range of computational binder design.
    DOI:  https://doi.org/10.1038/s41467-025-67866-3
  3. J Mass Spectrom. 2026 ;61(2): e70026
      Obesity is often linked to protein acetylation and induces intricate changes in post-translational modifications, affecting mitochondrial regulatory instability. Redox signaling is crucial for maintaining cellular homeostasis. The mechanism by which lysine acetylome drives redox signaling may elucidate the complexity of the biological networks underlying obesity. High-fat diet (HFD)-fed mouse livers were lysed, immunoprecipitated with lysine-acetyl antibody-conjugated beads, and labeled with isotopic 18O/16O for multiplexing. A total of 2282 proteins and 1384 Kac sites were identified, including 456 newly identified sites that were not matched in the dbPTM and iPTMnet databases. The expression levels of the acetylome were normalized to protein expression, and one-third of the acetylome was quantified. Differentially expressed acetylated proteins were annotated using Gene Ontology; the upregulated proteins belonged to the peroxisomal pathway. The three proteins involved in redox regulation, glutathione S-transferase theta-1, superoxide dismutase 1, and epoxide hydrolase 1, exhibited significant changes at specific sites with acetyl-lysine levels in HFD-fed mouse liver. Our data showed that investigating acetylation pathways can provide insights into the molecular mechanisms driving obesity and offer potential targets for therapeutic interventions.
    Keywords:  high‐fat diet; lysine acetylation; protein post‐translational modification
    DOI:  https://doi.org/10.1002/jms.70026
  4. bioRxiv. 2026 Jan 07. pii: 2026.01.06.697885. [Epub ahead of print]
      Glioma progression and resistance to temozolomide (TMZ) remain major clinical challenges. Here, we investigated whether dysregulated autophagy and cholesterol metabolism are coordinately remodeled during glioma progression and TMZ resistance. Tissue microarray analysis of astrocytoma and glioblastoma specimens revealed progressive autophagosome accumulation, reflected by increased LC3β puncta, coupled with impaired autophagic flux compared with adjacent normal brain tissue. These alterations intensified with tumor grade and were associated with upregulation of farnesyl diphosphate synthase (FDPS), linking malignant progression to cholesterol pathway remodeling. TMZ-resistant (R) glioblastoma cells exhibited epithelial-to-mesenchymal transition, mitotic quiescence, and mitochondrial remodeling consistent with a therapy-tolerant phenotype. Bioenergetic profiling demonstrated reduced respiratory reserve, diminished ATP-linked respiration, and elevated proton leak, indicating constrained metabolic flexibility. In parallel, impaired autophagy flux was associated with suppression of de novo cholesterol synthesis and transcriptional downregulation of SREBP-2 and LDL-R. Comprehensive lipidomic profiling revealed marked cholesterol metabolic reprogramming in R cells, characterized by accumulation of specific cholesteryl esters, including CE 22:5, CE 22:6, CE 22:4, and CE 20:4, despite reduced cholesterol biosynthesis. Pharmacologic inhibition of the mevalonate pathway with simvastatin significantly altered cholesteryl ester profiles but failed to restore autophagy flux or sensitize R cells to TMZ-induced apoptosis, even under combined TMZ-simvastatin treatment.
    Lay Abstract: As gliomas progress from astrocytoma to glioblastoma, autophagy becomes dysregulated and cholesterol metabolism is rewired. This coordinated remodeling supports tumor survival, metabolic plasticity, and resistance to temozolomide therapy.
    Highlights: Autophagy flux blockade intensifies during progression from astrocytoma to glioblastomaDysregulated autophagy is coupled to altered cholesterol metabolism in malignant gliomasTMZ-resistant glioblastoma cells undergo epithelial-to-mesenchymal transition and mitotic quiescenceResistant cells exhibit constrained bioenergetic capacity and mitochondrial remodelingImpaired autophagy suppresses de novo cholesterol synthesis and lipid recyclingLipidomics reveals accumulation of long-chain cholesteryl esters in TMZ-resistant cellsStatin-based cholesterol inhibition fails to resensitize glioblastoma cells to temozolomide.
    DOI:  https://doi.org/10.64898/2026.01.06.697885
  5. Sci Rep. 2026 Jan 14.
      Phytosesquiterpene lactones deoxyelephantopin (DET) and its derivative DETD-35 are reported to induce oxidative stress towards inhibiting triple-negative breast cancer (TNBC) cell activities. This study aimed to elucidate how DET and DETD-35 affect mitochondrial function and systemic metabolism in TNBC cells. DET and DETD-35 promoted mitochondrial superoxide production by upregulating expression of SOD1 and SOD2, induced permeability transition pore opening, and attenuated intracellular ATP levels. Neither compound interfered with mitochondrial respiration/bioenergetics in normal mammary MCF-10A cells. Comparative mitochondrial proteome and bioinformatic analyses showed significant deregulation of proteins related to the oxidative phosphorylation, depolarization of mitochondria, and apoptosis signaling in DET- or DETD-35-treated TNBC cells, and primary metabolomics revealed that both compounds deregulated metabolites dynamics and the corresponding metabolic pathways in TNBC cells. Knockdown of the PRKCA gene/protein involved in inducing mitochondrial toxicity in TNBC cells reversed cytotoxicity, apoptosis, and the levels of several metabolites induced by DET or DETD-35 in the cancer cells. Integrated Pearson's correlation and IPA network analyses of differentially expressed proteins and metabolites revealed the networks of ATP synthesis, energy homeostasis, and respiration, depolarization, and transmembrane potential in mitochondria highly correlated to the compound effects. Notable, DET/DETD-35 inhibited mitochondrial ATPase activity, and molecular modeling further predicted the binding sites of either compound with ATP synthase at the subunits α/β and c/a interfaces. The overexpression of ATP synthase-related proteins ATP5A1 and ATP5C1 in the tumor microenvironment of MDA-MB-231 xenograft mice were also significantly suppressed by DET and DETD-35 treatments. In summary, this study identifies DETD-35 and DET as novel ATPase inhibitors which are attributed to disrupting mitochondrial biogenetics and cellular metabolism and networking in TNBC cells.
    Keywords:  ATP synthase; Breast cancer; Metabolic reprogramming; Mitochondrial dysfunction; Mitochondrial proteome; Sesquiterpene lactone
    DOI:  https://doi.org/10.1038/s41598-026-35194-1
  6. bioRxiv. 2026 Jan 05. pii: 2026.01.05.697750. [Epub ahead of print]
      The cGAS/STING pathway is a critical signaling hub that orchestrates type I interferon (IFN) responses, autophagy, and programmed cell death in response to double-stranded DNA (dsDNA) or cyclic dinucleotides. While traditionally characterized as a sensor of foreign or mis-localized self dsDNA, recent evidence demonstrates that STING also integrates information about the homeostasis of cellular lipid biosynthesis into the innate inflammatory response. This integration occurs most notably through STING's sensitivity to de novo cholesterol synthesis. However, given that mammalian cells undergo widespread lipid metabolic reprogramming, characterized by alterations in the synthesis of many lipid species in addition to cholesterol, during processes such as malignant transformation to cancer or during infection by intracellular pathogens, we hypothesized that STING function may be regulated by perturbations in other undescribed lipid pathways. To investigate potential other facets of the STING-lipid interface, we have performed a targeted small molecule screen across multiple lipid metabolic pathways, including the mevalonate, PPAR (fatty acid), and arachidonic acid pathways. Our findings reveal that positively and negatively perturbing enzymes within these diverse lipid paths including lipoxygenases and cyclooxygenases can significantly modulate STING-dependent signal transduction and transcriptional programs, identifying metabolic nodes that link lipid homeostasis with innate immune signaling. These results suggest that existing lipid-lowering and metabolic therapies may have unappreciated immunomodulatory effects on STING applicable in cancer and infectious disease, offering new opportunities for therapeutic intervention.
    DOI:  https://doi.org/10.64898/2026.01.05.697750
  7. J Proteome Res. 2026 Jan 13.
      Conventional database search methods for proteomics struggle when tasked with identifying dozens or hundreds of modifications simultaneously. Open or error-tolerant searches can address this limitation but at the cost of increased difficulty in downstream interpretation of the results and quantification. We and others have previously described "mass offset" or multinotch searches that sit in between closed and open searches, allowing simultaneous search for hundreds of modifications with more straightforward downstream interpretation than open search. The original mass offset searches were closer to the open search, lacking the ability to restrict modifications to specific amino acids. Here, we describe a new "detailed" mass offset (DMO) search implemented in the MSFragger search engine, which allows each mass offset to have its own site restrictions and fragmentation rules. The benefits of the DMO search over existing mass offset searches are shown with three example searches of complex modification sets: nearly one hundred post-translational modifications, fast photochemical oxidation of proteins (FPOP)-derived modifications, and amino acid substitutions. The DMO search further improves the interpretability of results by reducing ambiguity in site localization, particularly when modifications have overlapping masses, and provides benefits that scale with the complexity of the search.
    Keywords:  PTMs; database search; mass offset; open search; proteomics; software
    DOI:  https://doi.org/10.1021/acs.jproteome.5c00775
  8. Free Radic Biol Med. 2026 Jan 12. pii: S0891-5849(26)00028-6. [Epub ahead of print]
      Cetuximab resistance in head and neck squamous cell carcinoma (HNSCC) is increasingly recognized as an adaptive state driven by metabolic and redox reprogramming that enables tumor cells to tolerate sustained oxidative and immune stress. Although lipid metabolism and PPARγ signaling have been implicated in therapeutic resistance, their functional contribution to drug-tolerant persister (DTP) cells and the role of peroxisomal fatty acid oxidation (FAO) remain poorly defined. In this study, we demonstrate that a redox-driven FABP1/PPARγ axis sustains peroxisome-centered FAO, GPX4-dependent antioxidant defense, and immune suppression in cetuximab-tolerant HNSCC. FABP1 expression was markedly elevated in cetuximab-tolerant DTP cell models and resistant patient tumors. Genetic silencing or pharmacological inhibition of FABP1 using a selective small-molecule inhibitor impaired tumorsphere formation, increased intracellular reactive oxygen species accumulation, and induced apoptotic cell death, accompanied by coordinated suppression of FAO-associated genes, including CPT1, ACSL family members, and acyl-CoA oxidase 1. In an orthotopic SCC9-DTP xenograft model established in NOD-SCID mice, FABP1 inhibition significantly attenuated tumor growth, disrupted metabolic-redox adaptation, and reduced tumor-associated macrophage polarization toward an immunosuppressive phenotype. Our findings identify the FABP1/PPARγ axis as a central regulator of peroxisome-centered FAO and redox buffering in cetuximab-tolerant DTP cells. Targeting FABP1 collapses this adaptive metabolic-redox program, restores vulnerability to oxidative stress, and alleviates immune suppression, highlighting peroxisomal lipid metabolism as a therapeutically actionable vulnerability in refractory HNSCC.
    Keywords:  FABP1; GPX4; HNSCC; PPARγ; cetuximab resistance; fatty acid oxidation; peroxisome; redox homeostasis; tumor-associated macrophage
    DOI:  https://doi.org/10.1016/j.freeradbiomed.2026.01.020
  9. Nat Metab. 2026 Jan 16.
      Hexokinase (HK) catalyses the phosphorylation of glucose to glucose 6-phosphate, marking the first step of glucose metabolism. Most cancer cells co-express two homologous HK isoforms, HK1 and HK2, which can each bind the outer mitochondrial membrane (OMM). CRISPR screens performed across hundreds of cancer cell lines indicate that both isoforms are dispensable for growth in conventional culture media. By contrast, HK2 deletion impaired cell growth in human plasma-like medium. Here we show that this conditional HK2 dependence can be traced to the subcellular distribution of HK1. Notably, OMM-detached (cytosolic) rather than OMM-docked HK supports cell growth and aerobic glycolysis (the Warburg effect), an enigmatic phenotype of most proliferating cells. We show that under conditions promoting increased translocation of HK1 to the OMM, HK2 is required for cytosolic HK activity to sustain this phenotype, thereby driving sufficient glycolytic ATP production. Our results reveal a basis for conditional HK2 essentiality and suggest that demand for compartmentalized ATP synthesis explains why cells engage in aerobic glycolysis.
    DOI:  https://doi.org/10.1038/s42255-025-01428-1
  10. Nucleic Acids Res. 2026 Jan 14. pii: gkaf1498. [Epub ahead of print]54(2):
      Molecular profiling of human primary cell types is essential for understanding human biology. We present a transcriptome and proteome map of 28 primary human cell types. Three major clusters of epithelial, endothelial, and mesenchymal cell types were observed in both the transcriptome and proteome levels along with the discovery of cell type enriched molecules including GRAP and C1orf116. The epithelial cell specific protein C1orf116 was further validated using immunohistochemistry across various human tissues. An exhaustive protein database search considering 39 post-translational modifications (PTMs) revealed novel insights into the PTM landscape including identification of understudied PTMs such as serine O-acetylation and histidine methylation. This also enabled comprehensive characterization of proteins with diverse PTMs. Interestingly, an unexpectedly higher frequency of dioxidation on tryptophan compared to methionine led to the identification of oxidative mitochondria complex subunit proteins. Further, a search strategy accounting for alternative translational start sites, splice junctions and translational readthrough refined genome annotation using proteomic evidence. For example, peptides from translational readthrough including extended sequence of LDHB and MDH1 were detected representing the first peptide-level evidence of these protein readthrough isoforms. Our comprehensive transcriptome and proteome data revealed cell type-specific molecular cues and heterogeneity, offering new insights into disease mechanisms often overlooked by tissue proteomics.
    DOI:  https://doi.org/10.1093/nar/gkaf1498
  11. FASEB J. 2026 Jan 31. 40(2): e71427
      Obesity has become a global epidemic and a major contributor to the development of Type 2 diabetes (T2D) through the promotion of insulin resistance. Emerging evidence has shown that GPX4 expression is reduced in macrophages under hyperglycemic conditions; however, the involvement of macrophage-specific GPX4 in obesity-associated insulin resistance remains unclear. We generated macrophage-specific Gpx4 knockout (Gpx4Mac-KO) mice and subjected both Gpx4Mac-KO and littermate Gpx4fl/fl mice to a high-fat diet (HFD) for 16 weeks. Metabolic parameters, adipose tissue morphology, hepatic lipid accumulation, and free fatty acid (FFA) metabolism were assessed. The results showed that macrophage-specific deletion of Gpx4 attenuated HFD-induced obesity and improved insulin sensitivity in mice in vivo. Gpx4-deficient mice exhibited lower levels of systemic inflammation, reduced adipocyte hypertrophy, and diminished hepatic steatosis. Deficiency of Gpx4 in macrophages affects FFA metabolism by regulating the expression of FFA breakdown-related genes, such as C/EBP-α, PPARγ, ATGL, Fabp4, and/or LPL, in white adipose tissue and the liver. These beneficial metabolic effects seemed to be associated with enhanced macrophage ferroptosis, suggesting a mechanistic link between Gpx4 deficiency, ferroptosis, and the alleviation of obesity-associated insulin resistance. Our findings identify macrophage GPX4 as a key mediator of obesity-induced insulin resistance and metabolic malfunction. Targeting macrophage GPX4 may represent a promising therapeutic strategy for the treatment of T2D.
    Keywords:  GPX4; ferroptosis; insulin resistance; macrophage; obesity
    DOI:  https://doi.org/10.1096/fj.202503596R
  12. Pharmacol Rev. 2025 Nov 20. pii: S0031-6997(25)07514-3. [Epub ahead of print]78(1): 100105
      Enhanced de novo lipogenesis is a hallmark of cancer cells, enabling their proliferation, metastasis, and resistance to therapy. Among key lipogenic enzymes, fatty acid synthase (FASN) is frequently overexpressed in cancer but minimally expressed in most normal adult tissues, making it an appealing drug target. Human FASN is the sole cytosolic type I enzyme responsible for the de novo synthesis of palmitate. It is a homodimer of 270 kDa multidomain protein, functioning like an automatic assembly line. Its acyl carrier protein domain serves as a flexible arm, transporting the elongating acyl chain through other enzymatic domains responsible for chain elongation and modification, including malonyl/acetyltransferase, β-ketoacyl synthase, enoyl reductase, β-ketoacyl reductase, dehydrase, and thioesterase. The process begins at the malonyl/acetyltransferase domain, where the acetyl and malonyl groups from acetyl-CoA and malonyl-CoA, respectively, are transferred to the acyl carrier protein. FASN has been validated to play vital roles in promoting cancer progression, supporting cancer cell survival, reprogramming lipid metabolism, modulating oncogenic signaling pathways, and inducing drug resistance. Over the past 2 decades, significant progress has been made in developing inhibitors targeting different domains of FASN, including structure-based drug design, repurposing existing drugs, and nature-derived compounds with FASN-inhibitory properties. Despite these efforts, only a handful of inhibitors have entered clinical trials, such as 3-V Biosciences-2640 (denifanstat) and repurposed omeprazole, and none have received regulatory approval to date. In this review, we critically evaluate FASN-targeting strategies, highlight domain-specific targeting challenges, and discuss emerging insights that may help overcome current limitations, aiming to guide future discovery and optimization of FASN-targeted therapeutics. SIGNIFICANCE STATEMENT: Enhanced lipogenesis and fatty acid synthase overexpression in cancer make this multidomain enzyme an attractive target for therapy and overcoming drug resistance. Despite progress with novel and repurposed inhibitors, none have gained approval. This review critically examines past efforts, current challenges, and offers insights to guide future development of effective fatty acid synthase-targeting cancer therapeutics.
    DOI:  https://doi.org/10.1016/j.pharmr.2025.100105
  13. FEBS J. 2026 Jan 16.
      The labile iron pool in the cell is required for ferroptosis, a form of regulated cell death resulting from excessive lipid peroxidation and membrane damage. Glutathione (GSH) is critical for lipid-peroxide scavenging, and cysteine is the rate-limiting amino acid in GSH synthesis. Cysteine metabolism intricately intertwines with iron metabolism, either directly by participating in assembly of the iron-sulfur cluster or indirectly through the pantothenate pathway and coenzyme A (CoA) synthesis. However, the regulation of iron homeostasis in cystine (Cys2)-deprivation-induced ferroptosis is poorly understood. Here, we show that Cys2 deprivation promotes ferroptosis, at least in part, by activating the iron-starvation response (ISR), and CoA can mitigate ferroptosis by suppressing the ISR. Mechanistically, Cys2 deprivation promotes the oxidation of cytosolic iron-sulfur clusters to activate the ISR; CoA and related small-molecule thiols in the pantothenate pathway suppress the ISR and ferroptosis by preventing the oxidation of iron-sulfur clusters in Cys2-deprived cells. Our findings provide important insight into the regulation of the ISR in Cys2-deprivation-induced ferroptosis, and show that CoA can protect cells from Cys2-deprivation-induced ferroptosis by suppressing the ISR.
    Keywords:  Coenzyme A; cysteine; cystine‐deprivation; ferroptosis; iron‐starvation response; iron–sulfur cluster; pantothenate pathway
    DOI:  https://doi.org/10.1111/febs.70411
  14. Nat Metab. 2026 Jan 15.
      Cachexia is a wasting disorder associated with high morbidity and mortality in patients with cancer. Tumour-host interaction and maladaptive metabolic reprogramming are substantial, yet poorly understood, contributors to cachexia. Here we present a comprehensive overview of the spatio-temporal metabolic reprogramming during cachexia, using integrated metabolomics, RNA sequencing and 13C-glucose tracing data from multiple tissues and tumours of C26 tumour-bearing male mice at different disease stages. We identified one-carbon metabolism as a tissue-overarching pathway characteristic for metabolic wasting in mice and patients and linked to inflammation, glucose hypermetabolism and atrophy in muscle. The same metabolic rewiring also occurred in five additional mouse models, namely Panc02, 8025, ApcMin, LLC and KPP, and a humanised cachexia mouse model. Together, our study provides a molecular framework for understanding metabolic reprogramming and the multi-tissue metabolite-coordinated response during cancer cachexia progression, with one-carbon metabolism as a tissue-overarching mechanism linked to wasting.
    DOI:  https://doi.org/10.1038/s42255-025-01434-3
  15. Nat Commun. 2026 Jan 14. 17(1): 229
      The mechanisms underlying the metabolic adaptation of myeloid cells within the tumor microenvironment remain incompletely understood. Here, we identify 6-phosphogluconate dehydrogenase (6PGD), a rate-limiting enzyme in the pentose phosphate pathway (PPP), as an important regulator of monocytic-myeloid derived suppressor cell (M-MDSC) function. Our findings reveal that tumor M-MDSCs upregulate 6PGD expression via IL-6/STAT3 signaling. Blocking 6PGD, using either genetic or pharmacological approaches, impairs the immunosuppressive function of M-MDSCs and suppresses tumor growth. Mechanistically, 6PGD inhibition leads to the accumulation of its substrate, 6-phosphogluconate (6PG), within M-MDSCs, activates the JNK1-IRS1 and PI3K-AKT-pDRP1 signaling pathways, leading to mitochondrial fragmentation and elevated mitochondrial reactive oxygen species (ROS). This metabolic shift drives M-MDSCs toward an M1-like proinflammatory phenotype. Furthermore, 6PGD blockade synergizes with anti-PD-1 immunotherapy in a preclinical tumor model, substantially improving therapeutic outcomes. Our data reveals 6PGD as a possible therapeutic target to disrupt M-MDSC function and improve cancer immunotherapy outcomes.
    DOI:  https://doi.org/10.1038/s41467-025-68102-8
  16. bioRxiv. 2026 Jan 08. pii: 2026.01.07.698253. [Epub ahead of print]
      Cell Communication Network factor 4 (CCN4/WISP1) is a matricellular protein secreted by cancer cells that is upregulated in essentially all invasive breast cancers and promotes immunosuppression in melanoma. Recent work suggests that limited anti-tumor immunity also associates with poor patient outcomes in patients with breast cancer. Motivated by increased CCN4 correlating with dampened anti-tumor immunity in primary breast cancer, we test for a direct causal link by knocking out CCN4 (CCN4 KO) in the Py230 and Py8119 mouse breast cancer models. Tumor growth is reduced when CCN4 KO breast cancer cells are implanted in immunocompetent but not in immunodeficient mice. Correspondingly in size-matched tumors, CD4+ and CD8+ T cells are significantly increased in CCN4 KO tumors while the myeloid compartment is shifted from polymorphonuclear- to monocytic-myeloid-derived suppressor cells (MDSC). This shift in the MDSC compartment is also associated with a significant reduction in splenomegaly. Among mechanisms linked to local immunosuppression, CCN4 knockout has a similar impact on the secretome of both breast cancer and melanoma cell lines. Overall, our results suggest that CCN4 promotes tumor-induced immunosuppression in the context of breast cancer and is a potential target for therapeutic combinations with immunotherapies.
    DOI:  https://doi.org/10.64898/2026.01.07.698253
  17. Int Immunopharmacol. 2026 Jan 14. pii: S1567-5769(25)02095-8. [Epub ahead of print]172 116106
       BACKGROUND: Pancreatic ductal adenocarcinoma (PDAC) undergoes profound metabolic reprogramming. This study aims to elucidate how PIK3CG deficiency drives glutamine (Gln) metabolic reprogramming in PDAC.
    METHODS: We first identified PIK3CG as a key differentially expressed gene in PDAC and confirmed that its expression level correlates with patient survival. We established both in vitro and in vivo PIK3CG-knockdown (PIK3CG-KD) models. Using these models, we assessed its regulatory effects on the Gln metabolic pathway, mitochondrial reactive oxygen species (mtROS) accumulation, mitochondrial membrane potential, and tumor cell pyroptosis. Moreover, we delineated the specific molecular mechanism linking PIK3CG to downstream signaling. This mechanism crucially involves GLS2, a key enzyme in glutamine metabolism.
    RESULTS: PIK3CG deficiency suppresses the mechanistic target of rapamycin complex 1 (mTORC1) pathway, leading to enhanced phosphorylation of S6K2. This disrupts the interaction between nuclear S6K2 (Glu163) and P53 (Arg273), ultimately inhibiting GLS2 transcription. Consequently, a series of metabolic disturbances ensue: glutamate (Glu) accumulates substantially, Gln catabolism is blocked, and its influx into the TCA cycle is restricted, resulting in reduced α-ketoglutarate (α-KG) levels. The deficiency in α-KG triggers a significant accumulation of mtROS. Notably, despite elevated ROS levels, pyroptosis is suppressed and accompanied by exacerbated inflammation. Conversely, GLS2 overexpression rescues all the aforementioned phenotypes induced by PIK3CG-KD-including tumor growth, elevated mtROS, suppression of pyroptosis, and inflammatory response-while restoring Gln metabolic homeostasis.
    CONCLUSION: Our study reveals a novel mechanism by which PIK3CG-KD regulates Gln metabolism and mitochondrial function via the S6K2/P53/GLS2 axis, providing a rationale for metabolic intervention and precision therapy in PIK3CG-deficient PDAC.
    Keywords:  GLS2; Glutamine metabolism; PIK3CG; Pancreatic ductal adenocarcinoma; Pyroptosis
    DOI:  https://doi.org/10.1016/j.intimp.2025.116106
  18. Liver Int. 2026 Feb;46(2): e70507
       BACKGROUND & AIMS: Metabolic dysfunction-associated steatotic liver disease (MASLD) spans from simple steatosis to metabolic dysfunction-associated steatohepatitis (MASH) and can progress to cirrhosis or hepatocellular carcinoma. Despite its prevalence, effective therapies are lacking. Recent genome-wide association studies identified a common missense variant (rs2642438) in the Mitochondrial Amidoxime Reducing Component 1 (MTARC1) gene that protects against liver cirrhosis without increasing cardiovascular disease risk. Biochemical and disease risk signatures associated with carriers of this missense variant also aligned with those of a known loss-of-function MTARC1 variant, suggesting mARC1 inhibition as a potential MASLD treatment.
    METHODS: To validate mARC1 loss-of-function as protective against MASLD, we generated Mtarc1 knockout (KO) mice and placed them on a choline-deficient, L-amino acid-defined, high-fat diet (CDAHFD). Effects of Mtarc1 KO on obesity and type 2 diabetes were explored using a high-fat diet. Hepatocytes from Mtarc1 KO mice were isolated to explore the molecular mechanisms by which Mtarc1 KO impacts lipid metabolism.
    RESULTS: Mtarc1 KO mice exhibited no vital growth or development defects. With a high-fat diet-induced obesity model, obese Mtarc1 KO mice exhibited reduced liver mass and lower cholesterol levels, with no effect on glucose homeostasis. In a CDAHFD-induced MASLD model, mARC1 deficiency significantly reduced liver steatosis, profibrosis, and inflammation. Untargeted metabolomics profiling further showed hepatic enrichment of phospholipids in Mtarc1 KO mice. Primary hepatocytes isolated from Mtarc1 KO mice exhibited reduced lipid droplet accumulation, decreased fatty acid uptake, and increased lipid secretion.
    CONCLUSIONS: These findings support mARC1 inhibition as a promising therapeutic strategy for MASLD/MASH.
    Keywords:   Mtarc1 ; metabolic dysfunction‐associated steatotic liver disease; phospholipid; profibrosis; steatosis
    DOI:  https://doi.org/10.1111/liv.70507
  19. J Cell Physiol. 2026 Jan;241(1): e70128
      Preservation of the insulin-sensitive glomerular podocyte is imperative for normal kidney function. The protein tyrosine phosphatases (PTPs), protein tyrosine phosphatase 1B (PTP1B), T-cell protein tyrosine phosphatase (TCPTP), and Src homology phosphatase 2 (SHP2) are established regulators of insulin signaling in vivo and implicated in renal function. However, knowledge gaps exist regarding the roles of these enzymes and their integrated modulation of signaling in podocytes. Accordingly, uncovering the mediators of PTP function is critical to elucidate their modes of action and help develop mechanism-based interventions for podocytopathies. We generated E11 podocyte cell lines expressing the substrate-trapping mutants of these PTPs and then used immunoprecipitation and mass spectrometry to identify their putative substrates. Bioinformatic analyses were used to decipher the pathways affected by these enzymes in the insulin-stimulated podocytes. We identified known and novel targets, some common across the three PTPs, others shared between two PTPs, and others unique to a single phosphatase. Additionally, cytoskeleton and cellular junction-associated pathways were significantly enriched among the phosphatases and their putative substrates. Moreover, we uncovered a signaling node that is likely key to the action of these PTPs, comprising the protein tyrosine kinase Src, cortactin, and lamin A/C, interconnected via vimentin. To further validate this, we demonstrated that vimentin is a substrate of SHP2 in podocytes. The current findings suggest that PTP1B, TCPTP, and SHP2 act coordinately and engage numerous targets to orchestrate an integrated response to insulin in podocytes. Notably, these enzymes are components of a crucial signaling node that modulates cytoskeletal and junctional proteins, thereby influencing podocyte function.
    Keywords:  diabetic nephropathy; insulin; podocytes; protein tyrosine phosphatases; substrate trapping
    DOI:  https://doi.org/10.1002/jcp.70128
  20. bioRxiv. 2026 Jan 06. pii: 2026.01.05.697775. [Epub ahead of print]
      Therapy resistance is the leading cause of cancer-related deaths. Drug-tolerant persister cells (DTPs) represent a major barrier to cancer cure, mediating resistance through adaptive cell state transitions and driving tumor progression. Here, we investigate metabolic differences between DTPs and drug-sensitive cancer cells using integrated fluxomics. Proteomic profiling and extracellular flux analyses revealed that DTPs upregulate glycolysis and gluconeogenesis while reducing oxidative phosphorylation, indicating a shift in central carbon metabolism. Isotope tracing and metabolic modeling demonstrate that DTPs utilize glucose to fuel the pentose phosphate pathway (PPP) to generate NADPH and metabolize glutamine to provide carbons for the PPP via gluconeogenesis. Integrating our multi-omic datasets into a genome-scale model identified that DTPs sustain antioxidant metabolism by decreasing fluxes of other NADPH-consuming reactions upon in silico PPP knockout. These findings reveal a systems-level shift in DTP metabolism that maintains antioxidant activity for cell survival, highlighting potential new targets and treatment paradigms to overcome therapy resistance.
    DOI:  https://doi.org/10.64898/2026.01.05.697775
  21. Chembiochem. 2026 Jan;27(1): e202500616
      Spatial proteomics has emerged as a powerful approach to systematically map the subcellular localization of thousands of proteins in parallel, providing insights into organelle composition, protein trafficking, and context-dependent relocalization events. Building on advances in mass spectrometry sensitivity, and acquisition as well as quantification strategies, organelle-resolved protein maps can now be generated with unprecedented depth and resolution, and recent workflows have expanded the applicability of spatial proteomics to diverse experimental and challenging contexts. Complementary bioinformatic pipelines enable the assignment of proteins to compartments, the detection of distribution shifts, and the integration of spatial data with other omics layers. Beyond fundamental cell biology, the technology holds great potential for clinical research, where limited input material and the complexity of primary samples pose specific challenges. Emerging low-input preparation methods, antibody-based organelle enrichment, and microscopy-guided approaches offer promising solutions, while robust, marker-independent data analysis will be essential to handle the biological variability of patient-derived samples. As protocols become more automated, low-input compatible, and bioinformatically standardized, spatial proteomics is poised to become a valuable tool for mechanistic disease research, biomarker discovery, and therapeutic target identification.
    Keywords:  fractionation; mass spectrometry; microscopy‐guided segmentation; organelle profiling; protein translocations; proteome profiling
    DOI:  https://doi.org/10.1002/cbic.202500616
  22. J Lipid Res. 2026 Jan 13. pii: S0022-2275(26)00006-4. [Epub ahead of print] 100980
       BACKGROUND: A high-fat diet (HFD) induces metabolic dysfunction early, before the onset of the classic obese phenotype. However, understanding this early process remains limited, and potential diagnostic systems are still poorly investigated, particularly in childhood obesity.
    METHODS: Continuous blood glucose monitoring was performed in mice to evaluate the early metabolic effects of HFD exposure. Metabolomic and transcriptomic analyses were conducted to characterize metabolic and transcriptional changes at various HFD feeding stages and investigate underlying mechanisms. Venn analysis was applied to identify metabolites specific to early HFD exposure. These metabolites were further compared with those detected in obese children to identify potential early-warning biomarkers of obesity.
    RESULTS: Week 3 of HFD feeding was identified as a critical turning point in metabolic dysfunction in mice. Metabolomic profiling revealed that significant metabolic remodeling had occurred before glucose intolerance, particularly involving alterations in tryptophan metabolism, polyamine metabolism, and glycerophospholipid metabolism. Moreover, 54 HFD-specific metabolites were identified during this early stage. Further analysis identified serotonin, formiminoglutamate, inosine and spermine as potential early-warning biomarkers for HFD-induced obesity. Finally, transcriptomic profiling revealed early activation of IL-17A and type I interferon pathways, implicating immune involvement in metabolic perturbations.
    CONCLUSIONS: Early HFD exposure induces metabolic reprogramming before the onset of glucose intolerance. These findings provide new insights into the mechanisms of diet-induced metabolic dysfunction and support the identification of potential biomarkers for early detection, particularly in childhood obesity.
    Keywords:  Dysglycemia; High-fat diet; Metabolic perturbations; Polyamine metabolism; Tryptophan metabolism
    DOI:  https://doi.org/10.1016/j.jlr.2026.100980
  23. Nat Metab. 2026 Jan 15.
      Nicotinamide adenine dinucleotide (NAD(H)) and its phosphorylated form NADP(H) are vitamin B3-derived redox cofactors essential for numerous metabolic reactions and protein modifications. Various health conditions are associated with disturbances in NAD+ homeostasis. To restore NAD+ levels, the main biosynthetic pathways have been targeted, with nicotinamide (Nam), nicotinamide riboside (NR) and nicotinamide mononucleotide (NMN) being the most prominent boosters. However, while many preclinical studies have examined the effects of these precursors, a direct comparison in humans is lacking, and recent rodent research suggests that the NAD+-boosting effects of NR and NMN may depend on their microbial conversion to nicotinic acid (NA), a mechanism not yet confirmed in humans. Here we show in a randomized, open-label, placebo-controlled study in 65 healthy participants that 14 days of supplementation with NR and NMN, but not Nam, comparably increases circulatory NAD+ concentrations in healthy adults. Unlike the chronic effect, only Nam acutely and transiently affects the whole-blood NAD+ metabolome. Using ex vivo fermentation with human microbiota, we identify that NR and NMN give rise to NA and specifically enhance microbial growth and metabolism. We further demonstrate ex vivo in whole blood that NA is a potent NAD+ booster, while NMN, NR and Nam are not. Ultimately, we propose a gut-dependent model for the modes of action of the three NAD+ precursors with NR and NMN elevating circulatory NAD+ via the Preiss-Handler pathway, while rapidly absorbed Nam acutely affects NAD+ levels via the salvage pathway. Overall, these results indicate a dual effect of NR and NMN and their microbially produced metabolite NA: a sustained increase in systemic NAD+ levels and a potent modulator of gut health. ClinicalTrials.gov identifier: NCT05517122 .
    DOI:  https://doi.org/10.1038/s42255-025-01421-8
  24. Breast Cancer Res. 2026 Jan 12. 28(1): 12
       BACKGROUND: Metastatic disease is the main cause of breast cancer (BC)-related deaths, but prediction of metastases remains challenging especially in the large and diverse group with estrogen receptor (ER)-positive, human epidermal growth factor receptor 2 (HER2)-negative tumors. Molecular tumor features beyond currently used markers could provide important information for stratifying metastatic risk. To allow for the discovery of new subtypes and molecular tumor features associated with metastatic spread, i.e., both lymph node and distant metastases, we here leverage advances in proteomic profiling of tumors.
    METHODS: We developed a protocol for proteome and phosphoproteome analysis using label-free data independent acquisition (DIA) liquid chromatography tandem mass spectrometry (LC-MS/MS) and integrated the generated data with parallel transcriptome data for the profiling of 182 ER-positive, HER2-negative primary BC tumors from the SCAN-B cohort.
    RESULTS: A total of 13,571 protein groups, 7107 phosphopeptides and 13,085 expressed genes were quantified in at least 70% of the samples. The data showed clear differences between invasive lobular carcinoma and no special type cancers, including the hallmark loss of E-cadherin expression and differences in catenin levels. We identified potential new subtypes with differential immune infiltration patterns and survival through unsupervised consensus clustering. Additionally, by adopting an integrative, multiomic data analysis workflow, we identified several potential protein markers of both lymph node and distant metastases. For lymph node metastasis, the level of phosphorylated ES8L2 serine at position 570 (multivariable p value = 0.05, HR = 0.61, 95% CI 0.38-0.99) was associated with improved recurrence-free survival, and showed decreased abundance in lymph node positive cases. For distant metastases, on the other hand, proteins belonging to the heat shock protein 90 family were associated with worse distant recurrence-free survival (multivariable p value = 0.0058, HR = 2.10, 95% CI 1.24-3.55), with significantly higher abundance levels in patients with a distant recurrence event. These correlations with survival could also be validated in multiple external cohorts.
    CONCLUSIONS: In summary, we present the most comprehensive matched multiomic dataset from ER-positive/HER2-negative BC tumors, not only serving as an invaluable resource for further advancing precision medicine but also allowing the discovery of potential biomarkers and providing unique insights into metastatic processes.
    TRIAL REGISTRATION: Sweden Cancerome Analysis Network-Breast: Genomic Profiling of Breast Cancer (SCAN-B), beginning 2010-08, NCT02306096.
    Keywords:  Automation; Biomarker discovery; Breast cancer; Deconvolution; Immune infiltration; Mass spectrometry; Metastasis; Multi-omics; Phosphoproteomics; Proteomics
    DOI:  https://doi.org/10.1186/s13058-025-02173-9
  25. ACS Chem Biol. 2026 Jan 13.
      S-acylation, often referred to as S-palmitoylation, is a reversible and dynamic posttranslational modification that corresponds to the addition of a long-chain fatty acid to cysteine (Cys) residues. Established mass spectrometry-based chemoproteomics methods have improved our understanding of the S-acylation proteome, notably by identifying hundreds of S-acylated proteins, sometimes with the modified Cys. However, the precise quantification of S-acylation levels for each Cys within a single sample remains challenging at the proteome level. Quantification of S-acylation levels is critical to further our understanding of protein S-acylation in cellular function and its role in health and diseases. We report here the development of an S-acylation quantification workflow based on the sequential labeling of free Cys and S-acylated Cys with isotopic labeling reagents. The workflow was extensively optimized, notably by comparing the number of sites identified with two alkyne-tagged Cys-reactive isotopic probes and four azido-tagged biotin-based capture reagents. By integrating this enhanced workflow with high-field asymmetric waveform ion mobility spectrometry (FAIMS) on LC-MS/MS instruments for the separation of labeled peptides, over 17,000 unique Cys could be quantified in biological samples. Application of the S-acylation quantification workflow to cellular proteomes allowed for the quantification of S-acylation levels in a HeLa proteome. We also identified dynamic S-acylation changes in response to autophagy induction.
    DOI:  https://doi.org/10.1021/acschembio.5c00824
  26. Redox Biol. 2025 Dec 19. pii: S2213-2317(25)00493-8. [Epub ahead of print]90 103980
      Thioredoxin reductases (cytosolic TXNRD1 and mitochondrial TXNRD2) are antioxidant enzymes often overexpressed in tumors, including triple negative breast cancer (TNBC), making them promising targets for cancer therapy. Inhibiting these enzymes may worsen the already elevated oxidative stress in cancer cells, ultimately leading to cell death through a pro-oxidant mechanism. However, selectively targeting TXNRDs has been challenging due to the traditional reliance on covalent inhibition strategies. Recent studies have identified a druggable allosteric pocket in this enzyme family, paving the way for the development of novel non-covalent inhibitors, referred to as TXNRD(i)s. These inhibitors have been tested in TNBC models and have demonstrated a range of anti-cancer effects. To understand the molecular and cellular consequences of TXNRD(i)s, we conducted unbiased transcriptomic analyses and found that the gene expression changes induced by TXNRD(i) treatment closely mirror those resulting from TXNRD1 silencing, reinforcing TXNRD1 as the primary therapeutic target. While TXNRD(i) treatment increases redox stress in TNBC cells, this is not the main driver of the anti-cancer effect. Instead, TXNRD(i)s potently inhibit cell proliferation and induce G1 phase cell cycle arrest. Notably, supplementing cells with exogenous deoxynucleotides restores cell viability, cell cycle progression and partially reverses cell death. These findings indicate that TXNRD(i)s impair ribonucleotide reductase activity and deplete endogenous deoxynucleotide pools as the main mechanism of anti-cancer effects. We further demonstrate that TXNRD(i)s inhibit both TXNRD1 and TXNRD2, and that dual inhibition is more effective in suppressing TNBC cell growth. In vivo, TXNRD(i) treatment significantly impairs TNBC xenograft tumor growth and reduces proliferation-related genes. Collectively, these findings challenge the prevailing paradigm that all TXNRD inhibitors function through a pro-oxidant mechanism, instead highlighting that non-covalent TXNRD(i)s exert their effects by blocking proliferation offering a compelling therapeutic strategy for TNBC and potentially other cancers with elevated TXNRD expression.
    DOI:  https://doi.org/10.1016/j.redox.2025.103980