bims-pideca 2025-11-23 papers

bims-pideca

Biomed News

on Class IA PI3K signalling in development and cancer

Issue of 2025–11–23
thirty-one papers selected by
Ralitsa Radostinova Madsen, MRC-PPU

Dietary protein governs the role of insulin signaling in the postprandial regulation of hepatic mTORC1.
AKT as a Therapeutic Target in Cancer.
Adenovirus E4ORF1 activates isoform-specific phosphatidylinositol 3-kinase signaling.
OmniPath: integrated knowledgebase for multi-omics analysis.
Vascular malformations: from genetics to therapeutics.
A new horizon unfolding for insulin signaling in health and disease.
Novel role for PI3Kβ in placental function through regulation of system A amino acid transporter expression, associated with embryonic lethality.
A microscopy-based CRISPR screening platform enables organellar functional genomics and illuminates ciliary biology.
Temporal reassignment and correspondence evaluation with quality control for time-course imaging of 3D cell culture.
Subcellular cartography of the phosphoinositide multiverse.
Phosphatidylserine and RhoB connect phosphatidylinositol 4-phosphate and phosphatidic acid metabolism at the plasma membrane.
Temporal photoproximity labeling of ligand-activated EGFR neighborhoods using MultiMap.
Driving cancer: Motor and adaptor protein dysregulation in endocytic receptor signalling.
FOXO1 links KRAS G12D and G12V alleles to glutamine and nitrogen metabolism in colorectal cancer.
SIGNOR 4.0: the 2025 update with focus on phosphorylation data.
Systems analysis reveals neuregulin-1 control of cardiomyocyte size and shape mediated by distinct PI3K and p38 pathways.
RAF inhibitors activate the integrated stress response by direct activation of GCN2.
Capivasertib-induced diabetic ketoacidosis in a patient with stage IV breast cancer: A case report.
Persistent memory in network topologies following temporary stimuli.
Spatial organization of phosphoinositide signaling.
Benchmarking informatics workflows for data-independent acquisition single-cell proteomics.
Transcriptional network analysis of PTEN-protein-deficient prostate tumors reveals robust stromal reprogramming and signs of senescent paracrine communication.
Synthetic signaling platform uncovers and rewires cellular responses to PD-1 perturbation.
Endothelial Cell Organization Drives Distinct Agonist-Specific Ca2+ Dynamics in Arteries and Veins.
Endothelial senescent-cell-specific clearance alleviates metabolic dysfunction in obese mice.
Mapping drug mechanisms with ProteomicsDB: unified omics and cell sensitivity data at scale.
Focal postnatal deletion of Tsc2 causes epilepsy.
Hepatic zonation determines tumorigenic potential of mutant β-catenin.
Structure-Guided Design of a Highly Selective PI3Kα Inhibitor Overcoming Metabolic Dysregulation with Potent Anti-breast Cancer Efficacy.
Cellular Morphometric Analysis (CellMorph)-a comprehensive imaging-based tool for quantifying cellular phenotype heterogeneity and dynamics across biological processes.
A tumor-selective mRNA system enables precision cancer treatment.

bioRxiv. 2025 Oct 03. pii: 2025.10.01.679861. [Epub ahead of print]

Dietary protein governs the role of insulin signaling in the postprandial regulation of hepatic mTORC1.

Krystle C Kalafut, Yann Cormerais, Madi Y Cissé, Samuel C Lapp, Karen E Inouye, Gökhan S Hotamışlıgil, Brendan D Manning.

The nutrient-sensing mechanistic target of rapamycin complex 1 (mTORC1) signaling pathway controls cellular and organismal growth and metabolism, while aberrant activation is linked to human disease, including metabolic disease. Cellular studies have established several regulatory mechanisms influencing mTORC1 activation, but the physiological signals that control mTORC1 at the organismal and tissue levels are less well defined. mTORC1 is dynamically regulated by fasting and feeding in metabolic tissues, with both nutrients and insulin proposed to activate mTORC1 in response to feeding. Here, a liver-specific mouse model that disconnects mTORC1 activation from AKT-mediated TSC2 phosphorylation is employed. This genetic mouse model demonstrates that AKT-mediated TSC2 phosphorylation is the predominant mechanism of hepatic mTORC1 induction by insulin but is dispensable for activation by feeding. Furthermore, dietary protein is critical and dictates the insulin-responsiveness of hepatic mTORC1 signaling. Contrary to dogma, hepatic mTORC1 signaling was not elevated in response to diet-induced obesity associated with the phenotypes of type-2 diabetes, including hyperinsulinemia, systemic insulin resistance, and hyperglycemia, and blocking hepatic AKT-TSC-mTORC1 signaling did not prevent these metabolic impairments. Evidence is also provided supporting a role for glucagon in hepatic mTORC1 suppression during fasting. This study reveals a hierarchy of physiological signals regulating hepatic mTORC1.

DOI: https://doi.org/10.1101/2025.10.01.679861
Curr Top Microbiol Immunol. 2025 Nov 19.

AKT as a Therapeutic Target in Cancer.

Khine N Myint, Igor Vivanco.

Aberrant activation of the PI3K pathway is one of the commonest oncogenic events in human cancer. AKT is a key mediator of PI3K oncogenic function, and as such, it has been intensively pursued as a therapeutic target. Despite the high frequency of AKT activation in human tumors, the clinical performance of AKT inhibitors remained largely disappointing for many years. However, the recent approval of the AKT inhibitor capivasertib (formerly AZD-5363) for the treatment of breast cancer provides clinical validation of its therapeutic relevance and raises the possibility that AKT inhibitors could still provide clinical benefit either as monotherapy in patients with the rare AKT-E17K mutation or in broader patient populations when combined with other agents. In this chapter, we review the evidence for AKT dependence in human tumors, the importance of genetic and cellular context in AKT dependence, and the challenges of translating AKT inhibition into therapeutic benefit.

DOI: https://doi.org/10.1007/82_2025_334
J Biol Chem. 2025 Nov 13. pii: S0021-9258(25)02799-1. [Epub ahead of print] 110947

Adenovirus E4ORF1 activates isoform-specific phosphatidylinositol 3-kinase signaling.

Fuqiang Geng, Mariko Kobayashi, Yang Lin, Jesus Maria Gomez-Salinero, Dominick Romano, Jean Kanyo, Jennifer Geng, Ying Liu, Michael Ginsberg, Jae-Hung Shieh, Kevin Chen, TuKiet T Lam, Arash Rafii, Sina Y Rabbany, Raphaël Lis, Shahin Rafii.

  The human adenovirus serotype 5 E4ORF1 (Ad5E4ORF1) protein promotes primary endothelial cell survival and angiocrine functions by hijacking the cellular phosphatidylinositol 3-kinase (PI3K)/AKT signaling pathway. However, the mechanism by which E4ORF1 activates PI3K in vascular cells remains largely unknown. Here we show that Ad5E4ORF1 recruits multiple host scaffold proteins, including DLG1, which facilitates AKT activation in response to both Ad5E4ORF1 and endogenous receptor agonists. Furthermore, Ad5E4ORF1 specifically engages the human PI3K isoform p110α-p85β through multi-domain interactions exclusively with p110α. Notably, E4ORF1 proteins from different adenoviral serotypes differentially interact with p110α, resulting in varying levels of AKT activation in endothelial cells. We propose that E4ORF1 specifically recognizes and allosterically activates p110α-p85β via direct multi-site contacts with p110α.

Keywords:  AKT; Adenovirus; DLG1; E4ORF1; angiogenesis; endothelium; phosphatidylinositol-3-kinase

DOI:  https://doi.org/10.1016/j.jbc.2025.110947
Nucleic Acids Res. 2025 Nov 18. pii: gkaf1126. [Epub ahead of print]

OmniPath: integrated knowledgebase for multi-omics analysis.

Dénes Türei, Jonathan Schaul, Nicolàs Palacio-Escat, Balázs Bohár, Yunfan Bai, Francesco Ceccarelli, Elif Çevrim, Macabe Daley, Melih Darcan, Daniel Dimitrov, Tunca Doğan, Daniel Domingo-Fernández, Aurelien Dugourd, Attila Gábor, Lejla Gul, Benjamin A Hall, Charles Tapley Hoyt, Olga Ivanova, Michal Klein, Toby Lawrence, Diego Mañanes, Dezső Módos, Sophia Müller-Dott, Márton Ölbei, Christina Schmidt, Bünyamin Şen, Fabian J Theis, Atabey Ünlü, Erva Ulusoy, Alberto Valdeolivas, Tamás Korcsmáros, Julio Saez-Rodriguez.

Analysis and interpretation of omics data largely benefit from the use of prior knowledge. However, this knowledge is fragmented across resources and often is not directly accessible for analytical methods. We developed OmniPath (https://omnipathdb.org/), a database combining diverse molecular knowledge from 168 resources. It covers causal protein-protein, gene regulatory, microRNA, and enzyme-post-translational modification interactions, cell-cell communication, protein complexes, and information about the function, localization, structure, and many other aspects of biomolecules. It prioritizes literature curated data, and complements it with predictions and large scale databases. To enable interactive browsing of this large corpus of knowledge, we developed OmniPath Explorer, which also includes a large language model agent that has direct access to the database. Python and R/Bioconductor client packages and a Cytoscape plugin create easy access to customized prior knowledge for omics analysis environments, such as scverse. OmniPath can be broadly used for the analysis of bulk, single-cell, and spatial multi-omics data, especially for mechanistic and causal modeling.

DOI: https://doi.org/10.1093/nar/gkaf1126
EMBO Mol Med. 2025 Nov 21.

Vascular malformations: from genetics to therapeutics.

Gabriel Morin, Ilaria Galasso, Guillaume Canaud.

  Vascular malformations (VMs) are congenital disorders characterized by structurally abnormal blood and lymphatic vessels. Advances in genetics have revealed that most sporadic VMs result from post-zygotic variants in genes involved in key endothelial signaling pathways, including the phosphoinositide-3-kinase (PI3K) and the mitogen-associated proliferation kinase (MAPK) pathways. As these variants are shared with cancer, genetics now have theragnostic impact by helping predict relevant targeted therapies. mTOR and PI3Kα inhibitors such as sirolimus and alpelisib have shown promising efficacy in slow-flow VMs, while reports have suggested that MAPK inhibitors such as trametinib may improve arteriovenous malformations. Despite these advances, several challenges remain, including obtaining accurate genetic diagnosis, enhancing treatment efficacy while mitigating drug-related toxicities, and personalizing multimodal treatment strategies. Emerging approaches such as mutant-selective inhibitors, proteolysis-targeting chimeras, and gene therapy hold promises for improving treatment specificity and minimizing adverse effects. This review provides an overview of the genetic bases of VMs, recent advances in targeted therapies, and future directions in the field, highlighting the ongoing evolution of precision medicine for VMs.

Keywords:  Mosaicism; PIK3CA; RAS; Targeted Therapies; Vascular Malformations

DOI:  https://doi.org/10.1038/s44321-025-00344-x
Mol Cell. 2025 Nov 20. pii: S1097-2765(25)00893-7. [Epub ahead of print]85(22): 4111-4113

A new horizon unfolding for insulin signaling in health and disease.

Morris F White.

Wang et al.1 use innovative computational methods to design polypeptides that bind to and activate the insulin receptor tyrosine kinase, revealing strategies to resolve the composite insulin signal into distinct components for therapeutic use.

DOI: https://doi.org/10.1016/j.molcel.2025.10.032
Cell Mol Life Sci. 2025 Nov 19. 82(1): 413

Novel role for PI3Kβ in placental function through regulation of system A amino acid transporter expression, associated with embryonic lethality.

Sarah E Conduit, Cindy X W Zhang, Wayne Pearce, Julie Guillermet-Guibert, Amanda N Sferruzzi-Perri, Bart Vanhaesebroeck.

  The placenta is essential for embryonic development, in part by mediating nutrient transfer from mother to embryo. Placental insufficiency is the most common cause of intrauterine growth restriction which has long-term health consequences lasting into adulthood. p110β is a class IA phosphoinositide 3-kinase (PI3K) catalytic subunit, a family of lipid kinases which are critical regulators of adult metabolism, immunity and embryonic and placental development. However, unlike the other class IA PI3K isoforms, the in vivo functions of p110β remain unclear. While homozygous p110β kinase-dead mice are mostly embryonically lethal, some survive into adulthood with no apparent phenotypes, other than reduced fertility. The mechanism(s) underlying this embryonic lethality remain unclear. Therefore, we performed an in-depth characterisation of p110β kinase-dead embryos, revealing a previously unrecognised role for p110β in controlling the expression of system A amino acid transporters. We show that homozygous p110β kinase-dead embryos are phenotypically normal, but growth-restricted and exhibit placental insufficiency. The placenta is small with a reduced nutrient storing junctional zone and downregulation of the system A amino acid transporters, required for maternal-to-embryo amino acid transfer. These data suggest defective amino acid transfer drives embryonic growth restriction and partial lethality of p110β kinase-dead embryos. This predominantly embryonic p110β phenotype is consistent with the notion that system A amino acid transporters are more critical during development than in adult physiology. The greater significance of p110β in development than in adult homeostasis may also help explain why p110β inhibitors, compared to inhibitors of other PI3K isoforms, are well-tolerated in adults.

Keywords:   PIK3CB ; Drug target; Inhibitor; Nutrient transporters; PI 3-kinase; Placenta

DOI:  https://doi.org/10.1007/s00018-025-05937-w
Dev Cell. 2025 Nov 20. pii: S1534-5807(25)00666-5. [Epub ahead of print]

A microscopy-based CRISPR screening platform enables organellar functional genomics and illuminates ciliary biology.

Jingbo Sun, Irem Sude Atiş, Stéfany L L Empke, Mustafa K Khokha, David K Breslow.

  Microscopy offers an indispensable technique for visualizing biological processes and for defining cytological abnormalities characteristic of disease. However, combining microscopy with the power of pooled CRISPR screening presents considerable technical challenges, hindering application of systematic genetic analysis to imaging-defined phenotypes. Here, we establish a fluorescence microscopy-based CRISPR screening platform that combines ease of implementation with flexible analysis of live-cell or antibody-based molecular markers, including post-translational modifications. Applying this methodology, we systematically identify regulators of primary cilium structure and function in human cells through targeted and genome-wide screens. We further show that integration of screens focused on distinct ciliary phenotypes yields multi-dimensional profiles that delineate precise gene functions. Among the identified hits, TZMP1 (SMIM27) encodes a microprotein at the ciliary transition zone that is required for ciliogenesis in human cells and for ciliary function in Xenopus embryos. More broadly, our approach provides a technological and conceptual strategy for microscopy-based functional genomics.

Keywords:  CRISPR screen; axoneme; cilia; ciliopathy; functional genomics; microprotein; optical screening; polyglutamylation; transition zone

DOI:  https://doi.org/10.1016/j.devcel.2025.10.015
Cell Rep Methods. 2025 Nov 18. pii: S2667-2375(25)00273-5. [Epub ahead of print] 101237

Temporal reassignment and correspondence evaluation with quality control for time-course imaging of 3D cell culture.

Eric M Cramer, Tamara Lopez-Vidal, Jeanette Johnson, Vania Wang, Daniel R Bergman, Ashani Weeraratna, Richard Burkhart, Elana J Fertig, Jacquelyn W Zimmerman, Laura M Heiser, Young Hwan Chang.

  Longitudinal imaging of 3D cell cultures like tumor organoids and spheroids offers crucial insights into cancer progression and treatment. However, spatial displacement during time-course imaging, caused by matrix detachment or experimental artifacts, can confound analyses. We present TRACE-QC, an application of the Procrustes technique to evaluate data integrity and rectify mislabeling in longitudinal imaging of 3D cell culture. Our algorithm integrates permutation-based optimization with Procrustes analysis. By using X and Y coordinates of images, it accurately reorders, matches, and aligns object positions across time points, correcting for global well rotations and translations, along with local spheroid movements. Validation with simulated data confirmed its accuracy and robustness. Applied to longitudinal imaging of tumor spheroids, our algorithm revealed frequent displacement among the spheroids between time points and corrected many mislabeled images. This computationally efficient and adaptable method needs no experimental adjustments and presents a readily accessible solution for data quality control.

Keywords:  3D cell culture; CP: imaging; Procrustes; cancer; extracellular matrix; imaging; organoid; quality control; spheroid; tumor

DOI:  https://doi.org/10.1016/j.crmeth.2025.101237
Biochim Biophys Acta Mol Cell Biol Lipids. 2025 Nov 16. pii: S1388-1981(25)00114-3. [Epub ahead of print] 159706

Subcellular cartography of the phosphoinositide multiverse.

Morgan M C Ricci, Claire C Weckerly, Gerald R V Hammond.

  Phosphoinositides (PPIn) are low-abundance phospholipids that define membrane identity and direct compartment-specific signaling across eukaryotic cells. Marking fifty years since Michell's seminal 1975 review, we re-evaluate how the subcellular localization of these lipids informs their function. Using a historical and mechanistic framework, we survey evidence for the steady-state distribution of all eight PPIn species and their key precursor, phosphatidic acid, emphasizing live-cell biosensor studies and kinase localization. We conclude that PI(4,5)P₂ and PIP₃ signaling remain largely confined to the plasma membrane, whereas PI4P and PI3P occupy distinct but complementary domains of the Golgi and endosomal systems, and PI(3,5)P₂ marks specialized late endosomal compartments. Together, these patterns reveal PPIn as spatial rather than purely temporal signaling molecules-an ATP-derived currency maintaining the ordered heterogeneity of eukaryotic membranes. Understanding how these pathways self-regulate will define the next generation of phosphoinositide biology.

Keywords:  Inositol lipids; Phosphoinositides

DOI:  https://doi.org/10.1016/j.bbalip.2025.159706
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
Nat Chem Biol. 2025 Nov 18.

Temporal photoproximity labeling of ligand-activated EGFR neighborhoods using MultiMap.

Zhi Lin, Wayne Ngo, Yu-Ting Chou, Harry Wu, Katherine J Susa, Young-Wook Jun, Trever G Bivona, Jennifer A Doudna, James A Wells.

Photoproximity labeling proteomics (PLP) methods have recently shown that cell surface receptors can form lateral interactome networks. Here, we present a paired set of PLP workflows that dynamically track neighborhood changes for oncogenic epidermal growth factor receptor (EGFR) over time, both outside and inside of cells. We achieved this by augmenting the multiscale PLP workflow we call MultiMap, where three photoprobes with different labeling ranges were photoactivated by one photocatalyst, eosin Y, anchored extracellularly and intracellularly on EGFR. We identified hundreds of neighboring proteins that changed within minutes to over 1 h after the addition of EGF. These neighborhoods reveal dynamic interactomes during early, middle and late signaling that drive phosphorylation, internalization, degradation and transcriptional regulation. This rapid 'molecular photographic' labeling approach provides snapshots of signaling neighborhoods, revealing their dynamic nature and potential for drug targeting.

DOI: https://doi.org/10.1038/s41589-025-02076-y
Curr Opin Cell Biol. 2025 Nov 17. pii: S0955-0674(25)00136-X. [Epub ahead of print]97 102598

Driving cancer: Motor and adaptor protein dysregulation in endocytic receptor signalling.

David H Kim, Shreya E Boby, Gregory M I Redpath, Vaishnavi Ananthanarayanan.

Receptor tyrosine kinases and other cell surface receptors are tightly regulated by endocytosis, which controls both the duration and spatial organisation of their downstream signalling. In cancers, altered internalisation and trafficking lead to sustained or misrouted signalling that promotes uncontrolled cell growth and survival. Motor proteins and their cargo adaptors are central to receptor signalling since they determine intracellular endosome positioning, recycling, and degradation. While their roles in intracellular transport have long been studied, the dysfunction of motors and adaptors in the context of aberrant receptor signalling and cancer progression has only recently begun to emerge. In this review, we highlight recent advances in understanding motor and adaptor function in healthy cells, discuss evidence implicating these proteins in oncogenic signalling, and consider how these insights may guide future directions in the field.

DOI: https://doi.org/10.1016/j.ceb.2025.102598
EMBO Rep. 2025 Nov 20.

FOXO1 links KRAS G12D and G12V alleles to glutamine and nitrogen metabolism in colorectal cancer.

Suzan Ber, Ming Yang, Marco Sciacovelli, Shamith Samarajiwa, Khushali Patel, Efterpi Nikitopoulou, Annie Howitt, Simon J Cook, Ashok R Venkitaraman, Christian Frezza, Alessandro Esposito.

  Mutations in KRAS, particularly at codon 12, are frequent in adenocarcinomas of the colon, lungs and pancreas, driving carcinogenesis by altering cell signalling and reprogramming metabolism. However, the specific mechanisms by which different KRAS G12 alleles initiate distinctive patterns of metabolic reprogramming are unclear. Using isogenic panels of colorectal cell lines harbouring the G12A, G12C, G12D and G12V heterozygous mutations and employing transcriptomics, metabolomics, and extensive biochemical validation, we characterise distinctive features of each allele. We demonstrate that cells harbouring the common G12D and G12V oncogenic mutations significantly alter glutamine metabolism and nitrogen recycling through FOXO1-mediated regulation compared to parental lines. Moreover, with a combination of small molecule inhibitors targeting glutamine and glutamate metabolism, we also identify a common vulnerability that eliminates mutant cells selectively. These results highlight a previously unreported mutant-specific effect of KRAS alleles on metabolism and signalling that could be potentially harnessed for cancer therapy.

Keywords:  Colorectal Cancer; FOXO Signalling; Glutamine Metabolism; Glutamine Synthase; KRAS Mutation

DOI:  https://doi.org/10.1038/s44319-025-00641-z
Nucleic Acids Res. 2025 Nov 17. pii: gkaf1237. [Epub ahead of print]

SIGNOR 4.0: the 2025 update with focus on phosphorylation data.

Prisca Lo Surdo, Marta Iannuccelli, Klas Karis, Eleonora Meo, Parnian Omidi, Marta Tosoni, Simone Graziosi, Simona Panni, Maria Teresa Fiorillo, Luana Licata, Francesca Sacco, Benjamin M Gyori, Livia Perfetto.

The SIGnaling Network Open Resource (SIGNOR 4.0, https://signor.uniroma2.it) is a database of manually curated causal interactions between biological entities. These signaling events are annotated along with their effect-denoting the activation or inactivation of a target entity-and mechanism through which it is mediated, such as phosphorylation, binding, or transcriptional regulation. The data is freely accessible and can be explored as customizable signaling networks, allowing users to adapt them for different modeling purposes. In our latest update (version 4.0), we improved our curation interface to include additional data-validation tools, integrated text-mining-assisted curation, increased our curation content, and expanded the scope of our curation efforts, with a particular emphasis on phosphorylation data. Furthermore, we developed a subdomain of SIGNOR, PhosphoSIGNOR, a dedicated user interface designed to enable targeted access to phosphorylation-specific information and network visualization. This expanded dataset allows for a more comprehensive mapping of signaling alterations and their associations with dysregulated cellular processes. The platform enables users to dynamically query phosphosite-specific data, examine context-dependent modifications, and integrate findings with known regulatory mechanisms. The PhosphoSIGNOR section of SIGNOR serves as an essential resource for cancer systems biology, offering an intuitive interface for hypothesis generation and mechanistic insights.

DOI: https://doi.org/10.1093/nar/gkaf1237
bioRxiv. 2025 Oct 03. pii: 2025.10.01.679873. [Epub ahead of print]

Systems analysis reveals neuregulin-1 control of cardiomyocyte size and shape mediated by distinct PI3K and p38 pathways.

Pichayathida Luanpaisanon, Philip M Tan, Karen A Ryall, James O'Hearn, Laura A Woo, Bryana N Harris, Bethany Wissmann, Alexander Paap, Matthew Rhoads, Jeffrey J Saucerman.

Cardiac hypertrophy is a common precursor to heart failure, but its cellular manifestations-changes in cardiomyocyte size and shape-are regulated by poorly understood signaling networks. Here, we combined high-content morphological profiling, proteomics, and systems modeling to characterize the diverse forms of hypertrophy induced by angiotensin II, endothelin-1, insulin growth factor-1, and neuregulin-1 (Nrg1). Reverse-phase protein array profiling and partial least squares regression modeling revealed that AKT, GSK3, and MAPK signaling are differentially regulated by hypertrophic agonists and are predictive of distinct phenotypic outcomes. Nrg1 uniquely induced cardiomyocyte elongation in both neonatal rat and human iPSC-derived cardiomyocytes, in addition to increasing cell area. Pharmacological perturbations demonstrated that Nrg1-induced elongation and area expansion both require PI3K activity, whereas p38 selectively mediates cell area. A logic-based network model incorporating dual-specificity phosphatases were sufficient to capture the amplifying PI3K and transient p38 signaling dynamics driving phenotypic changes. Together, these results identify distinct signaling cascades by which Nrg1 coordinates cardiomyocyte size and shape, providing mechanistic insight into how hypertrophic remodeling can be differentially regulated. This systems approach provides new insight into the pathways that drive distinct forms of cardiomyocyte hypertrophy, highlighting opportunities to selectively target maladaptive remodeling in heart failure.
Highlights: Reverse-phase protein arrays capture distinct signatures of cellular signaling in response to diverse hypertrophic ligands.Partial least squares regression model maps proteomic signatures to diverse patterns of cell morphology and gene expression.Neuregulin-1 induces elongation of rodent- and human-derived cardiomyocytes and markers of physiological hypertrophy.PI3K mediates both neuregulin-1-induced elongation and cell area, validating the PLSR model. In contrast, p38 regulates cell area but not elongation.Logic-based model demonstrates that the characterized mechanisms are sufficient to predict how distinct PI3K and p38 dynamics drive size and shape.

DOI: https://doi.org/10.1101/2025.10.01.679873
Nat Commun. 2025 Nov 17. 16(1): 10033

RAF inhibitors activate the integrated stress response by direct activation of GCN2.

Rebecca Gilley, Andrew M Kidger, Graham Neill, Eve Morrison, Paul Severson, Dominic P Byrne, Niall S Kenneth, Gideon Bollag, Chao Zhang, Taiana Maia de Oliveira, Patrick A Eyers, Richard Bayliss, Glenn R Masson, Simon J Cook.

Paradoxical activation of wild type RAF by chemical RAF inhibitors (RAFi) is a well-understood 'on-target' biological and clinical response. In this study, we show that a range of RAFi drive ERK1/2-independent activation of the Unfolded Protein Response (UPR), including expression of ATF4 and CHOP, that requires the translation initiation factor eIF2α. RAFi-induced ATF4 and CHOP expression was not reversed by inhibition of PERK, a known upstream activator of the eIF2α-dependent Integrated Stress Response (ISR). Rather, RAFi exposure activated GCN2, an alternate eIF2α kinase, leading to eIF2α-dependent (and ERK1/2-independent) ATF4 and CHOP expression. The GCN2 kinase inhibitor A-92, GCN2 RNAi, GCN2 knock-out or ISRIB (an eIF2α antagonist) all reversed RAFi-induced expression of ATF4 and CHOP indicating that RAFi require GCN2 to activate the ISR. RAFi also activated full-length recombinant GCN2 in vitro and in cells, generating a characteristic 'bell-shaped' concentration-response curve, reminiscent of RAFi-driven paradoxical activation of WT RAF dimers. Activation of the ISR by RAFi was abolished by a GCN2 kinase dead mutation. A M802A GCN2 gatekeeper mutant was activated at lower RAFi concentrations, demonstrating that RAFi bind directly to the GCN2 kinase domain; this is supported by mechanistic structural models of RAFi interaction with GCN2. Since the ISR is a critical pathway for determining cell survival or death, our observations may be relevant to the clinical use of RAFi, where paradoxical GCN2 activation is a previously unappreciated off-target effect that may modulate tumour cell responses.

DOI: https://doi.org/10.1038/s41467-025-65376-w
Am J Health Syst Pharm. 2025 Nov 15. pii: zxaf312. [Epub ahead of print]

Capivasertib-induced diabetic ketoacidosis in a patient with stage IV breast cancer: A case report.

Payton Mueller, Zoanne Harlas, John Carr.

   PURPOSE: Capivasertib is a selective pan-protein kinase B (AKT) inhibitor for hormone receptor-positive breast cancer. Cellular phosphoinositide 3-kinase and AKT activity plays an important role in glucose homeostasis. Additionally, AKT has a role in regulating hepatic glycogenolysis and glucose uptake via glycogen synthase kinase-3. Previous studies have found the incidence of hyperglycemia with capivasertib to be 13% to 49%.
SUMMARY: We report the case of a 74-year-old female with capivasertib-associated diabetic ketoacidosis (DKA) with evidence of extreme insulin resistance. The patient was started on capivasertib for stage IV breast cancer and experienced hyperglycemia 8 days after resuming the medication. Her initial blood glucose level was 632 mg/dL, with an anion gap of 29 mEq/L and a pH of 7.22. She was managed according to the institution's DKA protocol with a peak insulin infusion rate of 130 units/h (1.76 units/kg/h). The patient's blood glucose level improved after 40 hours on the continuous insulin drip, and she was discharged after 10 days with a prescription for sliding scale insulin and the instruction to discontinue capivasertib.
CONCLUSION: This case report provides evidence of extreme insulin resistance in a patient treated with capivasertib. Guidance on the management of acute hyperglycemia secondary to capivasertib is not currently established, and further research on optimal management of these acute crises is needed.

Keywords:  capivasertib; diabetic ketoacidosis; hyperglycemia; insulin resistance; phosphoinositide 3-kinases; protein kinase B

DOI:  https://doi.org/10.1093/ajhp/zxaf312
iScience. 2025 Nov 21. 28(11): 113765

Persistent memory in network topologies following temporary stimuli.

Federico Sevlever, Ariel Waisman, Santiago Miriuka, Alejandra C Ventura.

  Molecular memory in signaling and gene regulatory networks shapes how cells respond to transient inputs. Here, we present a mathematical framework to quantify memory as changes in system state after temporary stimulation. Using computational models, we show that circuits with positive feedback loops, particularly those enabling bistability, sustain long-term memory, while certain negative feedbacks can erase it. We further identify minimal network motifs that reliably confer memory, revealing symmetry between activating and inactivating mechanisms. In addition, oscillatory circuits can encode memory even without positive feedback, storing information in the phase of their oscillations. Applying this approach to mouse embryonic stem cells exposed to transient differentiation cues, we find that different genes display distinct degrees of memory retention, with some reflecting partial reversion and others indicating commitment to differentiation. This framework provides a unified way to compare memory across systems and highlights how circuit architecture influences information storage in biology.

Keywords:  Bioinformatics; Computermodeling; Systems biology

DOI:  https://doi.org/10.1016/j.isci.2025.113765
FEBS Lett. 2025 Nov 17.

Spatial organization of phosphoinositide signaling.

Siyu Lai, Wenbo Huang, Kangmin He.

  Mammalian cells express seven distinct phosphoinositide species: PI(3)P, PI(4)P, PI(5)P, PI(3,4)P2, PI(3,5)P2, PI(4,5)P2, and PI(3,4,5)P3. With the rapid development of labeling, imaging, and manipulation tools, our understanding of the spatial distribution, functions, and regulation of these phosphoinositides has advanced significantly. Tightly regulated by lipid kinases, phosphatases, and lipid transfer proteins, each phosphoinositide exhibits a unique yet dynamic spatial distribution at both subcellular and suborganelle levels. This distinct spatial organization is critical for controlling membrane trafficking, defining organelle identity and function, mediating signal transduction, and supporting other essential cellular processes. Dysregulation of spatial phosphoinositide signaling has been linked to various human diseases. In this review, we provide a brief overview of current insights into the spatial organization of phosphoinositide signaling, highlighting its key roles in regulating membrane dynamics and signal transduction at the plasma membrane, endosomes and lysosomes, the Golgi apparatus, the ER, and the nucleus.

Keywords:  endosome; nucleus; phosphoinositide; plasma membrane; signaling; spatial organization

DOI:  https://doi.org/10.1002/1873-3468.70227
Nat Commun. 2025 Nov 21. 16(1): 10276

Benchmarking informatics workflows for data-independent acquisition single-cell proteomics.

Jianwei Wang, Yi Huang, Fanghua Lu, Qinqin Xu, Zhuo Yang, Yirong Jiang, Shaowen Shi, Jianzhang Pan, Yi Yang, Qun Fang.

Recent years have seen a rise of single-cell proteomics by data-independent acquisition mass spectrometry (DIA MS). While diverse data analysis strategies have been reported in literature, their impact on the outcome of single-cell proteomic experiments has been rarely investigated. Here, we present a framework for benchmarking data analysis strategies for DIA-based single-cell proteomics. This framework provides a comprehensive comparison of popular DIA data analysis software tools and searching strategies, as well as a systematic evaluation of method combinations in subsequent informatic workflow, including sparsity reduction, missing value imputation, normalization, batch effect correction, and differential expression analysis. Benchmarking on simulated single-cell samples consisting of mixed proteomes and real single-cell samples with a spike-in scheme, recommendations are provided for the data analysis for DIA-based single-cell proteomics.

DOI: https://doi.org/10.1038/s41467-025-65174-4
Mol Oncol. 2025 Nov 17.

Transcriptional network analysis of PTEN-protein-deficient prostate tumors reveals robust stromal reprogramming and signs of senescent paracrine communication.

Ivana Rondon-Lorefice, Jose I Lopez, Aitziber Ugalde-Olano, Maite Zufiaurre, Ianire Astobiza, Natalia Martin-Martin, Laura Bozal-Basterra, Saioa Garcia-Longarte, Amaia Zabala-Letona, Sofia Rey, Aida Santos-Martin, Miguel Unda, Ana Loizaga-Iriarte, Mariona Graupera, Paolo Nuciforo, Arkaitz Carracedo, Isabel Mendizabal.

  Among the extensive genomic alterations in prostate cancer, phosphatase and tensin homolog (PTEN) deletion stands out as one of the most consistently observed events. PTEN loss in prostate tumors is primarily associated with cancer-cell proliferation and survival through the activation of the phosphoinositide 3-kinase (PI3K)-protein kinase B (AKT)-mechanistic target of rapamycin (mTOR) (PI3K-AKT-mTOR) signaling pathway. However, the use of PTEN as a robust biomarker in clinical practice is hampered by its complex epigenetic, transcriptional and post-translational regulation. In situ protein assessment by immunohistochemistry (IHC) captures PTEN protein status, but it does not report on associated tumor microenvironment remodeling. Here, we undertook an approach that combined PTEN immunoreactivity analysis with high-throughput transcriptional analysis to gain insights into the downstream functional effects of PTEN protein loss in primary tumors. Our extensive bioinformatic analyses highlighted stromal remodeling as a prominent cancer cell-extrinsic process associated with PTEN loss. By extending our transcriptomic computational strategy to Pten loss-driven murine prostate cancer, we validated the causal role of Pten in the stromal reaction observed in clinical specimens. Mechanistically, we provide experimental evidence for the activation of a paracrine program that encompasses enhanced transforming growth factor beta (TGF-β) signaling and that is compatible with the secretome of PTEN-deficient senescent cancer cells. Finally, our findings enable the sub-stratification of tumors with PTEN loss based on their senescence-associated stroma remodeling program to distinguish indolent from aggressive cases. Our study provides relevant biological context to the cellular and molecular alterations unleashed upon PTEN protein loss in prostate cancer.

Keywords:  PTEN protein loss; prostate cancer; stratification; stromal remodeling

DOI:  https://doi.org/10.1002/1878-0261.70164
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
Acta Physiol (Oxf). 2025 Dec;241(12): e70132

Endothelial Cell Organization Drives Distinct Agonist-Specific Ca2+ Dynamics in Arteries and Veins.

M D Lee, R A Clark, C Buckley, X Zhang, P Uhlen, C Wilson, J G McCarron.

   AIM: The endothelium regulates cardiovascular function by detecting and interpreting multiple extracellular signals from blood and surrounding tissues, even when these inputs are complex and conflicting. The major challenge faced by the endothelium is decoding this dynamic chemical environment to produce coordinated endothelial cellular responses. In addition to the problems of detection, extracellular signals must be processed correctly intracellularly to generate a functional outcome.
METHODS: Ca2+ imaging, network analysis and spectral graph theory across ~1000 endothelial cells in intact arteries and veins.
RESULTS: The venous endothelial cell population forms distinct, non-overlapping communities, each tuned to specific agonists. Within these communities, responsive cells act as bridges, linking members through the most direct communication route. Activation of one cell increases the likelihood of activation occurring in its neighbors, creating localized zones of high responsiveness. Only a small (5%) subset of cells responds to multiple activators. These multifunctional cells form unique connections that integrate and distribute signals between the agonist-specific sensing communities. We also show that different agonists elicit unique signaling patterns determined by the stimulus, not by intrinsic cellular properties. Finally, signal decoding strategies differ across vascular beds: venous endothelial cells rely on Ca2+ signal frequency, while arterial cells use signal amplitude.
CONCLUSION: The endothelium comprises functionally specialized populations. A small subset of pharmacologically distinct cells plays a key role in signal integration. These hubs are especially vulnerable to disconnection and dysfunction in disease, highlighting them as potential therapeutic targets. The findings presented reveal specialized encoding strategies that distinguish the arterio-venous axis.

Keywords:  arteries; calcium imaging; endothelial signaling; hub cells; network analysis; veins

DOI:  https://doi.org/10.1111/apha.70132
Cell Metab. 2025 Nov 20. pii: S1550-4131(25)00443-7. [Epub ahead of print]

Endothelial senescent-cell-specific clearance alleviates metabolic dysfunction in obese mice.

Masayoshi Suda, Selim Chaib, Larissa G P Langhi Prata, Yi Zhu, Utkarsh Tripathi, Karl H Paul, Allyson K Palmer, Tamar Pirtskhalava, Vagisha Kulshreshtha, Christina L Inman, Kurt O Johnson, Nino Giorgadze, Runqing Huang, Carolyn M Roos, Luisa F Leon-Sanchez, Jordan D Miller, Thomas White, Linshan Laux, Laura J Niedernhofer, Paul D Robbins, Sara Espinoza, Nicolas Musi, Sundeep Khosla, Stefan G Tullius, Tamar Tchkonia, James L Kirkland.

  Accumulation of senescent cells is a key contributor to multiple diseases across the lifespan, including metabolic dysfunction. We previously demonstrated that elimination of senescent cells using senolytic drugs alleviates obesity-induced metabolic dysfunction. However, the contribution of senescent endothelial cells to metabolic disorders remains elusive. Hence, we crossed mice that allow selective elimination of senescent cells (p16Ink4a-LOX-ATTAC mice) with Tie2-Cre mice (Tie2-Cre;p16Ink4a-LOX-ATTAC) to enable identification and inducible, selective elimination of p16Ink4a+ senescent endothelial cells. Targeted removal of senescent endothelial cells from obese Tie2-Cre;p16Ink4a-LOX-ATTAC mice attenuated the pro-inflammatory senescence-associated secretory phenotype and alleviated metabolic dysfunction. Conversely, transplanting senescent endothelial cells into lean mice caused adipose tissue inflammation and metabolic dysfunction. Consistent with these findings, the senolytic, fisetin, which targets senescent endothelial cells among other senescent cell types, reduced adipose tissue senescent endothelial cell abundance and improved glucose metabolism in obese mice or mice transplanted with senescent mouse endothelial cells. Our results indicate that specifically eliminating p16Ink4a+ senescent endothelial cells is a potential therapeutic strategy for metabolic disease.

Keywords:  SASP factors; TNFα; cellular senescence; diabetes; endothelial cells; fisetin; glucose intolerance; obesity; p16(Ink4a); senolytics

DOI:  https://doi.org/10.1016/j.cmet.2025.10.009
Nucleic Acids Res. 2025 Nov 17. pii: gkaf1265. [Epub ahead of print]

Mapping drug mechanisms with ProteomicsDB: unified omics and cell sensitivity data at scale.

Mario Picciani, Armin Soleymaniniya, Julian Müller, Amirhossein Sakhteman, Konstantinos Tzanakis, Judith Bernett, Elias Kahl, Firas Hamood, Johannes Kersting, Mohsen Pourjam, Luis Augusto Eijy Nagai, Markus List, Bernhard Kuster, Matthew The, Mathias Wilhelm.

Proteomic and phenotypic cell sensitivity datasets are increasingly important for understanding chemoproteomics and the underlying drug mechanisms of action. Yet, integrating such heterogeneous datasets remains challenging due to inconsistent annotations, incompatible IDs, and variable data processing methods. Here, a major update to ProteomicsDB (https://www.proteomicsdb.org) is presented that combines over 1300 proteomic and 1000 transcriptomic profiles with phenotypic cell sensitivity data across >1500 human cancer cell lines and 1470 drugs. Harmonizing cell line and drug names and applying a standardized normalization and refitting pipeline for dose-response curves enables consistent, statistically robust analysis across studies. Three new graphical user interfaces support interactive exploration of cell sensitivity data, exploring the protein targets and dose-resolved changes in protein expression in the presence of a drug, and comparing the expression profiles of cell lines. With this update, ProteomicsDB is strengthening its future role as a central hub for proteomics and multi-omics, providing researchers with a unified framework to explore phenotypic cell sensitivity in combination with dose-resolved expression proteomics at the molecular level, supporting biomarker discovery, drug repurposing, and precision medicine applications.

DOI: https://doi.org/10.1093/nar/gkaf1265
Front Mol Neurosci. 2025 ;18 1686023

Focal postnatal deletion of Tsc2 causes epilepsy.

Carlie McCoy, Mary Dusing, Lilian G Jerow, Grace C Winstel, Felix Zhan, Jason L Rogers, Madison Wesley, J Brian Otten, Steve C Danzer, Candi L LaSarge.

   Introduction: Tuberous sclerosis complex (TSC) is a genetic disorder caused by mutations in either the TSC1 or TSC2 genes. These mutations prevent the TSC1/TSC2 protein complex from forming, resulting in hyperactivation of the mechanistic target of rapamycin (mTOR) cell growth and protein synthesis pathway. Epilepsy is one of the most common neurological symptoms in TSC patients, often associated with focal cortical lesions. However, it is not fully established whether such focal abnormalities are sufficient on their own to generate seizures and associated behavioral deficits. Here, we created a novel mouse model to test the hypothesis that a focal, postnatal deletion of Tsc2 from cortical neurons is sufficient to induce an epileptogenic network and produce behavioral changes relevant to TSC.
Methods: Tsc2 was deleted from neurons in a focal area of the frontal cortex in Tsc2 fl/fl (fTSC2 KO) mice following neonatal bilateral AAV9-CaMKII-Cre-mCherry injections on postnatal day 2. One group of adult fTSC2 KO and Tsc2 wt/wt (control) mice was implanted with cortical electrodes for combined video-EEG monitoring. A separate group of control and fTSC2 KO mice, injected with a lower viral titer, underwent video recording and behavioral exploration analysis in a novel environment. Tissue was collected for histology.
Results: All adult fTSC2 KO mice implanted with cortical electrodes had seizures, whereas no control mice did. Histological analyses showed that virally infected cells in fTSC2 KO mice had enlarged somas and increased mTOR activation (pS6 expression). These fTSC2 KO mice also had decreased parvalbumin and somatostatin interneuron densities in the surrounding cortex. fTSC2 KO mice displayed increased anxiety-like behaviors, spending significantly less time in the center of the novel environment compared to controls.
Conclusion: A focal, postnatal deletion of Tsc2 from cortical neurons is sufficient to cause both epilepsy and behavioral deficits in mice. This model recapitulates key phenotypes of TSC, including abnormal cell growth, reduced inhibitory cell density, and increased microglia activation. This fTSC2 KO model is advantageous for delineating the cortical changes that support epilepsy and behavioral deficits in TSC, and for investigating possible targets for therapeutic intervention.

Keywords:  cortical development; epileptogenesis; mTOR; parvalbumin; somatostatin; tuberous sclerosis complex

DOI:  https://doi.org/10.3389/fnmol.2025.1686023
Nature. 2025 Nov 19.

Hepatic zonation determines tumorigenic potential of mutant β-catenin.

Alexander Raven, Kathryn Gilroy, Hu Jin, Joseph A Waldron, Holly Leslie, June Munro, Holly Hall, Rachel A Ridgway, Catriona A Ford, Doga C Gulhan, Nikola Vlahov, Megan L Mills, Andrew Hartley, Eve Anderson, Sheila Bryson, Nathalie Sphyris, Miryam Müller, Stephanie May, Barbara Cadden, Colin Nixon, Scott H Waddell, Rachel Guest, Luke Boulter, Nick Barker, Hans Clevers, Hao Zhu, Johanna Ivaska, Douglas Strathdee, Crispin J Miller, Nigel B Jamieson, Martin Bushell, Peter J Park, Thomas G Bird, Owen J Sansom.

Oncogenic mutations in phenotypically normal tissue are common across adult organs1,2. This suggests that multiple events need to converge to drive tumorigenesis and that many processes such as tissue differentiation may protect against carcinogenesis. WNT-β-catenin signalling maintains zonal differentiation during liver homeostasis3,4. However, the CTNNB1 oncogene-encoding β-catenin-is also frequently mutated in hepatocellular carcinoma, resulting in aberrant WNT signalling that promotes cell growth5,6. Here we investigated the antagonistic interplay between WNT-driven growth and differentiation in zonal hepatocyte populations during liver tumorigenesis. We found that β-catenin mutations co-operate with exogenous MYC expression to drive a proliferative translatome. Differentiation of hepatocytes to an extreme zone 3 fate suppressed this proliferative translatome. Furthermore, a GLUL and Lgr5-positive perivenous subpopulation of zone 3 hepatocytes were refractory to WNT-induced and MYC-induced tumorigenesis. However, when mutant CTNNB1 and MYC alleles were activated sporadically across the liver lobule, a subset of mutant hepatocytes became proliferative and tumorigenic. These early lesions were characterized by reduced WNT pathway activation and elevated MAPK signalling, which suppresses zone 3 differentiation. The proliferative lesions were also dependent on IGFBP2-mTOR-cyclin D1 pathway signalling, in which inhibition of either IGFBP2 or mTOR suppressed proliferation and tumorigenesis. Therefore, we propose that zonal identity dictates hepatocyte susceptibility to WNT-driven tumorigenesis and that escaping WNT-induced differentiation is essential for liver cancer.

DOI: https://doi.org/10.1038/s41586-025-09733-1
J Med Chem. 2025 Nov 17.

Structure-Guided Design of a Highly Selective PI3Kα Inhibitor Overcoming Metabolic Dysregulation with Potent Anti-breast Cancer Efficacy.

Yi Hou, Han Qin, Xinqing Zheng, Yasheng Zhu, Xiao Wang, Liping Wang, Wenjian Min, Shuyang Cao, Peng Yang.

Targeting oncogenic PI3Kα activation in PIK3CA-mutated breast cancer remains challenging due to metabolic toxicities of existing inhibitors. To address this, we designed A32, a novel PI3Kα-selective inhibitor, via scaffold hybridization and systematic optimization. A32 exhibited exceptional potency (PI3Kα IC50 = 2.5 nM) and selectivity (>400-fold over class I PI3K isoforms/mTOR). It operates through a dual mechanism: inhibiting PI3Kα kinase activity and selectively degrading the H1047R mutant p110α protein. In vitro, A32 showed robust antiproliferative activity (T47D IC50 = 157 nM; MCF7 IC50 = 373 nM), suppressed PI3K/AKT/mTOR signaling, induced G1 arrest, and inhibited migration. In vivo, A32 (100 mg/kg, p.o.) achieved 70.7% tumor growth inhibition in T47D xenografts, outperforming alpelisib (58.6%), without significant toxicity. Crucially, A32 (50 mg/kg) markedly reduced hyperglycemia risk versus alpelisib and displayed favorable pharmacokinetics. These findings establish A32 as a potent, selective, and metabolically safe PI3Kα inhibitor with a promising therapeutic profile.

DOI: https://doi.org/10.1021/acs.jmedchem.5c02352
FEBS J. 2025 Nov 18.

Cellular Morphometric Analysis (CellMorph)-a comprehensive imaging-based tool for quantifying cellular phenotype heterogeneity and dynamics across biological processes.

Henrique Quaiato de Oliveira, Solon Andrades da Rosa, Luiza Cherobini Pereira, Laura Boose de Mendonça, Juliete Scholl, Fabrício Figueiró, Thais Cardoso Bitencourt, Davi Piovesan Echevarria, João Luiz Aldinucci Buzzo, Jessica Boschini D'Agostin, Danieli Rosane Dallemole, Carolina Oliveira, Fernanda Simas, Fernanda Saez-Calazans, Débora Santos-Sousa, Guido Lenz, Eduardo C Filippi-Chiela.

  Understanding eukaryotic cell morphometry is fundamental to cell biology, as cells exhibit a broad range of sizes and shapes during processes such as senescence, cell death, mitosis, and migration. Dynamic changes in subcellular compartments and protein distribution also occur, impacting cytoplasmic and nuclear characteristics. Traditional measurement methods are often limited, highlighting the need for alternatives that comprehensively integrate data from both the cytosol and nuclei while tracking individual live cells over time. To address these limitations, we developed Cellular Morphometric Analysis (CellMorph), a novel tool designed to objectively assess multiple features of individual eukaryotic cells, including cell size, shape, cytosolic staining, and morphometry. CellMorph can analyze bright-field and fluorescent images, accommodating both nonstained cells and those expressing fluorescent reporters or chromogenic labels. We validated the tool using various cellular models and specific staining protocols that target fundamental processes such as apoptosis, autophagy, and senescence. CellMorph captures the intricate heterogeneity within cell populations by providing a multidimensional perspective on individual cellular features and their differential responses to various stresses. This capability to track phenotypic changes over time makes CellMorph particularly valuable for studying dynamic cellular responses. Detailed morphometric data are essential for investigating cellular behavior in pathogenic processes and responses to stressors, including therapies or environmental changes. By integrating multiple parameters, CellMorph represents a significant advancement in cell biology, offering researchers a powerful tool to explore the complexities of cellular morphometry effectively.

Keywords:  cell biology tool; cell state; cellular morphometry; phenotypic dynamic; single‐cell biology

DOI:  https://doi.org/10.1111/febs.70339
Mol Ther. 2025 Nov 15. pii: S1525-0016(25)00954-2. [Epub ahead of print]

A tumor-selective mRNA system enables precision cancer treatment.

Magdalena M Żak, Jimeen Yoo, Alberto Utrero-Rico, Wencke Walter, Gayatri Mainkar, Matthew Adjmi, Ann Anu Kurian, Ashikur Rahaman, Daniel Lozano Ojalvo, Jordi Ochando, Torsten Haferlach, Ramon E Parsons, Filip K Swirski, Lior Zangi.

mRNA has revolutionized vaccine development, demonstrating high efficacy and safety in COVID-19 vaccines, and is now being explored for broader therapeutic applications. However, while vaccines rely on widespread antigen expression, many therapeutic strategies-particularly in oncology-require precise, cell-selective gene expression. Here, we present the Selective modRNA Translation System (SMRTS), a versatile, engineered mRNA system that enables targeted gene expression in specific cell populations. As a proof of concept, we developed cancer-specific variants, bcSMRTS and ccSMRTS, for breast and colon cancer, respectively. Systemic delivery of lipid nanoparticle (LNP)-encapsulated SMRTS constructs yielded a 114-fold and 141-fold increase in tumor-specific expression in 4T1 and MC-38 models, respectively, while reducing off-target expression by over 380-fold. Therapeutic deployment of Pten ccSMRTS suppressed tumor growth by 45%, and combination with modRNA-derived anti-checkpoint inhibitor antibodies (modRNAbs) resulted in up to 93% tumor inhibition. Beyond oncology, SMRTS introduces a novel mRNA tool, providing a versatile system for cell-selective gene expression. By expanding the mRNA therapeutics toolbox, SMRTS paves the way for precise mRNA-based interventions across a wide range of disease settings.

DOI: https://doi.org/10.1016/j.ymthe.2025.11.015