bims-cesirm 2026-02-08 papers

bims-cesirm

Biomed News

on Cell Signaling mediated regulation of metabolism

Issue of 2026–02–08
33 papers selected by
Tigist Tamir, University of North Carolina

Dietary sulfur amino acid restriction improves glucose homeostasis through hepatic de novo serine synthesis.
Phosphoproteomics Analysis of Insulin-like Growth Factor-1 Signaling in Neuronal Cells.
Cross-tissue deep profiling of redox proteome in obese mice using enhanced resin-assisted capture and data-independent acquisition.
Splicing Factor SF3B4 Suppresses Pancreatic Cancer Growth and Migration by Inhibiting Autophagy.
AHCY: A Metabolic Gatekeeper at the Interface of Methylation, Redox Balance, and Cellular Stress Response.
Unsaturated Phosphorus Electrophiles to Probe Protein Tyrosine Phosphatases.
SLC6A6 imports taurine into mitochondria to sustain mitochondrial translation and tumour growth.
RNF90 promotes hepatic steatosis by degrading CPT1α to suppress fatty acid oxidation.
Trustworthy prediction of enzyme commission numbers using a hierarchical interpretable transformer.
Integrated Structural and Glycoproteomic Profiling Reveals Protein Conformational Remodeling and Biomarkers Across Alzheimer's Disease Progression.
Metabolic reprogramming in cancer: signaling pathways and therapeutic targets.
Transglutaminase 2 exacerbates ovarian cancer survival by directly inactivating GSK3β.
Complete Data Analysis Workflow for Quantitative DIA Mass Spectrometry Using Nextflow.
Reversible arginine methylation regulates mitochondrial IDH2 activity: coordinated control by CARM1 and KDM3A/4A.
Automatically Defining Protein Words for Diverse Functional Predictions Based on Attention Analysis of a Protein Language Model.
Analysis of the transcriptomic and metabolomic landscape of prostate cancer with different anatomical origins using snFLARE-seq and mxFRIZNGRND.
Chemical Proteomic Profiling of Lysine Benzoylation.
Changes in EGFR activity following CRISPR/Cas9-editing of the EGF binding domain.
Integrative metabolomic and single-cell transcriptomic analysis of recurrent condyloma acuminatum in humans.
Energetic stress in combination with impaired fatty acid oxidation induces sequestration of CoA and adaptation of CoA metabolism.
Cullin-3 adaptor SHKBP1 inhibits SQSTM1/p62 oligomerization and Keap1 sequestration.
Functional analysis of O-GlcNAcylation by networking of OGT interactors and substrates.
Decoding the Post-translational Modification Crosstalk: Functional Implications of Phosphorylation, Acetylation, and Methylation.
Spatiotemporal 4D Whole-cell Modeling of a Minimal Autotroph Reveals Central Carbon Metabolism Regulated Locally by Protein Megacomplexes via Post-translational Modifications under Light Disturbance.
Phosphorylation of Cyclophilin-D is Not Required for Regulation of The Mitochondrial Permeability Transition Pore by GSK3β.
Lactylation enhances YTHDF3 stability to promote cisplatin resistance via m6A-dependent KDM6B decay in bladder cancer.
Neoadjuvant endocrine treatment plus mammaglobin-A DNA vaccine induces antitumor immune responses in the primary tumor and peripheral blood of breast cancer patients: Insights from a phase 1b clinical trial.
SF3B1 Phosphorylation Prompts U2AF2 Dissociation for Widespread Control of pre-mRNA Splicing.
Recent advances in proximity labeling-based subcellular proteomic mapping.
Impact of obesity on aromatic amino acids and brain glucose during acute hyperglycemia.
Glucose Deprivation of Tumor Cells via Selective Nutrient Delivery: A Potential Therapy for Metastatic Breast Cancer.
Alteration of Flavin Homeostasis in Uterine Cancer.
A cell-based assay for retinaldehyde dehydrogenase activity: retinoid quantification as an alternative to current fluorescence-based approaches.

Mol Metab. 2026 Feb 03. pii: S2212-8778(26)00009-8. [Epub ahead of print] 102325

Dietary sulfur amino acid restriction improves glucose homeostasis through hepatic de novo serine synthesis.

Andres F Ortega, Cha Mee Vang, Ferrol I Rome, Kaitlyn M Andreoni, Aiden M Phoebe, Alisa B Nelson, Peter A Crawford, James J Galligan, Stanley Ching-Cheng Huang, Curtis C Hughey.

  Dietary sulfur amino acid restriction (SAAR) improves whole-body glucose homeostasis, elevates liver insulin action, and lowers liver triglycerides. These adaptations are associated with an increased expression of hepatic de novo serine synthesis enzymes, phosphoglycerate dehydrogenase (PHGDH) and phosphoserine aminotransferase 1 (PSAT1). This study tested the hypothesis that enhanced hepatic serine synthesis is necessary for glucose and lipid adaptations to SAAR. Hepatocyte-specific PSAT1 knockout (KO) mice and wild type (WT) littermates were fed a high-fat control or SAAR diet. In WT mice, SAAR increased liver PSAT1 protein (∼70-fold), serine concentration (∼2-fold), and 13C-serine (∼20-fold) following an intravenous infusion of [U-13C]glucose. The elevated liver serine and partitioning of circulating glucose to liver serine by SAAR were attenuated in KO mice. This was accompanied by a blunted improvement in glucose tolerance in KO mice fed a SAAR diet. Interestingly, SAAR decreased liver lysine lactoylation, a SAA-supported post-translational modification known to inhibit PHGDH enzymatic activity. This suggests dietary SAAR may increase serine synthesis, in part, by lowering lysine lactoylation. Beyond glucose metabolism, dietary SAAR reduced body weight, adiposity, and liver triglycerides similarly in WT and KO mice. Collectively, these results demonstrate that hepatic PSAT1 is necessary for glucose, but not lipid, adaptations to SAAR.

Keywords:  De novo serine synthesis; Glucose homeostasis; Liver intermediary metabolism; Sulfur amino acid restriction

DOI:  https://doi.org/10.1016/j.molmet.2026.102325
J Proteome Res. 2026 Feb 01.

Phosphoproteomics Analysis of Insulin-like Growth Factor-1 Signaling in Neuronal Cells.

Morgan J Rothschadl, Monica Sathyanesan, Samuel S Newton.

  Phosphorylation is a key post-translational modification that can impact the function of a protein and the outcome of cell signaling pathways. Using phosphoproteomics to characterize the phosphorylation changes downstream of trophic factor signaling is important for better understanding the pleiotropic actions of this class of molecules. Insulin-like growth factor-1 (IGF-1) is a trophic factor that can influence cellular growth and differentiation, and IGF-1 signaling in the brain has been linked to cognitive processes. While its main signaling molecules are well characterized, we sought to perform a more in-depth and unbiased analysis of the IGF-1 phosphoproteome in neuronal cells. To obtain insight into the IGF-1 signaling pathway in neuronal cells, we performed a quantitative mass spectrometric phosphoproteomics analysis in rat pheochromocytoma (PC-12) cells. Our results illustrate a diverse phosphoproteome downstream of IGF-1, with insight into novel phosphoprotein sites, such as Plcβ3 (Ser1105), that likely influence IGF-1 signaling in neuronal cells. We also identify a robust upregulation of the Rho GTPase cycle and an activation of synaptogenesis signaling downstream of IGF-1. These results pave the way for more targeted studies on specific phosphoprotein sites, which will facilitate a better understanding of how these phosphorylation events impact IGF-1-related signaling outcomes in neuronal cells.

Keywords:  IGF-1; PC-12; neuronal culture; phosphoproteomics; trophic factor

DOI:  https://doi.org/10.1021/acs.jproteome.5c00655
Redox Biol. 2026 Jan 28. pii: S2213-2317(26)00054-6. [Epub ahead of print]90 104056

Cross-tissue deep profiling of redox proteome in obese mice using enhanced resin-assisted capture and data-independent acquisition.

Jiyuan Liu, Xinbo Jiang, Yunyu Li, Liye Shen, Xiaoliang Li, Xiaohui Wang, Jinlong Wang.

  Cysteine thiol modification plays a critical role in the precise regulation of the cellular redox state. Existing redox proteomic methodologies are often limited by their efficiency, complexity, and cost. To overcome these limitations, we developed and synthesized a series of novel enrichment resins. Three of these resins demonstrated a markedly enhanced enrichment efficiency. The application of one such resin, coupled with data-independent acquisition, allowed the systematic and reproducible quantification and analysis of thiol sites on a large scale within a single experiment. We further employed this strategy in a murine model of obesity and identified over 40,000 thiol sites across five tissues. These findings highlight the resin's capability to identify and quantify a significant number of thiol sites, offering a valuable resource for comprehensive investigations into redox regulation and oxidative stress in obesity.

Keywords:  Data-independent acquisition; Enhanced resin-assisted capture; Obesity; Redox proteomics; Thiol sites enrichment

DOI:  https://doi.org/10.1016/j.redox.2026.104056
Anticancer Res. 2026 Feb;46(2): 737-747

Splicing Factor SF3B4 Suppresses Pancreatic Cancer Growth and Migration by Inhibiting Autophagy.

So-Hyun Choi, Jiyoon Seo, Seung Min Jeong.

   BACKGROUND/AIM: Pancreatic ductal adenocarcinoma (PDAC) is one of the most lethal malignancies, characterized by aggressive progression, profound chemoresistance and unique metabolic adaptations such as elevated autophagy. Although the splicing factor SF3B4 has been reported to function as an oncogene in other malignancies, its role in PDAC remains unclear. This study aimed to elucidate the functional and mechanistic significance of SF3B4 in PDAC.
MATERIALS AND METHODS: SF3B4 expression in PDAC was analyzed using patient datasets and experimental models. Functional assays including cell proliferation, colony formation, migration, and autophagy analyses were performed in PDAC cells. Reactive oxygen species (ROS) levels were evaluated. Sensitivity to 5-fluorouracil (5-FU) and apoptotic responses were also evaluated.
RESULTS: SF3B4 acts as a tumor suppressor in PDAC by inhibiting autophagy, a process that this cancer uniquely depends on for survival. SF3B4 overexpression inhibited proliferation, colony formation and migration of PDAC cells. Mechanistically, SF3B4 suppressed autophagic flux, resulting in increased ROS accumulation and subsequent inhibition of tumorigenic phenotypes. Treatment with the antioxidant N-acetylcysteine (NAC) rescued the tumor suppressive effects of SF3B4 overexpression. Moreover, SF3B4 overexpression sensitized PDAC cells to 5-FU, accompanied by enhanced apoptotic responses.
CONCLUSION: SF3B4 is a context-dependent splicing factor that functions as a tumor suppressor in PDAC by regulating autophagy and redox homeostasis. Targeting the SF3B4-autophagy-ROS axis may represent a promising strategy to suppress PDAC progression and overcome chemoresistance.

Keywords:  PDAC; ROS; SF3B4; autophagy; chemoresistance

DOI:  https://doi.org/10.21873/anticanres.17983
J Biol Chem. 2026 Feb 02. pii: S0021-9258(26)00090-6. [Epub ahead of print] 111220

AHCY: A Metabolic Gatekeeper at the Interface of Methylation, Redox Balance, and Cellular Stress Response.

Sarah C Stanhope, Vikki M Weake.

  S-Adenosylhomocysteinase (AHCY, also known as SAHH) is a highly conserved enzyme that catalyzes the reversible hydrolysis of S-adenosylhomocysteine (SAH) into adenosine and homocysteine. As the sole enzyme capable of catalyzing this reaction, AHCY modulates cellular methylation potential required for DNA, RNA, and protein methyltransferase activity. Recent discoveries, however, expand its role well beyond this canonical function, positioning AHCY as a metabolic gatekeeper that integrates one-carbon metabolism with epigenetic regulation, RNA processing, nucleotide balance, and redox signaling. This review brings together mechanistic, structural, and regulatory insights into AHCY while critically evaluating diverse biochemical and biophysical methods for assaying its activity. Comparative structural analyses uncover conserved tetrameric organization alongside species-specific adaptations in oligomeric state, NAD+ pocket accessibility, and C-terminal dynamics that shape enzyme catalytic efficiency and regulation. AHCY function is further fine-tuned through a wide spectrum of post-translational modifications and small-molecule interactions, linking it to transcriptional control, stress adaptation, and viral infection. By linking SAH turnover to methylation capacity and adenosine/homocysteine flux, AHCY coordinates metabolism with chromatin regulation and stress responses. These cross-cutting roles highlight how a single metabolic enzyme bridges catalysis, regulation, and disease. In doing so, AHCY exemplifies the broader principle that metabolic enzymes can have a central role as regulators of metabolic flux and cellular regulation, offering both mechanistic depth and translational promise as a therapeutic target.

Keywords:  S-Adenosylhomocysteinase (AHCY); S-Adenosylhomocysteinase Hydrolase (SAHH); enzymatic regulation; methylation potential; one-carbon metabolism; redox homeostasis

DOI:  https://doi.org/10.1016/j.jbc.2026.111220
Angew Chem Int Ed Engl. 2026 Feb 03. e21902

Unsaturated Phosphorus Electrophiles to Probe Protein Tyrosine Phosphatases.

Eleftheria Poulou, Max Ruwolt, Christian E Stieger, Kristin Kemnitz-Hassanin, Christian P R Hackenberger.

  Protein tyrosine phosphatases (PTPs) represent an important pharmacological target and subject of study. Although a number of broad-spectrum electrophilic, phosphotyrosine-mimicking probes have been developed to covalently capture the catalytic site of these enzymes, there is still a high demand for PTP probes with high target selectivity that are accessible in a synthetically straightforward way. Unsaturated phosphorus (V) (P(V)) compounds have recently emerged as powerful cysteine-selective bioconjugation reagents (P5-labeling). Herein, we introduce ethynyl-substituted aryl phosphonamidic and phosphonic acids as phosphotyrosine mimics, which serve as active-site-directed, covalent probes for tyrosine phosphatases. We show that these P(V) electrophiles can be readily incorporated into a peptide sequence, allowing proximity-enabled reactivity and selective targeting of the catalytic cysteine residue of an interacting phosphatase, as exemplified for PTP1B, a protein tyrosine phosphatase that acts as a key negative regulator of insulin signaling. Both ethynyl phosphonamidic acid and ethynyl phosphonic acid show no reactivity towards nontarget cysteine residues, though the phosphonamidic acid probe was notably less reactive toward its intended target. Proteomics experiments in human cell lysates demonstrated that the phosphonic acid probe selectively enriches its interacting phosphatase in the human proteome. Our study highlights a versatile strategy to obtain remarkably precise peptide-based PTP probes, thereby enabling the characterization of phosphatase interactions with high specificity.

Keywords:  activity‐based probes; phosphatase; phosphorus; proteomics; proximity‐induced reactivity

DOI:  https://doi.org/10.1002/anie.202521902
Nat Metab. 2026 Feb 06.

SLC6A6 imports taurine into mitochondria to sustain mitochondrial translation and tumour growth.

Liucheng Li, Jianwei You, Zi-Qing Chai, Xueshan Li, Xinlei Cai, Lin Wang, Fang Yang, Lingzhi Zhu, Wen Mi, Xinyi Xia, Haohang Yan, Fei Li, Juan Wang, Tong-Jin Zhao, Ligong Chen, Hongbin Ji, Pingyu Liu, Xiao-Long Zhou, Li Chen, Fuming Li.

Taurine plays a crucial role in mitochondrial translation. Mammalian cells obtain taurine via exogenous uptake mediated by the plasma membrane transporter SLC6A6 or via cytosolic biosynthesis. However, it remains unclear how taurine enters mitochondria and impacts cellular metabolism. Here we show that SLC6A6, but not exogenous taurine, is essential for mitochondrial metabolism and cancer cell growth. We discover that SLC6A6 also localizes to mitochondria and imports taurine for mitochondrial transfer RNA modifications. SLC6A6 deficiency specifically reduces mitochondrial taurine abundance and abrogates mitochondrial translation and cell proliferation. We identify protein kinase A as a regulator of SLC6A6 subcellular localization, as it promotes SLC6A6 presence at the plasma membrane while inhibiting its mitochondrial localization. Furthermore, we identify NFAT5 as a key regulator of mitochondrial function through SLC6A6 and demonstrate that targeting the NFAT5-SLC6A6 axis markedly impairs mitochondrial translation and tumour growth. Together, these findings suggest that SLC6A6 is a mitochondrial taurine transporter and an exploitable metabolic dependency in cancer.

DOI: https://doi.org/10.1038/s42255-026-01455-6
J Biol Chem. 2026 Feb 04. pii: S0021-9258(26)00101-8. [Epub ahead of print] 111231

RNF90 promotes hepatic steatosis by degrading CPT1α to suppress fatty acid oxidation.

Feng-Juan Yan, Ning Zhang, Shu-Han Li, Mei-Xin Huang, Meng-Meng Wu, Yu-Jie Yan, Xin Liu, Hao Lei.

  Hepatic fatty acid oxidation (FAO) is crucial for maintaining hepatic lipid homeostasis, and dysregulation of hepatic lipid metabolism is closely associated with metabolic dysfunction-associated fatty liver disease (MASLD). However, the molecular mechanisms governing FAO in hepatocytes remain incompletely understood. Here, we demonstrate that RNF90 is essential for FAO regulation, with its expression significantly upregulated in fatty liver. Further investigation revealed that RNF90 is transcriptionally activated by KLF5 and functions as an E3 ubiquitin ligase to promote the ubiquitin-dependent proteasomal degradation of CPT1α, a rate-limiting enzyme in mitochondrial FAO. Hepatocyte-specific RNF90 knockout significantly increased CPT1α protein expression, enhanced FAO activity, and alleviated hepatic steatosis, as evidenced by reduced hepatic lipid accumulation and TG levels. Conversely, overexpression of wildtype RNF90 (but not its E3 ligase-deficient mutant) exerted the opposite effects. Function rescue experiments further confirm that CPT1α is indispensable for RNF90-mediated regulation of FAO and protection against hepatic steatosis. Collectively, our study establishes RNF90 as a critical regulator of hepatic lipid metabolism and identifies the KLF5/RNF90/CPT1α axis as a potential therapeutic target for MASLD.

Keywords:  CPT1α; Fatty acid oxidation (FAO); Hepatic steatosis; KLF5; Metabolic dysfunction-associated fatty liver disease (MASLD); RNF90

DOI:  https://doi.org/10.1016/j.jbc.2026.111231
Nat Commun. 2026 Jan 30. 17(1): 1146

Trustworthy prediction of enzyme commission numbers using a hierarchical interpretable transformer.

Louis Dumontet, So-Ra Han, Jun Hyuck Lee, Tae-Jin Oh, Mingon Kang.

Accurate and trustworthy prediction of Enzyme Commission (EC) numbers is critical for understanding enzyme functions and their roles in biological processes. Despite the success of recently proposed deep learning-based models, there remain limitations, such as low performance in underrepresented EC numbers, lack of learning strategy with incomplete annotations, and limited interpretability. To address these challenges, we propose a hierarchical interpretable transformer model, HIT-EC, for trustworthy EC number prediction. HIT-EC employs a four-level transformer architecture that aligns with the hierarchical structure of EC numbers, and leverages both local and global dependencies within protein sequences for this multi-label classification task. We also propose a learning strategy to handle samples associated with incomplete EC numbers. HIT-EC, as an evidential deep learning model, produces trustworthy predictions by providing domain-specific evidence through a biologically meaningful interpretation scheme. The predictive performance of HIT-EC is assessed by multiple experiments: a cross-validation with a large dataset, a validation with external data, and a species-based performance evaluation. HIT-EC shows statistically significant improvement in predictive performance when compared to the current state-of-the-art benchmark models. HIT-EC's robust interpretability is further validated by identifying well-known conserved motifs and functional regions. HIT-EC is a robust, interpretable, and reliable solution for EC number prediction, with significant implications for enzymology, drug discovery, and metabolic engineering.

DOI: https://doi.org/10.1038/s41467-026-68727-3
ACS Cent Sci. 2026 Jan 28. 12(1): 75-87

Integrated Structural and Glycoproteomic Profiling Reveals Protein Conformational Remodeling and Biomarkers Across Alzheimer's Disease Progression.

Haiyan Lu, Ching-Yuan Yang, Hua Zhang, Xudong Shi, Penghsuan Huang, Peng-Kai Liu, Zicong Wang, Sanjay Asthana, Cynthia Carlsson, Ozioma Okonkwo, Lingjun Li.

Alzheimer's disease (AD) is characterized by progressive neurodegeneration and protein misfolding, yet the structural dynamics of proteins and their post-translational modifications during disease progression remain poorly understood. Here, we present an integrated structural and glycoproteomic analysis of paired serum and cerebrospinal fluid (CSF) samples from individuals across three clinical stages: normal cognition, mild cognitive impairment, and AD. Using limited proteolysis mass spectrometry (LiP-MS) combined with high-field asymmetric waveform ion mobility spectrometry and data-independent acquisition, we identified 54 proteins exhibiting structural alterations, two of which (clusterin and ceruloplasmin) showed structural changes in both serum and CSF. Furthermore, our findings reveal potential crosstalk between protein structural changes and N-glycosylation, supported by correlations between LiP-derived structural features and glycosylation patterns in key proteins, such as haptoglobin and kininogen-1. This study demonstrates that integrating structural proteomics with glycoproteomics in matched serum and CSF samples enhances biomarker discovery and provides novel insights into the molecular mechanisms of AD. Our approach offers a powerful platform for identifying robust, minimally invasive biomarkers and for understanding post-translational modification-induced protein remodeling in neurodegenerative diseases.

DOI: https://doi.org/10.1021/acscentsci.5c02048
Mol Cancer. 2026 Feb 03.

Metabolic reprogramming in cancer: signaling pathways and therapeutic targets.

Shi Dong, Taiyuan Li.



Keywords:  Cancer; Glucose; Glutamine; Lipid; Metabolic reprogramming; Polyamine; Tumor microenvironment

DOI:  https://doi.org/10.1186/s12943-026-02582-0
Cell Death Dis. 2026 Feb 02. 17(1): 199

Transglutaminase 2 exacerbates ovarian cancer survival by directly inactivating GSK3β.

Ho Lee, Joon Hee Kang, Hyun Jung Kim, Kyun Heo, Mi Kyung Park, Jeong Hwan Park, Byung Il Lee, Jong In Yook, Soo-Youl Kim.

Elevated expression of transglutaminase 2 (TGase 2, EC 2.3.2.13, protein-glutamine γ-glutamyltransferase, gene name TGM2) is known as one of the most upregulated genes during epithelial-mesenchymal transition (EMT) in ovarian cancer. Despite initial complete responses to conventional chemotherapy, ovarian cancer often recurs with metastasis, presenting a significant clinical challenge. Drug-resistant ovarian cancer cells exhibit markedly higher levels of TGase 2 compared to normal ovarian epithelium, which is associated with EMT activation, enabling them to evade chemotherapy effects. Intracellular TGase 2 is recognized as a key factor in maintaining the mesenchymal phenotype. Therefore, while EMT expression can be effectively reversed by inhibiting TGase 2, the underlying mechanism of this effect remains unclear. We found that TGase 2 promotes EMT by directly binding to glycogen synthase kinase-3β (GSK3β), promoting the stabilization of β-catenin. Domain mapping revealed that the N-terminus of TGase 2 interacts with the mid-region of GSK3β, leading to the autophagic degradation of GSK3β. Pharmacological disruption of this N-terminal interaction by streptonigrin, in combination with standard chemotherapy, extended overall survival in a xenograft model of ovarian cancer. This study identified TGase 2 as a pivotal regulator of EMT-driven metastasis and drug resistance.

DOI: https://doi.org/10.1038/s41419-026-08447-0
J Proteome Res. 2026 Feb 06.

Complete Data Analysis Workflow for Quantitative DIA Mass Spectrometry Using Nextflow.

Mats Perk, Sami Pietilä, Tommi Välikangas, Balazs Balint, Tomi Suomi, Laura L Elo.

  Data-independent acquisition (DIA) mass spectrometry is a technique used in proteomics to identify and quantify proteins in complex biological samples. While this comprehensive approach yields more complete and reproducible protein profiles than data-independent acquisition (DDA), the resulting data are substantially larger and more complex, presenting significant challenges for data analysis and interpretation. These challenges can be effectively addressed using dedicated workflow managers that support parallel execution of complex analysis pipelines on high-performance computing infrastructure. Nextflow, in particular, is well-suited for streamlining data analysis, as it automates key aspects of workflow management, allowing researchers to efficiently analyze large-scale data sets with minimal manual intervention. Here, we describe glaDIAtor-nf, a Nextflow version of our software package glaDIAtor for untargeted analysis of DIA mass spectrometry proteomics data. We first demonstrate its technical accuracy through rigorous testing on gold standard data sets. Building on this, we then reveal known proteome patterns from public breast cancer data that remained hidden in the processed data of the original study. This illustrates the potential of reanalyzing the accumulating public data, but also highlights the need for convenient tools to facilitate such reanalysis in large-scale.

Keywords:  data analysis; data-independent acquisition; mass spectrometry; nextflow; quantitative proteomics

DOI:  https://doi.org/10.1021/acs.jproteome.5c00266
Cell Death Dis. 2026 Feb 02. 17(1): 195

Reversible arginine methylation regulates mitochondrial IDH2 activity: coordinated control by CARM1 and KDM3A/4A.

Yena Cho, Jessica Winarto, Dae-Geun Song, Dong Hee Na, Kyo Bin Kang, Su-Nam Kim, Yong Kee Kim.

Mitochondria are essential for cellular homeostasis, supplying key metabolites and energy. While post-translational modifications regulate mitochondrial enzymes, their roles remain less explored compared to those in the nucleus and cytoplasm. Here, we demonstrate that reversible arginine methylation governs the activity of several mitochondrial enzymes, with a particular focus on isocitrate dehydrogenase 2 (IDH2). We identify coactivator-associated arginine methyltransferase 1 (CARM1) as a mitochondrial enzyme that asymmetrically dimethylates IDH2 at R188, leading to enzymatic inhibition while enhancing protein stability. This modification is dynamically reversed by the lysine demethylases KDM3A and KDM4A, which restore IDH2 activity. Notably, despite its reduced stability, demethylated IDH2 promotes α-ketoglutarate production, enhancing mitochondrial membrane potential and oxygen consumption. These findings highlight the critical role of reversible arginine methylation in fine-tuning mitochondrial enzyme function and maintaining mitochondrial homeostasis.

DOI: https://doi.org/10.1038/s41419-026-08444-3
Adv Sci (Weinh). 2026 Feb 05. e21970

Automatically Defining Protein Words for Diverse Functional Predictions Based on Attention Analysis of a Protein Language Model.

Hedi Chen, Jingrui Zhong, Xiaochun Zhang, Jingke Chen, Lin Guo, Xiaoliang Xiong, Xiaonan Zhang, Xiangyu Liu, Bailong Xiao, Boxue Tian.

  Understanding the relationship between protein sequence and function remains a longstanding challenge in bioinformatics, and to date the lion's share of related tools parse proteins at the domain or motif levels. Here, we define "protein words" as an alternative to "motif" for studying proteins and functional prediction applications. We first developed an unsupervised tool we term Protein Wordwise, which parses analyte protein sequences into protein words by analyzing attention matrices from a protein language model (PLM) through a community detection algorithm. We then developed a supervised sequence-function prediction model called Word2Function, for mapping protein words to GO terms through feature importance analysis. We compared the prediction performance of our protein word-based toolkit with a motif-based method (PROSITE) for multiple protein function datasets. We also assembled a functionally diverse data resource we term PWNet to support evaluation of protein words for predicting functional residues across 10 tasks (e.g., diverse biomolecular binding, catalysis, and ion-channel activity). Our toolkit outperforms PROSITE in all the examined datasets and tasks. By abandoning domains and instead using attention matrices from a PLM for automatic, systematic, and annotation-agnostic parsing of proteins, our toolkit both outperforms currently available tools for functional annotations at the residue and whole-protein levels and suggests innovative forms of protein analysis well-suited to the post-AlphaFold era of biochemistry.

Keywords:  attention analysis; community detection; protein function prediction; protein language model; protein words

DOI:  https://doi.org/10.1002/advs.202521970
Nat Commun. 2026 Feb 07.

Analysis of the transcriptomic and metabolomic landscape of prostate cancer with different anatomical origins using snFLARE-seq and mxFRIZNGRND.

Dongyin He, Haoran Hu, Kai Xiao, Yuhang Zhang, Yongbing Cheng, Shaozhuo Jiao, Yimei Hao, Yuanyuan Cai, Ziqun Liu, Xinran Yan, Qinsheng Chen, Xiyan Mu, Qi Wang, Shan Peng, Guoqin Sang, Xiaoling Zhi, Yanxia Chang, Qing Ye, Yuyao Yang, Meixia Che, Shengsong Huang, Hongqian Guo, Luonan Chen, Huiru Tang, Xuefeng Qiu, Zhenfei Li.

Prostate cancer cells of different anatomical locations display remarkable heterogeneity. This poses a challenge to the clinical relevance of pre-clinical models and the efficacy of contemporary therapeutic approaches. Here we develop the snFLARE-seq and mxFRIZNGRND methodologies to directly investigate the transcriptomic and metabolomic landscape of prostate cancer patients utilizing formalin-fixed paraffin-embedded (FFPE) specimens. A retrospective analysis reveals the clinical disparities of prostate cancer from peripheral zone (PZ), transition zone (TZ), and across PZ and TZ. The snFLARE-seq, refined for enhanced single-nucleus sequencing, unveils distinct cell type distributions and signaling pathways between PZ and TZ samples. Hormone therapy substantially affects cancer cells and microenvironment, leading to a polarized feature of epithelial cells and a subverted immune microenvironment. With improvements in metabolite extraction, mxFRIZNGRND reveals unique metabolic features of prostate cancer from different origins. The metabolomic results indicate that PZ cancer cells are in a metabolic-dormant status, which are probably awaken by hormone therapy. Integrative analysis of results from snFLARE-seq, mxFRIZNGRND, and TCGA database uncovers four metabolic pathways and related genes associated with disease aggressiveness. Our work could accelerate investigations on disease heterogeneity and evolution in real-world clinical settings, stimulating patient-specific precision healthcare solutions.

DOI: https://doi.org/10.1038/s41467-026-69347-7
J Proteome Res. 2026 Feb 04.

Chemical Proteomic Profiling of Lysine Benzoylation.

Xiaohan Song, Yuhan Lu, Panpan Peng, Binjing Chen, He Huang.

  Benzoylation (Kbz) is a physiologically relevant post-translational modification derived from the food additive sodium benzoate. While Kbz has been implicated in unique cellular regulatory processes, its substrate landscape and functional consequences remain poorly characterized. Conventional antibody-based enrichment methods for Kbz detection suffer from affinity bias and limited specificity. Here, we developed AyBz3, a bioorthogonal chemical probe enabling the unbiased mapping of Kbz across the proteome. Implementation of AyBz3 in HepG2 cells revealed 688 unique Kbz sites, significantly expanding the known benzoylome. Functional analysis revealed that Kbz-modified proteins are enriched in pathways related to protein translation and cell adhesion. Notably, we demonstrated that Kbz modification of nucleophosmin 1 (NPM1) impairs its molecular chaperone function toward p53, resulting in accelerated p53 degradation. Together, this study establishes AyBz3 as a powerful probe for unbiased benzoylome profiling and provides new insights into the regulatory roles of Kbz in cellular processes.

Keywords:  chemical proteomic; lysine benzoylation; nucleophosmin; substrates

DOI:  https://doi.org/10.1021/acs.jproteome.5c00792
Sci Rep. 2026 Jan 31.

Changes in EGFR activity following CRISPR/Cas9-editing of the EGF binding domain.

Jelena Popović, Anna Hahut, Gabriel E Torres, Andrew Vincent, Nashaly Soto-Echevarria, Brian Wray, Elizabeth T Bartom, Tatjana Paunesku, Chelain R Goodman, Gayle E Woloschak.

  Elevated Epidermal Growth Factor Receptor (EGFR) expression is observed in most cervical cancers, and it is frequently associated with poor clinical outcomes. The limited efficacy of existing EGFR-targeted therapies in cervical cancer highlights the need for a deeper understanding of EGFR role in this cancer type. To investigate EGFR separately from its interaction with Epidermal Growth Factor (EGF), we removed the key amino acids from the ligand bindings site. We used CRISPR/Cas9 genome editing to generate a panel of EGFR mutant cell lines and then sequenced and characterized them in detail. Studying the phenotypes of mutant cell clones, we show that a pair of amino acid substitutions L14R and Y45M within Domain I of EGFR protein completely disrupts EGF binding and changes EGFR subcellular distribution. A single substitution Y45M significantly reduced EGF binding but did not lead to subcellular redistribution of EGFR. Upon editing, EGFR mRNA and protein expression were decreased in mutant clones compared to wild type cells. Genome wide profiling of different CRISPR/Cas9 clones confirmed correct editing of EGFR with no off target CRISPR/Cas9 generated mutations. At the same time, spontaneous mutations that could impact cell phenotypes were detected in mutant clones. Disruption of ligand binding domain of EGFR by sequential knock in CRISPR/Cas9 genome editing altered subcellular localization and phosphorylation of EGFR in cervical cancer cells. The results presented here provide insights that may accelerate the development of CRISPR/Cas9-based therapies for EGFR-dependent cancers and reinforce the importance of thorough evaluation of CRISPR/Cas9-generated phenotypes.

Keywords:  CRISPR-Cas9; Cervical cancer; EGF binding; EGFR; ME180

DOI:  https://doi.org/10.1038/s41598-026-37579-8
Sci Rep. 2026 Feb 04.

Integrative metabolomic and single-cell transcriptomic analysis of recurrent condyloma acuminatum in humans.

Yushu Wei, Yaohan Xu, Chenxi Feng, Siji Chen, Jie Chen, Jiacheng Wang, Jingying Pan, Yinjing Song, Chunting Hua, Miaolian Cai, Hao Cheng, Jiang Zhu.

  Condyloma acuminatum (CA), primarily caused by low-risk HPV6/11, is a benign proliferative disease that is difficult to cure and prone to recurrence. However, the molecular and immune mechanisms underlying relapse remain unclear. We combined metabolomic profiling with single-cell RNA sequencing to investigate recurrence-associated changes. Metabolomics revealed dysregulation of ascorbate and aldarate, glycerophospholipid, purine, and arginine/proline metabolism in recurrent CA. Single-cell analysis identified altered expression of metabolism-related genes (AMD1, GSTM3, ALDH3A1, GPX1, GPX4) in keratinocytes, associated with hyperproliferation, impaired differentiation, and ferroptosis resistance. Immune profiling identified transcriptionally distinct myeloid subpopulations in recurrent CA lesions, including M2 macrophages and dendritic cells. KEGG analysis indicated enrichment of antigen processing, phagosome, and endocytosis pathways in M2 macrophages, and antigen processing and viral carcinogenesis in dendritic cells, suggesting altered immune regulatory states. Notably, the key polyamine biosynthesis regulator AMD1 was downregulated in both M2 macrophages and dendritic cells in recurrent lesions, paralleling metabolic evidence of altered arginine-polyamine pathways. These findings suggest that recurrent CA involves coordinated metabolic dysregulation across keratinocytes and immune cells, highlighting potential targets for immunometabolic intervention.

Keywords:  Condyloma acuminatum; Human papillomavirus; Immunometabolism; Metabolomics; Recurrence; Single-cell sequencing

DOI:  https://doi.org/10.1038/s41598-026-37989-8
FEBS J. 2026 Feb 07.

Energetic stress in combination with impaired fatty acid oxidation induces sequestration of CoA and adaptation of CoA metabolism.

Ligia Akemi Kiyuna, Christoff Odendaal, Madhulika Singh, Albert Gerding, Miriam Langelaar-Makkinje, Marianne van der Zwaag, Asmara Drachman, Vladimíra Cetkovská, Gaby Liem Foeng Kioen, Anne-Claire M F Martines, Nicolette C A Huijkman, Hein Schepers, Bart van de Sluis, Dirk-Jan Reijngoud, Ody C M Sibon, Amy C Harms, Thomas Hankemeier, Barbara M Bakker.

  Coenzyme A (CoA) is a vital cofactor involved in 8-10% of all metabolic reactions in human cells. Different inherited enzyme deficiencies in which the oxidation of acyl-CoAs is hampered have been hypothesised to share a phenotype characterised by toxic accumulation of acyl-CoA and a concomitant decline in free CoA (CoASH) levels, whereby CoASH becomes limiting for other metabolic reactions. This is referred to as CoASH sequestration. There is, however, limited experimental evidence for this hypothesis. Using a combination of approaches, we test this hypothesis in medium-chain acyl-CoA dehydrogenase deficiency (MCADD), the most common deficiency of mitochondrial fatty acid oxidation (mFAO), under energetic stress. Both in vitro MCAD-knockout (KO) HepG2 cells and a kinetic model of mFAO showed decreased CoASH, elevated medium-chain acyl-CoA, and decreased long-chain acyl-CoA levels. MCAD-KO mice exposed to fasting and cold as energetic stressors had a significantly increased total CoA pool and increased expression of CoA biosynthetic enzymes in the liver, indicative of an upregulated CoA biosynthesis. Expression of carnitine acyltransferases and acyl-CoA thioesterases, enzymes that liberate CoASH from acyl-CoAs, was also upregulated, suggesting an adaptive response of CoA metabolism to decreased CoASH. Finally, computational model simulations showed that a combination of elevated total CoA and thioesterase activity led to normalisation of both CoASH and medium-chain acyl-CoA levels. Together, the results provide the first evidence for the CoA sequestration hypothesis in MCADD. The observed adaptation of CoA metabolism under energetic stress may act as a compensatory response that counteracts CoASH depletion and accumulation of toxic medium-chain acyl-CoAs.

Keywords:  CASTOR; CoA metabolism; MCAD deficiency; inborn errors of metabolism; systems medicine

DOI:  https://doi.org/10.1111/febs.70442
J Cell Biol. 2026 Apr 06. pii: e202501207. [Epub ahead of print]225(4):

Cullin-3 adaptor SHKBP1 inhibits SQSTM1/p62 oligomerization and Keap1 sequestration.

Lin Luan, Xiaofu Cao, Zijun Xia, Shivanshi Vaid, Manuel D Leonetti, Jeremy M Baskin.

SQSTM1/p62 is a master regulator of the autophagic and ubiquitination pathways of protein degradation and the antioxidant response. p62 functions in these pathways via reversible assembly and sequestration of additional factors into cytoplasmic phase-separated structures termed p62 bodies. The physiological roles of p62 in these various pathways depend on numerous mechanisms for regulating p62 body formation and dynamics that are incompletely understood. Here, we identify a new mechanism for regulation of p62 oligomerization and incorporation into p62 bodies by SHKBP1, a cullin-3 E3 ubiquitin ligase adaptor, that is independent of its potential functions in ubiquitination. We map an SHKBP1-p62 protein-protein interaction outside of p62 bodies that limits p62 assembly into p62 bodies and affects the antioxidant response involving sequestration of Keap1 and nuclear translocation of Nrf2. These studies provide a non-ubiquitination-based mechanism for an E3 ligase adaptor in regulating p62 body formation and cellular responses to oxidative stress.

DOI: https://doi.org/10.1083/jcb.202501207
Nat Chem Biol. 2026 Feb 03.

Functional analysis of O-GlcNAcylation by networking of OGT interactors and substrates.

Matthew E Griffin, John W Thompson, Yao Xiao, Michael J Sweredoski, Elizabeth H Jensen, Rita B Aksenfeld, Helena Awad, Terry D Kim, Andrew L Schacht, Priya Choudhry, Yelena Koldobskaya, Brett Lomenick, Spiros D Garbis, Annie Moradian, Linda C Hsieh-Wilson.

The post-translational modification (PTM) of proteins by O-linked β-N-acetyl-D-glucosamine (O-GlcNAcylation) is widely found across the proteome and regulates diverse cellular processes, from transcription and translation to signal transduction and metabolism. However, most functional studies to date have focused on individual modifications, overlooking other simultaneous O-GlcNAcylation events that work together to coordinate cellular activities. Here we describe networking of O-GlcNAc transferase interactors and substrates (NOTISE), a systems-level approach that monitors O-GlcNAcylation rapidly and comprehensively across the proteome to reveal important functional and regulatory relationships. The NOTISE method integrates affinity purification-mass spectrometry and site-specific chemoproteomic technologies with network generation to connect putative upstream regulators and downstream targets of O-GlcNAcylation. The resulting data-rich networks identify critical conserved activities of O-GlcNAcylation and tissue-specific functions. This holistic and unbiased approach provides a broadly applicable framework to catalyze investigations into the functional roles of coordinated, multisubstrate PTMs in specific cellular and physiological contexts.

DOI: https://doi.org/10.1038/s41589-025-02108-7
J Phys Chem B. 2026 Feb 06.

Decoding the Post-translational Modification Crosstalk: Functional Implications of Phosphorylation, Acetylation, and Methylation.

Xuyang Qin, Shikha Nangia.

Post-translational modifications (PTMs) such as phosphorylation, acetylation, and methylation critically expand proteome function by regulating protein structure and interactions. Hydropathy changes serve as a main driving force; however, a quantitative, mechanistic understanding of how their distinct chemical changes alter local protein hydropathy remains limited. To bridge this gap, we extend the Protocol for Assigning a Residue's Character on a Hydropathy (PARCH) scale, a residue-level hydropathy scale, to systematically evaluate PTM-induced physicochemical changes. By applying this method, we quantify the effect and magnitude of hydropathy shifts at modification sites and map how these perturbations influence the local protein environment. Our analysis reveals that phosphorylation exerts a strong, consistent hydrophilic effect, significantly increasing PARCH values due to the introduction of a large, charged phosphate group. In contrast, N-lysine acetylation, which neutralizes charge, shows context-dependent effects, predominantly increasing the hydrophobicity but occasionally enhancing the local hydrophilicity. Methylation presents the most complex signature, with no uniform trend, where increased side chain bulk can paradoxically increase water exposure despite the modification's nonpolar nature. This study establishes the PARCH scale as a powerful quantitative tool for deciphering how PTMs regulate the local hydropathy landscape of proteins, providing a predictive foundation for understanding their structural, hydropathy, and functional consequences.

DOI: https://doi.org/10.1021/acs.jpcb.5c08630
bioRxiv. 2026 Jan 23. pii: 2026.01.21.700212. [Epub ahead of print]

Spatiotemporal 4D Whole-cell Modeling of a Minimal Autotroph Reveals Central Carbon Metabolism Regulated Locally by Protein Megacomplexes via Post-translational Modifications under Light Disturbance.

Connah G M Johnson, Aaron Chan, Jordan Rozum, August George, Amar D Parvate, Doo Nam Kim, Song Feng, Pavlo Bohutskyi, Zachary Johnson, Natalie Sadler, Marci Garcia, Xiaolu Li, Jesse Trejo, Ruonan Wu, William Sineath, Lindsey N Anderson, James E Evans, Angad P Mehta, Wei-Jun Qian, Zaida Luthey-Schulten, Margaret S Cheung.

Photosynthetic microorganisms rely on multiple pathways in central carbon metabolism to adapt to fluctuating light and energy availability across diel cycles. Mechanistic insight into the regulatory dynamics of this adaptation requires integrating processes spanning disparate timescales, from rapid redox-dependent post-translational modifications (PTMs) to slower changes in protein expression and metabolic pathway usage. To address this complexity beyond genome-based inference and traditional modeling, we develop a whole-cell four-dimensional (3D + time) model of the marine cyanobacterium Prochlorococcus marinus MED4 that explicitly represents the spatial organization of enzymatic and molecular processes in central carbon metabolism under light perturbation. We employ a perturbation-based research design to experimentally generate time-series, multi-omics measurements that provide molecular descriptors and cryo-ET images as constraints for this dynamic 4D framework. The integration of experiments and modeling across defined light regimes enables quantitative validation of system-level responses and forecasting under distinct light disturbances. We test the hypothesis that light-dependent redox PTMs regulating the structural assembly of a protein megacomplex, the "dark complex," modulate metabolic flux at a conserved regulatory node of the Calvin-Benson cycle (CBC) in cyanobacteria. Our model shows that subcellular spatial organization buffers rapid light-induced changes in thylakoid reaction rates, which are followed by redox-PTM-mediated sequestration or release of CBC enzymes in the dark complex, ultimately impacting carbon fixation dynamics within carboxysomes. Comparison with an equivalently parameterized well-mixed stochastic model demonstrates that post-translational regulation not only buffers transcriptional noise and diffusion-driven fluctuations but also stabilizes phenotypic outcomes, underscoring the importance of spatial heterogeneity in phenotypic robustness. This ability to probe adaptive, spatiotemporally resolved mechanisms in photosynthetic machinery and central carbon metabolism addresses a critical gap in genotype-to-phenotype inference and expands modeling and design capabilities for understudied or genetically intractable autotrophs such as P. marinus MED4.
Significance Statement: This work advances 4D whole-cell modeling by presenting the first spatiotemporal simulation of a photosynthetic autotroph using the Lattice Microbes platform. Using Prochlorococcus marinus MED4, we show that subcellular spatial organization of organelles, diffusion constraints, and redox regulation collectively shape central carbon metabolism across orders of magnitude in space and time. Through a perturbation-based strategy that generates multi-omics data sets over time, we construct and validate a spatially and temporally resolved model of MED4, constrained by high-resolution (10 nm) cryo-electron tomography. Our results highlight the importance of localized biochemical reactions and redox-dependent post-translational modification of enzymes in regulating carbon fixation in a noisy environment under light disturbance. This study establishes a spatiotemporal, whole-cell physiology modeling framework as a transformative tool for uncovering multiscale regulatory responses to environmental gradients.

DOI: https://doi.org/10.64898/2026.01.21.700212
bioRxiv. 2026 Jan 19. pii: 2026.01.15.699680. [Epub ahead of print]

Phosphorylation of Cyclophilin-D is Not Required for Regulation of The Mitochondrial Permeability Transition Pore by GSK3β.

Linda Alex, Paula J Klutho, Lihui Song, Manuel Gutiérrez-Aguilar, Christopher P Baines.

Genetic inhibition of cyclophilin D (CypD) delays the opening of the mitochondrial permeability transition pore (MPTP) and therefore reduces necrotic cell death. Elucidation of factors that impact CypD activity is therefore key to understanding the regulation of MPTP opening. Glycogen synthase kinase-3β (GSK3β) is a serine/threonine kinase that has been shown to modulate MPTP and cell death, potentially through phosphorylation of CypD. Therefore, we hypothesized that the mitochondrial fraction of GSK3β directly phosphorylates CypD and promotes opening of MPTP. Overexpression of full length GSK3β in mouse embryonic fibroblasts sensitized the MPTP and exacerbated oxidative stress-induced necrosis. In contrast, genetic inhibition of GSK3β protected against oxidant-induced cytotoxicity but did not affect the MPTP. Recombinant GSK3β could directly bind to and phosphorylate recombinant CypD. Mass spectrometry revealed several putative GSK3β phosphorylation sites on CypD. However, mutation of these sites did not affect the peptidyl prolyl isomerase activity of CypD and reconstitution of these phosphomutants in CypD-deficient cells increased MPTP sensitivity and oxidative-induced cell death to the same extent as wild-type CypD. Further, targeted overexpression of either wild-type or kinase-inactive GSK3β in the mitochondrial matrix did not impact MPTP or cell death. Moreover, while proteinase-K digestion of cardiac mitochondria showed a significant amount of GSK3β in the mitochondria, it was not localized to the matrix. Finally, overexpression of GSK3β was still able to increase MPTP sensitivity and oxidative stress-induced death in CypD-null cells. Taken together, these data indicate that, while GSK3β can modulate MPTP, this appears to be independent of GSK3β's interaction with, or phosphorylation of CypD.

DOI: https://doi.org/10.64898/2026.01.15.699680
Cancer Lett. 2026 Jan 30. pii: S0304-3835(26)00045-5. [Epub ahead of print]642 218282

Lactylation enhances YTHDF3 stability to promote cisplatin resistance via m6A-dependent KDM6B decay in bladder cancer.

Kai Yu, Jiazhu Sun, Jiawei Zhang, Yuchen Shi, Junyan Wang, Yuqing Wu, Dingheng Lu, Xinyang Niu, Yuxiao Li, Suyuelin Huang, Jihuan Yuan, Zhixiang Qi, Fenghao Zhang, Jiangfeng Li, Hong Chen, Ben Liu.

  Acquired resistance to cisplatin remains a major therapeutic challenge in muscle-invasive bladder cancer. Here, we demonstrate for the first time that lactate accumulation induces AARS2-dependent lactylation of the m6A reader YTHDF3, establishing lactylation as a previously unrecognized regulatory layer of this epitranscriptomic factor. YTHDF3 lactylation stabilizes the protein by antagonizing ubiquitin-mediated degradation. Importantly, a lactylation-deficient YTHDF3 mutant fails to confer cisplatin resistance, underscoring the functional importance of this modification. Mechanistically, lactylated YTHDF3 enhances its m6A-dependent recognition and decay of KDM6B RNA. The resulting downregulation of KDM6B suppresses CDKN1A transcription through impaired H3K27me3 demethylation, representing an epigenetic mechanism that weakens the DNA damage response and promotes chemoresistance. Functional assays further demonstrate that YTHDF3 knockdown enhances cisplatin sensitivity in bladder cancer cells and xenograft tumors, whereas enforced expression of KDM6B or CDKN1A phenocopies the cisplatin-sensitizing effect of YTHDF3 knockdown. Collectively, our findings define a lactate-AARS2-YTHDF3-KDM6B-CDKN1A axis that integrates metabolic reprogramming, m6A-dependent epitranscriptomic regulation, and epigenetic chromatin remodeling to drive cisplatin resistance in bladder cancer.

Keywords:  Bladder cancer; Cisplatin; H3K27me3; Lactylation; Ubiquitination; YTHDF3; m6A

DOI:  https://doi.org/10.1016/j.canlet.2026.218282
Cancer Immunol Res. 2026 Feb 06.

Neoadjuvant endocrine treatment plus mammaglobin-A DNA vaccine induces antitumor immune responses in the primary tumor and peripheral blood of breast cancer patients: Insights from a phase 1b clinical trial.

Rashmi Mishra, Foluso Ademuyiwa, Yilin Yang, John Herndon, Lijin Li, Cherease Street, Nancy Myers, Ina Chen, Xiuli Zhang, Ian S Hagemann, Feng Gao, Christopher A Miller, Narendra V Sankpal, Joel M Guthridge, Madelyn Carmody, Cynthia X Ma, Rama Suresh, Timothy P Fleming, Caleb Marlin, S Peter Goedegebuure, William E Gillanders.

Tumor-associated antigen (TAA) vaccines are being explored as a strategy to induce antitumor immune responses. Mammaglobin-A (Mam-A) is a TAA expressed in >50% of breast cancer (BC) patients. Previously, we have shown that Mam-A DNA vaccines induce antitumor immune responses in patients with stable metastatic disease. To further evaluate the potential of the Mam-A vaccine, we initiated a phase-1b clinical trial in estrogen receptor-positive BC patients prior to surgery. Eight patients were assigned to Arm 1 (neoadjuvant endocrine therapy alone) and 17 to Arm 2 (neoadjuvant endocrine therapy plus Mam-A vaccination); the final analysis included 8 patients from Arm 1 and 13 from Arm 2. Ex vivo ELISpot analysis of peripheral blood mononuclear cells demonstrated that Mam-A vaccination induced Mam-A-specific T cells in 8/13 patients. Intracellular cytokine staining, and Mam-A-specific tetramer staining revealed that vaccine-induced Mam-A-specific T cells included both CD4+ and CD8+ polyfunctional T cells. Finally, high-throughput imaging mass cytometry identified 24 cellular meta-clusters with features of tumor, immune, stromal, and endothelial cells and revealed an increased CD8+ T-cell prevalence in the tumor after Mam-A vaccination. In particular, vaccination was associated with the infiltration of PD-1+CD8+ T cells. In addition, post-vaccination tumor samples exhibited close spatial interactions between cytotoxic CD8+ T cells (CTL) and Mam-A+ tumor cells and between CTL and antigen-experienced CD4+ T cells. Together, these results suggest that Mam-A DNA vaccination elicits both systemic and intratumoral antitumor immune responses.

DOI: https://doi.org/10.1158/2326-6066.CIR-25-0666
bioRxiv. 2026 Jan 20. pii: 2026.01.19.700466. [Epub ahead of print]

SF3B1 Phosphorylation Prompts U2AF2 Dissociation for Widespread Control of pre-mRNA Splicing.

Christopher L Kirchhoff, Hannah R Powell, Justin W Galardi, Sarah Loerch, Mary J Pulvino, Jermaine L Jenkins, Paul L Boutz, Clara L Kielkopf.

Reversible pre-mRNA splicing factor phosphorylation is a well-documented feature of spliceosome assembly, activation, and disassembly, yet its functional and mechanistic roles are still emerging. SF3B1, a core spliceosome subunit, is extensively phosphorylated before the first catalytic step of pre-mRNA splicing. Intriguingly, most SF3B1 phosphorylation sites surround its binding sites for U2AF2, an early-stage pre-mRNA splicing factor. Here, we discovered that SF3B1 phosphorylation significantly decreases its association with U2AF2. We determined two crystal structures revealing electrostatic repulsion between an acidic U2AF2 α-helix and the negatively-charged phosphoryl group of SF3B1. Variants with amino acid substitutions that prevent or mimic SF3B1 phosphorylation perturbed thousands of splice sites, primarily those marked by uridine-rich splice site signals recognized by U2AF2. Collectively, our findings demonstrate a widespread but previously unrecognized role for SF3B1 phosphorylation as a gateway for U2AF2 dissociation so that pre-mRNA splicing can proceed.

DOI: https://doi.org/10.64898/2026.01.19.700466
Mol Cell Proteomics. 2026 Jan 28. pii: S1535-9476(26)00015-0. [Epub ahead of print] 101520

Recent advances in proximity labeling-based subcellular proteomic mapping.

Gang Wang, Jiapeng Liu, Xuege Sun, Wei Qin, Shuo Han, Peng Zou.

The spatial organization of the cellular proteome is vital for cellular physiology, as protein localization is closely linked to post-translational modifications, subcellular trafficking, and protein-protein interactions. Systematic profiling of these spatial features can greatly enhance our understanding of protein functions. Recent advances in enzyme-mediated proximity labeling (PL) techniques, such as TurboID and APEX2, have improved our ability to map subcellular proteomes in living cells. This review discusses emerging trends in PL methods, which now offer subcellular precision with multi-dimensional protein features, including post-translational modifications, trafficking, turnover, and interaction with other biomolecules. Additionally, new techniques such as photoactivatable PL (optoPL) and antibody-targeted PL (immunoPL) provide enhanced spatiotemporal control and allow for detailed subcellular proteome mapping without genetic manipulation.

DOI: https://doi.org/10.1016/j.mcpro.2026.101520
Am J Physiol Endocrinol Metab. 2026 Feb 04.

Impact of obesity on aromatic amino acids and brain glucose during acute hyperglycemia.

Brooke C Matson, Felona Gunawan, Douglas L Rothman, Graeme F Mason, Olga Ilkayeva, Christopher B Newgard, Janice J Hwang.

  Hyperaminoacidemia is an early hallmark of insulin resistance, with aromatic and branched chain amino acids particularly associated with insulin resistance and type 2 diabetes. We previously showed that healthy adults with obesity exposed to acute hyperglycemia have lower brain glucose levels measured by magnetic resonance spectroscopy (MRS) than lean controls, suggesting that a blunted brain response to hyperglycemia may be an early marker of insulin resistance. Here, in a secondary analysis of our prior study, we used targeted mass spectrometry-based metabolomics to measure plasma amino acids in participants with and without obesity to determine if changes in peripheral metabolites associated with early insulin resistance such as amino acids were associated with changes in brain glucose levels during hyperglycemia. There were few differences in baseline amino acids between groups, but acute hyperglycemia unveiled higher plasma concentrations of amino acids including cysteine, cystine, glutamic acid, glutamine, methionine, and aromatic amino acids in obesity. Plasma glucagon levels were also higher in obesity during acute hyperglycemia. Higher plasma concentrations of aromatic amino acids and glucagon were significantly correlated with lower brain glucose levels, illustrating parallel development of central and peripheral metabolic changes in obesity.

Keywords:  amino acids; brain glucose; glucagon; magnetic resonance spectroscopy; obesity

DOI:  https://doi.org/10.1152/ajpendo.00463.2025
Anticancer Res. 2026 Feb;46(2): 589-599

Glucose Deprivation of Tumor Cells via Selective Nutrient Delivery: A Potential Therapy for Metastatic Breast Cancer.

Kamran Shirbache, Kimiya Shirbacheh, Ali Rezvani, Ali Shirbacheh, Soha Razmjouei, Maryam Khosravian, Zahra Golestani Hotkani, Hamid Nasri.

   BACKGROUND/AIM: Metastatic breast cancer remains a major clinical challenge despite the availability of various chemotherapeutic agents. Current metabolic inhibitors have limitations, prompting the need for innovative strategies that selectively target tumor cells while sparing normal tissues. This study aimed to propose a novel approach focused on depriving tumor cells of glucose while ensuring nutrient delivery to normal cells.
MATERIALS AND METHODS: A comprehensive literature review was conducted using PubMed and Google Scholar. The proposed strategy involved focusing on studies that deplete glycogen stores in normal tissues through prolonged fasting, followed by administration of total parenteral nutrition (TPN) enriched with essential ingredients encapsulated in specialized liposomes. Three liposomal strategies were outlined: 1-pH-sensitive copolymer coating: liposomes coated with polyethylene glycol-poly-L-histidine (PEG-PLH) selectively release contents in normal tissues by binding glucose transporters (GLUTs) while avoiding tumor cell GLUTs. 2-Superhydrophobic fluorinated compounds: conjugation with trastuzumab targets HER2 ligands on tumor cells, preventing liposome accumulation in tumors. 3-Superhydrophobic Zwitterionic modifications: these create a hydration layer around liposomes, preventing passage through capillary walls and reducing tumor tissue accumulation.
RESULTS: The strategies were designed to selectively reduce glucose availability to tumor cells while preserving normal cellular metabolism. The proposed liposomal modifications theoretically enhance targeted delivery and minimize off-target effects, providing a novel framework for metabolic therapy in metastatic breast cancer.
CONCLUSION: This novel glucose-targeted liposomal approach shows potential to improve therapeutic specificity and efficacy in metastatic breast cancer. Further in vitro, in vivo, and clinical studies are warranted to validate its effectiveness and explore applicability to other solid tumors.

Keywords:  HER2+ tumors; Metastatic breast cancer; glucose deprivation; liposomes; review; selective nutrient delivery; targeted therapy

DOI:  https://doi.org/10.21873/anticanres.17971
Anticancer Res. 2026 Feb;46(2): 681-688

Alteration of Flavin Homeostasis in Uterine Cancer.

Alessia Nisco, Maria Tolomeo, Angela Sposato, Didier Paleni, Mariafrancesca Scalise, Maria Barile.

   BACKGROUND/AIM: Uterine cancer is the fourth most frequently diagnosed cancer in women, and continues to present significant clinical challenges, particularly in older populations. Tumor progression is tightly linked to metabolic adaptations, and emerging evidence points to an association between dysregulated vitamin B2 (riboflavin, Rf) metabolism and cancer development. Rf is an essential precursor of the flavin cofactors flavin mononucleotide (FMN) and flavin adenine dinucleotide (FAD), which are critical for cellular energy metabolism and redox balance. The aim of the study was to investigate whether uterine cancer tissues exhibit alterations in the expression of key regulators of flavin homeostasis - riboflavin transporters (RFVT1-3) and FAD synthase (FADS) - and to determine how these changes relate to intracellular flavin levels and to the expression of the FAD-dependent epigenetic enzyme lysine-specific demethylase 1 (LSD1).
MATERIALS AND METHODS: Paired samples of tumor tissue and surrounding normal mucosa from eight patients with uterine cancer were analyzed to evaluate the expression of: RFVTs by both RT-PCR and western blot; and FADS, and the FAD dependent enzyme lysine specific demethylase 1 (LSD1) by RT-PCR. Furthermore, we evaluated flavin cofactors levels by HPLC.
RESULTS: Quantitative analyses revealed a significant up-regulation of RFVT1 and RFVT3 at both mRNA and protein levels in tumor tissues, accompanied by markedly increased intracellular levels of Rf (3fold) and FAD (2.5fold). FADS, the enzyme responsible for FAD production and delivery to client flavoproteins, was also significantly overexpressed and correlated with elevated LSD1 expression.
CONCLUSION: A coordinated mechanism where uterine cancer cells adaptively up-regulate RFVTs, FADS, and LSD1 to meet their metabolic demands was revealed. These results provide insights into the metabolic vulnerabilities of uterine cancer and propose Rf metabolism and flavin-dependent processes as potential therapeutic targets.

Keywords:  FADS; LSD1; RFVT; Uterine cancer; flavins

DOI:  https://doi.org/10.21873/anticanres.17978
J Biol Chem. 2026 Jan 28. pii: S0021-9258(26)00081-5. [Epub ahead of print] 111211

A cell-based assay for retinaldehyde dehydrogenase activity: retinoid quantification as an alternative to current fluorescence-based approaches.

Julie Charpentier, Yan Lu, Serena Gallozzi, Shubhangi Seth, Mark P Hodson, James R Krycer, Severine Navarro.

The biologically active metabolite of Vitamin A, retinoic acid, is essential for regulating immune tolerance, development, and metabolism. A key regulator of retinoic acid signalling is its synthesis by retinaldehyde dehydrogenase, whose expression is tightly regulated and cell-type specific. Current cell-based assays for retinaldehyde dehydrogenase activity rely on fluorescent aldehyde substrates, which lack specificity, limiting their accuracy and interpretability. Here, we developed a sensitive, cell-based assay that directly quantifies retinaldehyde dehydrogenase activity by measuring a panel of retinoids, including all-trans-retinoic acid, using liquid chromatography-mass spectrometry. Employing cultured conventional dendritic cells, we demonstrate that retinoic acid synthesis is time-, substrate-, and enzyme-dependent. Compared to fluorescence-based assays, our assay avoided artefactual signals influenced by cell density and provided a direct, quantitative measure of enzymatic activity in the context of broader retinoid metabolism. This assay offers additional practical advantages, including flexibility in sample processing and compatibility with other downstream metabolite analyses. Together, our protocol provides a robust, specific, and functionally-relevant approach that complements existing fluorescence-based approaches to study retinoic acid biosynthesis in immune cells and beyond.

DOI: https://doi.org/10.1016/j.jbc.2026.111211