bims-cesirm 2026-01-11 papers

bims-cesirm

Biomed News

on Cell Signaling mediated regulation of metabolism

Issue of 2026–01–11
34 papers selected by
Tigist Tamir, University of North Carolina

Targeting DHODH Reveals a Metabolic Vulnerability in AR-positive and AR-negative Prostate Cancer Cells via Pyrimidine Synthesis and Metabolic Crosstalk with the TCA and Urea Cycles.
Nutrient requirements of organ-specific metastasis in breast cancer.
Bacterial ubiquitin ligase engineered for small molecule and protein target identification.
Integrative proteogenomic analysis provides molecular insights and clinical significance in gallbladder cancer.
13C-Isotope Tracing Structural Lipidomics for Resolving Phospholipid Metabolism Dynamics in Human Breast Cancer Cells.
Don't forget protein synthesis! Mitochondria of cancer cells import glutamine to fuel metabolism and to charge tRNAs for translation.
O-GlcNAcylation of XRCC4 controls its stability and confers resistance to DNA double-strand break damage in cancer cells.
Membrane editing with proximity labeling reveals regulators of lipid homeostasis.
Metabolic hijackers: how viral proteins redefine host cell landscapes.
Mitochondrial ROS-induced metabolic alterations differentially regulate ferroptosis sensitivity.
Amino Acid Metabolic Reprogramming in Clear Cell Renal Cell Carcinoma: Pathogenic Mechanisms and Therapeutic Targeting.
PHGDH at the crossroads: metabolic plasticity, metastatic paradoxes, and therapeutic reconnaissance in cancer.
A clickable CoQ imaging probe reveals that cellular uptake and lysosomal trafficking depend on CD36 and NPC1.
The clinically available supplement pyruvate enhances the therapeutic effect of bortezomib in MM by modulating mitochondrial metabolism.
Active aldehydes accelerate CD8+ T cell exhaustion by metabolic alteration in the tumor microenvironment.
Integrated Interactome and Phosphoproteome Analysis Reveals Novel MAP4K3-Regulated Pathways and Unexpected Cellular Roles for MAP4K3.
Identification and Regulation of a Hepatic Lipogenic Metabolon.
MolOrgGPT: De Novo Generation via Large Language Models and Reinforcement Learning.
Functional Impact of Glycosylation of LRIG1 on EGFR Proteostasis in Cancer.
Uncovering the potential of pathomics: prognostic prediction and mechanistic investigation of pancreatic cancer.
SLC25A11-mediated reprogramming of mitochondrial redox state and lipid peroxidation confers NRF2-dependent ferroptosis resistance in biliary tract cancer.
Cancer cells surviving cisplatin chemotherapy increase stress-induced OMA1 activity and mitochondrial fragmentation.
Multi-Omics Integration Identifies the Cholesterol Metabolic Enzyme DHCR24 as a Key Driver in Breast Cancer.
Targeting the Primordial Chaperone to Overcome Acquired Drug Resistance in Cancer: TG2-Mediated Autophagy.
Methionine synthase reductase regulates heterochromatin independently of methionine synthesis through mitochondrial homeostasis.
PTEN-loss confers dependence on the guanylate synthesis enzyme IMPDH in T-cell acute lymphoblastic leukemia.
Citrate Synthase Knockdown Suppresses Cell Proliferation and Induces Apoptosis in Select Human Cancer Cell Lines.
Acetylation of CPT1A reduces fatty acid oxidation and leads to dysfunctional renal tubular mitochondria in diabetic kidney disease.
Multi-omic analysis reveals nitric oxide dependent remodeling in classically activated macrophages and identifies negative regulation mediated by AKR1A1.
A Multifunctional PD-L1 Modulator for Metabolic Reprogramming to Induce Pyroptosis and Enhance Glutamine Inhibition-Mediated Antitumor Immunotherapy.
Chronic stress drives ovarian cancer progression via myeloid-derived suppressor cells infiltration and Notch signaling pathway activation.
Enhancing Sensitivity in Targeted Single-Cell Proteomics by Coupling a Dual Ion Funnel Interface with Triple Quadrupole Mass Spectrometer.
Targeting ceramide metabolism to restore hypoxia-induced apoptosis in p53-deficient colon cancer cells.
Temporal Multi-Omic Analysis Uncovers Sex-Biased Molecular Programs Underlying Skeletal Muscle Adaptation to Endurance Training.

Mol Metab. 2026 Jan 06. pii: S2212-8778(25)00223-6. [Epub ahead of print] 102316

Targeting DHODH Reveals a Metabolic Vulnerability in AR-positive and AR-negative Prostate Cancer Cells via Pyrimidine Synthesis and Metabolic Crosstalk with the TCA and Urea Cycles.

Maxime Labroy, Marc-Oliver Paré, Line Berthiaume, Mélissa Thomas, Cynthia Jobin, Alain Veilleux, Martin Pelletier, Frédéric Pouliot, Jean-Yves Masson, Étienne Audet-Walsh.

  Following recurrence, the cornerstone clinical therapy to treat prostate cancer (PCa) is to inhibit the androgen receptor (AR) signaling. While AR inhibition is initially successful, tumors will eventually develop treatment resistance and evolve into lethal castration-resistant PCa. To discover new anti-metabolic treatments for PCa, a high-throughput anti-metabolic drug screening was performed in PC3 cells, an AR-negative PCa cell line. This screening identified the dihydroorotate dehydrogenase (DHODH) enzyme as a metabolic vulnerability, using both AR-positive and AR-negative models, including the neuroendocrine cell line LASCPC-01 and patient-derived organoids. DHODH is required for de novo pyrimidine synthesis and is the sole mitochondrial enzyme of this pathway. Using extracellular flux assays and targeted metabolomics, DHODH inhibition was shown to impair the pyrimidine synthesis pathway, as expected, along with a significant reprogramming of mitochondrial metabolism, with a massive increase in fumarate (>10-fold). Using 13C6-glucose, it was shown that following DHODH inhibition, PCa cells redirect carbons from glucose toward biosynthetic pathways rather than the TCA cycle. In parallel, using 13C5-glutamine, it was shown that PCa cells use this amino acid to fuel a reverse TCA cycle. Finally, 13C1-aspartate and 15N1-glutamine highlighted the connection between pyrimidine synthesis and the urea cycle, redirecting pyrimidine synthesis intermediates toward the urea cycle as a stress response mechanism upon DHODH inhibition. Consequently, combination therapies targeting DHODH and glutamine metabolism were synergistic in impairing PCa cell proliferation. Altogether, these results highlight DHODH as a metabolic vulnerability of AR-positive and AR-negative PCa cells by regulating central carbon and nitrogen metabolism.

Keywords:  BAY-2402234; DHODH; NEPC; androgen receptor; aspartate; cancer metabolism; castration-resistant prostate cancer; glucose; glutamine; mitochondria; neuroendocrine differentiation; neuroendocrine prostate cancer; nucleotide synthesis; prostate cancer

DOI:  https://doi.org/10.1016/j.molmet.2025.102316
Nature. 2026 Jan 07.

Nutrient requirements of organ-specific metastasis in breast cancer.

Keene L Abbott, Sonu Subudhi, Raphael Ferreira, Yetiş Gültekin, Sophie C Steinbuch, Muhammad Bin Munim, Diya L Ramesh, Sophie E Honeder, Ashwin S Kumar, Michelle Wu, Jacob A Hansen, Anna Shevzov-Zebrun, Edrees H Rashan, Kian M Eghbalian, Sharanya Sivanand, Anna M Barbeau, Lisa M Riedmayr, Mark Duquette, Ahmed Ali, Nicole Henning, Sonia E Trojan, Millenia Waite, Tenzin Kunchok, Mayu A Nakano, Florian Gourgue, Gino B Ferraro, Brian T Do, Virginia Spanoudaki, Francisco J Sánchez-Rivera, Xin Jin, George M Church, Rakesh K Jain, Matthew G Vander Heiden.

Cancer metastasis is a major contributor to patient morbidity and mortality1, yet the factors that determine the organs where cancers can metastasize are incompletely understood. Here we quantify the absolute levels of 124 metabolites in multiple tissues in mice and investigate how this relates to the ability of breast cancer cells to grow in different organs. We engineered breast cancer cells with broad metastatic potential to be auxotrophic for specific nutrients and assessed their ability to colonize different tissue sites. We then asked how tumour growth in different tissues relates to nutrient availability and tumour biosynthetic activity. We find that single nutrients alone do not define the sites where breast cancer cells can grow as metastases. In addition, we identify purine synthesis as a requirement for tumour growth and metastasis across many tissues and find that this phenotype is independent of tissue nucleotide availability or tumour de novo nucleotide synthesis activity. These data suggest that a complex interplay between multiple nutrients within the microenvironment dictates potential sites of metastatic cancer growth, and highlights the interdependence between extrinsic environmental factors and intrinsic cellular properties in influencing where breast cancer cells can grow as metastases.

DOI: https://doi.org/10.1038/s41586-025-09898-9
EMBO J. 2026 Jan 03.

Bacterial ubiquitin ligase engineered for small molecule and protein target identification.

James S Ye, Abir Majumdar, Brenden C Park, Miles H Black, Ting-Sung Hsieh, Adam Osinski, Kelly A Servage, Kartik Kulkarni, Jacinth Naidoo, Neal M Alto, Margaret M Stratton, Dominique Alfandari, Joseph M Ready, Krzysztof Pawłowski, Diana R Tomchick, Vincent S Tagliabracci.

  The Legionella SidE effectors ubiquitinate host proteins independently of the canonical E1-E2 cascade. Here we engineer the SidE ligases to develop a modular proximity ligation approach for the identification of targets of small molecules and proteins, which we call SidBait. We validate the method with known small molecule-protein interactions and use it to identify CaMKII as an off-target interactor of the breast cancer drug ribociclib. Structural analysis and activity assays confirm that ribociclib binds the CaMKII active site and inhibits its activity. We further customize SidBait to identify protein-protein interactions and discover the F-actin capping protein (CapZ) as a target of the Legionella effector RavB during infection. Structural and biochemical studies indicate that RavB allosterically binds CapZ and decaps actin, thus functionally mimicking eukaryotic CapZ interacting proteins. Collectively, our results establish SidBait as a reliable tool for identifying targets of small molecules and proteins.

Keywords:   Legionella ; Actin Capping; Kinase Inhibitor; Target Identification

DOI:  https://doi.org/10.1038/s44318-025-00665-0
Cancer Cell. 2026 Jan 08. pii: S1535-6108(25)00548-3. [Epub ahead of print]

Integrative proteogenomic analysis provides molecular insights and clinical significance in gallbladder cancer.

Zile Fu, Yuanli Song, Fen Liu, Lv Chen, Shangli Cai, Peng Cui, Guoqiang Wang, Wenchuan Xie, Shu Zhang, Li Ding, Pei Wang, Bing Zhang, Henry Rodriguez, Feiling Feng, Xufeng Zhang, Wei Gong, Qiang Gao, Daming Gao, Hu Zhou, Jia Fan.

  Gallbladder cancer (GBC) is a highly aggressive malignancy with dismal outcomes. To dissect its molecular characteristics and identify potential therapeutic avenues, we performed proteogenomic characterization of 195 tumors and 135 adjacent non-cancerous gallbladder tissues. Integrative analyses highlighted TP53 and ELF3 mutations as key drivers disrupting signaling and metabolism. ErbB2 amplification, a pivotal genomic event, was associated with reduced canonical PI3K/AKT and RAS/MAPK/ERK signaling yet enhanced proliferative activity. We discovered potential gain-of-function mutations in ErbB2 and ErbB3 predicted to enhance ErbB2-ErbB3 heterodimer activity. ACAT1 and PHGDH were identified as metabolic drivers of GBC liver invasion. Integrated molecular and immune subtyping delineated four distinct multi-omics and immune microenvironment subtypes, each carrying prognostic and therapeutic relevance. Although rare, neuroendocrine GBC was separately characterized, revealing MEIS1 as a potential regulator of neuroendocrine-like features. Together, this study establishes a proteogenomic landscape of GBC, providing biological insights and guiding future translational efforts.

Keywords:  gallbladder cancer; immune subtypes; multi-omics subtypes; proteogenomics

DOI:  https://doi.org/10.1016/j.ccell.2025.12.014
Anal Chem. 2026 Jan 09.

13C-Isotope Tracing Structural Lipidomics for Resolving Phospholipid Metabolism Dynamics in Human Breast Cancer Cells.

Zhuoning Xie, Qirui Yu, Simin Cheng, Dan Li, Zheng Ouyang, Xiaoxiao Ma.

Phospholipid metabolic homeostasis is critical, yet its dynamic regulation at the structural level remains poorly characterized, particularly from the perspective of metabolic flux analysis. This study presents an RPLC-PB-MS/MS workflow integrating 13C-glucose isotope tracing and the Paternò-Büchi (PB) reaction for comprehensive investigation of de novo phospholipid synthesis. By precisely mapping 13C labeling sites, we revealed distinct metabolic rates for various PL structural components. The glycerol backbone showed the fastest metabolism, while within phospholipid acyl chains, SFAs showed a greater contribution to 13C labeling compared to MUFAs. Furthermore, we quantified the labeling rates of PL C═C location isomers, highlighting dynamic regulation at the C═C location level. Notably, certain low-abundance n-7 isomers exhibited rapid turnover, suggesting potential functional roles in membrane remodeling or signaling. Analysis of three human breast cancer cell lines (MCF-7, MDA-MB-468, and BT-474) further revealed significant differences in PL metabolism dynamics, with MCF-7 cells showing initially rapid but transient labeling after passage, while MDA-MB-468 cells maintained sustained high fluxes. These findings provide insights into the structural specificity and dynamic regulation of phospholipid metabolism in cancer, offering potential therapeutic implications.

DOI: https://doi.org/10.1021/acs.analchem.5c06789
Mol Cell. 2026 Jan 08. pii: S1097-2765(25)01013-5. [Epub ahead of print]86(1): 6-8

Don't forget protein synthesis! Mitochondria of cancer cells import glutamine to fuel metabolism and to charge tRNAs for translation.

Yury S Bykov, Johannes M Herrmann.

In this issue of Molecular Cell, Zhu et al.1 show that mitochondria of cancer cells rely on the import of glutamine not only to fuel metabolite synthesis via the tricarboxylic acid cycle but also to charge mt-tRNAGln to allow mitochondrial protein synthesis and respiration.

DOI: https://doi.org/10.1016/j.molcel.2025.12.014
Cell Death Dis. 2026 Jan 09. 17(1): 22

O-GlcNAcylation of XRCC4 controls its stability and confers resistance to DNA double-strand break damage in cancer cells.

Jeong Yeon Ko, Tae Hyun Kweon, Hyeryeon Jung, Jingu Kang, Yeolhoe Kim, Yun Ju Kim, Donghyuk Shin, Seong Wook Yang, Myeong Min Lee, Jun Young Hong, Jae-Min Lim, Eugene C Yi, Jin Won Cho, Won Ho Yang.

X-ray repair cross-complementing protein 4 (XRCC4), a non-homologous end-joining protein involved in DNA double-strand break repair, is highly expressed in human cancer cells and tissues. A prior OGT interactome study identified XRCC4 as a candidate for O-GlcNAcylation. O-GlcNAcylation levels, a post-translational modification found on nuclear and cytosolic proteins, are also elevated in various cancers. However, the direct regulatory mechanism linking O-GlcNAcylation to XRCC4 function in cancer cells remains unclear. Here, we found that XRCC4 is O-GlcNAcylated at threonine 308, enhancing its stability by inhibiting TRIM21-mediated ubiquitin-dependent proteasomal degradation. O-GlcNAcylation elevated XRCC4 protein levels during DNA double-strand break damage, thereby conferring resistance to such damage. Additionally, XRCC4 Thr308 O-GlcNAcylation promotes cancer proliferation, invasion, and in vivo tumor growth. These findings suggest that downregulating O-GlcNAcylation on XRCC4 could be a potential therapeutic strategy to increase cancer sensitivity to chemotherapy or radiotherapy.

DOI: https://doi.org/10.1038/s41419-025-08209-4
Nat Chem Biol. 2026 Jan 07.

Membrane editing with proximity labeling reveals regulators of lipid homeostasis.

Reika Tei, Xiang-Ling Li, Lin Luan, Jeremy M Baskin.

Cellular lipid metabolism is subject to strong homeostatic regulation, but the players involved in and mechanisms underlying these pathways remain largely uncharacterized. Here we develop a 'feeding-fishing' approach coupling membrane editing using optogenetic lipid-modifying enzymes (feeding) with organelle membrane proteomics through proximity labeling (fishing) to elucidate molecular players and pathways involved in the homeostasis of phosphatidic acid (PA), a multifunctional lipid central to glycerolipid metabolism. This approach identified several PA-metabolizing enzymes and lipid transfer proteins enriched in and depleted from PA-fed membranes. Mechanistic analysis revealed that PA homeostasis in the cytosolic leaflets of the plasma membrane and lysosomes is mediated by both local PA metabolism and the action of lipid transfer proteins that carry out interorganelle lipid transport before subsequent metabolism. More broadly, the interfacing of membrane editing to controllably modify membrane lipid composition with organelle membrane proteomics using proximity labeling represents a strategy for revealing mechanisms governing lipid homeostasis.

DOI: https://doi.org/10.1038/s41589-025-02104-x
J Virol. 2026 Jan 09. e0055625

Metabolic hijackers: how viral proteins redefine host cell landscapes.

Adam Hafner, Rebekah L Mokry, John G Purdy, Christiane E Wobus.

  Viruses are metabolic engineers of host cells. As obligate intracellular pathogens, they rely on host cell metabolism for efficient viral replication. The manipulation of host metabolic processes is a strategy shared among diverse virus families to secure the necessary resources for replicating new genomes, building more virus particles, and supporting cell growth and proliferation. Key metabolic pathways targeted by viruses for disruption and manipulation are glycolysis, glutaminolysis, and lipid metabolism. However, the mechanisms behind virus-induced metabolic reprogramming and the viral proteins mediating it remain poorly understood. This review explores how specific viral proteins reshape the metabolic milieu of host cells during viral infections. We also highlight common themes and outline gaps in knowledge to stimulate further investigations into how viral proteins manipulate host metabolism. Such mechanistic insights will deepen our understanding of virus-host interactions and may reveal novel therapeutic targets.

Keywords:  RNA and DNA virus proteins; cellular metabolism; glutaminolysis; glycolysis; lipid metabolism

DOI:  https://doi.org/10.1128/jvi.00556-25
bioRxiv. 2025 Dec 23. pii: 2025.12.21.695848. [Epub ahead of print]

Mitochondrial ROS-induced metabolic alterations differentially regulate ferroptosis sensitivity.

Somesh Banerjee, Matthew Ryan Smith, Yining Irene Wang, Michael Wang, Derrik Gratz, Gregory K Tharp, Sumin Kang, Peijian He.

Ferroptosis is an iron-catalyzed lipid peroxidation (LP)-dependent cell death. Induction of mitochondrial ROS (mtROS) is crucial in the execution of ferroptosis, but the underlying mechanism remains unclear. Through utilizing the hepatocyte model and RNA-seq analysis, we determined mtROS-dependent metabolic changes that modulate ferroptosis sensitivity. Elevated mtROS production and LP suppressed glycolysis, fatty acid oxidation, and citric acid cycle activity, representing adaptive responses that protect cells from ferroptosis. On the other hand, mtROS-driven signaling impaired glutathione biosynthesis and downregulated genes involved in coenzyme Q10 (CoQ) biosynthesis, including those in the mevalonate pathway and CoQ8A, a key stabilizer of the CoQ biosynthetic complex. Importantly, silencing CoQ8A expression enhanced, whereas overexpression of CoQ8A reduced, ferroptosis susceptibility of hepatocytes and various cancer cell types. The mtROS-mediated downregulation of CoQ8A was dependent on farnesoid X receptor (FXR) and retinoid X receptors (RXRs). Collectively, our findings highlight that mtROS promotes ferroptosis, at least in part, by suppressing glutathione and CoQ biosynthesis.

DOI: https://doi.org/10.64898/2025.12.21.695848
Cancer Lett. 2026 Jan 04. pii: S0304-3835(26)00007-8. [Epub ahead of print] 218244

Amino Acid Metabolic Reprogramming in Clear Cell Renal Cell Carcinoma: Pathogenic Mechanisms and Therapeutic Targeting.

Junzhe Xie, Fangjing Ni, Jialiang Shao, Dongliang Zhang, Tuanjie Guo, Xiang Wang.

  Kidney cancer is a major global health burden, with clear cell renal cell carcinoma (ccRCC) as the most common and aggressive subtype. Beyond the typical alterations of high glucose uptake and lipid accumulation, amino acid metabolism dysregulation in ccRCC is also gradually being uncovered. Pathways involving glutamine, cystine, serine, glycine, branched-chain amino acids, methionine, aspartate, arginine, proline and tryptophan are extensively rewired. These alterations enable cancer cells to sustain proliferation and biosynthesis, maintain redox balance, remodel the immune microenvironment, and develop resistance to therapy. At the same time, such reprogramming creates metabolic dependencies and vulnerabilities, including glutamine and cystine addiction as well as arginine auxotrophy. Dysregulation of key enzymes such as GLS1, ASS1 and IDO1 further highlights potential therapeutic targets. Exploiting these vulnerabilities through metabolic inhibitors or rational combinations with targeted and immunotherapy holds promise for overcoming resistance and improving outcomes in ccRCC.

Keywords:  amino acid metabolism; clear cell renal cell carcinoma; metabolic reprogramming; therapeutic vulnerability

DOI:  https://doi.org/10.1016/j.canlet.2026.218244
J Biomed Sci. 2026 Jan 05. 33(1): 5

PHGDH at the crossroads: metabolic plasticity, metastatic paradoxes, and therapeutic reconnaissance in cancer.

Liang Hao, Bai-Qiang Li, Shi-Yang Lu, Zhong-Cai An, Zheng-Yuan Yin, Zhen-Xian Du, Hua-Qin Wang.

  Phosphoglycerate dehydrogenase (PHGDH), the rate-limiting enzyme of the serine biosynthesis pathway (SSP), is a central metabolic hub and multifunctional oncoprotein that drives tumorigenesis through both canonical and non-canonical mechanisms. This review outlines the multi-level regulation of PHGDH, covering epigenetic remodeling (DNA hypomethylation, H3K4me3/H3K36me3 dynamics), transcriptional control (ATF4, MYC, EWS-FLI1), post-transcriptional fine-tuning (m6A/m5C modifications, RNA-binding proteins), and post-translational modifications (ubiquitination, methylation, phosphorylation). Together, these regulatory layers allow cancer cells to adapt metabolically to microenvironmental stress. Beyond its fundamental role in supplying nucleotides, maintaining redox homeostasis, and supporting one-carbon metabolism, PHGDH also performs moonlighting function. For example, its translocation to the nucleus inhibits PARP1 to sustain oncogenic transcription, while its presence in mitochondria helps remodel electron transport chains to promote metastasis. Critically, PHGDH exhibits a therapeutic paradox wherein its inhibition can synergize with chemotherapy, radiotherapy, and immunotherapy across diverse malignancies, yet tumors develop resistance via metabolic plasticity, or by selection of PHGDH-low metastatic clones. The clinical translation of PHGDH inhibitors is further challenged by inherent neurotoxicity risks, as neurons rely on de novo serine synthesis. To address these challenges, we propose a precision roadmap that integrates spatial multi-omics, AI-driven allosteric inhibitor design, dynamic biosensing (e.g., 18F-metabolite PET), and biomarker-stratified clinical trials. By reconciling the dual nature of PHGDH biology, we can transform this metabolic linchpin from a confounding paradox into a clinically actionable vulnerability.

Keywords:  Metastatic heterogeneity; Neurotoxicity paradox; PHGDH; Precision metabolic oncology; Serine biosynthesis pathway; Spatial multi-omics

DOI:  https://doi.org/10.1186/s12929-025-01205-y
Redox Biol. 2025 Nov 26. pii: S2213-2317(25)00449-5. [Epub ahead of print]89 103936

A clickable CoQ imaging probe reveals that cellular uptake and lysosomal trafficking depend on CD36 and NPC1.

Irene Liparulo, Arkadiy Bazhin, Grace Katherine Van Wyhe, Amanda Lestari Gunawan, Neville Dadina, Justin Hyunwoo Kwon, Alanna Schepartz, Elena Goun, Andreas Stahl.

Coenzyme Q (CoQ) is a crucial lipid-soluble antioxidant and electron transporter vital for mitochondrial respiration and cellular redox balance. Despite the role of CoQ in oxidative phosphorylation being well established, the mechanisms by which CoQ is internalized, distributed among subcellular compartments, and trafficked to mitochondria remain poorly defined. Here, we present the development of a minimally modified, azide-tagged CoQ analogue that enables high-resolution visualization of CoQ localization using fluorescence-based imaging. Using this probe, we focus our investigation on brown adipose tissue (BAT), a mitochondria-rich, highly metabolically active tissue with elevated CoQ demand. On a cellular level, we demonstrate that CoQ is internalized via receptor-mediated endocytosis, predominantly localizing to lysosomes. Genetic knockdown and pharmacological studies identify CD36 and NPC1 as essential transporters in this process. Our work provides both a technical advance for the redox biology field, with the development and characterization of a CoQ probe, and the essential new biological insight that NPC1 is linked to CoQ homeostasis and thus provides a foundation for further dissection of CoQ biology in health and disease.

DOI: https://doi.org/10.1016/j.redox.2025.103936
Cancer Lett. 2026 Jan 07. pii: S0304-3835(26)00008-X. [Epub ahead of print] 218245

The clinically available supplement pyruvate enhances the therapeutic effect of bortezomib in MM by modulating mitochondrial metabolism.

Chenggong Tu, Arne Van der Vreken, Sylvia Faict, Gamze Ates, Ann Massie, Kim De Veirman, Elke De Bruyne, Karin Vanderkerken, Eline Menu.

  Multiple myeloma (MM) is a hematological malignancy characterized by plasma cells residing in the bone marrow. Despite advancements in treatment, including proteasome inhibitors (PIs) such as bortezomib (Bz), drug resistance remains a major challenge. Metabolic reprogramming supports MM survival and drug resistance, with mitochondria emerging as promising therapeutic targets through their control of OXPHOS and mitochondrial reactive oxygen species (Mito-ROS). Using metabolic flux analyses, flow cytometry, and Western blot analysis, we identified pyruvate as a central metabolic intermediate, which not only enhances mitochondrial respiration and Mito-ROS production, but also the Integrated Stress Response (ISR) pathway. Conversely, metformin, an inhibitor of OXPHOS, was still able to activate the ISR pathway, but rather reduced Bz-induced cytotoxicity by decreasing both protein synthesis, and ROS production. Results were confirmed on primary murine and patient samples. Moreover, analysis of the CoMMpass study revealed that patients with prolonged progression-free survival under PI treatment showed enrichment in OXPHOS-related gene, highlighting the importance of mitochondrial metabolism in regulating MM responses to Bz. These data suggest that targeting pyruvate metabolism to increase ROS production could offer a strategy to enhance Bz activity in MM.

Keywords:  ISR; bortezomib; metformin; multiple myeloma; pyruvate

DOI:  https://doi.org/10.1016/j.canlet.2026.218245
Nat Immunol. 2026 Jan 07.

Active aldehydes accelerate CD8+ T cell exhaustion by metabolic alteration in the tumor microenvironment.

Yasuharu Haku, Koji Kitaoka, Koki Ichimaru, Tomoko Hirano, Jun Wang, Kazuhiro Sonomura, Asuka Maruo, Shuhei Hirose, Yu Wang, Katsuhiro Ito, Tomohiro Kozuki, Keiko Yurimoto, Mai Kiyono, Hidetaka Kosako, Toshi Menju, Hiroshi Date, Takashi Kobayashi, Koichi Omori, Tomonori Yaguchi, Tasuku Honjo, Kenji Chamoto.

Glycolysis and mitochondrial fatty acid oxidation (FAO) regulate CD8+ T cell differentiation, but how this metabolic balance regulates T cell exhaustion is unclear. PD-1 signaling inhibits glycolysis and enhances FAO. Here, we show that CD8+ T cells in tumors adhere to glycolysis with attenuated FAO despite high PD-1 expression. Active aldehydes, final products of lipid peroxidation, accumulate in CD8+ T cells in proportion to their level of exhaustion, defined by mitochondrial mass and potential. Aldehydes promote glycolysis and inhibit FAO in T cells. Mice deficient in an FAO enzyme in T cells generate more acrolein, a representative aldehyde, enhancing T cell exhaustion and attenuating antitumor immunity. Acrolein is generated partly from mitochondria and damages mitochondrial architecture. Inhibitors of lipid peroxidation or aldehydes enhanced PD-1-blockade by rectifying metabolic imbalance. Therefore, active aldehydes resulting from FAO impairment can cause a vicious cycle of metabolic imbalance that leads to T cell exhaustion.

DOI: https://doi.org/10.1038/s41590-025-02370-w
FASEB J. 2026 Jan 15. 40(1): e71415

Integrated Interactome and Phosphoproteome Analysis Reveals Novel MAP4K3-Regulated Pathways and Unexpected Cellular Roles for MAP4K3.

Mary Rose Branch, Byeonggu Cha, Luke C Bartelt, Wen-Chuan Shen, Albert R La Spada.

  MAP4K3, also known as germinal-center kinase-like kinase (GLK), is a member of the Ste20 sub-family of MAPKs. Numerous studies have shown that MAP4K3 is required for mTORC1 activation in response to amino acids, and MAP4K3 represses autophagy by initiating inhibitory suppression of transcription factor EB. Furthermore, MAP4K3 is ubiquitously expressed; thus, MAP4K3 likely plays a central role in regulating the metabolic disposition of the cell. To define the basis for MAP4K3 regulation of these cellular pathways and to identify novel cellular processes subject to MAP4K3 regulation, we performed mass spectrometry interactome analysis of MAP4K3 and unbiased phosphoproteomics to define the MAP4K3 phosphoproteome landscape. MAP4K3 interactome and phosphoproteome analysis confirmed the existence of numerous MAP4K3 interactors and substrates involved in mTORC1 regulation, while suggesting a potential role for MAP4K3 in controlling the subcellular localization of mTORC1 via phosphorylation of Mios, a component of the GATOR2 complex. In addition to linking MAP4K3 to processes occurring at the lysosome, MAP4K3 interactome and phosphoproteome data revealed an unexpected role for MAP4K3 in the nucleus, implicating MAP4K3 in DNA damage response and repair. When we examined MAP4K3 subcellular localization, we confirmed that MAP4K3 is present in the nucleus, and found that MAP4K3 interacts with the DNA damage response regulator PARP1. Our unbiased interactome and phosphoproteome analysis of MAP4K3 provides a powerful resource for further study of MAP4K3 function in the mTORC1 pathway, but also in the regulation of DNA damage response and repair pathways in the nucleus.

Keywords:  DNA repair; MAP kinase kinase kinase kinase 3 (MAP4K3); interactome; lysosome; mechanistic target of rapamycin complex 1 (mTORC1); nucleus; phosphoproteomics; proteomics

DOI:  https://doi.org/10.1096/fj.202501003R
bioRxiv. 2026 Jan 05. pii: 2025.12.30.696908. [Epub ahead of print]

Identification and Regulation of a Hepatic Lipogenic Metabolon.

Xiaotong Zhu, William B McKean, Tam Tran, Xiaorong Fu, Jay D Horton, Chai-Wan Kim.

De novo lipogenesis (DNL) plays a key role in the excessive fat accumulation present in Metabolic Dysfunction-Associated Steatotic Liver Disease (MASLD). Most mechanistic studies and experimental strategies for improving hepatic steatosis in MASLD have focused on the transcriptional regulation of enzymes involved in DNL and triglyceride (TG) synthesis. Here, we provide evidence for a post-translational mechanism that enhances fatty acid (FA) and TG synthesis through the assembly of a multi-protein lipogenic metabolon in liver. Under anabolic conditions, acetyl-CoA carboxylase 1 (ACC1) interacts with additional key enzymes in the DNL and TG synthesis pathway. Immunofluorescence and electron microscopy reveal that this lipogenic metabolon localizes around lipid droplets (LDs) and in proximity to mitochondria and LD interfaces in the anabolic state. The formation of the lipogenic metabolon facilitates the efficient transfer of FA synthesis intermediates to enhance lipogenic flux. These findings uncover a new nutrient-responsive, post-translational regulatory mechanism for hepatic lipogenesis and highlight the lipogenic metabolon as a potential therapeutic target for metabolic liver diseases.

DOI: https://doi.org/10.64898/2025.12.30.696908
J Chem Inf Model. 2026 Jan 07.

MolOrgGPT: De Novo Generation via Large Language Models and Reinforcement Learning.

Pablo Varas Pardo, Oscar Toledano, Guillermo Marcos-Ayuso, David Quesada, Nuria E Campillo.

We present a general framework for the de novo design of small molecules with desirable chemical properties, developed to aid the creation of novel chemical entities with potential therapeutic use. The system is built upon a foundational Large Language Model trained on a large comprehensive chemical database capable of generating structurally diverse and synthetically accessible compounds. It is then fine-tuned through reinforcement learning to enhance its capacity to generate molecules tailored to specific biological targets. As a case study, we apply this framework to design molecules targeting key proteins involved in Alzheimer's disease. The generated compounds underwent molecular docking studies to assess their binding affinities and prioritize candidates with optimal predicted interactions. The top-ranked molecules were further analyzed based on their binding modes and key molecular interactions with the target proteins. The results suggest that our generative model produces viable, drug-like molecules with favorable interactions, underscoring its potential as a valuable tool in early stage drug discovery.

DOI: https://doi.org/10.1021/acs.jcim.5c02400
J Biochem. 2026 Jan 07. pii: mvag001. [Epub ahead of print]

Functional Impact of Glycosylation of LRIG1 on EGFR Proteostasis in Cancer.

Jumpei Kondo, Himari Nagao, Koki Oyama, Akari Minamiura, Shuto Aoki, Daisuke Sakon, Honoka Nakayama, Shinji Takamatsu, Eiji Miyoshi.

  LRIG1, a membrane glycoprotein, has emerged as a significant stem cell marker and negative regulator of receptor tyrosine kinases (RTKs), including EGFR. Glycosylation is a major post-translational modification, which plays a crucial role in protein function and stability. In cancer biology, abnormal glycosylation can contribute to pathogenesis, which can also serve as a biomarker in clinical setting. Here, we aimed to investigate the effects of glycosylation on LRIG1 functions. Through database analysis and experimental approaches, we focused on evolutionarily conserved glycosylation sites of LRIG1, particularly N74 in humans. We found that a mutation of the N74 glycosylation site (N74Q) enhances LRIG1's binding to EGFR and promotes EGFR degradation. Furthermore, we identified a naturally occurring splice variant of LRIG1 lacking the 72-bp exon 2, which includes the N74 site, that shows similar enhanced EGFR binding and degradation. Our findings suggest that the absence of glycosylation at N74 site enhances LRIG1-EGFR binding, providing an example of glycosylation negatively regulating protein-protein interaction. This mechanism provides insights into the importance of glycosylation deficiency in cancer biology.

Keywords:  Alternative Splicing; Cancer; Glycosylation; Protein degradation; Proteostasis

DOI:  https://doi.org/10.1093/jb/mvag001
J Pathol. 2026 Jan 08.

Uncovering the potential of pathomics: prognostic prediction and mechanistic investigation of pancreatic cancer.

Long Liu, Xiaohong Zhao, Fabiao Zhang, Yuxi Huang, Qi Wang, Zheping Fang, Yu Zhu, Yu Zhang.

  A machine learning-based pathomics model was investigated for its value and biological significance in predicting overall survival (OS) after surgery in pancreatic cancer patients. Data from 173 patients with pancreatic ductal adenocarcinoma (PDAC) who underwent surgery and continued follow-up in two centers were retrospectively analyzed. Pathomics parameters of both the tumor and peritumor were measured in all patients, and the optimal pathomics score (Pathscore) was calculated using five machine learning methods. The best Pathscore was then combined with multiple clinical parameters to analyze its incremental value and to construct a comprehensive nomogram. TCGA data, multiplex immunofluorescence, spatial analysis, and single-cell sequencing were used to explore the biological mechanisms of pathomics. In predicting OS, pathomics parameters from the tumor and peritumoral regions provided complementary prognostic information. The LASSO-based combined model achieved the best predictive accuracy. Multivariate Cox regression analysis identified T-stage, N-stage, CA19-9, and Pathscore as independent predictors of OS in patients with PDAC. The integrated nomogram demonstrated superior and more stable predictive performance. Analysis of the TCGA dataset suggested that the pathomics model was associated with the immune status of pancreatic cancer, a finding supported by trends in the validation cohort. Spatial analysis and single-cell analysis further revealed a strong association between the Pathscore and immune cell infiltration, in particular CD8+ T cells. Machine learning-based pathomics models can help to predict the immune status and OS of patients with PDAC. The integration of pathomics with clinical parameters provides a robust basis for immune evaluation, prognostic prediction, and therapeutic decision-making in PDAC. © 2026 The Pathological Society of Great Britain and Ireland.

Keywords:  biological mechanism; immunity; machine learning; pancreatic cancer; pathomics; prognostic model pathomics; survival

DOI:  https://doi.org/10.1002/path.70011
Cell Mol Biol Lett. 2026 Jan 09.

SLC25A11-mediated reprogramming of mitochondrial redox state and lipid peroxidation confers NRF2-dependent ferroptosis resistance in biliary tract cancer.

Yu-Yu Lin, Han-Hsi Kuo, Zhao-Jing He, Hsin-Yi Chung, Cheorl-Ho Kim, Yi-Ru Pan, Meng-Ju Wu, Ming-Hsien Chan, Chun-Nan Yeh, Nai-Jung Chiang, Ming-Huang Chen, Yu-Chan Chang.



Keywords:  Biliary tract cancer; Ferroptosis; Mitochondrial homeostasis; NRF2; SLC25A11

DOI:  https://doi.org/10.1186/s11658-025-00843-2
Sci Rep. 2026 Jan 06.

Cancer cells surviving cisplatin chemotherapy increase stress-induced OMA1 activity and mitochondrial fragmentation.

Melvin Li, Chenille A McCullum, Louis T A Rolle, Qin Ni, Zhuoxu Ge, Sean X Sun, Kenneth J Pienta, Sarah R Amend.

  Cancer is one of the leading causes of deaths worldwide. Once cancer cells acquire therapy resistance, they become the main driver of cancer lethality in patients. Thus, mechanisms of therapy resistance must be investigated to improve patient outcomes. Mitochondria are critical organelles in the cellular stress responses, undergoing dynamic morphological and functional changes in response to external stimuli. We and others have identified a chemotherapy-resistant cancer cell state where cells that survive treatment exhibit a dramatic increase in cell size and remain non-proliferative for weeks. In this study, we demonstrate that cancer cells that enter this resistant cell state in response to cisplatin increase OMA1 activity and decrease mitochondrial fusion and function to combat oxidative stress. These findings contribute to further understanding the role of the mitochondrial stress responses in therapy resistance in cancer and provide a potential therapeutic avenue to targeting cancer cells that enter this chemotherapy-resistant cell state.

Keywords:  Cancer; Mitochondrial dynamics; Mitochondrial morphology; OMA1; OPA1; Oxidative stress

DOI:  https://doi.org/10.1038/s41598-025-33677-1
Biology (Basel). 2025 Dec 25. pii: 40. [Epub ahead of print]15(1):

Multi-Omics Integration Identifies the Cholesterol Metabolic Enzyme DHCR24 as a Key Driver in Breast Cancer.

Mingfei Xu, Jinghua Hu, Lulan Pu, Jiayou Liu, Yanhong Yang, Qianqian Li, Jingwen Chen, Shishan Deng, Chaoyue Liu.

  Dysregulated cholesterol metabolism is a hallmark of breast cancer (BC), but its key molecular mediators remain unclear. Using an integrated multi-omics approach, including Mendelian randomization, transcriptomic/proteomic database screening, functional assays, and clinical correlation, we identified the cholesterol biosynthesis enzyme DHCR24 as a central metabolic-immune mediator. We found that high DHCR24 mRNA expression is associated with poorer patient prognosis and is elevated in luminal and HER2+ subtypes. Surprisingly, DHCR24 knockdown enhanced malignant phenotypes in MCF7 cells, contrasting its pro-tumor role in patients. Integrated analysis resolved this paradox, revealing that DHCR24 promotes BC progression non-cell-autonomously by remodeling an immunosuppressive tumor microenvironment, rather than by intrinsically driving cancer cell proliferation. Mechanistically, DHCR24 depletion upregulated TP53 and downregulated SQLE. This study establishes DHCR24 as a pivotal metabolic-immune node and a promising therapeutic target for disrupting the cholesterol-immune axis in luminal and HER2+ BC.

Keywords:  DHCR24; bioinformatics; breast cancer; cholesterol metabolism; mendelian randomization; multi-omics; therapeutic target

DOI:  https://doi.org/10.3390/biology15010040
Biomol Ther (Seoul). 2026 Jan 01. 34(1): 6-17

Targeting the Primordial Chaperone to Overcome Acquired Drug Resistance in Cancer: TG2-Mediated Autophagy.

Soo-Youl Kim.

  The transglutaminase family is roughly 250 million years old. Horseshoe crabs have been described as a 'living fossil' and have remained virtually unchanged since first appearing around the Triassic period. The horseshoe crab, a living fossil, carries a primitive form of TG that helps it defend against infection and survive. Transglutaminase 2 (TG2, EC 2.3.2.13, gene name TGM2) is mainly known as a cross-linking enzyme in vertebrates. Although TG2 is not an oncogene, its high levels are linked to worse outcomes in many cancers. However, how TG2 cross-linking activity relates to its role in promoting cancer growth remains unclear. A recent discovery sheds light on this. In ovarian cancer cells, TG2 binds directly to GSK3β, leading to its removal by autophagosomes, which activates β-catenin. Stopping this interaction allows GSK3β levels to recover, thereby decreasing β-catenin activity. Even in the absence of cross-linking, cancer cells use TG2 as a chaperone to promote growth and support metastasis. This suggests intracellular calcium levels are too low for TG2 to perform cross-linking. It also indicates that anticancer treatments may increase TG2 levels in cancer cells, helping them recover by removing tumor suppressors. As a result, TG2 plays a role in developing drug resistance, acting as a primitive systemic defense mechanism linked with survival signals. I suggest that blocking TG2 binding, combined with inhibiting autophagy or alternative signaling pathways, is essential for effectively overcoming drug resistance, since it is rooted in TG2's primordial role.

Keywords:  Cancer; Drug resistance; GSK3β; NFκB; Transglutaminase; p53

DOI:  https://doi.org/10.4062/biomolther.2025.247
bioRxiv. 2025 Dec 23. pii: 2025.12.19.695597. [Epub ahead of print]

Methionine synthase reductase regulates heterochromatin independently of methionine synthesis through mitochondrial homeostasis.

Fernanda Rezende Pabst, Andrey Tvardovskiy, Iratxe Estibariz, Veronica Finazzi, Pauline Couacault, Anna Artati, Michael Witting, Antonio Scialdone, Till Bartke, Daphne Selvaggia Cabianca.

Metabolic enzymes can influence chromatin organization by modulating the availability of key metabolites, yet how specific metabolic reactions affect chromatin function remains poorly understood. Here, we show that in Caenorhabditis elegans, the methionine-cycle enzyme methionine synthase reductase (MTRR-1/MSR) regulates heterochromatin independently of methionine synthesis. Loss of MTRR-1, but not of the methionine synthase METR-1/MS, specifically reduces heterochromatic histone methylation, derepresses repetitive elements, and causes developmental delay. Multi-omics profiling revealed that mtrr-1 mutants activate transcriptional programs associated with mitochondrial stress and accumulate long-chain acylcarnitines, indicating disrupted mitochondrial homeostasis. Functional assays confirmed altered mitochondrial respiration in mtrr-1 mutants, while direct perturbation of mitochondrial function was sufficient to induce heterochromatin defects. Together, our results reveal a previously unrecognized mitochondria-to-chromatin axis controlled by the methionine-cycle enzyme MTRR-1/MSR.

DOI: https://doi.org/10.64898/2025.12.19.695597
bioRxiv. 2025 Dec 24. pii: 2025.12.22.696045. [Epub ahead of print]

PTEN-loss confers dependence on the guanylate synthesis enzyme IMPDH in T-cell acute lymphoblastic leukemia.

Rayees A Padder, Thu Le Le, Emily Hyde, Maria E D Rubio, Eric Chiles, Namratha Sheshadri, Kelly Mulraney, Wei-Xing Zong, Xiaoyang Su, Daniel Herranz, Alexander J Valvezan.

Loss of the tumor suppressor PTEN is common in T-cell acute lymphoblastic leukemia (T-ALL), and is associated with poor prognosis. PTEN-loss drives robust activation of AKT/mTORC1 signaling to promote leukemic cell growth. We find that PTEN-loss in T-ALL confers dependence on the guanylate nucleotide synthesis enzyme inosine 5'-monophosphate dehydrogenase (IMPDH) for cell growth and viability. This metabolic vulnerability is dependent on sustained mTORC1 signaling and can be exploited using clinically approved IMPDH inhibitors to selectively kill PTEN-deficient T-ALL cells, and extend survival in genetic and xenograft T-ALL models in mice. Mechanistically, IMPDH inhibitors cause early DNA replication stress, followed by DNA damage. In contrast to treatment with mTORC1 inhibitors, these events culminate in robust and selective cell death in PTEN-deficient T-ALL cells. These findings reveal a targetable metabolic vulnerability in T-ALL, which could provide rationale for repurposing clinically approved IMPDH inhibitors.

DOI: https://doi.org/10.64898/2025.12.22.696045
Int J Mol Sci. 2025 Dec 21. pii: 83. [Epub ahead of print]27(1):

Citrate Synthase Knockdown Suppresses Cell Proliferation and Induces Apoptosis in Select Human Cancer Cell Lines.

Xiaoxiao Zhang, Siyu Qu, Huanhuan Zhong, Yulu Yang, Bo Cheng, Yan Zeng.

  Citrate synthase (CS) catalyzes the first reaction in the tricarboxylic acid (TCA) cycle and is one of the rate-limiting and regulatory enzymes of the TCA cycle. How CS influences human cells beyond its direct roles in carbohydrate metabolism and energy production is poorly understood. In this study, we used RNA interference (RNAi) to knockdown CS expression in three diverse human cancer cell lines, HCT116, HT-1080, and HepG2, and assessed changes in their cellular behaviors. In all three cell lines, the loss of CS led to are duction in cell proliferation, increased apoptosis, lower mitochondrial membrane potentials, higher reactive oxygen species (ROS) production, and reduced ATP levels. We then performed transcriptome analyses in the three cell lines, identified pathways related to the cell cycle and apoptosis that might elucidate the mechanisms underlying those cellular changes, and further verified the mRNA expression changes in specific genes associated with the apoptotic pathways. Taken together, our results suggest that CS regulates a broad spectrum of human cellular processes.

Keywords:  apoptosis; citrate synthase; the TCA cycle; the cell cycle

DOI:  https://doi.org/10.3390/ijms27010083
Biochem Pharmacol. 2026 Jan;pii: S0006-2952(25)00730-0. [Epub ahead of print]243(Pt 1): 117465

Acetylation of CPT1A reduces fatty acid oxidation and leads to dysfunctional renal tubular mitochondria in diabetic kidney disease.

Siyao Sun, Sen Liu, Shiyan Ruan, Hongli Zhou, Xiangfei Cui, Ning Lu, Liu Hong, Miaomiao Lu.

  Diabetic kidney disease (DKD), a major diabetic complication driving chronic and end-stage renal disease, involves disrupted proximal tubular energy metabolism. This study investigated the pathogenic role ofcarnitine palmitoyltransferase-1A (CPT1A) acetylation-a mitochondrial enzyme governing the rate-limiting step of fatty acid oxidation (FAO)-in DKD progression. Utilizingdb/dbmice to establishin vivoDKD models, we assessed renal fibrosis via histology/Western blotting and performedproteome-wide acetylation profiling. Parallelin vitroanalyses employed high-glucose (30 mM, 48 h)-treated human proximal renal tubular cells. Functional consequences oflysine 584 (K584) acetylationwere evaluated using lentiviral-mediated K584R point mutation. Results demonstrated: (1) Global protein hyperacetylation in DKD mice, with CPT1A identified as the most significantly hyperacetylated mitochondrial protein; (2) Downregulated CPT1A expression in renal tubular epithelia of both murine and human DKD tissues; (3) Association of CPT1A hyperacetylation with elevated α-smooth muscle actin, fibronectin, and reactive oxygen species (ROS), alongside reduced mitochondrial membrane potential, FAO, and fatty acid synthesis; (4) K584R mutation attenuated CPT1A acetylation, enhancing fatty acid synthase activity and FAO while reducing ROS and fibrosis markers. We conclude thatCPT1A acetylation at K584critically drives DKD pathogenesis and represents a promising biomarker/therapeutic target.

Keywords:  Acetylation modification; CPT1A; Diabetic kidney disease; Fatty acid oxidation; Mitochondria

DOI:  https://doi.org/10.1016/j.bcp.2025.117465
bioRxiv. 2026 Jan 01. pii: 2025.12.31.697202. [Epub ahead of print]

Multi-omic analysis reveals nitric oxide dependent remodeling in classically activated macrophages and identifies negative regulation mediated by AKR1A1.

Nicholas L Arp, Uzziah S Urquiza, Marcel Morgenstern, Jonathan H Schrope, James A Votava, Steven V John, Jack J Stevens, Anna Huttenlocher, Joshua J Coon, Jing Fan.

Nitric oxide (NO•) is an important signaling molecule in many biological processes, including immune response. During response to classical activation stimuli lipopolysaccharide (LPS) and interferon-γ (IFNγ), macrophages generate NO• via inducible nitric oxide synthase (iNOS). To comprehensively define the effects of NO•, we applied a multi-omic strategy integrating proteomics and transcriptomics to profile murine macrophages across conditions with or without LPS/IFNγ-activation, with or without iNOS expression or exogenous NO• donor treatment. The results revealed NO• has broad, yet selected and controlled, regulatory effects, playing a key role in coordinating the systematic remodeling during macrophage classical activation. Among the proteins that are most suppressed in a NO•-dependent manner, electron transport chain (ETC) is the most enriched. NO• drives complex-specific remodeling of ETC, causing selected downregulation of complex I, II, and IV, through a different combination of transcriptional and post-transcriptional mechanisms for each complex. Functionally, we found NO• is required, but not sufficient, for the strong suppression of cellular respiration upon macrophage activation. Among the most consistently upregulated proteins are many enzymes involved in redox defense. AKR1A1 was identified as a top hit. We found Akr1a1 induction requires both NO• and LPS/IFNγ stimulation. The S-nitroso-CoA reductase activity of AKR1A1 mitigates NO•-driven inhibition of pyruvate dehydrogenase complex by limiting the inhibitory modifications targeting its lipoyl cofactor. Knocking out Akr1a1 causes accelerated remodeling of TCA cycle, dysregulated immunoregulatory metabolite level, and altered functional gene expression and cytokine production at later stage of immune response. Thus, the NO•-dependent upregulation of AKR1A1 forms a negative regulatory loop to fine-tune NO•-mediated metabolic and functional remodeling during immune response. Together, this work provided a systems-level map of NO•-dependent regulation, revealed the crosstalk between NO• and immune signaling, and demonstrated mechanisms providing redox adaptation and precise control of NO•'s effects.

DOI: https://doi.org/10.64898/2025.12.31.697202
Acta Biomater. 2026 Jan 07. pii: S1742-7061(26)00012-7. [Epub ahead of print]

A Multifunctional PD-L1 Modulator for Metabolic Reprogramming to Induce Pyroptosis and Enhance Glutamine Inhibition-Mediated Antitumor Immunotherapy.

Jialing Guo, Ligang Wu, Jieke Zhang, Xiaodi Zhang, Bin Du.

  Metabolic interference strategies offer promising interventions in tumor therapy. However, inhibiting glutamine metabolism can upregulate Programmed Cell Death Ligand 1 (PD-L1), resulting in immune evasion and limiting the efficacy of glutamine inhibitors. Here, a nano-modulator with multi-enzyme interactions, DPG@COD/CuMOF@Dz, is introduced. It combines metabolic management and immunotherapy by incorporating copper metal-organic framework nanoparticles containing cholesterol oxidase (COD) and DNAzyme (Dz), as well as particles modified with DSPE-PEG-glutamine (DPG). Once internalized, the nano-modulator releases COD, Cu²⁺, and Dz in response to the high intracellular GSH environment. Cu²⁺ activates Dz, which inhibits glutaminase production and glutamine metabolism in cancer cells. Meanwhile, COD depletes cholesterol from cancer cell membranes, decreasing PD-L1 stability and abundance. COD produces hydrogen peroxide, which combines with Cu²⁺ via Fenton-like processes to produce ·OH, raising intracellular reactive oxygen species (ROS) levels. Additionally, GLS Dz effectively suppresses glutamine metabolism, thereby diminishing intracellular glutathione (GSH) synthesis and disrupting the redox homeostasis in cancer cells. These cascading events collectively initiate pyroptosis and immunogenic cell death (ICD), which not only attenuates PD-L1-mediated immune evasion but also provokes a robust antitumor immune response. Notably, combination therapy employing the nano-modulator and an αPD-1 antibody achieved a remarkable tumor inhibition rate of 93.7%. This work presents a promising strategy to overcome the challenges associated with glutamine blockade, offering an innovative therapeutic paradigm for the treatment of breast cancer. STATEMENT OF SIGNIFICANCE: This study develops a novel nano-modulator (DPG@COD/CuMOF@Dz) that co-targets glutamine metabolism and PD-L1 stability via cholesterol depletion for enhanced cancer immunotherapy. By integrating enzymatic activity and metal-organic frameworks for synergistic redox disruption and immune activation, it overcomes limitations of conventional inhibitors and offers a "three-in-one" strategy to reverse immunosuppression. This work provides new insights into metabolic-immune crosstalk and presents a promising combinatory platform to boost immune checkpoint therapy.

Keywords:  DNAzyme; Glutamine inhibition; pyroptosis; tumor immunotherapy

DOI:  https://doi.org/10.1016/j.actbio.2026.01.004
Front Immunol. 2025 ;16 1593299

Chronic stress drives ovarian cancer progression via myeloid-derived suppressor cells infiltration and Notch signaling pathway activation.

Yadiel A Rivera-López, Alanis P Torres-Rosado, Jaydiel A Casiano-Martínez, Luinet L Meléndez-Rodríguez, Raian Imad-Hamad, Sofía M Hernández-Carrasquillo, Luis M Rivera-Pérez, Melanie Ortiz-León, Orlando I Torres-Rodríguez, Alexandra N Aquino-Acevedo, Yesenia Castillo-Ocampo, Grace Duffey, Jaileene Pérez-Morales, Mary K Townsend, Lauren C Peres, Paulo C Rodriguez, Shelley S Tworoger, Guillermo N Armaiz-Pena.

   Background: Ovarian cancer (OC) is a leading cause of cancer-related death among women, with elevated levels of stress hormones linked to OC progression and immune evasion in the tumor microenvironment (TME). Chronic psychosocial stress has been associated with the expansion of immunosuppressive myeloid-derived suppressor cells (MDSCs), which promote tumor growth and negatively impact patient outcomes. This study tested how chronic daily restraint stress affected ovarian cancer progression, Notch signaling, and MDSCs in the OC TME. We hypothesized that chronic stress increases MDSCs infiltration in the TME, enhances Notch signaling in OC cells, and promotes cancer progression.
Methods: Female C57BL/6 mice were injected with ID8Luc or IG10Luc OC cells and subjected to daily restraint stress. We also isolated bone marrow from naïve C57BL/6 mice to differentiate myeloid cell precursors into MDSCs. These cells were then exposed to norepinephrine (NE), epinephrine (EPI), or corticosterone (CC). To further evaluate the effects of stress hormones on the dysregulation of the Notch signaling pathway, we treated OC cells with NE, EPI, or CC.
Results: Chronic daily restraint stress increased MDSCs infiltration and enriched polymorphonuclear (PMN)-MDSCs in the TME and bone marrow in both models. Ex vivo studies demonstrated an increased enrichment of PMN-MDSCs along with a reduction of mononuclear (M)-MDSCs in the groups treated with stress hormones, particularly CC. Our results showed that stress hormones significantly increased the expression of notch intracellular domain (NICD) in OC cells. Additionally, we observed increased mRNA levels of Notch1, Jagged2, and Hes1, along with elevated NICD and HES1 protein levels, mediated by CC-induced GSK3β phosphorylation. Pharmacological inhibition of NICD and gLucocorticoid receptors blocked the CC-induced Notch pathway activation via GSK3β phosphorylation. Moreover, tumors from mice subjected to restraint stress had elevated expression of Notch1, Jagged 2, NICD, HES1, GR, ADRB2, and pS9-GSK3β.
Conclusion: These data indicate that chronic stress leads to MDSCs infiltration and suppressive activity, which contributes to an immunosuppressive TME and OC progression.

Keywords:  GSK3β; MDSCs; Notch; chronic stress; corticosterone; epinephrine; norepinephrine; ovarian cancer

DOI:  https://doi.org/10.3389/fimmu.2025.1593299
bioRxiv. 2026 Jan 02. pii: 2026.01.02.697431. [Epub ahead of print]

Enhancing Sensitivity in Targeted Single-Cell Proteomics by Coupling a Dual Ion Funnel Interface with Triple Quadrupole Mass Spectrometer.

Sehong Min, Pearl Kwantwi-Barima, Issac K Attah, Thomas L Filmore, Matthew J Gaffrey, Reta Birhanu Kitata, Yehia M Ibrahim, Tujin Shi.

Single-cell proteomics (SCP) has emerged as a powerful approach for understanding cellular heterogeneity and biological processes at unprecedented resolution. However, the extremely limited protein content of individual cells (femtogram to picogram levels) pushes current mass spectrometry instrumentation to its sensitivity limits, creating a critical analytical bottleneck. While selected reaction monitoring (SRM) using triple quadrupole (QqQ) instruments offers advantages in sensitivity and reproducibility for targeted proteomics quantification, SRM still struggles with sensitivity for quantification of moderate- or low-abundance proteins from single-cell sample amounts. Here, we report the development and systematic evaluation of a dual ion funnel interface designed to address the sensitivity limitation by significantly enhancing ion transmission efficiency in commercial QqQ mass spectrometers. The dual ion funnel interface, composed of a curved S-funnel followed by a conventional ion funnel, improves ion transmission efficiency while reducing chemical noise through selective ion focusing. The performance of the dual ion funnel interface was systematically compared to standard interface on a TSQ Vantage platform across samples with different levels of complexity. The dual funnel interface demonstrated to provide up to 25-fold improvement in sensitivity across a wide range of protein concentrations in different biological matrices (low complex mouse macrophage and high complex human cells). Critically, enhanced sensitivity was accompanied by increased analytical reproducibility with lower coefficient of variations. Most importantly, the dual funnel interface enabled reliable quantification of low-abundance proteins that were barely detectable or not detected by the standard interface, extending analysis to single-cell equivalent amounts while maintaining excellent reproducibility. These results demonstrate that the dual funnel interface addresses the critical bottleneck in quantitative targeted proteomics, providing a technological foundation for ultrasensitive targeted SCP that requires both high sensitivity and robust quantitative performance.

DOI: https://doi.org/10.64898/2026.01.02.697431
PLoS One. 2026 ;21(1): e0340295

Targeting ceramide metabolism to restore hypoxia-induced apoptosis in p53-deficient colon cancer cells.

Karen Mechleb, Nancy Hourani, Maya Fakhry, Osama A Alyamani, Rouba Hage-Sleiman, Hicham Younes, Antoine Abou Fayad, Nadia Soudani, Amer Sakr, Nadine Darwiche, Georges Nemer, Raya Saab, Marguerite Mrad, Ghassan Dbaibo.

Hypoxic stress in solid tumors triggers growth arrest and apoptosis through p53 activation and stabilization. This environment inactivates p53 and drives the expansion of p53-mutant clones, which accentuate tumor aggressiveness. Ceramide, a signaling sphingolipid, was previously identified as a downstream collaborator with p53 in the stress-induced apoptosis and cell cycle arrest. Among sphingolipids, the balance between pro- and anti-apoptotic products, dictated by the expression and activity of appropriate enzymes, helps determine cell fate in response to hypoxia. The current study aimed to understand the role of ceramide in HCT116 human colon cancer cells response to hypoxia in the presence or absence of p53, and to determine whether the modulation of ceramide metabolism could sensitize the resistant p53-deficient cells to hypoxia-induced cell death. We observed that HCT116 p53-deficient cells were resistant to hypoxic cell death. We explored the role of ceramide in this response by screening for different sphingolipid metabolites through liquid-chromatography-mass spectrometry, and by measuring the expression of key enzymes involved in ceramide biosynthesis and breakdown. We also evaluated the changes in the cellular response to hypoxia associated with introduction of sphingolipid metabolites or with modulating the activity of related sphingolipid-metabolizing enzymes. In hypoxic p53-deficient cells, ceramide was synthesized via the de novo pathway through the action of ceramide synthases and dihydroceramide desaturase (DEGS1) driving the evasion of hypoxia-induced apoptosis. Among the accumulating ceramide species in p53 deficient cells, C24-ceramide was the most abundant and possibly contributing to their resistance. Tipping the sphingolipid balance in favor of pro-apoptotic sphingolipids, through the addition of C6 ceramide or sphingosine, or through the combined pharmacologic inhibition of DEGS1 and sphingosine kinase 1, helped circumvent the cellular resistance to hypoxia-induced apoptosis in cells lacking p53. Therefore, modulating sphingolipid metabolism may be a viable approach in the treatment of solid tumors with hypoxic regions.

DOI: https://doi.org/10.1371/journal.pone.0340295
bioRxiv. 2025 Dec 27. pii: 2025.12.26.696612. [Epub ahead of print]

Temporal Multi-Omic Analysis Uncovers Sex-Biased Molecular Programs Underlying Skeletal Muscle Adaptation to Endurance Training.

MoTrPAC study group

Background: Exercise training is known to benefit health and reduce disease risk. While skeletal muscle adaptations are fundamental to many of the health benefits of exercise training, the common and sex-specific molecular regulators that mediate these adaptations remain to be fully elucidated.
Methods: To this end, we leveraged skeletal muscle multi-omics data generated by the Molecular Transducers of Physical Activity Consortium (MoTrPAC), where 6 month-old male and female rats endurance trained for 1, 2, 4, or 8 weeks. Our objective was to identify shared and sex-specific multi-omic molecular responses to endurance training in skeletal muscle, and relate them to phenotypic adaptations.
Results: We identified largely sexually-conserved transcriptomic and proteomic pathway enrichments in the gastrocnemius , which correlated with skeletal muscle responses from a published exercise study in humans. We uncovered sex-consistent post-translational modifications, including decreased oxidation of MYH2 and deacetylation of the β-oxidation enzyme HADHA. Pathway enrichment analyses revealed sex-specific remodeling across the acetylome, redox proteome, and phosphoproteome; females decreased mitochondrial protein cysteine oxidation and increased mitochondrial cristae proteins, indicative of enhanced redox buffering and mitochondrial efficiency. Despite decreases in cysteine oxidation of key mitochondrial proteins, females displayed increases in the cysteine oxidation of proteins involved in glucose catabolism relative to males after 8 weeks of training, suggestive of sex-biased subcellular reactive oxygen species generation. Males demonstrated earlier induction of mitochondrial transcripts and predicted activation of mTOR. Although the increase in mitochondrial protein abundance was more modest in males, there was greater oxidation of mitochondrial proteins in response to training compared to females.
Conclusions: This work shows a large portion of the adaptive response to endurance training in skeletal muscle is shared between females and males, while there are distinct and nuanced sex-specific adaptations that are evident, particularly at the level of post-translational regulation.

DOI: https://doi.org/10.64898/2025.12.26.696612