bims-cesirm 2025-12-28 papers

bims-cesirm

Biomed News

on Cell Signaling mediated regulation of metabolism

Issue of 2025–12–28
23 papers selected by
Tigist Tamir, University of North Carolina

Beyond Bioenergetics: Emerging Roles of Mitochondrial Fatty Acid Oxidation in Stress Response and Aging.
GCDH Promotes Breast Cancer Glutaminolysis Reprogramming by Inducing GLS1 Expression Through Histone Crotonylation at Its Promoter Region.
Dynamic and differential renal cortical cell-specific mitochondrial metabolism in response to fasting.
PIPI-C: A combinatorial optimization framework for identifying post-translational modification hot-spots in mass spectrometry data.
Bioinformatic analysis of metastasis-associated metabolic landscape reveals an oncogenic role for the transsulfuration pathway.
Proteomics analysis reveals progesterone receptor induced mitochondria-mediated apoptosis in breast cancer cells.
Plasma plasmalogen levels and risk of lymph node positive breast cancer.
Temporal Profiling of Peroxynitrite-Mediated Protein Nitration and Phosphorylation Using Proteomics Analysis.
Modanovo: A Unified Model for Post-Translational Modification-Aware de Novo Sequencing Using Experimental Spectra from In Vivo and Synthetic Peptides.
Characterizing the Effects of Protein Glycosylation Perturbation on Phosphorylation Signaling.
MoSAIC: An Integrated and Modular Workflow for Confident Analysis of Protein Post-Translational Modification Landscapes.
Assessing the relation between protein phosphorylation, AlphaFold3 models, and conformational variability.
Stable de novo protein design via joint conformational landscape and sequence optimization.
Post-transcriptional modifications integration for ligand-receptor cellular network inference.
A reversible feedback mechanism regulating mitochondrial heme synthesis.
Mitochondrial control of fuel switching via carnitine biosynthesis.
Automated Mag-Net Enrichment Unlocks Deep and Cost-Effective LC-MS Plasma Proteomics.
The protein denitrosylase SCoR2 regulates lipogenesis and fat storage.
LEM4 interacts with β-catenin and promotes β-catenin-dependent transcription activity to confers ribociclib resistance in breast cancer cells.
Glucose Induces DNMT1/IMPDH2-Dependent Metabolic Memory in Endothelial Cells Upon Reprograming Nucleotide Metabolism.
Transsulfuration metabolism is essential for ferroptosis resistance in quiescent endothelial cells.
The ACSL family: Bridging fatty acid metabolism and cell death in cancer progression.
Cystathionine Beta-Synthase Promotes Anoikis Resistance and Transcoelomic Metastasis in Ovarian Cancer via the SP1-ITGB1 axis.

Cells. 2025 Dec 09. pii: 1956. [Epub ahead of print]14(24):

Beyond Bioenergetics: Emerging Roles of Mitochondrial Fatty Acid Oxidation in Stress Response and Aging.

Surim Bang, So-Hyun Choi, Seung Min Jeong.

  Mitochondrial fatty acid oxidation (FAO) has long been recognized as a central pathway for energy production, providing acetyl-CoA, NADH, and FADH2 to sustain cellular growth and survival. However, recent advances have revealed that FAO exerts far broader roles beyond bioenergetics. FAO contributes to redox balance by generating NADPH for antioxidant defense, regulates protein acetylation through acetyl-CoA availability, and modulates stress signaling pathways to support cellular adaptation under nutrient or genotoxic stress. These emerging insights establish FAO as a metabolic hub that integrates energy homeostasis with redox regulation, epigenetic modification, and stress responses. Dysregulation of FAO has been increasingly implicated in aging and diverse pathologies, including cellular senescence, obesity, cancer and fibrosis. In this review, we highlight recent findings and provide an updated perspective on the expanding roles of mitochondrial FAO in stress responses and aging, with particular emphasis on its potential as a therapeutic target in age-associated diseases.

Keywords:  acetylation; age-related diseases; fatty acid oxidation; redox homeostasis; stress response

DOI:  https://doi.org/10.3390/cells14241956
Cancer Manag Res. 2025 ;17 3185-3196

GCDH Promotes Breast Cancer Glutaminolysis Reprogramming by Inducing GLS1 Expression Through Histone Crotonylation at Its Promoter Region.

Jianan Zhang, Mengsha Zou.

   Objective: Glutaryl-CoA dehydrogenase (GCDH) is a mitochondrial enzyme involved in lysine and tryptophan catabolism, yet its role in cancer metabolism remains poorly understood. This study aimed to investigate the function of GCDH in regulating glutamine metabolism and proliferation in breast cancer cells, and to elucidate its molecular mechanism via epigenetic modulation of glutaminase 1 (GLS1).
Methods: GCDH expression was silenced using siRNAs in human breast cancer cell lines MCF-7 and MDA-MB-231. Cell proliferation was assessed using CCK-8 and EdU assays. Glutamine metabolism was analyzed by quantifying intracellular levels of glutamine, glutamate, α-ketoglutarate (α-KG), and ATP. In vivo effects were evaluated using a xenograft model in BALB/c nude mice. Chromatin immunoprecipitation (ChIP), luciferase reporter assays, and Western blotting were performed to explore the epigenetic regulation of GLS1. Functional interaction between GCDH and GLS1 was further validated through overexpression and knockdown studies, and the requirement for GCDH's enzymatic activity was tested using a catalytically inactive mutant.
Results: GCDH knockdown significantly suppressed proliferation in MCF-7 and MDA-MB-231 cells (p<0.001), decreased EdU incorporation (p<0.01), and impaired glutamine metabolism, as indicated by elevated intracellular glutamine and reduced levels of glutamate, α-KG, and ATP (all p<0.05). In vivo, GCDH depletion led to reduced tumor growth and weight (p<0.001), with altered metabolic profiles consistent with impaired glutaminolysis (decreased α-KG, p<0.05). Mechanistically, GCDH silencing reduced global and GLS1 promoter-specific H3K27 crotonylation (p<0.01), suppressing GLS1 transcriptional activity (p<0.001). Overexpression of GLS1 reversed the metabolic and proliferative deficits induced by GCDH knockdown. Furthermore, wild-type GCDH overexpression, but not a catalytically inactive mutant, partially restored glutamate production and ATP levels in GLS1-deficient cells (p<0.05), indicating a functional interplay that depends on GCDH's enzymatic activity.
Conclusion: GCDH promotes breast cancer cell proliferation and metabolic activity by enhancing glutaminolysis through epigenetic upregulation of GLS1 via histone crotonylation. Critically, this novel metabolic-epigenetic axis requires the catalytic function of GCDH. These findings not only reveal a novel metabolic-epigenetic axis driven by a specific mitochondrial enzyme but also suggest GCDH as a potential therapeutic target in breast cancer.

Keywords:  breast cancer; epigenetic regulation; glutamine metabolism; histone crotonylation

DOI:  https://doi.org/10.2147/CMAR.S552195
Am J Physiol Renal Physiol. 2025 Dec 22.

Dynamic and differential renal cortical cell-specific mitochondrial metabolism in response to fasting.

Kyle Feola, Andrea Henning Venable, Mina Rasouli, Julie Do, Tatyana Broomfield, Claire Llamas, Dana Straus, Joshua C Russell, Prashant Mishra, Behzad Najafian, Sarah C Huen.

  The metabolic health of the kidney is directly correlated to the risk of progressive kidney disease. Our understanding of the metabolic processes that fuel the diverse functions of the kidney is limited by the kidney's structural and functional heterogeneity, especially in key metabolic organelles like the mitochondria. As the kidney contains many different cell types, we sought to determine the intra-renal mitochondrial heterogeneity that contributes to cell-specific metabolism. To interrogate this, we utilized a recently developed mitochondrial tagging technique, MITO-Tag, to isolate kidney cell-type specific mitochondria. Here, we investigated mitochondrial functional capacities and the metabolomes of the early and late proximal tubule (PT) and the distal convoluted tubule (DCT). The conditional MITO-Tag transgene was combined with Slc34a1-CreERT2, Ggt1-Cre, or Pvalb-Cre transgenes to generate mouse models capable of cell-specific isolation of hemagglutinin (HA)-tagged mitochondria from the early PT, late PT, or the DCT, respectively. Functional assays measuring mitochondrial respiratory and fatty acid oxidation (FAO) capacities and metabolomics were performed on anti-HA immunoprecipitated mitochondria from kidneys of ad libitum fed and 24-hour fasted male mice. The renal MITO-Tag models targeting the early PT, late PT, and DCT revealed differential mitochondrial respiratory and FAO capacities which dynamically changed during fasting conditions. The renal MITO-Tag model captured differential mitochondrial metabolism and functional capacities across the early PT, late PT, and DCT at baseline and in response to fasting.

Keywords:  cellular metabolic heterogeneity; kidney; metabolism; mitochondria; tubular epithelium

DOI:  https://doi.org/10.1152/ajprenal.00235.2025
Mol Cell Proteomics. 2025 Dec 22. pii: S1535-9476(25)00593-6. [Epub ahead of print] 101494

PIPI-C: A combinatorial optimization framework for identifying post-translational modification hot-spots in mass spectrometry data.

Shengzhi Lai, Shuaijian Dai, Peize Zhao, Chen Zhou, Ning Li, Weichuan Yu.

  Post-translational modifications (PTMs) are pivotal in cellular regulations, and their crosstalk is related to various diseases such as cancer. Given the prevalence of PTM crosstalk within close amino acid ranges, identifying peptides with multiple PTMs is essential. However, this task is an NP-hard combinatorial problem with exponential complexity, posing significant challenges for existing analysis methods. Here, we introduce PIPI-C (PTM-Invariant Peptide Identification with a Combinatorial model), a novel search engine that addresses this challenge through a mixed-integer linear programming (MILP) model, thereby overcoming the limitations of existing approaches that struggle with high-order PTM combinations. Rigorous validation across diverse datasets confirms PIPI-C's superior performance in detecting PTM combinations. When applied to over 72 million mass spectra of three human cancers-lung squamous cell carcinoma (LSCC), colorectal adenocarcinoma (COAD), and glioblastoma (GBM)-PIPI-C reveals significantly upregulated PTM combinations. In LSCC, 50% of 860 upregulated unique PTM site patterns (UPSPs) (when comparing cancer vs. normal samples) carried at least two PTMs, including literature-supported crosstalks such as di-methylation with trifluoroleucine substitution and amidation with proline-to-valine substitution. Similar findings in COAD and GBM highlight PIPI-C's utility in uncovering cancer-relevant PTM combination landscapes. Overall, PIPI-C provides a robust mathematical framework for decoding complex PTM patterns, advancing our understanding of PTM-driven cellular processes in diseases.

Keywords:  Computational proteomics; Mixed integer linear programming (MILP); PTM crosstalk; Peptide identification; Post-translational modification (PTM)

DOI:  https://doi.org/10.1016/j.mcpro.2025.101494
bioRxiv. 2025 Dec 10. pii: 2025.12.07.692828. [Epub ahead of print]

Bioinformatic analysis of metastasis-associated metabolic landscape reveals an oncogenic role for the transsulfuration pathway.

Jonathan K Yan, Ying Yang, Wenqi Wang.

Cancer metastasis is a leading cause of cancer-related deaths, while its underlying mechanisms remain incompletely understood. To colonize distant organs, cancer cells reprogram their metabolism to adapt to diverse environmental challenges. Therefore, elucidating the metabolic pathways that drive cancer metastasis will uncover novel biomarkers and therapeutic targets. In this study, we integrated published datasets and systematically analyzed metabolites across multiple cancer cell lines. This large-scale bioinformatic analysis revealed distinct metabolites and metabolic pathways associated with organ-specific metastasis, and underscored the crucial role of tissue of origin in shaping the metabolic landscape of metastatic tumors. Notably, the transsulfuration pathway (also known as the cysteine and methionine metabolism) was strongly enriched in cancer cells with high metastatic potential. We validated this finding in pancreatic cancer, where the pathway enzyme cystathionine β-synthase (CBS) and its metabolic products were highly expressed in metastatic cancer cells. Targeting the transsulfuration pathway either by methionine deprivation or pharmacological inhibition of CBS significantly impaired the migration and invasion of metastatic pancreatic cancer cells. Taken together, our study not only provides a global view of the altered metabolic landscape in metastasis, but also identifies the transsulfuration pathway as an oncogenic driver and a therapeutic target for pancreatic cancer metastasis.

DOI: https://doi.org/10.64898/2025.12.07.692828
Sci Rep. 2025 Dec 24. 15(1): 44446

Proteomics analysis reveals progesterone receptor induced mitochondria-mediated apoptosis in breast cancer cells.

Qian Yee Woo, Pheck Khee Lau, Bernett Teck Kwong Lee, Natasa Bajalovic, Shi Hao Lee, Kye Siong Leong, Kai Yee Pow, Simra Hanan, Wei Meng, Soak Kuan Lai, Valerie Cl Lin.

The progesterone receptor (PR) expression is associated with disease-free survival in breast cancer. Yet, PR is known to elicit the activation of pro-tumor or anti-tumor signalling pathways. To gain a comprehensive understanding of intrinsic activities of PR, we conducted a global profiling of PR-regulated proteins using Tandem Mass Tag (TMT) proteomics in MCF-7 cells with elevated PR levels. The analysis identified reliably and reproducibly 4,915 PR-regulated proteins and 678 phosphorylated peptides in response to progestin R5020. Consistent with its growth inhibitory activity, PR broadly reduced levels of proteins for cell division, including CDKs, cyclins, DNA replication factors, and proteins involved in chromatin condensation, spindle assembly and chromosome segregation. PR also induced previously reported upregulation of pro-growth proteins such as EGFR, IRS2, and CCND1, but the upregulations are functionally futile due partly to inhibitory phosphorylation. Importantly, PR regulated 200 mitochondrial proteins including proapoptotic factors BNIP3, NIX, AIF/AIFM1, AIFM2, ENDOG, HtrA2/Omi, and Smac/DIABLO, culminating in mitochondria-mediated apoptosis independent of caspases. In conclusion, this proteomics study achieved to date the most comprehensive understanding of PR-regulated molecular networks that are strongly anti-proliferative and proapoptotic with pivotal involvement of mitochondria. PR agonists warrant evaluation for the treatment of breast cancer with high PR expression.

DOI: https://doi.org/10.1038/s41598-025-28183-3
bioRxiv. 2025 Dec 15. pii: 2025.12.11.693510. [Epub ahead of print]

Plasma plasmalogen levels and risk of lymph node positive breast cancer.

Mahsa Yavari, Kristen D Brantley, Alanis Carmona, Marie Sabatier, Yanshan Liang, June Monge-Lorenzo, Jordan Torpey, Krystina J Szylo, Midori Flores, Mario Palma, Cameron S Fraser, Milena Chaufan, Mayher Kaur, Lewis Hendrianto, Whitney Henry, Sheng Tony Hui, Raphaël Rodriguez, Walter C Willett, Julian Avila-Pacheco, Clary B Clish, A Heather Eliassen, Oana A Zeleznik, Jessalyn Ubellacker.

Lymph node involvement is a key predictor of poor breast cancer prognosis. Systemic lipid alterations can contribute to cancer cell survival in lymph nodes, but their relevance in humans remains unclear. Here, we combine human epidemiologic analyses from the Nurses' Health Study 2 and complementary mechanistic studies in mouse models to investigate how systemic lipid profiles relate to lymph node positive breast cancer. We show that in pre-diagnostic human plasma (n=511), lower levels of phosphatidylethanolamine (PE) and phosphatidylcholine (PC)-enriched plasmalogens are associated with increased risk of lymph node positivity, with stronger associations in samples collected closer to diagnosis. Consistent with the human data, lower levels of PE and PC-enriched plasma plasmalogens are found in mice with nodal involvement. Furthermore, in mice, dietary PUFA depletion reduces lipid oxidation in breast cancer cells in lymph nodes and promotes their survival and metastatic spread. These findings suggest that reduced levels of PE and PC-plasmalogens and decreased PUFA availability creates a lipid environment that enables breast cancer lymph node involvement.

DOI: https://doi.org/10.64898/2025.12.11.693510
J Proteome Res. 2025 Dec 22.

Temporal Profiling of Peroxynitrite-Mediated Protein Nitration and Phosphorylation Using Proteomics Analysis.

Yating Yao, Shuang Wang, Jingyi Li, Xiaohua Wang, Jinghua Yang.

  Peroxynitrite is capable of inducing protein nitration, which alters protein structure and interferes with signaling pathways dependent on phosphorylation. This study aims to investigate the effects of peroxynitrite-driven nitration and phosphorylation on proteins in HEK293T cells. Through label-free quantitative mass spectrometry, we successfully identified over 5,000 proteins from 0.5 μg of cell extracts collected at five different time intervals (0, 2, 15, 30, and 60 min) after exposure to peroxynitrite. We found that protein expression profiles from 2 to 60 min were distinct from those at 0 min. LC-MS/MS was also applied to quantify and map the nitration and phosphorylation sites. Analysis of protein nitration and phosphorylation revealed distinct temporal profiles, suggesting that nitration may contribute to the altered phosphorylation of the same protein or its interacting proteins. This study provides valuable insights for further mechanistic studies in peroxynitrite-related pathways.

Keywords:  mass spectrometry; peroxynitrite; post-translational modifications; protein nitration; protein phosphorylation; temporal profiling

DOI:  https://doi.org/10.1021/acs.jproteome.5c00417
Mol Cell Proteomics. 2025 Dec 24. pii: S1535-9476(25)00600-0. [Epub ahead of print] 101501

Modanovo: A Unified Model for Post-Translational Modification-Aware de Novo Sequencing Using Experimental Spectra from In Vivo and Synthetic Peptides.

Daniela Klaproth-Andrade, Yanik Bruns, Wassim Gabriel, Christian Nix, Valter Bergant, Andreas Pichlmair, Mathias Wilhelm, Julien Gagneur.

Post-translational modifications (PTMs) play a central role in cellular regulation and are implicated in numerous diseases. Database searching remains the standard for identifying modified peptides from tandem mass spectra, but is hindered by the combinatorial expansion of modification types and sites. De novo peptide sequencing offers an attractive alternative, yet existing methods remain limited to unmodified peptides or a narrow set of PTMs. Here, we curated a large dataset of spectra from endogenous and synthetic peptides from ProteomeTools spanning 19 biologically relevant amino acid-PTM combinations, covering phosphorylation, acetylation, and ubiquitination. We used this dataset to develop Modanovo, an extension of the Casanovo transformer architecture for de novo peptide sequencing. Modanovo achieved robust performance across these amino acid-PTM combinations (median area under the precision-coverage curve 0.92), while maintaining performance on unmodified peptides (0.93), nearly identical to Casanovo (0.94). The model outperformed π-PrimeNovo-PTM and InstaNovo-P and showed increased precision and complementarity to the database search tool MSFragger. Robustness was confirmed across independent datasets, particularly at peptide lengths frequently represented in the curated dataset. Applied to a phosphoproteomics dataset from monkeypox virus-infected cells, Modanovo recovered numerous confident peptides not reported by database search, including new viral phosphosites supported by spectral evidence, thereby demonstrating its complementarity to database-driven identification approaches. These results establish Modanovo as a broadly applicable model for comprehensive de novo sequencing of both modified and unmodified peptides.

DOI: https://doi.org/10.1016/j.mcpro.2025.101501
bioRxiv. 2025 Dec 20. pii: 2025.12.18.695253. [Epub ahead of print]

Characterizing the Effects of Protein Glycosylation Perturbation on Phosphorylation Signaling.

Effram Wei, Hongyi Liu, Michael Betenbaugh, Hui Zhang.

Protein glycosylation and phosphorylation constitute two pervasive regulatory layers in mammalian cells, yet the effects that protein glycosylation play in phosphorylation signaling remain poorly understood. Here we show that controlled perturbation of N-linked glycan biosynthesis through glycoengineering fundamentally rewires phosphorylation signaling networks in human cells. Using comprehensive proteomics approaches, we simultaneously profiled the global proteome, glycoproteome, and phosphoproteome in engineered HEK293 cells designed to eliminate core fucosylation while enhancing sialylation and reducing GlcNAc branching complexity. Glycoengineering emerged as the dominant source of molecular variation across all datasets, with over 9,800 intact glycopeptides identified of which 3,400 are significantly altered, establishing a remodeled baseline cellular state. Upon serum stimulation, engineered cells not only exhibited markedly decreased phosphorylation responses compared to wild-type cells, but comprehensively re-wired to prefer signaling away from canonical EGFR/mTOR growth pathways. These findings establish a systematic framework for targeting glycosylation-phosphorylation regulation and nominate glycan-dependent signaling nodes as potential therapeutic vulnerabilities in glycosylation-remodeled disease states.

DOI: https://doi.org/10.64898/2025.12.18.695253
Mol Cell Proteomics. 2025 Dec 24. pii: S1535-9476(25)00601-2. [Epub ahead of print] 101502

MoSAIC: An Integrated and Modular Workflow for Confident Analysis of Protein Post-Translational Modification Landscapes.

Yuanwei Xu, Lijun Chen, T Mamie Lih, Yingwei Hu, Hui Zhang.

  Investigating multiple protein post-translational modifications (PTMs) is critical for unraveling the complexities of protein regulation and the dynamic interplay among PTMs, a growing focus in proteomics. However, simultaneous analysis of diverse PTMs remains a significant technical challenge, as existing workflows struggle to balance throughput, sensitivity, and reproducibility, particularly when sample amounts are limited. To address these limitations, we present MoSAIC, a multi-PTM workflow integrating co-enrichment strategies, multiplexing, fractionation, hybrid data acquisition, and unified data analysis, optimized for clinically relevant biological samples. This approach targets phosphorylation, glycosylation, acetylation, and ubiquitination, enabling comprehensive interrogation of these modifications simultaneously. Compared to the traditional CPTAC workflow, MoSAIC doubles PTM coverage (4 vs. 2 PTMs) while maintaining the same instrument time (24 MS runs), achieving increased identifications of PTM-modified peptides. By leveraging fractionation and tandem mass tag (TMT) labeling, we achieved concurrent identification and quantification of PTM-specific peptides from the same sample, enhancing throughput and data consistency. This robust workflow addresses key limitations in multi-PTM proteomics, providing a cost-effective and efficient platform to advance biological and clinical research.

Keywords:  Acetylation; Data-dependent acquisition (DDA); Data-independent acquisition (DIA); Glycosylation; Mass spectrometry (MS); PTM crosstalk; Phosphorylation; Post-translational modifications (PTMs); Proteomics workflow; Tandem mass tag (TMT); Ubiquitination

DOI:  https://doi.org/10.1016/j.mcpro.2025.101502
Protein Sci. 2026 Jan;35(1): e70376

Assessing the relation between protein phosphorylation, AlphaFold3 models, and conformational variability.

Pathmanaban Ramasamy, Jasper Zuallaert, Lennart Martens, Wim F Vranken.

  Proteins perform diverse functions critical to cellular processes. Transitions between functional states are often regulated by post-translational modifications (PTMs) such as phosphorylation, which dynamically influence protein structure, function, folding, and interactions. Dysregulation of PTMs can therefore contribute to diseases such as cancer and Alzheimer's. However, the structure-function relationship between proteins and their modifications remains poorly understood due to a lack of experimental structural data, the inherent diversity of PTMs, and the dynamic nature of proteins. Recent advances in deep learning, particularly AlphaFold, have transformed protein structure prediction with near-experimental accuracy. However, it remains unclear whether these models can effectively capture PTM-driven conformational changes, such as those induced by phosphorylation. Here, we systematically evaluated AlphaFold models (AF2, AF3-non phospho, and AF3-phospho) to assess their ability to predict phosphorylation-induced structural diversity. By analyzing experimentally derived conformational ensembles, we found that all models predominantly aligned with dominant structural states, often failing to capture phosphorylation-specific conformations. Despite its phosphorylation-aware design, AF3-phospho predictions provided only modest improvement over AF2 and AF3-non phospho predictions. Our findings highlight key challenges in modeling PTM-driven structural landscapes and underscore the need for more adaptable structure prediction frameworks capable of capturing modification-induced conformational variability.

Keywords:  AlphaFold3; conformational diversity; phosphorylation; post‐translational modifications (PTMs); protein structures

DOI:  https://doi.org/10.1002/pro.70376
Nat Commun. 2025 Dec 24.

Stable de novo protein design via joint conformational landscape and sequence optimization.

Yehlin Cho, Justas Dauparas, Kotaro Tsuboyama, Gabriel J Rocklin, Sergey Ovchinnikov.

Generative protein modeling provides advanced tools for designing diverse protein sequences and structures. However, accurately modeling the conformational landscape and designing sequences remain critical challenges: ensuring that the designed sequence reliably folds into the target structure as its most stable conformation, and optimizing the sequence for a given suboptimal fixed input structure. In this study, we present a systematic analysis of jointly optimizing sequence-to-structure and structure-to-sequence mappings. This approach enables us to find optimal solutions for modeling the conformational landscape. We validate our approach with large-scale protein stability measurements, demonstrating that joint optimization is superior for designing stable proteins using a joint model (TrRosetta and TrMRF) and for achieving high accuracy in stability prediction when jointly modeling (half-masked ESMFold pLDDT + ESM2 Pseudo-likelihood). We further investigate features of sequences generated from the joint model and find that they exhibit higher frequencies of hydrophilic interactions, which may help maintain both secondary structure registry and pairing-features not captured by structure-to-sequence modeling alone.

DOI: https://doi.org/10.1038/s41467-025-66526-w
Mol Cell Proteomics. 2025 Dec 19. pii: S1535-9476(25)00592-4. [Epub ahead of print] 101493

Post-transcriptional modifications integration for ligand-receptor cellular network inference.

Pierre Giroux, Morgan Maillard, Jacques Colinge.

Cell-cell communications are widely explored to understand tissue homeostasis and diseases. Numerous computational tools have been developed to infer cellular interactions from transcriptomic or proteomic expression data. However, proteins often carry post-translational modifications (PTMs) that can induce conformational switches and alter their functional properties. A key challenge remains to incorporate PTM data in the inference and analysis of cellular interactions. Here, we propose an extension of our previously published tool BulkSignalR to integrate PTM information in ligand-receptor interactions and downstream pathways predictions. This new functionality is compatible with bulk and single-cell data, and it supports all types of PTMs. Based on two illustrative datasets, we show that this new feature provides deeper insights into biological pathway regulation, and that PTM integration helps reducing false positive results occasionally produced by standard approaches.

DOI: https://doi.org/10.1016/j.mcpro.2025.101493
J Biol Chem. 2025 Dec 22. pii: S0021-9258(25)02941-2. [Epub ahead of print] 111089

A reversible feedback mechanism regulating mitochondrial heme synthesis.

Iva Chitrakar, Alexis B Roberson, Pedro H Ayres-Galhardo, Breann L Brown.

  Proper heme biosynthesis is essential for numerous cellular functions across nearly all life forms. In humans, dysregulated heme metabolism is linked to multiple blood diseases, neurodegeneration, cardiovascular disease, and metabolic disorders. Erythroid heme production begins with the rate-limiting enzyme Aminolevulinic Acid Synthase (ALAS2) in the mitochondrion. Although prior studies discuss the regulation of ALAS2 in the nucleus and cytoplasm, its modulation as a mature mitochondrial matrix enzyme remains poorly understood. We report that heme binds mature human ALAS2 with high affinity, acting as a reversible mixed inhibitor that reduces enzymatic activity. Structural modeling supports the hypothesis that two flexible regions of ALAS2 interact with heme, locking the enzyme in an inactive conformation and occluding the active site. Our work reveals a negative feedback mechanism for heme synthesis, offering insights into the spatial regulation of ALAS2 and the maturation of the essential heme cofactor.

Keywords:  Heme; aminolevulinic acid; enzyme inhibition; enzymology; erythropoiesis; heme regulatory motif; protein structure and function; pyridoxal 5-phosphate

DOI:  https://doi.org/10.1016/j.jbc.2025.111089
bioRxiv. 2025 Dec 20. pii: 2025.12.16.694762. [Epub ahead of print]

Mitochondrial control of fuel switching via carnitine biosynthesis.

Christopher Auger, Hiroshi Nishida, Bo Yuan, Guilherme Martins Silva, Masanori Fujimoto, Mark Li, Daisuke Katoh, Dandan Wang, Melia Granath-Panelo, Jihoon Shin, Anthony Verkerke, Alexander Banks, Sheng Tony Hui, Lijun Sun, Jin-Seon Yook, Rose Witte, Shingo Kajimura.

Metabolic adaptation to environmental changes, such as fasting and cold exposure, involves a dynamic shift in fuel utilization from glucose to fatty acid oxidation, a process that relies on carnitine-mediated fatty acid oxidation in mitochondria. While dietary sources of animal origin (e.g., red meat) contribute to the carnitine pool, de novo carnitine synthesis from trimethyllysine (TML) is essential, particularly for those whose dietary sources are vegetables and fruits that contain negligible amounts of carnitine. However, the molecular pathway of de novo carnitine synthesis and its physiological significance remain poorly understood. Here, we showed that SLC25A45 is a mitochondrial TML carrier that controls de novo carnitine biosynthesis in vivo. Genetic loss of SLC25A45 results in systemic carnitine and acylcarnitine deficiency, leading to impaired fatty acid oxidation and thermogenesis during cold adaptation, while promoting glucose catabolism. Notably, Slc25a45-deficient mice maintained a high respiratory exchange ratio and impaired lipid mobilization following treatment with a GLP1 receptor agonist (GLP-1RA), rendering them resistant to GLP-1RA-induced adipose tissue loss. Together, the present study identifies SLC25A45 as a regulatory checkpoint in fuel switching during adaptation, with implications for systemic energy balance and response to GLP-1RA-mediated anti-obesity therapy.

DOI: https://doi.org/10.64898/2025.12.16.694762
J Proteome Res. 2025 Dec 21.

Automated Mag-Net Enrichment Unlocks Deep and Cost-Effective LC-MS Plasma Proteomics.

Erkka Järvinen, Xiaonan Liu, Markku Varjosalo, Salla Keskitalo.

  Plasma is an ideal material for proteomics due to its diverse protein content reflecting physiological and pathological states and its compatibility with minimally invasive sampling. Deep proteomic profiling of plasma is limited by high-abundant proteins that mask the detection of low-abundant proteins. To overcome this, we compared five plasma protein enrichment methods, Mag-Net, ENRICHplus, ENRICHiST, EasySep, and EXONET, against neat plasma using LC-MS proteomics. All five methods substantially increased protein identifications, with Mag-Net, ENRICHplus, EasySep, and EXONET yielding up to 4200 proteins per sample, over 7-fold more than neat plasma, using a 44 min gradient on the Evosep One and data-independent acquisition on the timsTOF Pro 2. These methods enriched extracellular vesicle-associated proteins while effectively depleting high-abundant proteins. To further enhance performance and scalability, we optimized the Mag-Net protocol by increasing the plasma-to-bead ratio and automated the workflow, including Evotip loading, on the Biomek i5 liquid handler. The automated Mag-Net, combined with the Orbitrap Astral mass spectrometer, yielded up to 4500 proteins per sample with a throughput of 100 samples per day. The workflow demonstrated high reproducibility and a remarkably low total cost of just a few dollars per sample. Newer enrichment methods (Proteonano, P2-iST Plasma, and P2) showed improved plasma proteome coverage compared with Mag-Net but are likely to incur higher costs. The streamlined Mag-Net enrichment strategy enables affordable, scalable, high-throughput LC-MS plasma proteomics, supporting biomarker discovery across large cohorts.

Keywords:  Biomek; DIA-NN; EXONET; Mag-Net; automation; dia-PASEF; extracellular vesicles (EVs); mass spectrometry; neat plasma; plasma proteomics

DOI:  https://doi.org/10.1021/acs.jproteome.5c00420
Sci Signal. 2025 Dec 23. 18(918): eadv0660

The protein denitrosylase SCoR2 regulates lipogenesis and fat storage.

Nicholas M Venetos, Colin T Stomberski, Hua-Lin Zhou, Zhaoxia Qian, Precious J McLaughlin, Puneet K Bansal, John Feczko, Ilya Bederman, Hoa Nguyen, Alfred Hausladen, Joseph C Schindler, Zachary W Grimmett, Henri Brunengraber, Richard T Premont, Jonathan S Stamler.

Lipid homeostasis is subject to control by posttranslational modification machinery, such as sirtuin deacetylases that reverse coenzyme A (CoA)-dependent acetylation. Here, we showed that a mammalian denitrosylase (SCoR2), which counteracts CoA-dependent S-nitrosylation, promoted both fat storage and lipogenesis to impair metabolic health. In mice, SCoR2 protein abundance correlated with body mass, and deleting or pharmacologically inhibiting SCoR2 prevented both diet-induced obesity and metabolic dysfunction-associated steatotic liver disease (MASLD). Loss of SCoR2 in adipocytes promoted the S-nitrosylation of the actin cytoskeletal regulator myosin 9, which inhibited the activity of the lipogenesis-promoting transcription factors PPARγ, SREBP1, and CEBPα to prevent fat storage. In hepatocytes, inhibition of SCoR2-mediated denitrosylation of lipogenic enzymes reduced fat synthesis and induced fat oxidation. In humans, an obesity-linked polymorphism was associated with increased SCoR2 mRNA expression, and in patient adipose and liver tissues, SCoR2 protein or mRNA abundance directly correlated with adipocyte size or MASLD. These results indicate that SCoR2 regulates nutrient metabolism, similar to sirtuins, and is a potential drug target for obesity and MASLD.

DOI: https://doi.org/10.1126/scisignal.adv0660
Sci Rep. 2025 Dec 24. 15(1): 44435

LEM4 interacts with β-catenin and promotes β-catenin-dependent transcription activity to confers ribociclib resistance in breast cancer cells.

Qi Tang, Xintong Zhao, Hui Li, Jiaqian Liao, Bingyu Ouyang, Chunxiao Ma, Dedian Chen.

  Background Ribociclib, a CDK4/6 inhibitor, is a targeted therapy for breast cancer management. However, acquired resistance to ribociclib is a common clinical challenge. This study aimed to investigate the role of LEM-Domain Protein 4 (LEM4), a nuclear envelope protein, in mediating ribociclib resistance in breast cancer cells and elucidate the underlying molecular mechanisms. Methods LEM4 expression was analyzed in breast cancer patient samples and cell lines. Ribociclib-resistant MCF-7 and T47D cell lines were established, and the effects of LEM4 knockdown on drug sensitivity, apoptosis, and β-catenin signaling were evaluated using in vitro cytotoxicity, co-immunoprecipitation, β-catenin transcription activity and in vivo tumor formation assays. Results LEM4 was found to be overexpressed in breast cancer tissues and cell lines, and its high expression correlated with worse overall survival in patients. Ribociclib-resistant breast cancer cells demonstrated significantly elevated LEM4 expression levels, and LEM4 silencing re-sensitized drug-resistant cells to ribociclib-induced cytotoxicity and apoptosis in vitro and in vivo. Mechanistically, LEM4 interacted with β-catenin, increasing its protein stability, nuclear translocation, and transcriptional activity. Inhibition of β-catenin signaling reversed ribociclib resistance. Conclusion This study identifies LEM4 as a key mediator of ribociclib resistance in breast cancer cells through its interaction with β-catenin and subsequent activation of β-catenin signaling. Targeting the LEM4/β-catenin axis represents a potential therapeutic strategy to overcome ribociclib resistance in breast cancer.

Keywords:  Breast cancer; LEM4; Ribociclib resistance; Targeted therapy; Β-catenin

DOI:  https://doi.org/10.1038/s41598-025-28139-7
FASEB J. 2026 Jan 15. 40(1): e71374

Glucose Induces DNMT1/IMPDH2-Dependent Metabolic Memory in Endothelial Cells Upon Reprograming Nucleotide Metabolism.

Sampara Vasishta, Ganesha Poojary, Sarmeela Sharma, Sarah Michael Gomes, Sharath Mohan Bhat, Sandeep Mallya, Prashanth Adiga, Shashikiran Umakanth, Saumya Jakati, Brijesh Takkar, Inderjeet Kaur, Manjunath B Joshi.

  Type 2 diabetic (T2D) individuals are predisposed to enduring vascular complications despite therapeutic/lifestyle intervention due to 'metabolic memory', an epigenetic reprogramming in various cell/tissue types. The present study examined the potential role of DNMT isoforms in regulating glucose-induced metabolic memory and associated changes in endothelial metabolism leading to diabetic complications. The study involved micro/macro vascular endothelial cells (ECs), high-fat diet (HFD)-induced diabetic mouse models, and subjects with diabetic retinopathy (DR) at varying enforced levels of glycemia. Immunoblotting and HPLC-based analysis were performed to examine the expression of DNMT isoforms and global DNA methylation levels. Reactive oxygen species (ROS) and inflammatory mediators were analyzed by Spectramax and multiplex ELISA respectively. Cell cycle analysis and angiogenesis assays were performed by flowcytometry and 3D spheroid assays. Integrated omics analysis using LC-MS and RRBS was performed to identify metabolic and epigenomic signatures of metabolic memory. Candidate genes were validated in clinically characterized individuals with DR by RT-PCR. High glucose and AGEs persistently elevated expression of the DNMT1 but not DNMT3A and DNMT3B despite glucose normalization. Global DNA methylation, DNA synthesis, angiogenesis, oxidative stress, inflammatory mediators, and nucleotide metabolism intermediates were elevated and sustained despite glucose normalization. Metabolic memory was associated with differential methylation of genes associated with vascular functions and nucleotide metabolism. We observed persistent DNA methylation of IMPDH2, the rate-limiting enzyme of purine metabolism. DNMT1 and IMPDH2 were elevated in retinal and umbilical vein endothelial cells in vitro, as well as retinal and aortic tissues of the HFD mice despite dietary intervention, which were reduced upon treatment with 5-aza-2'-deoxycytidine. IMPDH2 transcripts were elevated in subjects with DR undergoing antidiabetic therapy and in the exosomes derived from the vitreous of subjects with proliferative DR. Mycophenolate mofetil, a pharmacological inhibitor of IMPDH2, decreased sustained levels of DNMT1 and impeded sprout formation in 3D endothelial cultures induced by transient hyperglycemic conditions. Our study provides novel insights into the biology of metabolic memory by identifying IMPDH2 regulated by DNMT1 during epigenetic and metabolic reprogramming, with clinical relevance to the pathogenesis of DR.

Keywords:  DNA methylation; endothelium; exosomes; metabolic memory; nucleotide metabolism; retinopathy

DOI:  https://doi.org/10.1096/fj.202502260RR
Cell Death Dis. 2025 Dec 20.

Transsulfuration metabolism is essential for ferroptosis resistance in quiescent endothelial cells.

Roxana Elena Oberkersch, Jacopo Lidonnici, Sebastiano Andreuzza, Eleonora Zambon, Gabriele Imperato, Silvia Pedretti, Nico Mitro, Massimo Mattia Santoro.

Angiogenesis, the formation of new blood vessels from pre-existing ones, is a crucial process involved in both physiological and pathological contexts. During angiogenesis, quiescent endothelial cells (QECs) forming the vascular bed begin to proliferate and switch their metabolism to support anabolic and energetic needs in response to growth factors and hypoxic conditions. Recent research has demonstrated that ferroptosis, an iron-dependent form of cell death mediated by lipid peroxidation, can affect angiogenesis. Cysteine, a thiol-containing amino acid, is crucial for the synthesis of sulfur-containing biomolecules that control ferroptosis. Glutathione (GSH), a reducing tripeptide containing a cysteine residue, serves as a cofactor for the enzyme glutathione peroxidase 4 (GPX4) to donate electrons to peroxides of polyunsaturated fatty acyl phospholipids. Cysteine can be acquired from its extracellular oxidized form, cystine, via the glutamate-cystine antiporter (system xCT) or synthesized de novo via the transsulfuration pathway (TSP). However, whether proliferating ECs (PECs) and QECs differentially modulate the cysteine/GSH/GPX4 axis to protect themselves from ferroptosis is still unknown. Our findings revealed that PECs primarily utilize extracellular cystine to synthesize GSH, which is essential for avoiding ferroptosis. In contrast, QECs exhibit a resilient response to cystine starvation by activating the TSP. Interestingly, chronic and severe hypoxia induces ferroptosis resistance in PECs exposed to cystine limitation, mimicking the metabolic profile of QECs. Molecularly, QECs exhibit high NRF2 expression necessary to support TSP under cystine limitation and protect QECs from ferroptosis. In vivo experiments confirm the susceptibility of ECs to cell death by xCT inhibition in a retinal model of sprouting angiogenesis. These findings highlight differential regulation of cysteine metabolism in PECs and QECs and suggest that the cysteine/GSH/GPX4 axis could be a potential therapeutic target for diseases involving angiogenesis.

DOI: https://doi.org/10.1038/s41419-025-08333-1
Metabolism. 2025 Dec 18. pii: S0026-0495(25)00340-3. [Epub ahead of print]176 156470

The ACSL family: Bridging fatty acid metabolism and cell death in cancer progression.

Ziqi Yu, Lifeng Zhang, Bo Jiang, Lu Zhang, Minghui Chen, Mei Song.

  Fatty acids (FAs) are indispensable for cellular homeostasis and centered in anabolic and catabolic pathways that are tightly governed by long-chain acyl-CoA synthetases (ACSLs). These enzymes drive fatty acid β-oxidation (FAO) to generate energy, remodel cell membrane phospholipid composition to dictate ferroptosis susceptibility, coordinate steroidogenesis and eicosanoid biosynthesis, and mediate metabolic reprogramming, thus acting as a central nexus between FAs metabolism and cell death. Dysregulation of ACSLs across malignancies fosters oncogenic dependency on metabolic reprogramming, influencing tumor progression, immune modulation, and therapy resistance, offering a rationale for anticancer therapeutic opportunities. Here, we delineate the decisive roles of ACSLs in the metabolic fate of FAs and cell death execution. We dissect their tumorigenic mechanisms through metabolic rewiring and cell death modulation, with an emphasis on ACSLs-mediated crosstalk between ferroptosis and cancer immunity. Furthermore, we discuss the potential of ACSLs-targeted agents in tumor therapy and the treatment of ferroptosis-associated pathologies, offering actionable insights for clinical translation.

Keywords:  ACSL; Cancer therapy; Fatty acid metabolism; Ferroptosis; Regulated cell death

DOI:  https://doi.org/10.1016/j.metabol.2025.156470
bioRxiv. 2025 Dec 15. pii: 2025.12.12.694000. [Epub ahead of print]

Cystathionine Beta-Synthase Promotes Anoikis Resistance and Transcoelomic Metastasis in Ovarian Cancer via the SP1-ITGB1 axis.

Pallab Shaw, Arpan Dey Bhowmik, Akrit Pran Jaswal, Rameswari Velayutham, Srikanth Chiliveru, Samantha Ricketts, Chao Xu, Danny N Dhanasekaran, Resham Bhattacharya, Priyabrata Mukherjee, Shailendra Kumar Dhar Dwivedi, Geeta Rao.

Anoikis resistance is crucial for ovarian cancer (OvCa) transcoelomic metastasis, during which exfoliated OvCa cells survive as spheroids before invading the omentum. Here, we demonstrate that cystathionine β-synthase (CBS), an H2S-producing transsulfuration pathway enzyme, is a key determining factor of OvCa spheroidal viability and metastatic potential. Analysis of publicly available patient datasets, as well as an in-house tissue microarray revealed that high CBS expression positively correlates with poor progression-free survival and clinically observed peritoneal/omental metastasis. Integrated functional and proteomic analyses indicated that CBS silencing induces apoptosis in 2D monolayers. Consistent with this, CBS silencing in spheroids caused apoptosis along and disrupted spheroid architecture. Mechanistically, this phenotype was associated with downregulation of oncogenic stemness and epithelial-mesenchymal transition. Further, through proteomic and bioinformatic analyses, we identified ITGB1 to be the hub protein in OvCa spheroidogenesis. Interestingly, knockdown of CBS led to abrogation of the ITGB1-mediated downstream pathway. Moreover, by proteomic and network analyses, we identified SP1 as a key transcriptional regulator of CBS-induced pro-spheroidal transcriptional programs of stemness and invasiveness. Stabilization of SP1 through persulfidation by H2S supplementation restored spheroidal viability and underlying protein signaling. Further, our results reveal that loss of CBS through ITGB1 repression disrupts spheroid architecture, leading to reduced metastatic docking on the murine omental surface in vivo . Collectively, these findings establish CBS as a central regulator of anoikis resistance and OvCa transcoelomic dissemination, highlighting the therapeutic potential of targeting the CBS-SP1-ITGB1 axis to attenuate metastatic spread.

DOI: https://doi.org/10.64898/2025.12.12.694000