bims-pideca Biomed News
on Class IA PI3K signalling in development and cancer
Issue of 2025–07–27
twelve papers selected by
Ralitsa Radostinova Madsen, MRC-PPU
  1. Optimizing PH Domain-Based Biosensors for Improved Plasma Membrane PIP3 Measurements in Mammalian Cells.
  2. VE-PTP controls a fluid shear stress set point that governs cell morphological responses through Tie-2.
  3. Molecular glues that facilitate RAS binding to PI3Kα promote glucose uptake without insulin.
  4. mTORC1 senses glutamine and other amino acids through GCN2.
  5. A subset of neutrophil phagosomes is characterised by pulses of Class I PI3K activity.
  6. A gain-of-function PIK3CD variant, R512W, impairs T cell function through polyamine-dependent metabolic dysregulation.
  7. High-resolution spatial mapping of cell state and lineage dynamics in vivo with PEtracer.
  8. From Harmony to Discord: Multicellular Coordination in Tissues and Its Rewiring in Cancer.
  9. eIF4A controls translation of estrogen receptor alpha and is a therapeutic target in advanced breast cancer.
  10. PTEN modulates urinary tract infection susceptibility and shapes urothelial antibacterial defenses.
  11. Alternative to the statistical mass confusion of testing for "no effect".
  12. SPIDR enables multiplexed mapping of RNA-protein interactions and uncovers a mechanism for selective translational suppression upon cell stress.
  1. Cells. 2025 Jul 21. pii: 1125. [Epub ahead of print]14(14):
    Optimizing PH Domain-Based Biosensors for Improved Plasma Membrane PIP3 Measurements in Mammalian Cells.
    Amir Damouni, Dániel J Tóth, Aletta Schönek, Alexander Kasbary, Adél P Boros, Péter Várnai.
      Phosphoinositide-binding pleckstrin homology (PH) domains interact with both phospholipids and proteins, often complicating their use as specific lipid biosensors. In this study, we introduced specific mutations into the phosphatidylinositol 3,4,5-trisphosphate (PIP3)-specific PH domains of protein kinase B (Akt) and general receptor for phosphoinositides 1 (GRP1) that disrupt protein-mediated interactions while preserving lipid binding, in order to enhance biosensor specificity for PIP3, and evaluated their impact on plasma membrane (PM) localization and lipid-tracking ability. Using bioluminescence resonance energy transfer (BRET) and confocal microscopy, we assessed the localization of PH domains in HEK293A cells under different conditions. While Akt-PH mutants showed minimal deviations from the wild type, GRP1-PH mutants exhibited significantly reduced PM localization both at baseline and after stimulation with epidermal growth factor (EGF), insulin, or vanadate. We further developed tandem mutant GRP1-PH domain constructs to enhance PM PIP3 avidity. Additionally, our investigation into the influence of ADP ribosylation factor 6 (Arf6) activity on GRP1-PH-based biosensors revealed that while the wild-type sensors were Arf6- dependent, the mutants operated independently of Arf6 activity level. These optimized GRP1-PH constructs provide a refined biosensor system for accurate and selective detection of dynamic PIP3 signaling, expanding the toolkit for dissecting phosphoinositide-mediated pathways.
    Keywords:  ADP ribosylation factor 6 (Arf6); bioluminescence resonance energy transfer (BRET); biosensor; confocal microscopy; general receptor for phosphoinositides 1 (GRP1); phosphatidylinositol 3,4,5-trisphosphate (PIP3); phosphoinositide (PI); pleckstrin homology (PH) domain; protein kinase B (Akt)
    DOI:  https://doi.org/10.3390/cells14141125
  2. Front Cell Dev Biol. 2025 ;13 1603517
    VE-PTP controls a fluid shear stress set point that governs cell morphological responses through Tie-2.
    Keisuke Shirakura, Mana Ghanbarpour Houshangi, Kevin G Peters, Dietmar Vestweber.
      Blood flow differs between arteries and veins, hence endothelial cells in these vessels are exposed to different magnitudes of shear stress. Deviation from physiological blood flow triggers vascular remodeling, with increased or decreased flow leading to outward or inward remodeling, to adjust lumen diameter and thereby re-establish physiological shear stress. Based on this, it is assumed that endothelial cells in different vessels differ in their sensitivity to different shear stress levels. Expression levels of VEGFR3 were previously demonstrated to determine the threshold or set point for endothelial cell type specific shear stress sensitivity. Here we show, that the receptor type tyrosine phosphatase VE-PTP and the tyrosine kinase receptor Tie-2 represent another, new signaling system, that determines sensitivity and cellular responsiveness to different shear stress magnitudes or flow set points. We found that increased shear stress levels cause increased levels of VE-PTP endocytosis, which trigger, a similarly graded increase of Tie-2 activity, stimulation of FOXO1 nuclear exclusion and activation of autophagy. The VE-PTP/Tie-2 signaling mechanism controls cell alignment and elongation dependent on the magnitude of shear stress. In addition, VE-PTP/Tie-2 controls shear stress-induced cellular morphological changes independent of VEGFR2. Thus, VE-PTP/Tie-2 is a novel signaling mechanism which determines shear stress sensitivity and morphological responses of endothelial cells.
    Keywords:  Tie-2; VE-PTP; cell alignment and elongation; shear stress; vascular remodeling
    DOI:  https://doi.org/10.3389/fcell.2025.1603517
  3. Science. 2025 Jul 24. 389(6758): 402-408
    Molecular glues that facilitate RAS binding to PI3Kα promote glucose uptake without insulin.
    Koji Terayama, Shinji Furuzono, Nicole Fer, Wupeng Yan, Lucy C Young, Daniel J Czyzyk, Ruby Goldstein de Salazar, Masato Sasaki, Akihiro Uozumi, Masahiro Konishi, Shoichi Kanda, Yoshitaka Sogawa, Mitsuhiro Yamaguchi, Takashi Tsuji, Junichi Kuroyanagi, Mayumi Hayashi, Yuji Ogura, Dhirendra K Simanshu, Kazuishi Kubota, Jun Tanaka, Frank McCormick.
      While exploring strategies to control blood glucose concentrations in diabetes, we identified so-called molecular glues D223 and D927 that promote glucose uptake in the absence of insulin. They act by increasing the binding affinity of phosphoinositide 3-kinase α (PI3Kα) catalytic subunit p110α to canonical small guanosine triphosphatase RAS proteins and to RRAS, RRAS2, and MRAS by three orders of magnitude. The compounds bind to the RAS-binding domain of p110α, stabilizing the secondary structures of the PI3Kα in a RAS-binding conformation and forming direct interactions with RAS residues tyrosine-40 and arginine-41. In vivo, D927 mimicked the effects of insulin: It rapidly lowered blood glucose concentrations, enhanced glucose metabolism in normal and Zucker fatty rats, and improved hyperglycemia in models of type 1 and type 2 diabetes, even in insulin-deficient diabetic animals.
    DOI:  https://doi.org/10.1126/science.adr9097
  4. EMBO J. 2025 Jul 21.
    mTORC1 senses glutamine and other amino acids through GCN2.
    Gianluca Figlia, Sandra Müller, Fabiola Garcia-Cortizo, Marilena Neff, Glynis Klinke, Gernot Poschet, Aurelio A Teleman.
      mTORC1 promotes cell growth when nutrients such as amino acids are available. While dedicated sensors relaying availability of leucine, arginine and methionine to mTORC1 have been identified, it is still unclear how mTORC1 senses glutamine, one of its most potent inducers. Here, we find that glutamine is entirely sensed through the protein kinase GCN2, whose initial activation is not triggered by depletion of glutamine itself, but by the concomitant depletion of asparagine. In turn, GCN2 leads to a succession of events that additively inhibit mTORC1: within 1 h, GCN2 inhibits mTORC1 through the Rag GTPases, independently of its function as an eIF2α kinase. Later, GCN2-mediated induction of ATF4 upregulates Ddit4 followed by Sestrin2, which together cause additional mTORC1 inhibition. Additionally, we find that depletion of virtually any other amino acid also inhibits mTORC1 through GCN2. GCN2 and the dedicated amino acid sensors thus represent two independent systems that enable mTORC1 to perceive a wide spectrum of amino acids.
    Keywords:  Amino Acid Sensors; Asparagine; GCN2; Glutamine; mTORC1
    DOI:  https://doi.org/10.1038/s44318-025-00505-1
  5. Dis Model Mech. 2025 Jul 22. pii: dmm.052042. [Epub ahead of print]
    A subset of neutrophil phagosomes is characterised by pulses of Class I PI3K activity.
    Clare F Muir, Constantino Carlos Reyes-Aldasoro, Tomasz K Prajsnar, Bartosz J Michno, Justyna Cholewa-Waclaw, Yin X Ho, Audrey Bernut, Catherine A Loynes, Stone Elworthy, Kieran A Bowden, Ashley J Cadby, Lynne R Prince, Jason S King, Felix Ellett, Alison M Condliffe, Stephen A Renshaw.
      Class I PI3kinases coordinate the delivery of microbicidal effectors to the phagosome by forming phosphatidylinositol (3, 4, 5)-trisphosphate (PIP3). However, the dynamics of PIP3 in neutrophils during a live bacterial tissue infection are unknown. We have therefore developed an in vivo, live zebrafish infection model that enables visualisation of dynamic changes in Class 1 PI3kinases (PI3K) signalling on neutrophil phagosomes in real-time. We have identified that on approximately 12% of neutrophil phagosomes PHAkt-eGFP, a reporter for Class 1 PI3K signalling, repeatedly fades and re-recruits in pulsatile bursts. This phenomenon occurred on phagosomes containing live and dead bacteria as well as beads, and was dependent on the activity of the Class 1 PI3K isoform, PI3kinase γ. Detailed imaging suggested that pulsing phagosomes represent neutrophils transiently reopening and reclosing phagosomes, a conclusion supported by observations that a subset of phagosomes in human neutrophils rapidly accumulate dye from the extracellular space. Therefore, we propose that some neutrophil phagosomes remain unsealed and are consequently able to exchange contents with the extracellular environment, with implications for phagosome fate and communication with surrounding cells.
    Keywords:  Neutrophils; Phagocytosis; Phagosome maturation; Phosphatidylinositol (3,4,5)-trisphosphate; Zebrafish
    DOI:  https://doi.org/10.1242/dmm.052042
  6. Biochem Biophys Res Commun. 2025 Jul 17. pii: S0006-291X(25)01093-9. [Epub ahead of print]778 152378
    A gain-of-function PIK3CD variant, R512W, impairs T cell function through polyamine-dependent metabolic dysregulation.
    Kyoko Kiyota, Hiroshi Shiraishi, Shiho Ohno, Yasuhiro Soga, Nobuyuki Shimizu, Hiroyuki Yatsuka, Masanori Inoue, Takashi Takeno, Wang Hongxia, Adiana Mutamsari Witaningrum, Reiko Hanada, Yoshiki Yamaguchi, Kenji Ihara, Toshikatsu Hanada.
      We previously reported a patient harboring a novel heterozygous phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit delta (PIK3CD) missense variant (p.R512W) who presented with autoimmune features including Kawasaki disease, immune thrombocytopenic purpura, and systemic lupus erythematosus, without the classical signs of immunodeficiency typically associated with activated PI3Kδ syndrome (APDS). To elucidate the molecular mechanisms underlying this phenotype, we conducted functional and structural analyses of the R512W variant. Overexpression of mutant human p110δ (R512W) in a murine T cell line resulted in increased PIP3 accumulation and AKT phosphorylation, consistent with a gain-of-function effect. However, T cells expressing R512W exhibited paradoxical dysfunction, including reduced IL-2 production, impaired proliferation, increased PD-1 expression, and apoptosis, which are hallmarks of a T cell exhaustion-like state. A transcriptomic analysis revealed downregulation of polyamine biosynthesis genes, such as Odc1, Amd1, and Smox, along with reduced intracellular polyamine levels. Supplementation of the culture medium with spermidine partially rescued the proliferative defects, suggesting reversible metabolic insufficiency. Structural modeling indicated that R512W may alter the conformation of the helical domain of p110δ, potentially contributing to its hyperactivation. Unlike canonical APDS-associated mutations, the R512W variant appears to uncouple PI3K hyperactivation from effective T cell responses, resulting in immune dysregulation through both signaling and metabolic pathways. This autoimmune-dominant phenotype underscores mutation-specific clinical heterogeneity within the PIK3CD-associated disease spectrum. These findings reveal a novel link between aberrant PI3K signaling and polyamine metabolism, and suggest that targeting metabolic pathways may hold therapeutic potential in select cases of PI3K-driven autoimmunity.
    Keywords:  APDS; PIK3CD; Polyamines; T cell; p110δ
    DOI:  https://doi.org/10.1016/j.bbrc.2025.152378
  7. Science. 2025 Jul 24. eadx3800
    High-resolution spatial mapping of cell state and lineage dynamics in vivo with PEtracer.
    Luke W Koblan, Kathryn E Yost, Pu Zheng, William N Colgan, Matthew G Jones, Dian Yang, Arhan Kumar, Jaspreet Sandhu, Alexandra Schnell, Dawei Sun, Can Ergen, Reuben A Saunders, Xiaowei Zhuang, William E Allen, Nir Yosef, Jonathan S Weissman.
      Charting the spatiotemporal dynamics of cell fate determination in development and disease is a long-standing objective in biology. Here we present the design, development, and extensive validation of PEtracer, a prime editing-based, evolving lineage tracing technology compatible with both single-cell sequencing and multimodal imaging methodologies to jointly profile cell state and lineage in dissociated cells or while preserving cellular context in tissues with high spatial resolution. Using PEtracer coupled with MERFISH spatial transcriptomic profiling in a syngeneic mouse model of tumor metastasis, we reconstruct the growth of individually-seeded tumors in vivo and uncover distinct modules of cell-intrinsic and cell-extrinsic factors that coordinate tumor growth. More generally, PEtracer enables systematic characterization of cell state and lineage relationships in intact tissues over biologically-relevant temporal and spatial scales.
    DOI:  https://doi.org/10.1126/science.adx3800
  8. Cancer Res. 2025 Jul 23.
    From Harmony to Discord: Multicellular Coordination in Tissues and Its Rewiring in Cancer.
    Merve Dede, Vakul Mohanty, Ken Chen.
      Tissue function emerges from coordinated interactions among diverse cell types, but how these interactions are structured and rewired in disease remains unclear. In a recent study, Shi and colleagues introduce CoVarNet, a computational framework that maps reproducible multicellular modules (CMs) across 35 human tissues using single-cell and spatial transcriptomics. These CMs, spanning immune, stromal, and endothelial cells, exhibit functional organization across tissue systems and dynamically respond to biological transitions such as aging and menopause. Importantly, cancer progression is marked by a breakdown of tissue-specific CMs and the emergence of a convergent cancer-associated ecosystem, cCM02. This rewiring reflects a fundamental reorganization of tissue architecture during malignancy and provides new opportunities for diagnostics and therapeutic targeting. The study signifies a conceptual advance from cell-centric to ecosystem-level biology and offers a generalizable framework for integrating multimodal data to dissect tissue-level coordination. Here, we discuss how CoVarNet redefines our understanding of tissue organization, its translational implications in oncology, and unresolved questions in modular tissue biology.
    DOI:  https://doi.org/10.1158/0008-5472.CAN-25-3155
  9. Proc Natl Acad Sci U S A. 2025 Jul 29. 122(30): e2424286122
    eIF4A controls translation of estrogen receptor alpha and is a therapeutic target in advanced breast cancer.
    Jacob A Boyer, Ezra Y Rosen, Malvika Sharma, Madeline A Dorso, Nicholas Mai, Corina Amor, Jason M Reiter, Ram Kannan, Sunyana Gadal, Jianing Xu, Matthew Miele, Zhuoning Li, Xiaoping Chen, Qing Chang, Fresia Pareja, Stephan Worland, Douglas Warner, Sam Sperry, Gary G Chiang, Peggy A Thompson, Guangli Yang, Ouathek Ouerfelli, Alexander Drilon, Elisa de Stanchina, Hans-Guido Wendel, Sarat Chandarlapaty, Neal Rosen.
      Most breast cancers depend on hormone-stimulated estrogen receptor alpha (ER) activity and are sensitive to ER inhibition. Resistance can arise from activating mutations in the gene encoding ER (ESR1) or from reactivation of downstream targets. Newer ER antagonists occasionally show efficacy but are largely ineffective as single agents in the long term. Here, we show that ER translation is eIF4E/cap-independent yet sensitive to inhibitors of the translation initiation factor eIF4A. EIF4A inhibition reduces the expression of ER and cell cycle regulators such as cyclin D1. This leads to growth suppression in ligand-independent breast cancer models, including those driven by ER mutants and fusion proteins. Efficacy is enhanced by adding the ER degrader, fulvestrant. The combination further lowers ER expression and blocks tumor growth in vitro and in vivo. In an early clinical trial (NCT04092673), the eIF4A inhibitor zotatifin was combined with either fulvestrant or fulvestrant plus CDK4 inhibitor, abemaciclib, in patients with acquired resistance to these agents. Multiple clinical responses including a handful of durable regressions were observed, with little toxicity. Thus, eIF4A inhibition could be useful for treating ER+ breast cancer resistant to other modalities.
    Keywords:  breast cancer; eIF4A; estrogen receptor; translation; zotatifin
    DOI:  https://doi.org/10.1073/pnas.2424286122
  10. Life Sci Alliance. 2025 Oct;pii: e202503292. [Epub ahead of print]8(10):
    PTEN modulates urinary tract infection susceptibility and shapes urothelial antibacterial defenses.
    Aaron Simoni, M Skye Bochter, Sarah Linn-Peirano, Kristin Salamon, Brian Becknell, Hanna Cortado, Ashley R Jackson, Laura Schwartz, John David Spencer.
      Despite advancements in our understanding of urinary tract infection (UTI) pathogenesis, UTIs remain a leading cause of morbidity, partly because of an incomplete understanding of the molecular pathways governing bladder antibacterial defenses. Here, we demonstrate that phosphatase and tensin homolog (PTEN), a negative regulator of PI3K/Akt signaling, is a critical modulator of bladder urothelial immune defenses and vulnerability to UTIs caused by uropathogenic Escherichia coli (UPEC). PTEN silencing in human bladder urothelial cells increases susceptibility to UPEC in vitro, and urothelial-specific PTEN knockout mice exhibit increased bacterial titers in the urine, bladder, and kidneys after in vivo transurethral UPEC infection. Mechanistically, PTEN deficiency enhances Akt phosphorylation, amplifying NFκB and FAK activity. Silencing NFκB or FAK in PTEN-deficient cells restores resistance to UPEC. These findings establish PTEN as an important regulator of bladder urothelial defenses, balancing immune activation and urothelial structural integrity to protect against UTI.
    DOI:  https://doi.org/10.26508/lsa.202503292
  11. J Cell Biol. 2025 Aug 04. pii: e202403034. [Epub ahead of print]224(8):
    Alternative to the statistical mass confusion of testing for "no effect".
    Josh L Morgan.
      In cell biology, statistical analysis means testing the hypothesis that there was no effect. This weak form of hypothesis testing neglects effect size, is universally misinterpreted, and is disastrously prone to error when combined with high-throughput cell biology. The solution is for analysis of measurements to start and end with an interpretation of effect size. In this manuscript, I walk through some of the common critiques of significance testing and how they relate to experimental cell biology. I argue that careful consideration of effect size should be returned to its central position in the planning and discussion of cell biological research. To facilitate this shift in focus, I recommend replacing P values with confidence intervals as cell biology's default statistical analysis.
    DOI:  https://doi.org/10.1083/jcb.202403034
  12. Cell. 2025 Jul 21. pii: S0092-8674(25)00743-3. [Epub ahead of print]
    SPIDR enables multiplexed mapping of RNA-protein interactions and uncovers a mechanism for selective translational suppression upon cell stress.
    Erica Wolin, Jimmy K Guo, Mario R Blanco, Isabel N Goronzy, Darvesh Gorhe, Wenzhao Dong, Andrew A Perez, Abdurrahman Keskin, Elizabeth Valenzuela, Ahmed A Abdou, Carl R Urbinati, Ross Kaufhold, H Tomas Rube, Jailson Brito Querido, Mitchell Guttman, Marko Jovanovic.
      RNA-binding proteins (RBPs) regulate all stages of the mRNA life cycle, yet current methods generally map RNA targets of RBPs one protein at a time. To overcome this limitation, we developed SPIDR (split-and-pool identification of RBP targets), a highly multiplexed split-pool method that profiles the binding sites of dozens of RBPs simultaneously. SPIDR identifies precise, single-nucleotide binding sites for diverse classes of RBPs. Using SPIDR, we uncovered an interaction between LARP1 and the 18S rRNA and resolved this interaction to the mRNA entry channel of the 40S ribosome using cryoelectron microscopy (cryo-EM), providing a potential mechanistic explanation for LARP1's role in translational suppression. We explored changes in RBP binding upon mTOR inhibition and identified that 4EBP1 preferentially associates with translationally repressed mRNAs upon mTOR inhibition. SPIDR has the potential to significantly advance our understanding of RNA biology by enabling rapid, de novo discovery of RNA-protein interactions at an unprecedented scale.
    Keywords:  CLIP; LARP1; RNA; RNA-binding proteins; mTOR; ribosome; translation
    DOI:  https://doi.org/10.1016/j.cell.2025.06.042
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