bims-cesirm 2025-11-23 papers

bims-cesirm

Biomed News

on Cell Signaling mediated regulation of metabolism

Issue of 2025–11–23
thirty-six papers selected by
Tigist Tamir, University of North Carolina

Ribonuclease RNase Z is an evolutionarily conserved deAMPylase.
The dynamics of ubiquitination and its role within the proteome of extracellular vesicles.
Succinate puts the brakes on de novo purine synthesis.
Mitochondrial Transfer Rescues Respiration to Support De Novo Pyrimidine Biosynthesis and Tumor Progression.
SLC45A4 encodes a peroxisomal putrescine transporter that promotes GABA de novo synthesis.
BRSK2 plays a role in autophagy and cancer cell growth and survival under nutrient deprivation stress via the PIK3C3 pathway.
De novo design of phospho-tyrosine peptide binders.
Path-based quantification of activation and repression in Boolean models using BooLEVARD.
Targeting plasticity in the pyrimidine synthesis pathway potentiates macrophage-mediated phagocytosis in pancreatic cancer models.
Glutamine-Dependent Slc25a39-Nrf2 Axis Couples Mitochondrial Dynamics with Metabolic Reprogramming to Establish Myogenic Commitment.
Longitudinal transformation of mitochondrial metabolism during neurogenesis.
c-Abl Kinase Targets Tight Junction Protein ZO-2 in Regulation of Cell Migration and Morphology.
The cyclic peptide mallotumide A inhibits colon and breast cancer cell growth and motility by targeting cellular respiration and lipogenesis.
Androgen receptor drives polyamine synthesis creating a vulnerability for prostate cancer.
Targeted Metabolomic Methods for 13C Stable Isotope Labeling with Uniformly Labeled Glucose and Glutamine Using Liquid Chromatography-Tandem Mass Spectrometry (LC-MS/MS).
Phosphatidylserine and RhoB connect phosphatidylinositol 4-phosphate and phosphatidic acid metabolism at the plasma membrane.
Adipose Tissue Overexpression of Nicotinamide Phosphoribosyltransferase Prevents Metabolic Dysfunction in Obese Mice.
Synthetic signaling platform uncovers and rewires cellular responses to PD-1 perturbation.
Metabolic STAMP for deciphering GPCR-regulated insulin secretion by pancreatic β cells.
System analysis links SMARCD3 regulons to growth signaling and MEK inhibitor response in everolimus-resistant ER+ breast cancer cells.
Proteomics of Prostate Cancer Tissue Small Extracellular Vesicles Reveal Alteration of Metabolism.
Glutamine antagonism suppresses tumor growth in adrenocortical carcinoma through inhibition of de novo nucleotide biosynthesis.
Glyceraldehyde-3-phosphate dehydrogenase homologs as bifunctional gatekeepers of metabolic segregation in Pseudomonas putida.
How one nutrient controls cell size.
Mapping the Subtype-Specific PARP1 ADP-ribosylated Proteome in Breast Cancer Cells.
DRESIS 2.0: the comprehensive landscape of drug resistance information.
CoDIAC: A comprehensive approach for interaction analysis provides insights into SH2 domain function and regulation.
Proteomics data imputation with a deep model that learns from many datasets.
GLP1 Receptor Agonism Alters Growth and Therapeutic Response in Prostate Cancer.
Breast cancer cell coculture induces normal lung fibroblast transition to CAFs, promoting tumor cell dormancy and therapy resistance.
The denitrosylase SCoR2 controls cardioprotective metabolic reprogramming.
Pharmacological Stimulation of GPER Reverses Mitochondrial Dysfunction in the Hearts of Ovariectomized Type 2 Diabetic Rats.
Computational design of pH-sensitive binders.
Biologically explainable multi-omics feature demonstrates greater learning potential by identifying tissue of origin, stages, and subtypes for pan-cancer classification.
Single-cell mapping of alternative splicing linked to checkpoint immunotherapy response.
Desaturase-dependent secretory functions of hepatocyte-like cells control systemic lipid metabolism during starvation in Drosophila.

Proc Natl Acad Sci U S A. 2025 Nov 25. 122(47): e2515155122

Ribonuclease RNase Z is an evolutionarily conserved deAMPylase.

Meghomukta Mukherjee, Alex Pon, Timea Goldberg, Krzysztof Pawłowski, Anju Sreelatha.

  Protein AMPylation is a highly conserved posttranslational modification in which adenosine monophosphate (AMP) is covalently attached to protein substrates. Our studies revealed that the mitochondrial AMPylase, Selenoprotein O (SelO), regulates cellular metabolism and oxidative stress response through AMPylation of key metabolic enzymes. Remarkably, SelO-mediated AMPylation is conserved in bacteria and humans, yet the enzyme that removes the AMP from modified proteins remains unknown. We show that the ribonuclease, RNase Z, is both necessary and sufficient to catalyze deAMPylation of AMPylated substrates. These results establish RNase Z as a moonlighting enzyme with previously unrecognized functional roles beyond tRNA processing, expanding our understanding of its biological significance. Furthermore, identification of an evolutionarily conserved deAMPylase highlights the importance of reversible AMPylation as a biological regulatory mechanism, akin to well-studied post translational modifications such as protein phosphorylation.

Keywords:  AMPylation; Endonuclease; RNase BN; adenylylation; selenoprotein O

DOI:  https://doi.org/10.1073/pnas.2515155122
J Proteomics. 2025 Nov 13. pii: S1874-3919(25)00193-9. [Epub ahead of print]323 105566

The dynamics of ubiquitination and its role within the proteome of extracellular vesicles.

Orlando Morales-Tarré, Xitlally Popa-Navarro, Alberto Paradela, Magdalena Hernández-Ortiz, Oscar Arrieta, Fernando Corrales, Sergio Encarnación-Guevara.

  Ubiquitination is a multifaceted post-translational modification that plays a crucial role in regulating the degradation of unnecessary cellular proteins and is involved in various cellular processes, including protein export via extracellular vesicles. We investigate how alterations in the intracellular levels of ubiquitinated proteins affect vesicle protein content in BEAS-2B cells. We increased the intracellular levels of ubiquitinated proteins by inhibiting proteasomal degradation with MG-132 and by blocking deubiquitinating enzymes using PR-619. Using centrifugation and ultracentrifugation, were isolate various vesicle types, specifically the largest vesicles (enriched in plasma membrane-derived microvesicles) and the smallest vesicles (enriched in endosomal exosomes). High-resolution mass spectrometry-based proteomics was utilized to quantify their protein content. The content of extracellular vesicles changed in response to both treatments, reflecting cellular changes and the export of stress signals. The increase in intracellular levels of ubiquitinated proteins induced metabolic stress in the cells, generally leading to a reduction in protein translation, an enhanced response to oxidative stress, changes in membrane transport, and alterations in cell-microenvironment interactions. The modifications observed in the vesicular proteome suggest that ubiquitination plays a significant role in regulating protein export. This regulation can be mastered for diagnostic purposes and for describing cells and tissues through liquid biopsies. SIGNIFICANCE: Ubiquitination is one of the most abundant post-translational modifications in cells, and its role, beyond marking proteins for degradation, is not fully understood. Characterizing the effect of this modification on protein export to extracellular vesicles can shed light on how a cell selects its contents to influence its microenvironment, send signals to distant tissues, or interact with the immune system. This is particularly relevant in the context of pathologies such as cancer, which hijacks the cellular vesicle-producing machinery and adapts it to its needs to influence the remodeling of its surroundings. Understanding how a cell regulates the specific contents of its vesicles may point the way toward the development of treatments or superior diagnostic and classification tools.

Keywords:  BEAS-2B; Exosomes; Extracellular vesicles; Mass spectrometry; Microvesicles; Proteomics; Ubiquitination

DOI:  https://doi.org/10.1016/j.jprot.2025.105566
Mol Cell. 2025 Nov 20. pii: S1097-2765(25)00861-5. [Epub ahead of print]85(22): 4109-4110

Succinate puts the brakes on de novo purine synthesis.

Timothy C Kenny, Kıvanç Birsoy.

In this issue of Molecular Cell, Nengroo et al.1 report that the tricarboxylic acid (TCA) cycle enzyme succinate dehydrogenase (SDH) is essential for de novo purine synthesis, revealing a previously unrecognized metabolic dependency in cancer that can be leveraged therapeutically.

DOI: https://doi.org/10.1016/j.molcel.2025.10.020
Cancer Res. 2025 Nov 17.

Mitochondrial Transfer Rescues Respiration to Support De Novo Pyrimidine Biosynthesis and Tumor Progression.

Maria Dubisova, Klara Bohacova, Zuzana Nahacka, Daniel Kraus, Jaromir Novak, Sarka Dvorakova, Petra Brisudova, Natalie Danesova, Saba Selvi, Mariia Hrysiuk, Berwini B Endaya, Panagiotis Botsios, Dan-Diem Thi Le, Monika Novotna, Sona Vodenkova, Jaroslav Truksa, Karel Chalupsky, Krystof Klima, Jan Prochazka, Radislav Sedlacek, Francesco Mengarelli, Patrick Orlando, Luca Tiano, Stepana Boukalova, Michael V Berridge, Renata Zobalova, Jiri Neuzil.

Cancer cells with severe defects in mitochondrial DNA (mtDNA) can import mitochondria via horizontal mitochondrial transfer (HMT) to restore respiration. Mitochondrial respiration is necessary for the activity of dihydroorotate dehydrogenase (DHODH), an enzyme of the inner mitochondrial membrane that catalyzes the fourth step of de novo pyrimidine synthesis. Here, we investigated the role of de novo synthesis of pyrimidines in driving tumor growth in mtDNA-deficient (ρ0) cells. While ρ0 cells grafted in mice readily acquired mtDNA, this process was delayed in cells transfected with alternative oxidase (AOX), which combines the functions of mitochondrial respiratory complexes III and IV. The ρ0 AOX cells were glycolytic but maintained normal DHODH activity and pyrimidine production. Deletion of DHODH in a panel of tumor cells completely blocked or delayed tumor growth. The grafted ρ0 cells rapidly recruited tumor-promoting/stabilizing cells of the innate immune system, including pro-tumor M2 macrophages, neutrophils, eosinophils, and mesenchymal stromal cells (MSCs). The ρ0 cells recruited MSCs early after grafting, which were potential mitochondrial donors. Grafting MSCs together with ρ0 cancer cells into mice resulted in mitochondrial transfer from MSCs to cancer cells. Overall, these findings indicate that cancer cells with compromised mitochondrial function readily acquire mtDNA from other cells in the tumor microenvironment to restore DHODH-dependent respiration and de novo pyrimidine synthesis. The inhibition of tumor growth induced by blocking DHODH supports targeting pyrimidine synthesis as a potential widely applicable therapeutic approach.

DOI: https://doi.org/10.1158/0008-5472.CAN-24-0737
Nat Commun. 2025 Nov 20. 16(1): 10198

SLC45A4 encodes a peroxisomal putrescine transporter that promotes GABA de novo synthesis.

Cecilia Colson, Yujue Wang, James Atherton, Nisha Rani Dahiya, Davood Kharaghani, Xiaoyang Su.

Solute carriers (SLC) are membrane proteins that facilitate the transportation of ions and metabolites across either the plasma membrane or the membrane of intracellular organelles. With more than 450 human genes annotated as SLCs, many of them are still orphan transporters without known biochemical functions. We develop a metabolomic-transcriptomic association analysis, and we find that the expression of SLC45A4 has a strong positive correlation with the cellular level of γ-aminobutyric acid (GABA). Using mass spectrometry and the stable isotope tracing approach, we demonstrate that SLC45A4 promotes GABA de novo synthesis through the Arginine/Ornithine/Putrescine (AOP) pathway. SLC45A4 functions as a putrescine transporter localized to the peroxisome membrane to facilitate GABA production. Taken together, our results reveal a biochemical mechanism where SLC45A4 controls GABA production.

DOI: https://doi.org/10.1038/s41467-025-62721-x
Sci Rep. 2025 Nov 19. 15(1): 40651

BRSK2 plays a role in autophagy and cancer cell growth and survival under nutrient deprivation stress via the PIK3C3 pathway.

Aparna Maiti, Alison D Axtman, Rongrong Wu, Lydia J B Redman, Kazuaki Takabe, Aimee B Stablewski, Li Yan, Michael J Ciesielski, Jianmin Zhang, Sharon S Evans, Pawel Kalinski, Nitai C Hait.

  Macroautophagy/autophagy is a stress-responsive lysosomal catabolic pathway that promotes cellular homeostasis and tumor cell survival, but its role in breast cancer progression and metastasis remains unclear. Here, we show that a brain-specific serine/threonine protein kinase, BRSK2, a marker of aggressive metastatic disease in breast cancer patients, is crucial in regulating autophagy. BRSK2 is overexpressed in aggressive cancer and is associated with reduced disease-specific survival. BRSK2 also regulates basal autophagy and activates AKT, STAT3, and NF-κB-mediated cancer cell survival pathways. In addition, BRSK2 overexpression increases the levels of inflammatory cytokines and chemokines in breast cancer cells. Downregulation of BRSK2 using specific siRNAs or the BRSK2 kinase small-molecule inhibitor GW296115 markedly reduced nutrient-deprivation stress-mediated autophagy, cell growth, and metastatic potential, and enhanced breast cancer cell apoptosis. Endogenous BRSK2 is associated with the Vps34-class III PI3K-Beclin-1-ATG14 autophagy signaling complexes that could protect cancer cells from nutrient-deprivation stress. Our findings demonstrate the key role of the BRSK2-mediated protective autophagy and cell growth and survival under nutrient deprivation stress via survival signals, e.g., PI3K/AKT or STAT3-NF-kB, in aggressive breast cancer cells.

Keywords:  Autophagy; BRSK2; Breast cancer; Cell survival; Nutrient-deprivation stress

DOI:  https://doi.org/10.1038/s41598-025-24354-4
bioRxiv. 2025 Sep 30. pii: 2025.09.29.678898. [Epub ahead of print]

De novo design of phospho-tyrosine peptide binders.

Magnus S Bauer, Jason Z Zhang, Kejia Wu, Gyu Rie Lee, Brian Coventry, Kody A Klupt, Jiuhan Shi, Rafael I Brent, Xinting Li, Carolina Moller, Nicole Roullier, Dionne K Vafeados, Indrek Kalvet, Rebecca K Skotheim, Siyu Zhu, Amir Motmaen, Luca C Herrmann, Pascal Sturmfels, Doug Tischer, Han Raut Altae-Tran, David Juergens, Rohith Krishna, Woody Ahern, Jason Yim, Asim K Bera, Alex Kang, Emily Joyce, Andrew Lu, Lance Stewart, Frank DiMaio, David Baker.

Phosphorylation on tyrosine is a key step in many signaling pathways. Despite recent progress in de novo design of protein binders, there are no current methods for designing binders that recognize phosphorylated proteins and peptides; this is a challenging problem as phosphate groups are highly charged, and phosphorylation often occurs within unstructured regions. Here we introduce RoseTTAFold Diffusion 2 for Molecular Interfaces (RFD2-MI), a deep generative framework for the design of binders for protein, ligand, and covalently modified protein targets. We demonstrate the power and versatility of this method by designing binders for four critical phosphotyrosine sites on three clinically relevant targets: Cluster of Differentiation 3 (CD3ε), Epidermal Growth Factor Receptor (EGFR) and Insulin Receptor (INSR). Experimental characterization shows that the designs bind their phospho-tyrosine containing targets with affinities comparable to native binding sites and have negligible binding to non-phosphorylated targets or phosphopeptides with different sequences. X-ray crystal structures of generated binders to CD3ε and EGFR are very close to the design models, demonstrating the accuracy of the design approach. RFD2-MI provides a generalizable all-atom diffusion framework for probing and modulating phosphorylation-dependent signaling, and more generally, for developing research tools and targeted therapeutics against post-translationally modified proteins.

DOI: https://doi.org/10.1101/2025.09.29.678898
NPJ Syst Biol Appl. 2025 Nov 19. 11(1): 129

Path-based quantification of activation and repression in Boolean models using BooLEVARD.

Marco Fariñas, Eirini Tsirvouli, John Zobolas, Tero Aittokallio, Åsmund Flobak, Kaisa Lehti.

Boolean models are a powerful resource for studying dynamic processes of biological systems. However, their inherent discrete nature limits their ability to capture continuous aspects of signal transduction, such as signal strength or protein activation levels. Although existing tools provide some path exploration capabilities that can be used to explore signal transduction circuits, the computational workload often requires simplifying assumptions that compromise the accuracy of the analysis. Here, we introduce BooLEVARD, a Python package designed to efficiently quantify the number of paths leading either to node activation or repression in Boolean models, which offers a more detailed and quantitative perspective on how molecular signals propagate through signaling networks. By focusing on the collection of non-redundant paths directly influencing Boolean outcomes, BooLEVARD enhances the precision of signal strength representation. We showcase the application of BooLEVARD in studying cell-fate decisions using a Boolean model of cancer metastasis, demonstrating its ability to identify critical signaling events. In addition, through a second use case, we demonstrated BooLEVARD's capability to scale efficiently across increasingly large and connected Boolean models. Through these properties, BooLEVARD provides a distinctive tool for quantitative analysis of signaling dynamics within Boolean models, which can increase our understanding of disease development and drug responses. BooLEVARD is freely available at https://github.com/farinasm/boolevard .

DOI: https://doi.org/10.1038/s41540-025-00605-y
J Clin Invest. 2025 Nov 17. pii: e193370. [Epub ahead of print]135(22):

Targeting plasticity in the pyrimidine synthesis pathway potentiates macrophage-mediated phagocytosis in pancreatic cancer models.

Jie Zhao, Xinghao Li, Xinyu Li, Pengfei Ren, Yilan Wu, Hao Gong, Lijian Wu, Junran Huang, Saisai Wang, Ziwei Guo, Mo Chen, Zexian Zeng, Deng Pan.

  Macrophage-mediated phagocytosis plays a critical role in the elimination of cancer cells and shaping antitumor immunity. However, the tumor-intrinsic pathways that regulate cancer cell sensitivity to macrophage-mediated phagocytosis remain poorly defined. In this study, we performed a genome-wide CRISPR screen in murine pancreatic cancer cells cocultured with primary macrophages and identified that disruption of the tumor-intrinsic pyrimidine synthesis pathway enhances phagocytosis. Mechanistically, we discovered that macrophages inhibit the pyrimidine salvage pathway in tumor cells by upregulating Upp1-mediated uridine degradation through cytokines TNF-α and IL-1. This shift increased tumor cells' reliance on de novo pyrimidine synthesis. As a result, tumor cells with impaired de novo pyrimidine synthesis showed depleted UMP and displayed enhanced exposure of phosphatidylserine (PtdSer), a major "eat-me" signal, thereby promoting macrophage-mediated phagocytosis. In multiple pancreatic cancer models, Cad-deficient tumors exhibited markedly reduced tumor burden with increased levels of phagocytosis by macrophages. Importantly, the Cad-mediated suppression of pancreatic cancer was dependent on TAMs and cytokines IL-1 and TNF-α. Pharmacological inhibition of DHODH, which blocks de novo pyrimidine synthesis, similarly decreased tumor burden with enhanced phagocytosis in pancreatic cancer models. These findings highlight the critical role of the tumor-intrinsic pyrimidine synthesis pathway in modulating macrophage-mediated antitumor immunity, with potential therapeutic implications.

Keywords:  Cancer immunotherapy; Immunology; Innate immunity; Macrophages; Metabolism; Oncology

DOI:  https://doi.org/10.1172/JCI193370
bioRxiv. 2025 Oct 04. pii: 2025.10.02.680066. [Epub ahead of print]

Glutamine-Dependent Slc25a39-Nrf2 Axis Couples Mitochondrial Dynamics with Metabolic Reprogramming to Establish Myogenic Commitment.

Brian Kelly, Chia-Hua Wu, Kaan I Eskut, Elizabeth McCauley, Sajina Dhungel, Samantha Pavlecic, Grace Bieghler, Jelena Perovanovic, Dean Tantin, Jakub Famulski, Jeramiah Smith, Chintan Kikani.

Myogenic commitment is a decisive and irreversible step in skeletal muscle regeneration, necessitating proliferating myoblasts to integrate metabolic cues with nuclear transcriptional programs. Among amino acids, glutamine is uniquely positioned to influence this transition by coupling energy production to macromolecule biosynthesis and epigenetic regulation. We reasoned that myoblasts must sense glutamine availability to ensure orderly progression toward commitment, and we tested this by examining the molecular consequences of acute glutamine withdrawal. We find that continued glutamine oxidation is required to sustain glycolysis, maintain mitochondrial fission, and preserve a redox balance that supports progression towards myogenic commitment. In its absence, myoblasts undergo a reductive shift, characterized by mitochondrial elongation, membrane depolarization, and suppression of glycolysis, ultimately leading to growth arrest. Transcriptomic profiling reveals reduced MyoD and MKi67 , accompanied by increased Sprouty1 levels, defining a reversible non-proliferative state that resembles but is distinct from quiescent and reserve cells. We term this state Poised Metabolic Arrest (PMA), a cellular response to glutamine limitation during myogenic progression. Mechanistically, PMA is driven by Nrf2-dependent increased glutathione (GSH) biosynthesis and upregulation of mitochondrial GSH carrier Slc25a39 when glutamine is limited. Depleting mitochondrial glutathione or silencing Slc25a39 forces exit from PMA. However, this premature exit compromises subsequent differentiation potential, indicating PMA serves to preserve differentiation competence when glutamine is limited. Consistent with this, both loss and overexpression of Slc25a39 impair myoblast differentiation in vitro and disrupt regeneration in vivo. Together, these data suggest that a reciprocal Slc25a39-Nrf2 redox axis functions as a nutrient-dependent checkpoint, coupling glutamine availability to mitochondrial remodeling and metabolic reprogramming, necessary to establish irreversible myogenic commitment.

DOI: https://doi.org/10.1101/2025.10.02.680066
Proc Natl Acad Sci U S A. 2025 Nov 25. 122(47): e2517961122

Longitudinal transformation of mitochondrial metabolism during neurogenesis.

Donghoon Lim, Sewon Park, Jong Seung Lee, Hyo Jin Gwon, Yunwoo Nam, Suhyuk Choi, Jongwon Kim, Yeonsu Kim, Geonwoo Park, Woo Yang Pyun, Hyun Woo Park, Seung-Woo Cho, Hyun S Ahn.

  Neural stem cells (NSCs) are valuable in the quest to conquer neurodegenerative diseases due to their capability to reconstruct the damaged neuronal networks. However, deep understanding of the intercellular signaling mechanism controlling the lineage and fate of the stem cells is required before potential clinical applications. Here, we applied nondestructive and label-free electrochemical methods for the longitudinal tracking of NSC respiratory metabolism. Sharp change in the oxygen utilization pattern was observed concomitant to stemness loss and onset of differentiation, suggesting metabolic reprogramming in the transition. Intra- and extracellular profiling of mitochondrial metabolites revealed molecular preference in the extracellular transport rates. Electrochemical emulation of the metabolite release pattern induced acceleration of neurite growth in nearby cells, suggesting paracrine signaling system mediated by mitochondrial metabolites.

Keywords:  intercellular signaling; neurogenesis; reactive oxygen species; scanning electrochemical microscopy

DOI:  https://doi.org/10.1073/pnas.2517961122
FASEB J. 2025 Nov 30. 39(22): e71214

c-Abl Kinase Targets Tight Junction Protein ZO-2 in Regulation of Cell Migration and Morphology.

Doo Eun Choi, Bomi Gweon, Jacob Notbohm, Heejin Kim, Xue-Song Liu, Jeffrey J Fredberg.

  c-Abl is a non-receptor tyrosine kinase involved in the regulation of cell migration and morphogenesis, but the underlying mechanism remains unclear. Here, we report the identification of tight junction protein ZO-2 as a bona fide substrate of c-Abl. We show that c-Abl directly binds to and phosphorylates the C-terminus of ZO-2. In addition, c-Abl stimulates the activity of JAK1, which subsequently phosphorylates the N-terminus of ZO-2. Using the RNAi-mediated knockdown/rescue strategy, we demonstrate that c-Abl regulates cellular morphology and migration through targeting ZO-2 for phosphorylation. c-Abl activity is also associated with decreased traction forces exerted on the cell substrate, thus corroborating c-Abl kinase activity-mediated inhibition of cell migration. Collectively, our data uncover ZO-2 as a novel mediator for c-Abl-dependent regulation of cell migration.

Keywords:  ZO‐2; cell migration; cell morphology changes; c‐Abl; tyrosine kinase

DOI:  https://doi.org/10.1096/fj.202402159R
Sci Rep. 2025 Nov 19. 15(1): 40774

The cyclic peptide mallotumide A inhibits colon and breast cancer cell growth and motility by targeting cellular respiration and lipogenesis.

Chayanee Laowittawat, Natthapat Sawektreeratana, Kanlaya Katewongsa, Pattaree Payomhom, Sakchai Hongthong, Vichai Reutrakul, Chutima Kuhakarn, Sarawut Jitrapakdee.

  We have recently isolated, and determined the structure of a cycloheptapeptide, Mallotumide A from the Mallotus spodocarpus root extract. Here we reported the anti-cancer activity of Mallotumide A in highly invasive colon cancer, HCT116 and triple-negative breast cancer, MDA-MB-231 cell lines. Mallotumide A, at concentrations of 1 nM and 10 nM, completely inhibited the clonogenic growth, migration, and invasion of HCT116 and MDA-MB-231 cells, respectively. While the compound interfered with cell cycle progression without inducing apoptosis, exposure to 10 nM Mallotumide A for 48 h reduced the expression of two key lipogenic enzymes, ACC1 and FASN, by approximately 50% in both cell lines. The downregulation of ACC1 and FASN was accompanied by a 50% reduction in intracellular triglyceride levels while the cholesterol levels remained unaffected. Mallotumide A also moderately decreased AMP-activated protein kinase (AMPK) and ATP levels. Extracellular flux analysis revealed that acute exposure of both cancer cell lines to 1 nM and 10 nM Mallotumide A for 24 h markedly lowered the oxygen consumption rate. This was accompanied by reductions in basal and ATP-linked respiration, maximal respiration, and mitochondrial spare respiratory capacity. Mallotumide A also decreased the extracellular acidification rate, affecting both basal glycolysis and the glycolytic reserve. These findings suggest that the anti-cancer effects of Mallotumide A are associated with disruptions in cellular energy metabolism and the de novo lipogenesis pathway in cancer cells. This study underscores the potential of Mallotumide A as a novel anti-cancer agent.

Keywords:  Anticancer; Cancer; Cyclic peptide; Mallotumide A; Natural product

DOI:  https://doi.org/10.1038/s41598-025-24547-x
Cancer Res. 2025 Nov 21.

Androgen receptor drives polyamine synthesis creating a vulnerability for prostate cancer.

Rajendra Kumar, Sheila Jonnatan, David E Sanin, Varsha Vakkala, Anoushka Kadam, Shivani Kumar, D Marc Rosen, Susan L Dalrymple, Liang Zhao, Jackson R Foley, Cassandra E Holbert, Ashley Nwafor, Srushti Kittane, Elizabeth Penner, Petya Apostolova, Samuel Warner, Chi V Dang, Eneda Toska, Elizabeth A Thompson, John T Isaacs, Angelo M De Marzo, W Nathaniel Brennen, Erika L Pearce, Tracy Murray Stewart, Robert A Casero, Samuel R Denmeade, Laura A Sena.

Supraphysiological androgen (SPA) treatment can paradoxically restrict growth of castration-resistant prostate cancer with high androgen receptor (AR) activity, which is the basis for use of Bipolar Androgen Therapy (BAT) for patients with this disease. While androgens are widely appreciated to enhance anabolic metabolism, how SPA-mediated metabolic changes alter prostate cancer progression and therapy response is unknown. Here, we report that SPA markedly increased intracellular and secreted polyamines in prostate cancer models. AR binding at enhancer sites upstream of the ODC1 promoter increased the abundance of ornithine decarboxylase (ODC), a rate-limiting enzyme of polyamine synthesis, and de novo synthesis of polyamines from arginine. SPA-stimulated polyamines enhanced prostate cancer fitness, as dCas9-KRAB-mediated inhibition of AR regulation of ODC1 or direct ODC inhibition by difluoromethylornithine (DFMO) increased efficacy of SPA. Mechanistically, AR activation combined with loss of negative feedback by polyamines increased the activity of S-adenosylmethionine decarboxylase 1 (AMD1), leading to depletion of its substrate S-adenosylmethionine and global protein methylation. These data provided the rationale for a clinical trial testing the safety and efficacy of BAT in combination with DFMO for patients with metastatic castration-resistant prostate cancer. Pharmacodynamic studies of this therapeutic combination in the first five patients on trial indicated that this approach effectively depleted polyamines in plasma. Thus, the AR potently stimulates polyamine synthesis, which constitutes a vulnerability in prostate cancer treated with SPA that can be targeted therapeutically.

DOI: https://doi.org/10.1158/0008-5472.CAN-25-1532
J Proteome Res. 2025 Nov 20.

Targeted Metabolomic Methods for 13C Stable Isotope Labeling with Uniformly Labeled Glucose and Glutamine Using Liquid Chromatography-Tandem Mass Spectrometry (LC-MS/MS).

Erin Q Jennings, W Kimryn Rathmell, Jeffrey C Rathmell.

  Heavy carbon labeling has emerged as a popular way to study metabolic diseases. However, most carbon labeling techniques use untargeted mass spectrometry, which typically requires dependence on a research core and specialized software. By combining published 13C labeling patterns and known enzyme reactions, an optimized targeted mass spectrometry method was generated to measure stable isotope labeling with carbon-13 through glycolysis, the tricarboxylic acid cycle, the hexosamine biosynthetic pathway, and glutaminolysis using uniformly labeled glucose or glutamine. This method provides a novel and adaptable approach to investigate pointed hypotheses on the utilization of glucose or glutamine in disease states and models.

Keywords:  carbon tracing; stable isotope labeling; tandem mass spectrometry; targeted metabolomics

DOI:  https://doi.org/10.1021/acs.jproteome.5c00514
bioRxiv. 2025 Oct 02. pii: 2025.09.30.679611. [Epub ahead of print]

Phosphatidylserine and RhoB connect phosphatidylinositol 4-phosphate and phosphatidic acid metabolism at the plasma membrane.

Shiying Huang, Yeun Ju Kim, Xiaofu Cao, Timothy W Bumpus, Mira Sohn, Matthew Tyler Menold, Ryan S Dale, Jin Joo Kang, Saori Uematsu, Shagun Gupta, Shu-Bing Qian, Haiyuan Yu, Tamas Balla, Jeremy M Baskin.

Cells tightly control the homeostatic levels and subcellular localizations of membrane phospholipids through the regulation of the activities of numerous lipid-metabolizing enzymes and lipid transfer proteins. Yet, the mechanisms by which lipid imbalances are sensed and corrected to establish and maintain homeostasis are, in most cases, unknown. Here we present an expanded view of plasma membrane (PM) phosphoinositide metabolism by revealing an unexpected metabolic connection between two key anionic lipids in this membrane, phosphatidylinositol 4-phosphate (PI4P) and phosphatidic acid (PA). PM pools of PI4P are generated by PI 4-kinase Type IIIα (PI4KIIIα/PI4KA), an essential enzyme whose partial dysfunction leads to numerous hereditary human diseases. We find that depletion of PI4P by pharmacological inhibition of PI4KA increases the activity of phospholipase Ds (PLDs) and the levels of their lipid product, PA, in the PM. Guided by RNA-seq analysis and proximity labeling proteomics, we elucidate how cells connect this PI4P decrease to a compensatory increase in PA levels. Loss of PM PI4P induces a concomitant decrease of phosphatidylserine (PS) levels, and this metabolic rewiring activates a reciprocal relationship between PS synthesis and PLD-mediated PA generation. These metabolic changes also lead to transcriptional and translational upregulation of the small GTPase RhoB, which enhances PLD-mediated PA synthesis and subsequent actin cytoskeletal remodeling. Our study reveals how disease-relevant perturbation of phosphoinositide synthesis induces an integrated response that ultimately boosts levels of PA, a key anionic lipid and metabolic intermediate in phosphoinositide resynthesis.

DOI: https://doi.org/10.1101/2025.09.30.679611
bioRxiv. 2025 Oct 02. pii: 2025.09.30.679563. [Epub ahead of print]

Adipose Tissue Overexpression of Nicotinamide Phosphoribosyltransferase Prevents Metabolic Dysfunction in Obese Mice.

Daniel Ferguson, Elise I Gadson, Kathleen R Markan, Jun Yoshino, Maxwell Lin, Mohammad Habibi, Snigdha Tiash, Xiaoxia Cui, Evguenia Kouranova, Edziu Franczak, Qiuyuan Guo, Jill Kealing, Terri A Pietka, Kim H H Liss, John P Thyfault, Gary J Patti, Brian N Finck, Clair Crewe, Sandip Mukherjee.

Nicotinamide adenine dinucleotide (NAD+) is a vital coenzyme and a central factor in energy metabolism. Nicotinamide phosphoribosyltransferase (NAMPT) maintains the cellular NAD+ pool by synthesizing the NAD+ precursor, nicotinamide mononucleotide (NMN), and diminished adipocyte NAMPT activity has been implicated in aging- and obesity-related metabolic dysfunction. Herein, we examined the effects of overexpressing or knocking out NAMPT in adipocytes on metabolic dysfunction and interorgan communication in mice. We generated new adipocyte-specific NAMPT overexpressing( ANOV ) mice model. Male ANOV mice are protected from diet-induced metabolic dysfunction including adipose tissue inflammation, glucose intolerance, and insulin resistance. In contrast female ANOV mice were less protected from metabolic dysfunction, possibly due to higher endogenous expression of NAMPT in WT female mice. Livers of ANOV mice showed improved insulin signaling, increased NAD content, and reduced steatosis, suggesting that NAMPT regulates interorgan communication between adipocytes and hepatocytes. Extracellular vesicles (EV) isolated from ANOV mice enhanced insulin signaling in HepG2 cells and improved glucose tolerance in WT obese mice. In contrast, EV from ANKO mice suppressed HepG2 insulin signaling and inhibition of EV release improved glucose tolerance in ANKO female mice. Collectively, these data highlight a novel mechanism by which adipocyte NAD+ metabolism regulates systemic metabolic dysfunction via EVs.

DOI: https://doi.org/10.1101/2025.09.30.679563
bioRxiv. 2025 Oct 03. pii: 2025.10.01.679874. [Epub ahead of print]

Synthetic signaling platform uncovers and rewires cellular responses to PD-1 perturbation.

Zhixing Ma, Lars Hellweg, Susanna K Elledge, Jasper B Lee, Maria Caterina Rotiroti, Kai W Wucherpfennig, Robbie G Majzner, Xin Zhou.

Tyrosine phosphorylation motifs are central regulators of cell signaling, yet methods to selectively detect and reprogram these events have been lacking. Here we introduce Sphyder (Selective PHosphotYrosine DEtection and Rewiring), which enables precise detection of signaling at the resolution of individual phosphorylation motifs. Using Sphyder biosensors, we resolved phosphorylation dynamics and uncovered regulatory mechanisms of the checkpoint receptor PD-1 in living cells. Sphyder also provided a framework for reconstructing phosphosignaling pathways. With this approach, we redirected PD-1 signaling from immunosuppressive to immunoactivating outputs and engineered synthetic receptors that linked extracellular sensing to customized transcriptional programs. In addition, Sphyder biosensors revealed previously unrecognized mechanisms of the PD-1/VEGF bispecific antibody Ivonescimab, showing that it induces VEGF-dependent clustering, phosphorylation, and degradation of PD-1. These findings may underlie its promising clinical activity relative to conventional PD-1 blockade. Together, our study establishes a broadly applicable strategy for sensing and reprogramming cell signaling, while also providing mechanistic insights into a new class of immune checkpoint inhibitors of major clinical interest.

DOI: https://doi.org/10.1101/2025.10.01.679874
bioRxiv. 2025 Oct 04. pii: 2025.10.03.680349. [Epub ahead of print]

Metabolic STAMP for deciphering GPCR-regulated insulin secretion by pancreatic β cells.

Mohammad Ovais Aziz-Zanjani, Rachel E Turn, Yan Hang, Anushweta Asthana, Leilani Elizabeth LaBrie, Mohammadamin Mobedi, Lucy Artemis Xu, Michael Krawitzky, Seung K Kim, Peter K Jackson.

Pancreatic β cells integrate glucose and metabolic cues to regulate insulin secretion, a process disrupted in T2D. GPCRs play a critical role in fine-tuning insulin release, yet the mechanisms by which ciliary ( e.g., FFAR4) and non-ciliary ( e.g ., GLP1-R) GPCRs coordinate GSIS remains unclear. In this study, we employed Metabolic-STAMP (Synchronized Temporal-Spatial Analysis via Microscopy and Phosphoproteomics) in both mouse β cells (MIN6) and primary human islets to map the dynamic signaling networks governing GSIS and to link transient phosphorylation events to their functional outcomes. We systematically interrogated GPCR-mediated phosphorylation events through selective pharmacological inhibitors, resolving signaling hierarchies and consensus patterns across multiple pathways. Our multi-modal approach uncovered key insulin-secretion-associated PTMs, linked phosphorylation targets with phenotypic organelle dynamics, and provided mechanistic insights into how GLP1-R versus FFAR4 modulates GSIS through shared and GPCR-specific phospho-signatures. We highlighted key examples of stimulus-specific regulation by high glucose alone versus GPCR stimulation, including context-specific activation of the classic ERK signaling pathway, compartmentalized PKA signaling, pathway specificity in organelle dynamics and inter-organellar contacts, and HDAC6/ATAT-mediated regulation of microtubule acetylation. Collectively, these findings provided a blueprint for deconvolving pathway specificity of β cell GPCR signaling, illuminated regulatory nodes that program insulin release, and offered new therapeutic targets to enhance β-cell function .

DOI: https://doi.org/10.1101/2025.10.03.680349
Cell Rep Med. 2025 Nov 18. pii: S2666-3791(25)00498-7. [Epub ahead of print]6(11): 102425

System analysis links SMARCD3 regulons to growth signaling and MEK inhibitor response in everolimus-resistant ER+ breast cancer cells.

Eric F Medina, Elena Farmaki, Jason I Griffiths, Andrea H Bild, Aritro Nath.

  Estrogen receptor-positive breast cancer (ER+BC) accounts for ∼70% of all breast tumors, and 20%-40% of patients develop metastases. Everolimus is an mammalian target of rapamycin (mTOR) inhibitor used in combination with exemestane for metastatic ER+BC. However, resistance remains common and leads to poor survival outcomes. To uncover resistance mechanisms, we analyze transcriptomic profiles from everolimus-sensitive and -resistant ER+BC cell lines. Our study uncovers persistent activation of a growth-factor signaling meta-phenotype in resistant cells involving IGF1R, ESR1, and mitogen-activated protein kinase (MAPK) pathways. We identify SMARCD3 regulons linked to this meta-phenotype. Additionally, we find SMARCD3 regulon activity elevated in everolimus-refractory patient tumors. Importantly, we show that SMARCD3 regulon activation was correlated with sensitivity to several known MEK1/2 inhibitors, including trametinib. Combining trametinib with everolimus treatment significantly reduces resistant cell growth. Our results demonstrate that everolimus-resistant ER+BC cells evade therapy via alternate growth-factor signaling linked to activation of SMARCD3 regulons, which can be therapeutically targeted using MEK1/2 inhibitors.

Keywords:  ER+ breast cancer; MEK1/2 inhibitors; SMARCD3 regulon; everolimus resistance; growth-factor signaling; therapeutic targeting; transcriptomics

DOI:  https://doi.org/10.1016/j.xcrm.2025.102425
Proteomics. 2025 Nov 17. e70081

Proteomics of Prostate Cancer Tissue Small Extracellular Vesicles Reveal Alteration of Metabolism.

Lijuan Yu, Ting Ding, Roger Olofsson Bagge, Lei Zheng, Xiaoke Hao.

  Prostate cancer (PCa) is a leading male malignancy worldwide, with metabolic reprogramming being a critical hallmark of its progression. Extracellular vesicles (EVs) derived from tissues directly reflect the tumor microenvironment, offering unique insights into cancer pathophysiology that are unattainable through cell line or biofluid-derived EVs. However, the functional roles of tissue-derived EVs in PCa metabolism remain poorly understood. Leveraging our expertise in murine PCa model establishment and EV isolation from prostate tissue, this study aimed to characterize functional differences between PCa and normal prostate tissue via proteomic analysis of tissue-derived sEVs. We orthotopically implanted luciferase-labeled PCa cells into nude mice to establish an in situ PCa model, confirmed tumor formation via in vivo imaging, and harvested tissues after 4 weeks. sEVs were isolated using ultracentrifugation combined with an iodixanol density cushion and characterized by transmission electron microscopy, nanoparticle tracking analysis, and protein marker profiling. Proteomic analysis identified 28 upregulated and 24 downregulated proteins in PCa-derived sEVs compared to normal controls. Subcellular localization revealed enrichment in the cytoplasm, while pathway analysis highlighted significant involvement in metabolic processes, particularly glycolysis, amino acid biogenesis, carbon metabolism, and pyruvate metabolism. Our study establishes a robust method for isolating prostate tissue sEVs and provides the first evidence that PCa tissue-derived sEVs exhibit profound metabolic pathway alterations. These findings enhance our understanding of PCa progression mechanisms and may facilitate the development of novel diagnostic biomarkers and therapeutic strategies targeting metabolic dysregulation in PCa. SUMMARY: In this study, we created a method to isolate prostate tissue small EVs, based on our knowledge of the murine prostate cancer model building. Our data suggested that prostate tissue small EVs proteins significantly changed in many metabolism pathways, such as Glycolysis, Biogenesis of amino acids, Carbon metabolism and Pyruvate metabolism. In this study, we are the first to report prostate tissue-derived EVs proteins enriched in alterations of cancer metabolism. These differential proteins in PCa tissue EVs reflect metabolic changes in PCa and may provide insights into the development of early diagnostic biomarkers or novel therapeutic strategies.

Keywords:  Glycolysis; prostate cancer; tissue EVs; tumor metabolism

DOI:  https://doi.org/10.1002/pmic.70081
bioRxiv. 2025 Sep 29. pii: 2025.09.28.674326. [Epub ahead of print]

Glutamine antagonism suppresses tumor growth in adrenocortical carcinoma through inhibition of de novo nucleotide biosynthesis.

Vasileios Chortis, Kleiton Silva Borges, Cong-Hui Yao, Claudio Ribeiro, Luis Fernando Nagano, Mesut Berber, Alessandro Prete, Lukáš Najdekr, Michail E Klontzas, Andris Jankevics, Pedro Vendramini, Jean Lucas Kremer, Liam Kelley, Sathuwarman Raveenthiraraj, Stylianos Tsagarakis, Magdalena Macech, Ivana D Pupovac, Thomas G Papathomas, Betul Haykir, Catherine Winder, Marcus Quinkler, M Conall Dennedy, Grethe Å Ueland, Felix Beuschlein, Antoine Tabarin, Martin Fassnacht, Angela E Taylor, Darko Kastelan, Urszula Ambroziak, Dimitra A Vassiliadi, Katja Kiseljak-Vassiliades, Irina Bancos, Diana L Carlone, Warwick B Dunn, Wiebke Arlt, Marcia C Haigis, David T Breault.

Dysregulation of cellular metabolism is a hallmark of cancer, which remains poorly understood in adrenocortical carcinoma (ACC). Here, we dissected ACC metabolism by integrating transcriptional profiling from human and mouse ACC, targeted tissue metabolomics from a mouse ACC model, and untargeted serum metabolomics from a large patient cohort, providing cross-species validation of metabolic rewiring in ACC. This study revealed global metabolic dysregulation, involving glutamine-dependent pathways such as non-essential amino-acid and hexosamine biosynthesis, nucleotide metabolism, and glutathione biosynthesis, suggesting glutamine catabolism is a critical metabolic vulnerability in ACC. Treatment with glutamine antagonists 6-Diazo-5-Oxo-L-Norleucine (DON) and JHU-083 elicited robust anti-tumor responses. Mechanistic studies revealed DON's anti-tumor effect was primarily driven by selective inhibition of glutamine-fueled de novo nucleotide biosynthesis. Additionally, DON led to DNA damage, which yielded potent synergism with inhibition of the DNA damage response pathway. Collectively, this work highlights glutamine metabolism as a central metabolic dependency and therapeutic target in ACC.

DOI: https://doi.org/10.1101/2025.09.28.674326
Proc Natl Acad Sci U S A. 2025 Nov 25. 122(47): e2513479122

Glyceraldehyde-3-phosphate dehydrogenase homologs as bifunctional gatekeepers of metabolic segregation in Pseudomonas putida.

Nanqing Zhou, Caroll M Mendonca, Austin L Carroll, Stefan Pate, Manuel Nieto-Domínguez, Xinyu Chen, Lichun Zhang, Kelly P Teitel, Nienke K Dekker, Joshua R Elmore, Pablo I Nikel, Jacob R Waldbauer, Adam M Guss, Niall M Mangan, Ludmilla Aristilde.

  Metabolically versatile Pseudomonas species can assimilate various glycolytic and gluconeogenic substrates. Simultaneous assimilation is known to segregate carbons from each substrate type into different metabolic pathways. However, the mechanisms of this metabolic segregation remain unresolved. Here, we investigate Pseudomonas putida KT2440 during processing of the sugar glucose through glycolysis versus the phenolic acid ferulate through gluconeogenesis. Metabolome profiling reveals up to twofold less tricarboxylic acid cycle metabolites but up to 10-fold higher metabolites of upper glycolysis, pentose-phosphate, and Entner-Doudoroff pathways in glucose-grown cells compared to ferulate-grown cells. After 13C-substrate switching, kinetic isotopic profiling captures rapid assimilation of new substrate carbons into initial catabolic pathways, but incorporation into downstream pathways is absent or incomplete. Proteomics identifies a 22-fold higher abundance of one homolog of glyceraldehyde-3-phosphate dehydrogenase (GAPDH, GapA) in cells fed on glucose relative to ferulate, while abundance of another homolog (GapB) remains unchanged. Growth phenotypes and quantitative metabolomics for single and double knockout mutants of these GAPDH homologs indicate only GapA involvement in glycolytic flux, which can be compensated by the Entner-Doudoroff pathway, and distinct preference of GapB with minimal role of GapA for gluconeogenic flux. Accordingly, growth of triple knockout mutant with deletion of gapA, gapB, and edd is possible only when glycolytic and gluconeogenic substrates are provided together to meet metabolic demands in a segregated fashion, but metabolic tradeoffs lead to slow growth. A mathematical, experimentally constrained, model of the GAPDH node shows that tuning of GapA and GapB concentrations enables transition between flux regimes for nutritional adaptability.

Keywords:  carbon switch; gluconeogenesis; glycolysis; metabolomics; proteomics

DOI:  https://doi.org/10.1073/pnas.2513479122
Elife. 2025 Nov 19. pii: e109482. [Epub ahead of print]14

How one nutrient controls cell size.

Angela Montero, Lydia W S Finley.

  The metabolic fate of a nutrient called pyruvate determines how big cells become.

Keywords:  D. melanogaster; biochemistry; cell biology; cell growth; chemical biology; genetics; hepatocytes; human; pyruvate metabolism; redox state; translation

DOI:  https://doi.org/10.7554/eLife.109482
bioRxiv. 2025 Sep 30. pii: 2025.09.30.679484. [Epub ahead of print]

Mapping the Subtype-Specific PARP1 ADP-ribosylated Proteome in Breast Cancer Cells.

Sneh Koul, Minjung Kwon, Poulami Tapadar, Yangyang Dai, Tulip Nandu, Dan Huang, Cristel V Camacho, W Lee Kraus.

  Breast cancers are molecularly heterogeneous, with subtype-specific differences in transcriptional programs, chromatin architecture, and therapeutic responses. While PARP1 has been extensively studied in the context of DNA repair, emerging evidence implicates its catalytic activity in a broader set of cellular processes, including the regulation of gene expression. Here, we employed an NAD analog-sensitive PARP1 (asPARP1) chemical genetics approach combined with mass spectrometry to map the ADP-ribosylated proteome across six human breast cancer cell lines representing luminal and basal/triple negative subtypes. We identified thousands of PARP1 substrates and hundreds of Glu/Asp ADPRylation sites, revealing both shared and subtype-specific modifications in cell lines maintained under basal growth conditions. Luminal-specific substrates were enriched in chromatin and transcriptional regulators, whereas basal-specific substrates were preferentially linked to translation and RNA processing, highlighting lineage-dependent PARP1 activity. Transcription factors emerged as major substrates, with TFAP2A serving as a proof-of-concept; it is selectively ADPRylated in luminal cells and inhibition of PARP1-mediated ADPRylation modulates its promoter occupancy in a subtype-specific manner. Our data provide a new resource for studying subtype-specific PARP1-mediated ADPRylation in breast cancer cells. Collectively, our findings expand the conceptual framework for PARP1 function beyond DNA repair, offering mechanistic insights into subtype-specific gene regulation and potential determinants of PARP inhibitor sensitivity in breast cancer.

Keywords:  ADP-ribosylation (ADPRylation); Breast cancer; Cell growth; Chromatin remodeling complex; Gene regulation; Histone; Histone modifying enzymes; PARP1; Transcription; Transcription factor

DOI:  https://doi.org/10.1101/2025.09.30.679484
Nucleic Acids Res. 2025 Nov 20. pii: gkaf1219. [Epub ahead of print]

DRESIS 2.0: the comprehensive landscape of drug resistance information.

Xiuna Sun, Zhangle Wei, Xinyuan Yu, Kaixuan Liu, Shun Yao, Zheng Ni, Hanbing Wang, Ziming Zhao, Yinpeng Zhang, Yuxuan Liu, Hanlu Ding, Yintao Zhang, Zhiguo Liu, Mang Xiao, Feng Zhu.

Elucidating mechanisms of drug resistance is key for overcoming resistance, guiding drug design, and enabling accurate resistance prediction. Recently, disease metabolic reprogramming has emerged as a novel mechanism of resistance, which enables disease cells to adapt to therapeutic resistance by altering energy production pathways, cellular signaling, and biosynthesis processes. Moreover, protein structure alterations also play a pivotal role in resistance study, facilitating mechanistic understanding, and structure-based target discovery. In other words, integrating these recently accumulated critical data is essential for enriching the landscape of drug resistance data. Therefore, in this study, DRESIS was a significant update by providing (i) 236 molecules that drive metabolic reprogramming and confer resistance to 168 drugs, together with a detailed mechanism, (ii) 2228 protein structural variants implicated in resistance to 671 drugs across 238 diseases, and (iii) greatly expanded landscapes of drug resistance information, now featuring 398 newly added key drug-resistant molecules, 356 drugs with the latest published resistance mechanisms, and 81 new drug-resistant disease categories. All in all, DRESIS 2.0 is expected to serve as a valuable resource for the scientific community and provide important support in tackling the global challenge of drug resistance, which is now publicly accessible at https://idrblab.org/dresis/.

DOI: https://doi.org/10.1093/nar/gkaf1219
Sci Signal. 2025 Nov 18. 18(913): eads8396

CoDIAC: A comprehensive approach for interaction analysis provides insights into SH2 domain function and regulation.

Alekhya Kandoor, Gabrielle Martinez, Julianna M Hitchcock, Savannah Angel, Logan Campbell, Saqib Rizvi, Kristen M Naegle.

Protein domains are conserved structural and functional units that serve as the building blocks of proteins. Through evolutionary expansion, domain families are represented by multiple members in diverse configurations with other domains, evolving new specificities for their interacting partners. Here, we developed a structure-based interface analysis to map domain interfaces from experimental and predicted structures, including interfaces with macromolecules and intraprotein interfaces. We hypothesized that contact mapping of domains could yield insights into domain selectivity and the conservation of domain-domain interfaces across proteins and identify conserved posttranslational modifications (PTMs) relative to interaction interfaces, enabling the inference of specific effects as a result of PTMs or mutations. We designed this modular approach as an open-source Python package called Comprehensive Domain Interface Analysis of Contacts (CoDIAC) and applied it to the family of human Src homology 2 (SH2) domains, a modular unit central to phosphotyrosine-mediated signaling. CoDIAC revealed coordinated regulation of SH2 domain binding interfaces by tyrosine and serine/threonine phosphorylation and acetylation that may underlie binding selectivity. These findings suggest that multiple signaling systems can regulate protein activity and SH2 domain interactions in a coordinated manner. Applying CoDIAC to the study of other protein domains should provide insights into their binding interfaces and molecular interactions.

DOI: https://doi.org/10.1126/scisignal.ads8396
Mol Cell Proteomics. 2025 Nov 17. pii: S1535-9476(25)00560-2. [Epub ahead of print] 101461

Proteomics data imputation with a deep model that learns from many datasets.

Lincoln Harris, William S Noble.

Missing values are a major challenge in the analysis of mass spectrometry proteomics data. Missing values hinder reproducibility, decrease statistical power for identifying differentially abundant proteins and make it challenging to analyze low-abundance proteins. We present Lupine, a deep learning-based method for imputing, or estimating, missing values in quantitative proteomics data. Lupine is, to our knowledge, the first imputation method that is designed to learn jointly from many datasets, and we provide evidence that this approach leads to more accurate predictions. We validated Lupine by applying it to tandem mass tag data from >1,000 cancer patient samples spanning ten cancer types from the Clinical Proteomics Tumor Atlas Consortium. Lupine outperforms the state-of-the-art for proteomics imputation, uniquely identifies differentially abundant proteins and Gene Ontology terms and learns a meaningful representation of proteins and patient samples. Lupine is implemented as an open-source Python package.

DOI: https://doi.org/10.1016/j.mcpro.2025.101461
Endocr Relat Cancer. 2025 Nov 19. pii: ERC-25-0185. [Epub ahead of print]

GLP1 Receptor Agonism Alters Growth and Therapeutic Response in Prostate Cancer.

Soumen Bera, Lisa Gutgesell, Brynne Darden, Robert M Sargis, Mark Maienschein-Cline, Charles E Gaber, Natalie Reizine, Donald J Vander Griend, Jordan E Vellky.

  The burgeoning metabolic benefits of GLP1 receptor (GLP1R) agonists have led to their widespread use for treatment of type 2 diabetes mellitus and obesity. While the pharmacological GLP1R agonist semaglutide primarily activates GLP1R signaling in the pancreas, GLP1R is also expressed in advanced prostate cancer where GLP1R agonism could directly alter cellular signaling. Because metabolic disorders and their treatment are common among those with prostate cancer, understanding the effects of semaglutide in prostate cells is critical for deciphering its systemic effects and delineating potential impacts on prostate cancer outcomes. In prostate cancer models, semaglutide decreased cell proliferation, glycolytic function, and phospho-kinase-mediated signaling. This overall suppression of signaling downstream of GLP1R is consistent with inhibitory GPCR signaling, which was confirmed by reduced cAMP levels. Further, cell proliferation was decreased with semaglutide alone and in combination with enzalutamide, supporting that GLP1R agonism may provide therapeutic benefit as a standalone treatment or to augment the therapeutic benefits of androgen receptor signaling inhibitors (ARSI). Interestingly, in a trans-differentiation model (n=55), GLP1R and AR expression were negatively correlated, while GLP1R and NEPC markers (DLL3, ASCL1) were positively correlated, suggesting an association between GLP1R and neuroendocrine differentiation. Bioinformatic analyses on publicly-available patient RNA-sequencing data (n=664) identified significantly higher GLP1R expression in advanced prostate cancer vs. benign prostate, where it was associated with negative Notch signaling. Taken together, our data support a model wherein GLP1R agonism blocks oncogenic signaling pathways and growth of prostate cancer cells that could be exploited therapeutically for men with advanced prostate cancer.

Keywords:  Castration-resistant prostate cancer; Neuroendocrine prostate cancer; advanced prostate cancer; incretin mimetics; metabolic co-morbidities

DOI:  https://doi.org/10.1530/ERC-25-0185
Proc Natl Acad Sci U S A. 2025 Nov 25. 122(47): e2423894122

Breast cancer cell coculture induces normal lung fibroblast transition to CAFs, promoting tumor cell dormancy and therapy resistance.

Marika L Klosowski, Kathryn E Cronise, Eric P Palmer, Kelly McAuliffe, Claire Stratton, Kelsie Sparks, Kendall T Malmstrom, Gwyneth Knott-Byars, Qiong Zhou, Hector Esquer, Daniel V LaBarbera, Daniel P Regan.

  Cancer-associated fibroblasts (CAFs) shape the tumor microenvironment of primary breast tumors to promote tumor progression and therapy resistance. While the lung is a top metastatic site in breast cancer, the origins of lung metastasis-associated fibroblasts and their influence on disseminating tumor cell outgrowth and chemoresistance are poorly understood. Here, we demonstrate the applicability of 2-dimensional and 3-dimensional cocultures of primary human lung fibroblasts (LF) and breast cancer cells (BCC) as models of tumor-stromal interactions in lung metastatic breast cancer. Using these models, we find that BCC lines representing clinically relevant molecular subtypes differentially induce CAF-like phenotypes in primary LFs corresponding with their propensity for lung metastasis. Furthermore, we identify a mechanism by which juxtacrine signaling from LFs to triple negative breast cancer (TNBC) cells promotes expansion of prognostic dormant-like cell subpopulations and instigates autophagy-dependent therapy resistance via integrin and Janus kinase1/2 signaling. A high content kinase inhibitor compound library screen using this model identifies vacuolar protein sorting 34 as a therapeutic vulnerability unique to BCC-LF interaction whose inhibition can resensitize TNBC cells to chemotherapy and relieve LF-mediated extrinsic therapy resistance. Therefore, we propose coculture of primary human LFs and BCC as a reductionist model of interactions between tumor cells and lung-resident stroma and a tool for therapeutic and mechanistic discovery in lung metastatic breast cancer.

Keywords:  breast cancer; cancer-associated fibroblast; lung; metastasis; model

DOI:  https://doi.org/10.1073/pnas.2423894122
Elife. 2025 Nov 17. pii: RP106601. [Epub ahead of print]14

The denitrosylase SCoR2 controls cardioprotective metabolic reprogramming.

Zachary W Grimmett, Rongli Zhang, Hua-Lin Zhou, Qiuying Chen, Dawson Miller, Zhaoxia Qian, Justin Lin, Riti Kalra, Steven S Gross, Walter J Koch, Richard T Premont, Jonathan S Stamler.

  Acute myocardial infarction (MI) is a leading cause of morbidity and mortality, and therapeutic options remain limited. Endogenously generated nitric oxide (NO) is highly cardioprotective, but protection is not replicated by nitroso-vasodilators (e.g., nitrates, nitroprusside) used in clinical practice, highlighting specificity in NO-based signaling and untapped therapeutic potential. Signaling by NO is mediated largely by S-nitrosylation, entailing specific enzymes that form and degrade S-nitrosothiols in proteins (SNO-proteins), termed nitrosylases and denitrosylases, respectively. SNO-CoA Reductase 2 (SCoR2; product of the Akr1a1 gene) is a recently discovered protein denitrosylase. Genetic variants in SCoR2 have been associated with cardiovascular disease, but its function is unknown. Here, we show that mice lacking SCoR2/AKR1A1 exhibit robust protection in an animal model of MI. SCoR2 regulates ketolytic energy availability, antioxidant levels, and polyol homeostasis via S-nitrosylation of key metabolic effectors. Human cardiomyopathy shows reduced SCoR2 expression and an S-nitrosylation signature of metabolic reprogramming, mirroring SCoR2-/- mice. Deletion of SCoR2 thus coordinately reprograms multiple metabolic pathways-ketone body utilization, glycolysis, pentose phosphate shunt, and polyol metabolism-to limit infarct size, establishing SCoR2 as a novel regulator in the injured myocardium and a potential drug target.

Keywords:  S-nitrosylation; denitrosylase; human; ischemia–reperfusion; medicine; metabolic reprogramming; mouse; myocardial infarction

DOI:  https://doi.org/10.7554/eLife.106601
J Biochem Mol Toxicol. 2025 Dec;39(12): e70619

Pharmacological Stimulation of GPER Reverses Mitochondrial Dysfunction in the Hearts of Ovariectomized Type 2 Diabetic Rats.

Nahlah Fahad-Alreshidi, Refaat A Eid, Abdullah M K Albloshi, Saud S Alharbi, Sultan Mohammed Alanazi, Thamer Alsufayan, Musaad B Alsahly, Mirwais Ramozi.

  Postmenopausal diabetic women face an increased risk of cardiovascular diseases due to estrogen deficiency and metabolic dysfunction. Mitochondrial calcium homeostasis is essential for the viability and energy production of cardiomyocytes; however, the regulation of this process in estrogen-deficient diabetic hearts is not well understood. This study aimed to explore the effects of activating the G protein-coupled estrogen receptor 1 (GPER) on cardiac mitochondrial calcium regulation via the mitochondrial calcium uniporter (MCU) in ovariectomized rats with type 2 diabetes (OVX-T2D). T2D was induced using a high-fat diet combined with a single dose of streptozotocin (30 mg/kg). The animals were divided into three groups: OVX, OVX + T2D, and OVX + T2D treated with the GPER agonist G1. Our findings indicate that GPER activation significantly increased MCU expression in the heart, mediated by the cAMP/PKA/CREB signaling cascade. This increase was associated with enhanced activity of tricarboxylic acid (TCA) cycle enzymes (PDH and α-KGDH) and improved mitochondrial ATP production. Additionally, G1 treatment reduced oxidative stress markers (MDA) and increased the activity of antioxidant enzymes (SOD), suggesting a better mitochondrial redox balance. Notably, GPER stimulation also suppressed caspase-3 expression, indicating a reduction in apoptosis within cardiac tissue. These results demonstrate that GPER activation restores mitochondrial calcium uptake and enhances mitochondrial function in the diabetic postmenopausal heart. This study highlights a novel regulatory mechanism where GPER enhances cardiac mitochondrial resilience through MCU upregulation and related metabolic and antiapoptotic pathways. Targeting GPER may emerge as a promising therapeutic strategy for alleviating diabetic cardiomyopathy in postmenopausal women.

Keywords:  GPER; cardiovascular diseases; mitochondrial calcium uniporter; oxidative stress; type 2 diabetes

DOI:  https://doi.org/10.1002/jbt.70619
bioRxiv. 2025 Sep 29. pii: 2025.09.29.678932. [Epub ahead of print]

Computational design of pH-sensitive binders.

Green Ahn, Brian Coventry, Ella Haefner, Shayan Sadre, Jenny Hu, Mimosa Van, Buwei Huang, Isaac Sappington, Adam J Broerman, Mauriz A Lichtenstein, Matthias Glögl, Inna Goreshnik, Dionne Vafeados, David Baker.

pH gradients are central to physiology, from vesicle acidification to the acidic tumor microenvironment. While therapeutics have been developed to exploit these pH changes to modulate activity across different physiological environments, current approaches for generating pH-dependent binders, such as combinatorial histidine scanning and display-based selections, are largely empirical and often labor-intensive. Here we describe two complementary principles and associated computational methods for designing pH-dependent binders: (i) introducing histidine residues adjacent to positively charged residues at binder-target interfaces to induce electrostatic repulsion and weaken binding at low pH, and (ii) introducing buried histidine-containing charged hydrogen-bonding networks in the binder core such that the protein is destabilized under acidic conditions. Using these methods, we designed binders that dissociate at acidic pH against ephrin type-A receptor 2, tumor necrosis factor receptor 2, interleukin-6, proprotein convertase subtilisin/kexin type 9, and the interleukin-2 mimic Neo2. Fusions of the designs to pH-independent binders of lysosomal trafficking receptors function as catalytic degraders, inducing target degradation at substoichiometric levels. Our methods should be broadly useful for designing pH-sensitive protein therapeutics.

DOI: https://doi.org/10.1101/2025.09.29.678932
Sci Rep. 2025 Nov 18. 15(1): 40627

Biologically explainable multi-omics feature demonstrates greater learning potential by identifying tissue of origin, stages, and subtypes for pan-cancer classification.

Sana Munquad, Bikash Kumar Dash, Sayan Sengupta, Vishal Singh, Yerra Ushakiran, Asim Bikas Das.

  Cancer is a complex disease characterized by uncontrolled cell growth, which can invade surrounding tissues and spread to distant organs. Most of the conventional methods of diagnosis fails to identify the primary organ when cancer spreads to other organs, thereby adding another level of complexity for cancer detection. It is also critical to determine the stages and subtypes of cancer, and develop a clinically applicable model for precision therapy. With a dataset of 7632 samples from 30 different cancer originating from distinct organs, we have constructed a deep learning framework to solve all of these challenges. We have applied a hybrid feature selection method to identify cancer-associated features in the transcriptome, methylome, and microRNA datasets. This was achieved by combining both gene set enrichment analysis and Cox regression analysis to build an explainable AI model. We performed the early integration using an autoencoder to embed the cancer-associated multi-omics data into a lower-dimensional space; an ANN classifier was constructed using the latent features. In addition to correctly classifying 30 different cancer types by their tissue of origin, our framework also identifies individual subtypes and stages of cancer with an accuracy ranging from 87.31% to 94.0% and 83.33% to 93.64%, respectively. The current model demonstrates higher accuracy even when tested with external datasets, and shows better stability and accuracy in making predictions compared to the existing models. This approach offers explainable strategies for selecting features in AI-based prediction of tumor types for personalized therapy, aiding clinicians in making real-time treatment decisions.

Keywords:  Cancer tissue of origin; Deep-learning; Epigenomics; Genomics; Stage; Subtypes

DOI:  https://doi.org/10.1038/s41598-025-24352-6
Nucleic Acids Res. 2025 Nov 13. pii: gkaf1171. [Epub ahead of print]53(21):

Single-cell mapping of alternative splicing linked to checkpoint immunotherapy response.

Jieyi Xiong, Orian Bricard, Ingrid Arijs, Jonas Demeulemeester, Chen Gu, Bernard Thienpont, Danie Daaboul, Ayse Bassez, Oliver Bechter, Joanna Poźniak, Hanne Vos, Ines Nevelsteen, Sofie Torfs, Sara Aibar Santos, Qing Lan, Yong Hou, Lore Van Oudenhove, Gitta Boons, Junbin Qian, Stein Aerts, Ann Smeets, Jean-Christophe Marine, Diether Lambrechts.

Evidence suggests that alternative RNA splicing (AS) plays a critical role in tumor biology and may contribute to the generation of tumor antigens. Here, we develop a method to detect AS in short-read single-cell 5'-RNA-sequencing data, allowing us to uniquely characterize the heterogeneity and dynamic changes in AS in individual cell types within the tumor microenvironment. We identify numerous splicing events specific to either cancer cells or stromal cell types or for triple-negative versus estrogen receptor-positive breast cancers (BCs). By correlating these splice events with expression of splicing regulators in individual cells, we also identify their potential mediators. For instance, we identify and functionally validate the Epithelial Splicing Regulatory Protein-1 (ESRP1) to drive AS in BCs responding to immune checkpoint blockade (ICB). Prioritization of splicing events based on their likelihood to represent tumor antigens reveals that their aggregated load also correlates with high immune activity in multiple cancers, while also predicting expansion of T cells in BCs receiving ICB and prolonging long-term survival of cancer patients treated with ICB. Collectively, our method provides a framework for analyzing AS in single-cell data and defines a key role for AS in the response to ICB.

DOI: https://doi.org/10.1093/nar/gkaf1171
Nat Commun. 2025 Nov 21.

Desaturase-dependent secretory functions of hepatocyte-like cells control systemic lipid metabolism during starvation in Drosophila.

Jiayi Li, Kerui Huang, Indira Dibra, Ying Liu, Norbert Perrimon, Matias Simons.

Similar to the mammalian hepatocytes, Drosophila oenocytes accumulate fat during fasting, but it is unclear how they communicate with the fat body, the major lipid source. Using a modified protocol for prolonged starvation, we show that knockdown of the sole delta 9 desaturase, Desat1 (SCD in mammals), specifically in oenocytes leads to more saturated lipids in the hemolymph and reduced triacylglycerol storage in the fat body as well as reduced survival. We further show that the insulin antagonist ImpL2 (IGFBP7 in mammals) is secreted from oenocytes during starvation in a Desat1-dependent manner. Flies with oenocyte-specific knockdown and overexpression of ImpL2 exhibit higher and lower sensitivity to starvation, lower and higher triacylglycerol levels as well as higher and lower levels of bmm during starvation, respectively. Overall, this study highlights the importance of Desat1 in maintaining the proper functioning of oenocytes and the central role of oenocytes in the regulation of fat body lipid metabolism during periods of prolonged starvation.

DOI: https://doi.org/10.1038/s41467-025-66571-5