bims-cesirm 2025-11-16 papers

bims-cesirm

Biomed News

on Cell Signaling mediated regulation of metabolism

Issue of 2025–11–16
seventeen papers selected by
Tigist Tamir, University of North Carolina

Redox Regulation of Cell Migration via Nischarin S-glutathionylation.
Glyoxalase 1 is a pro-adipogenic gene.
Heat shock protein DNAJA2 controls insulin signaling and glucose homeostasis by preventing spontaneous insulin receptor endocytosis.
Uridine-sensitized screening identifies demethoxy-coenzyme Q and NUDT5 as regulators of nucleotide synthesis.
Discovery and Profiling of Protein Cysteine S-2-Carboxypropylation.
Potassium-Hydroxide-Based Extraction of Nicotinamide Adenine Dinucleotides from Biological Samples Offers Accurate Assessment of Intracellular Redox Status.
TXNIP upregulation controls metabolism and cell cycle during androgen deprivation therapy in prostate cancer.
SQOR as a metabolic rheostat of H2S: structure, redox homeostasis, and disease therapy.
Integrating machine learning and experimental validation identifies a post-translational modification gene signature for prognosis and treatment response in breast cancer.
β-Hydroxybutyrylation Links Ketone Metabolism to Mitochondrial Remodeling in Diabetic Cardiomyopathy.
Novel therapeutic strategies for targeting fatty acid oxidation in cancer.
Decoding spliceosome inhibition: Isobaric tag-based proteomic profiling of pladienolide B treated human cell lines.
Targeting polyamine metabolism and ferroptosis enhances the efficacy of KRAS-targeted therapy depending on KEAP1 status.
Androgen receptors promote oxidative phosphorylation and resistance to palmitate lipotoxicity in ER-mutant breast cancer.
Complete end-to-end learning from protein feature representation to protein interactome inference.
Proteomic sensors for quantitative multiplexed and spatial monitoring of kinase signaling.
Linoleic Acid Potentiates Response to Chemotherapy in Biliary Tract Cancer Through RARγ Activation.

Free Radic Biol Med. 2025 Nov 08. pii: S0891-5849(25)01348-6. [Epub ahead of print]

Redox Regulation of Cell Migration via Nischarin S-glutathionylation.

Madhu C Shivamadhu, Dhanushika S K Kukulage, Rayavarapu Padmavathi, Daniel Oppong, Faezeh Mashhadi Ramezani, Denaye N Eldershaw, Brett M Collins, Young-Hoon Ahn.

  Reactive oxygen species (ROS) are central players in redox signaling, controlling all biological processes in human health. Many reports demonstrated that ROS play essential roles in regulating cell migration and invasion, while contributing to cancer progression and metastasis, potentially via inducing protein cysteine oxidative modifications. Nevertheless, specific redox players involved in cell migration and invasion remain ill-defined. In this report, we found that Nischarin (NISCH), established as a tumor suppressor, is susceptible to S-glutathionylation, selectively at Cys185 located near its leucine-rich repeat (LRR) domains, which are implicated in protein-protein interactions with Rac1 and PAK1. We demonstrated that epithelial breast cancer cell lines, MCF7 and MDA-MB-231, expressing NISCH wild-type (WT), compared to its cysteine mutant (C185S), exhibit increased migration and invasion in response to oxidative stress, such as limited glucose. Mechanistically, NISCH S-glutathionylation reduced its binding to Rac1 and PAK1, without altering its binding to integrin α5. The dissociation of NISCH led to the activation of Rac1 and PAK1, resulting in the localization of Rac1 to the cell periphery, which facilitates lamellipodia formation. The activated PAK1 increased the phosphorylation of the LIMK1-cofilin axis, thereby further enhancing actin filament dynamics that promote cell migration. Based on the mechanistic analysis, we produced an engineered NISCH construct, composed of the N-terminal PX and LRR domains. We demonstrated that the engineered NISCH PX-LRR constructs, particularly one lacking the S-glutathionylation site (i.e., C185S), can suppress the migration, invasion, and colony formation of MDA-MB-231 cells, regardless of the presence of oxidative stress. Our data reports a new redox player in cell migration and invasion, while supporting the potential application of NISCH-derived protein-based therapeutics for breast cancer.

Keywords:  IRAS; Nischarin; S-glutathionylation; cell migration and invasion; redox signaling

DOI:  https://doi.org/10.1016/j.freeradbiomed.2025.11.013
J Biol Chem. 2025 Nov 07. pii: S0021-9258(25)02778-4. [Epub ahead of print] 110926

Glyoxalase 1 is a pro-adipogenic gene.

Marissa N Trujillo, Wei-Chen Zhang, Emely A Hoffman, Naoya Kitamura, Aiden M Phoebe, James J Galligan.

  Diabetes is one of the most prevalent and wide-spread diseases, with the majority of cases stemming from prolonged obesity. Obesity occurs through the expansion of adipose tissue in an unhealthy and dysfunctional manner, where patients develop inflammation and insulin resistance. Diabetic patients have increased levels of the reactive glycolytic by-product, methylglyoxal (MGO), and its resulting post-translational modifications (PTMs) compared to non-diabetic patients. To combat this, cells are equipped with the glyoxalase cycle, consisting of two enzymes, glyoxalase 1 (GLO1) and GLO2, to reduce the levels of MGO. Previous work has identified a putative role for MGO in the pathologies associated with obesity. We thus sought to interrogate the role of GLO1 in the context of adipogenesis using GLO1 knockout (GLO1-/-) 3T3-L1 preadipocytes. These cells have elevated, physiologically relevant, levels of MGO and MGO-derived PTMs. When differentiated to mature adipocytes, GLO1-/- cells fail to accumulate lipid, despite significant elevations in MGO. We also show a restoration of MGO-derived PTMs in GLO1-/- cells following differentiation. Proteomic analysis reveals significant enrichment in glycolytic and TCA cycle enzymes in WT cells compared to GLO1-/- cells after differentiation. Lastly, immunoblotting shows decreased AKT phosphorylation and reduced glucose uptake in differentiated GLO1-/- cells. Taken together, our data identifies a putative pro-adipogenic role for GLO1 and MGO in adipogenesis.

Keywords:  GLO1; Glyoxalase; glycation; glycerol; methylglyoxal

DOI:  https://doi.org/10.1016/j.jbc.2025.110926
Nat Commun. 2025 Nov 13. 16(1): 9973

Heat shock protein DNAJA2 controls insulin signaling and glucose homeostasis by preventing spontaneous insulin receptor endocytosis.

Yuanhua Qin, Wenjun Wu, Kequan Lin, Anthony J Davis, Yaping Huang.

Dysregulation of heat shock protein DNAJA2 induces genomic instability and was consequently hypothesized to promote tumorigenesis. However, DNAJA2 knockout mice do not develop cancer but exhibit neonatal lethality and the underlying mechanism remains unknown. Here, we demonstrate that DNAJA2 maintains homeostatic glucose metabolism by regulating insulin signaling. Mechanistically, DNAJA2 binds to the insulin receptor (IR) and prevents adaptor protein 2 (AP2)-mediated spontaneous IR endocytosis by inhibiting the IR-AP2 interaction. Thus, DNAJA2 defects lead to reduced IR localization on the plasma membrane and suppression of the insulin-stimulated signaling cascade, thereby inhibiting glycogen synthesis and storage in the liver during embryogenesis, further resulting in neonatal lethality of DNAJA2-deficient mice. Analysis of public datasets reveals a strong association between DNAJA2 and metabolic phenotypes, including type 2 diabetes mellitus (T2DM) and obesity, in both humans and mice. In conclusion, our study elucidates the mechanism by which DNAJA2 regulates IR endocytosis, insulin signaling and glucose metabolism, shedding light on the pathogenesis of metabolic disorders.

DOI: https://doi.org/10.1038/s41467-025-64948-0
Nat Metab. 2025 Nov 13.

Uridine-sensitized screening identifies demethoxy-coenzyme Q and NUDT5 as regulators of nucleotide synthesis.

Abigail Strefeler, Zakery N Baker, Sylvain Chollet, Mads M Foged, Rachel M Guerra, Julijana Ivanisevic, Hector Gallart-Ayala, David J Pagliarini, Alexis A Jourdain.

Rapidly proliferating cells require large amounts of nucleotides, making nucleotide metabolism a widely exploited therapeutic target against cancer, autoinflammatory disorders and viral infections. However, regulation of nucleotide metabolism remains incompletely understood. Here, we reveal regulators of de novo pyrimidine synthesis. Using uridine-sensitized CRISPR-Cas9 screening, we show that coenzyme Q (CoQ) is dispensable for pyrimidine synthesis, in the presence of the demethoxy-CoQ intermediate as alternative electron acceptor. We further report that the ADP-ribose pyrophosphatase NUDT5 directly binds PPAT, the rate-limiting enzyme in purine synthesis, which inhibits its activity and preserves the phosphoribosyl pyrophosphate (PRPP) pool. In the absence of NUDT5, hyperactive purine synthesis exhausts the PRPP pool at the expense of pyrimidine synthesis, which promotes resistance to purine and pyrimidine nucleobase analogues. Of note, the interaction between NUDT5 and PPAT is disrupted by PRPP, highlighting an intricate allosteric regulation. Overall, our findings reveal a fundamental mechanism of nucleotide balance and position NUDT5 as a regulator of nucleobase analogue metabolism.

DOI: https://doi.org/10.1038/s42255-025-01419-2
Molecules. 2025 Oct 31. pii: 4255. [Epub ahead of print]30(21):

Discovery and Profiling of Protein Cysteine S-2-Carboxypropylation.

Jiabao Song, Kejun Yin, Ronghu Wu, Y George Zheng.

  Methacrylyl-CoA is a key metabolic intermediate in the valine catabolic pathway. Its accumulation has been found to be cytotoxic and associated with pathological conditions. Nevertheless, detailed biological effects of methacrylyl-CoA and methacrylate in human physiology and pathology are poorly understood. We propose that the electrophilicity of the alkene bond in the methacrylyl group can react with the cysteine residues in proteins resulting in an unexplored protein post-translational modification (PTM), cysteine S-2-carboxypropylation (C2cp). To test and validate this mechanistic hypothesis, we experimentally detected and profiled S-2-carboxypropylated proteins from the complex cellular proteome with the design and application of a bioorthogonal chemical probe, N-propargyl methacrylamide. We tested the probe in different mammalian cell models and demonstrated its versatility and sensitivity to protein cysteine S-2-carboxypropylation. We established quantitative chemical proteomics for global and site-specific profiling of protein S-2-carboxypropylation, which successfully identified 403 S-2-carboxypropylated proteins and 120 cysteine modification sites from HEK293T cells. Through bioinformatic analysis, we found that C2cp-modified proteins were involved in a variety of critical cellular functions including translation, RNA splicing, and protein folding. Our chemoproteomic studies demonstrating the proteome-wide distribution of cysteine S-2-carboxypropylation provide a new biochemical mechanism for the functional investigation of methacrylyl-CoA and understanding valine-related metabolic disorders.

Keywords:  PTM; chemical proteomics; cysteine S-2-carboxypropylation (C2cp); methacrylyl-CoA; valine metabolism

DOI:  https://doi.org/10.3390/molecules30214255
Int J Mol Sci. 2025 Oct 24. pii: 10371. [Epub ahead of print]26(21):

Potassium-Hydroxide-Based Extraction of Nicotinamide Adenine Dinucleotides from Biological Samples Offers Accurate Assessment of Intracellular Redox Status.

Tamas Faludi, Daniel Krakko, Jessica Nolan, Robert Hanczko, Akshay Patel, Zach Oaks, Evan Ruggiero, Joshua Lewis, Xiaojing Wang, Ting-Ting Huang, Ibolya Molnar-Perl, Andras Perl.

  The reduced form of nicotinamide adenine dinucleotide phosphate (NADPH) is a primary electron donor for both antioxidant enzymes, such as glutathione reductase, and pro-oxidant enzymes, such as NADPH oxidases that produce reactive oxygen species (ROS) and nitric oxide synthases that generate nitric oxide which act as signaling molecules. Monitoring NADPH levels, NADPH/NADP+ ratio, and especially distinguishing from NADH, provides vital information about cellular redox status, energy generation, survival, lineage specification, and death pathway selection. NADPH detection is key to understanding metabolic reprogramming in cancer, aging, and cardiovascular, hormonal, neurodegenerative, and autoimmune diseases. Liquid chromatography combined with mass spectrometry (LC-MS) is crucial for NADPH detection in redox signaling because it offers the high sensitivity, specificity, and comprehensive profiling needed to quantify this vital but labile redox cofactor in complex biological samples. Using hepatoma cell lines, liver tissues, and primary hepatocytes from mice lacking transaldolase or nicotinamide nucleotide transhydrogenase, or having lupus, this study demonstrates that accurate measurement of NADPH depends on its preservation in reduced form which can be optimally achieved by extraction of metabolites in alkaline solution, such as 0.1 M potassium hydroxide (KOH) in comparison to 80% methanol (MeOH) alone or 40:40:20 methanol/acetonitrile/formic acid solution. While KOH extraction coupled with hydrophilic interaction liquid chromatography (HILIC) and mass spectrometry most reliably detects NADPH, NADP, NADH, NAD, polyamines, and polyols, MeOH extraction is best suited for detection of glutathione and overall discrimination between complex metabolite extracts. This study therefore supports performing parallel KOH and MeOH extractions to enable comprehensive metabolomic analysis of redox signaling.

Keywords:  NAD; NADH; NADP; NADPH; alkaline extraction; formic acid extraction; hepatocellular carcinoma; hepatocyte; liver; lupus; methanol extraction; transaldolase

DOI:  https://doi.org/10.3390/ijms262110371
Cell Death Dis. 2025 Nov 10. 16(1): 817

TXNIP upregulation controls metabolism and cell cycle during androgen deprivation therapy in prostate cancer.

Sergio Alcon-Rodriguez, Juan C Mayo, Pedro Gonzalez-Menendez, Iván Fernandez-Vega, David Hevia, Sheila Fernandez-Vega, Alba Moran-Alvarez, Daniela Pineda-Cevallos, Miguel Alvarez-Mugica, Pablo Rodriguez-Gonzalez, Belen Garcia-Soler, Jorge Zamora, Jose M C Tubio, Rosa M Sainz, Isabel Quiros-Gonzalez.

Thioredoxin-Interacting Protein (TXNIP) is an arrestin at the crossroad of redox and glycolytic metabolisms. Prostate cancer (PCa) exhibits a unique metabolic profile due to the glycolytic nature of healthy prostate tissue. We hypothesize that TXNIP plays a pivotal role in the progression of PCa to castration-resistant prostate cancer (CRPC), an incurable stage of the disease characterized by profound metabolic reprogramming and independence from androgens. Only a subset of patients progresses to CRPC, and current stratification tools lack robust biomarkers. TXNIP expression is directly suppressed by androgens and diminishes during tumor initiation and progression, as demonstrated in both human samples and a prostate adenocarcinoma mouse model (TRAMP). TXNIP regulates glucose metabolism by sequestering the glucose transporter GLUT1 away from the membrane, shifting metabolism from glycolysis to glutaminolysis. Nuclear-localized TXNIP induces cell cycle arrest through the upregulation of p27kip1 which is downregulated together with TXNIP in CRPC. The response to androgen deprivation therapy (ADT) strongly depends on TXNIP expression. In the murine model, TXNIP levels were significantly higher in ADT responders compared to non-responders. Furthermore, TRAMP-Txnip-/- prostate tumors exhibited a poorer response to ADT, with increased Ki67 and enhanced viability. In clinical samples, all patients on relapse showed low levels of TXNIP and progressed to CRPC. Our findings identify TXNIP as a critical regulator of cell cycle and glucose metabolism in PCa and emphasize for the first time its essential role in mediating therapeutic responses to ADT.

DOI: https://doi.org/10.1038/s41419-025-08128-4
Front Cell Dev Biol. 2025 ;13 1685252

SQOR as a metabolic rheostat of H2S: structure, redox homeostasis, and disease therapy.

Ming-Hui Peng, Kai-Lun Zhang, Zhong-Wu Ma, He-Wei Zhang, Shi-Wei Guan, Hai-Bo Yu.

  Sulfide:quinone oxidoreductase (SQOR) is an inner-mitochondrial-membrane enzyme that couples hydrogen sulfide oxidation to the coenzyme Q pool, thereby linking sulfur metabolism with cellular bioenergetics and redox control. Recent structural and mechanistic advances-most notably the catalytic cysteine trisulfide-clarify how membrane context and substrate availability tune catalytic flux, yet debate persists over the physiological sulfur acceptor (glutathione versus sulfite) and how microenvironments route sulfide. SQOR also shapes ferroptosis: by using hydrogen selenide to reduce ubiquinone, it elevates ubiquinol and suppresses lipid peroxidation independently of glutathione peroxidase-4. We synthesize cross-system disease evidence-brain (hypoxia/ischemia, neuroinflammation), heart (divergent roles in acute ischemia-reperfusion versus chronic failure), kidney (mitochondrial dysfunction and cGAS-STING(cyclic GMP-AMP synthase-stimulator of interferon genes)-driven fibrosis), gastrointestinal tract (stage-specific effects in colorectal cancer and impaired detoxification in ulcerative colitis), bone/metabolic disorders, and the male reproductive system-highlighting SQOR's bidirectional pathology when hydrogen sulfide is excessive or depleted. Viewing SQOR as a "metabolic rheostat" reconciles these paradoxes and underscores therapeutic opportunities: metabolic supplementation (e.g., coenzyme Q10), selective inhibition or activation, and context-matched modulation. We further propose companion diagnostics that quantify sulfur/selenium species and enzyme activity to enable patient stratification and de-risk clinical translation.

Keywords:  coenzyme Q10; colorectal cancer; ferroptosis; hydrogen sulfide (H2S); mitochondrial bioenergetics; sulfide oxidation pathway; sulfide:quinone oxidoreductase (SQOR); ulcerative colitis

DOI:  https://doi.org/10.3389/fcell.2025.1685252
Sci Rep. 2025 Nov 14. 15(1): 39962

Integrating machine learning and experimental validation identifies a post-translational modification gene signature for prognosis and treatment response in breast cancer.

Lina Zhao, Lijuan Song, Hongzhi Wang, Wen Tian, Junfeng Xi, Bo Zhang, Yue Cai, Lei Hou.

  Breast cancer (BC) is the most prevalent malignancy among women, and the steadily increasing disease burden has garnered considerable global attention. Post-translational modifications (PTMs) are critical in the initiation and progression of BC. This study aimed to elucidate the associations between diverse PTMs and the prognosis of patients with BC. We collected genes associated with multiple PTMs and evaluated the activity of each PTM using GSVA. We aggregated PTM scores to derive the PTMS and identified differentially expressed genes between the high- and low-PTMS groups. A PTM-related gene signature (PTMRS) was developed based on the optimal combination among 117 machine learning models, and its predictive performance was benchmarked against other published signatures. In addition, we investigated the associations between PTMRS, tumor immunity, and treatment response. Gene expression across different cell types was evaluated using single-cell and spatial transcriptomic analyses. Gene expression levels in cancerous and paired adjacent noncancerous tissues were validated by PCR. The results of GSVA showed that most of the PTMs were dysregulated in cancer. Tumor immunity levels were elevated in the low-PTMS group compared with the high-PTMS group. The PTMRS comprised five genes: SLC27A2, TNFRSF17, PEX5L, FUT3, and COL17A1. The predictive performance of the PTMRS exceeded that of the clinical profile and 14 other published gene signatures. Patients in the high-PTMRS group exhibited poorer prognosis and reduced anti-tumor immunoreactivity. In addition, patients in the low-PTMRS group showed improved responses to chemotherapy and immune checkpoint inhibitors. Spatial transcriptomics analysis revealed that SLC27A2 exhibited higher expression in malignant spots, whereas COL17A1 and TNFRSF17 showed lower expression in malignant spots. SLC27A2 mRNA expression was elevated in tumor tissues relative to adjacent noncancerous tissues, whereas the mRNA expression levels of the other four genes were decreased. This study reveals the important role of PTMs in BC prognosis and provides new perspectives for the prognostic assessment of BC patients as well as personalized treatment.

Keywords:  Breast cancer; Gene signature; Machine learning; Post-translational modification; Prognosis

DOI:  https://doi.org/10.1038/s41598-025-23772-8
Diabetes. 2025 Nov 10. pii: db250496. [Epub ahead of print]

β-Hydroxybutyrylation Links Ketone Metabolism to Mitochondrial Remodeling in Diabetic Cardiomyopathy.

Haoran Jing, Meixin Shi, Ye Wang, Rongyi Cao, Xiaoxue Li, Xin Zhong, Shiyun Dong, Can Wei.

Diabetic cardiomyopathy (DbCM) is characterized by metabolic remodeling and energetic stress independent of coronary artery disease. Increased reliance on fatty acid and ketone body metabolism has been observed in DbCM, but the regulatory mechanisms linking altered substrate use to myocardial dysfunction remain poorly understood. In particular, lysine β-hydroxybutyrate (Kbhb), a ketone body-derived, posttranslational modification, has emerged as a potentially critical regulator but has not been fully investigated. We conducted a comprehensive multiomics study integrating metabolomics, transcriptomics, proteomics, and Kbhb-specific proteomics on myocardial tissues in a well-established mouse model of DbCM. Kbhb-modified proteins were systematically mapped and quantified, followed by motif, subcellular localization, and protein-protein interaction analyses. DbCM cardiac tissue exhibited coordinated upregulations of fatty acid β-oxidation, ketone metabolism, and tricarboxylic acid cycle activity at the transcriptomic, proteomic, and metabolomic levels. Kbhb profiling revealed extensive mitochondrial protein modification, with Atp5f1a-K239 identified as a key modification site strongly correlated with β-hydroxybutyrate and isocitric acid concentrations. This study identifies Kbhb as a potential metabolic-epigenetic modifier linking ketone body availability to the regulation of mitochondrial proteins in DbCM. Our findings provide novel insights into metabolic-epigenetic cross talk and identify potential therapeutic targets for interventions to restore mitochondrial function in alleviating diabetic heart disease.
ARTICLE HIGHLIGHTS: We performed a multiomics study to better understand dysfunctions in diabetic cardiomyopathy (DbCM) and specifically identify links between lysine β-hydroxybutyrylation (Kbhb), a ketone body-derived, posttranslational modification, and cardiac dysfunction. DbCM cardiac tissue exhibited coordinated upregulations of fatty acid β-oxidation, ketone metabolism, and tricarboxylic acid cycle activity at the transcriptomic, proteomic, and metabolomic levels. Mitochondrial proteins showed that high Kbhb modification and modification of the Atp5f1a-K239 site were strongly correlated with high β-hydroxybutyrate and isocitric acid concentrations. This study identifies Kbhb modification of mitochondrial proteins as a potential mechanism linking ketone body availability to mitochondrial function in DbCM.

DOI: https://doi.org/10.2337/db25-0496
Biomark Res. 2025 Nov 11. 13(1): 145

Novel therapeutic strategies for targeting fatty acid oxidation in cancer.

Yan Wang, Mengsi Zhang, Jihong Liu, Chenglong Li, Na Sun, Xiujuan Wu, Chengfang Wang, Xuanni Tan, Yi Yang, Xiaowei Qi, Yi Zhang.

  Metabolic rewiring is a defining feature of malignant cells, enabling them to dynamically exploit nutrient resources to meet bioenergetic problems at different growth stages. Beyond the classical Warburg effect, recent studies have shown that neoplasms demonstrate a marked dependency on lipid metabolism, using free fatty acids to support cellular proliferation and regeneration via fatty acid oxidation (FAO). As a central component of lipid metabolism, FAO exerts dual immunomodulatory functions within tumors. Although numerous studies have described the enzymatic reactions of the FAO pathway in different malignancies, relatively few have investigated the pharmacological disruption of these enzymatic checkpoints and the resulting immunological consequences. Moreover, existing therapeutic strategies have failed to achieve a risk-benefit balance, limiting the clinical translation of FAO-directed approaches. To better understand the therapeutic implications of FAO, we investigated the mechanistic pathways mediated by mitochondrial rate-limiting enzymes, with a particular focus on the carnitine palmitoyltransferase 1 enzyme family-the critical gatekeeper controlling the entry of fatty acids into mitochondrial oxidation instead of CPT2. We comprehensively evaluated its role in tumor biology and also highlight future research directions to inform rational intervention strategies.

Keywords:  Cancer; Carnitine palmitoyltransferase 1; Fatty acid oxidation; Targeted therapy; Tumor microenvironment

DOI:  https://doi.org/10.1186/s40364-025-00855-2
J Proteomics. 2025 Nov 10. pii: S1874-3919(25)00192-7. [Epub ahead of print] 105565

Decoding spliceosome inhibition: Isobaric tag-based proteomic profiling of pladienolide B treated human cell lines.

Xcanda Ixchel Herrera Lopez, Karina Martinez-Perez, Sanjukta Guha Thakurta, Benjamin Levi, Joao A Paulo.

  Pladienolide B (Pla-B) is a potent splicing modulator that has shown promise in cancer treatment, but its cellular effects remain incompletely understood. We investigated the dose-associated effect of Pla-B on human cell lines using isobaric tag-based quantitative proteomics and phosphoproteomics techniques. We quantified over 10,000 proteins and 19,000 phosphorylation events in SH-SY5Y cells, revealing dose-associated changes in protein abundance and phosphorylation status. Low Pla-B concentrations induced significant alterations in nuclear proteins, specifically those involved in transcription and cell division. Higher concentrations led to more extensive proteome remodeling, affecting chromatin-associated proteins and transcription. Phosphoproteome analysis uncovered alterations in the phosphorylation states of proteins including the splicing factor subunit SF3B, suggesting complex regulation of signaling pathways. Our findings reveal the detailed proteomic landscape of Pla-B's effects, offering insights into its role in the global proteome, which may guide future therapeutic applications and rational drug design.

Keywords:  Phosphoproteomics; Pladienolide B; SF3B complex; Spliceosome; Splicing modulation

DOI:  https://doi.org/10.1016/j.jprot.2025.105565
Nat Commun. 2025 Nov 11. 16(1): 9923

Targeting polyamine metabolism and ferroptosis enhances the efficacy of KRAS-targeted therapy depending on KEAP1 status.

Yunyi Bian, Guangyao Shan, Guoshu Bi, Zhijie Xu, Jiaqi Liang, Yuanliang Yan, Wei Guo, Qihai Sui, Yanjun Yi, Haochun Shi, Tao Lu, Huan Zhang, Qun Wang, Hong Fan, Wei Jiang, Cheng Zhan.

The resistance to KRAS-targeted therapies, particularly due to co-occurring gene mutations, remains a significant challenge. Through a metabolite library screening, we reveal that polyamines sensitize KRAS inhibitors only in KRASMU/KEAP1WT cells but not in KRASMU/KEAP1MU cells. Transcriptome sequencing and metabolome profiling pinpoint SAT1, the key enzyme in polyamine metabolism, as essential for this divergence. In KRASMU/KEAP1WT context, treatment of KRAS inhibitors activates JNK/c-Jun pathway and SAT1 expression, while the augmented SAT1 facilitates polyamine metabolism and KRAS inhibitors-induced ferroptosis. Conversely, in KRASMU/KEAP1MU cells, activated JNK promotes the degradation of NRF2, thereby inhibiting SAT1 expression. Our results further demonstrate that polyamine supplementation enhances KRAS-targeted therapy in KRASMU/KEAP1WT resistant cells, patient-derived organoids, xenografts, and spontaneously tumorigenic mice, while KRASMU/KEAP1MU models require lentivirus or adeno-associated virus-mediated SAT1 overexpression prior to polyamine treatment, to augment ferroptosis and drug sensitivity. Our findings highlight SAT1-mediated polyamine metabolism as a promising target in precision treatments for KRAS-mutant cancers.

DOI: https://doi.org/10.1038/s41467-025-65441-4
Endocrinology. 2025 Nov 11. pii: bqaf168. [Epub ahead of print]

Androgen receptors promote oxidative phosphorylation and resistance to palmitate lipotoxicity in ER-mutant breast cancer.

Dane T Sessions, Dillon P Boulton, Nicole S Spoelstra, M Cecilia Caino, Min Yu, Andrew Goodspeed, Jennifer K Richer.

  Aromatase inhibitors (AI) are first-line therapy for postmenopausal women with estrogen receptor-expressing (ER+) breast cancer (BC). AI therapy effectively reduces recurrence and extends lifespan for patients with ER+ breast cancer through long term estrogen deprivation (LTED) resulting from inhibition of the enzyme aromatase that converts androgens to estrogens. However, up to 50% of ER+ BC recurs as AI resistant metastatic disease within 10 years of diagnosis. AI resistant BC upregulates androgen receptors (AR) and mitochondrial oxidative phosphorylation (OXPHOS) and requires OXPHOS and fatty acid oxidation (FAO). The liver and lung, common ER+ BC metastatic sites, have high abundance of the saturated fatty acid palmitate (PA). We asked whether AR signaling regulates OXPHOS in the context of LTED. Using mutant ER-expressing MCF7 and T47D BC cell lines with AR antagonism via the anti-androgen enzalutamide and with shRNA knockdown, we demonstrate that AR supports cell growth, OXPHOS, FAO, and resistance to PA lipotoxicity. We identify AR as a positive regulator of the carnitine acyltransferase family enzyme CRAT that promotes OXPHOS capacity. These studies identify AR as pro-tumor in the LTED setting and as a therapeutic target for ER-mutant BC that develops under the selective pressure of AI therapy.

Keywords:  androgen receptor; breast cancer; estrogen receptor; fatty acid oxidation; mitochondria; oxidative phosphorylation

DOI:  https://doi.org/10.1210/endocr/bqaf168
Gigascience. 2025 Jan 06. pii: giaf122. [Epub ahead of print]14

Complete end-to-end learning from protein feature representation to protein interactome inference.

Yu-Hsin Chen, Chien-Fu Liu, Jun-Yi Leu, Huai-Kuang Tsai.

   BACKGROUND: Co-fractionation coupled with mass spectrometry (CF-MS) is a powerful strategy for mapping protein-protein interactions (PPIs) under near-physiological conditions. Despite recent progress, existing analysis pipelines remain constrained by reliance on handcrafted features, sensitivity to experimental noise, and an inherent focus on pairwise interactions, which limit their scalability and generalizability. To address these difficulties, we introduce FREEPII (Feature Representation Enhancement End-to-End Protein Interaction Inference), a unified deep learning framework that integrates CF-MS data with sequence-derived features to learn biologically meaningful protein-level representations for accurate and efficient inference of PPIs and protein complexes.
RESULTS: FREEPII employs a convolutional neural network architecture to learn protein-level representations directly from raw data, enabling feature sharing across interaction pairs and reducing computational complexity. To enhance robustness against CF-MS noise, protein sequences are introduced as auxiliary input to enrich the feature space with complementary biological cues. The supervised protein embeddings further encode network-level context derived from complex annotations, allowing the model to capture higher-order interactions and enhance the expressive power of protein representations. Extensive benchmarking demonstrates that FREEPII consistently outperforms state-of-the-art CF-MS analysis tools, capturing more biologically coherent and discriminative protein features. Cross-dataset evaluations further reveal that integrating multimodal data from diverse experimental contexts substantially improves the generalization and sensitivity of data-driven models, offering a scalable, cross-species strategy for reliable protein interaction inference.
CONCLUSIONS: FREEPII provides a unified computational framework that integrates CF-MS data and sequence-derived features to learn discriminative and biologically consistent protein representations. By leveraging multimodal inputs through a coherent deep learning architecture, the model achieves accurate and scalable inference of PPIs and protein complexes across species. Its modality-aware design and supervised protein embeddings capture higher-order interaction contexts, ensuring robust generalization and reliable discovery of novel interactions. Overall, FREEPII offers a flexible and extensible foundation for data-driven exploration of protein interaction networks.

Keywords:  co-fractionation coupled with mass spectrometry analysis; convolutional neural network; end-to-end learning; protein interactome inference; representation learning

DOI:  https://doi.org/10.1093/gigascience/giaf122
Nat Commun. 2025 Nov 13. 16(1): 9902

Proteomic sensors for quantitative multiplexed and spatial monitoring of kinase signaling.

William J Comstock, Marcos V A S Navarro, Deanna V Maybee, Yiseo Rho, Mateusz Wagner, Khoula Jaber, Yingzheng Wang, Marcus B Smolka.

Understanding kinase action requires precise quantitative measurements of their activity in vivo. In addition, the ability to capture spatial information of kinase activity is crucial to deconvolute complex signaling networks, interrogate multifaceted kinase actions, and assess drug effects or genetic perturbations. Here we develop a proteomic kinase activity sensor technique (ProKAS) for the analysis of kinase signaling using mass spectrometry. ProKAS is based on a tandem array of peptide sensors with amino acid barcodes that allow multiplexed analysis for spatial, kinetic, and screening applications. We engineered a ProKAS module to simultaneously monitor the activities of the DNA damage response kinases ATR, ATM, and CHK1 in response to genotoxic drugs, while also uncovering differences between these signaling responses in the nucleus, cytosol, and replication factories. Furthermore, we developed an in silico approach for the rational design of specific substrate peptides expandable to other kinases. Overall, ProKAS is a versatile system for systematically and spatially probing kinase action in cells.

DOI: https://doi.org/10.1038/s41467-025-65950-2
FASEB J. 2025 Nov 30. 39(22): e71232

Linoleic Acid Potentiates Response to Chemotherapy in Biliary Tract Cancer Through RARγ Activation.

Yinye Yao, Chunjing Xu, Yongfu Shao, Xiaoqing Xu, Qian Yin, Xinyuan Cao, Meifang Zheng, Duqin Zhao, Wangye Zheng, Jiaojiao Ni, Jieer Ying, Yunben Yang.

  Biliary tract cancer (BTC) remains highly challenging owing to its poor prognosis. Although gemcitabine plus cisplatin (Gem/Cis) represents a standard chemotherapy option, treatment resistance significantly limits the outcomes. Metabolic reprogramming influences therapeutic response; however, the specific metabolic determinants of chemosensitivity in BTC are poorly defined. Using untargeted metabolomics followed by targeted validation, we found that plasma linoleic acid (LA) levels were significantly elevated in patients with chemotherapy-responsive BTC. LA supplementation led to tumor accumulation and synergistically enhanced Gem/Cis-induced cytotoxicity in vitro and in vivo. Mechanistic investigations revealed that LA activated retinoic acid receptor gamma (RARγ), and pharmacological or genetic ablation of RARγ abolished the chemosensitizing effects of LA, establishing RARγ as an important mediator. Activation of the LA-RARγ axis orchestrated a dual proapoptotic and pro-immune transcriptional program. This resulted in increased cancer cell apoptosis and a remodeled immune microenvironment, characterized by reduced PD-L1 expression and enhanced CD8+ T cell activation. Taken together, this study identified LA as a novel metabolic modulator that potentiates chemotherapy response in BTC through RARγ activation, orchestrating a dual antitumor response by promoting cancer cell apoptosis and enhancing antitumor immunity.

Keywords:  apoptosis; biliary tract cancer; chemotherapy; linoleic acid; retinoic acid receptor gamma; tumor microenvironment

DOI:  https://doi.org/10.1096/fj.202502665R