bims-pideca Biomed News
on Class IA PI3K signalling in development and cancer
Issue of 2026–07–26
eighteen papers selected by
Ralitsa Radostinova Madsen, MRC-PPU



  1. Cancer Sci. 2026 Jul 19.
      PTEN (phosphatase and tensin homolog deleted on chromosome ten) is a tumor suppressor, the function of which is impaired in many diverse cancers. It has phosphoinositide lipid phosphatase activity by which it suppresses activation of the oncogenic PI3K signaling network but in vitro also displays activity against protein substrates and is able to auto-dephosphorylate its Thr366 residue. Here we generate germline knock-in mice expressing PTEN-Y138L, a mutant enzyme which selectively lacks protein phosphatase activity and retains lipid phosphatase activity. Homozygous PtenY138L/Y138L mice die in utero before E10.5. Primary MEFs and thymocytes with only a single PtenY138L allele display normal low levels of AKT phosphorylation indicating effective regulation of PI3K signaling by endogenous PTEN-Y138L in vivo. Heterozygous Pten+/Y138L mice have reduced overall survival compared to wild-type littermates and develop tumors in multiple organs. Our data imply that in addition to its lipid phosphatase activity, the protein phosphatase activity of PTEN is also required for normal embryonic development and tumor suppression.
    Keywords:  AKT; PI3K; PTEN; mice; phosphatase
    DOI:  https://doi.org/10.1111/cas.70476
  2. J Cell Biol. 2026 Sep 07. pii: e202604036. [Epub ahead of print]225(9):
      Primordial germ cells (PGCs) are the first cells specified in the Drosophila embryo and are precursors to the germline. Their formation requires suppression of somatic fates, achieved by degrading the receptor tyrosine kinase Torso at the posterior pole through the ubiquitin ligase adaptor germ cell-less (GCL). Although Torso is known to antagonize PGC formation, the underlying mechanisms remained unclear. Here, we combine optogenetic Ras activation and Ras effector loop mutants to show that Ras suppresses PGC formation independently of the canonical Raf/MEK/ERK pathway. We identify an unexpected early role for Torso in activating phosphoinositide 3-kinase (PI3K), generating membrane domains enriched in phosphatidylinositol (3,4,5)-trisphosphate (PIP3). Elevated PI3K activity disrupts PGC formation, while reduced PI3K activity creates ectopic PGCs. We demonstrate that GCL remodels the posterior pole membrane by suppressing Torso-dependent PI3K activation. Clearing PIP3 enables myosin II enrichment, allowing for PGC formation. Together, our findings reveal how antagonistic Torso and GCL activities establish the soma-germline boundary by organizing cortical lipids.
    DOI:  https://doi.org/10.1083/jcb.202604036
  3. Sci Rep. 2026 Jul 19.
      The epidermal growth factor receptor (EGFR) and hepatocyte growth factor receptor (c-Met/MET) are receptor tyrosine kinases (RTKs) whose signalling depends on endocytic routing, and impaired down-regulation can drive tumour progression and therapy resistance, including MET-driven bypass of EGFR inhibition. However, how routing states couple to signalling and lipid programs, and how this differs between receptors under matched conditions, remains unclear. Using a chemically diverse annotated inhibitor library, we performed time-resolved, pathway-focused high-content imaging in A549 cells to compare co-varying phenotypes across matched EGFR and c-Met assay systems. Late receptor persistence defined operational degradation-inhibitor phenotypes that were heterogeneous and dispersed across a fused phenotypic atlas. Despite this heterogeneity, matched degradation-inhibitor sets showed receptor-selective lipid-trafficking coupling: EGFR persistence was associated with reduced phosphatidylinositol 4,5-bisphosphate-linked readouts and signalling biases, whereas c-Met persistence aligned with increased perinuclear phosphatidylinositol 4-phosphate heterogeneity and altered transferrin-recycling readouts. These results provide a comparative imaging framework for mapping RTK trafficking states and nominate phosphoinositide-linked features as candidate readouts of trafficking rewiring in cancer-relevant contexts.
    Keywords:  Cell Painting; EGFR; Endocytic trafficking; High-content screening; Phosphoinositides; c-Met/MET
    DOI:  https://doi.org/10.1038/s41598-026-61308-w
  4. Dev Cell. 2026 Jul 21. pii: S1534-5807(26)00240-6. [Epub ahead of print]
      Inflammation in the pancreas drives acinar-to-ductal metaplasia (ADM), a progenitor-like state that can be hijacked by mutant Kras in the formation of pancreatic ductal adenocarcinoma. How these cell fate decisions vary according to KRAS mutation remains poorly understood. To define mutation-specific lineage reversion and tumor initiation, we implement Ptf1a-tdTomato mice and multiple KRAS mutants across several genetic, pharmacologic, and inflammatory perturbations in vivo. Whereas KRASG12D co-opts injury to enable lineage reversion, enhancer reprogramming, and tumor initiation, KRASG12R/V cannot sustain dedifferentiated and neoplastic transcriptional and epigenetic programs. Specifically, KRASG12R/V mutants fail to invoke robust EGFR, AKT, and RAC1/VAV1 signaling and to license Pou2f3 and Vav1 in chromatin, such that only constitutive AKT activation is sufficient to rescue the tumorigenic potential of KRASG12Rin vivo. As the marked heterogeneity among KRAS variants begins early in tumorigenesis, these data are crucial to deciphering mutation-specific oncogenic trajectories and directing the implementation of KRAS-directed therapeutics.
    Keywords:  EGFR; G12R; KRAS; RAC1; VAV1; acinar-ductal metaplasia; epigenetic reprogramming; inflammation; lineage reversion; pancreatic ductal adenocarcinoma
    DOI:  https://doi.org/10.1016/j.devcel.2026.06.016
  5. Proc Natl Acad Sci U S A. 2026 Jul 28. 123(30): e2602436123
      Receptor tyrosine kinases (RTKs) are key therapeutic targets in cancer, diabetes, and other diseases. With only one transmembrane α-helix-compared with seven in G-protein-coupled receptors-RTKs are thought to be activated by ligand-induced dimerization. Complicating this view, however, one of the best-studied RTKs, the insulin receptor (IR), forms allosterically regulated covalent dimers. Moreover, noncovalent "preformed" dimers have frequently been reported for the sequence-related epidermal growth factor receptor (EGFR), one of the first RTKs for which ligand-induced dimerization was described. Here, we describe a detailed structural view of a preformed EGFR dimer. Using cryo-EM, we describe how the Caenorhabditis elegans EGFR (LET-23) dimerizes without ligand. We show that preformed dimer formation modulates ligand sensitivity in vivo, but is not required for signaling itself. We also elucidate substantial ligand-induced conformational changes in LET-23 required for signaling. Our structures reveal unexpected similarities between regulation of LET-23 and the IR, suggesting that LET-23 may represent an evolutionary "missing link" between the IR and EGFR families. In the absence of ligand, intermolecular interactions within preformed receptor dimers hold the extracellular juxtamembrane regions far apart to separate the intracellular kinase domains so that they remain inactive. Ligand binding disrupts these interactions to remove the restraints on the kinase domains, which then can associate to become activated. Our analysis further suggests a unified model for the allosteric activation of preformed RTK dimers that has important implications for understanding cell-surface EGFR.
    Keywords:  EGFR; cryo-EM; growth factor signaling; preformed dimers; receptor tyrosine kinases
    DOI:  https://doi.org/10.1073/pnas.2602436123
  6. Nature. 2026 Jul 22.
    Liver Cancer Evolution Consortium
      Human cancers are heterogeneous1. Dissecting how germline genetic variation and environmental factors shape tumour evolution using human datasets is limited by inherent diversity in genetic backgrounds2 and environmental exposures3-5. Here, to overcome these limitations, we re-ran early tumour evolution hundreds of times in diverged inbred mouse strains, generating matched histology and whole-genome and transcriptome sequences. The sex, environment and carcinogenic exposures were all controlled, and the study design allowed us to capture genetic variation comparable with that observed across human populations while exploiting the nested hierarchical structure of strain-litter-animal-tumour relationships. Our analyses reveal that epistatic interactions between genetic background and acquired somatic mutations result in population-specific disease progression, including choice of driver mutations, occurrence of whole-genome duplication and subclonal selection dynamics that mirror both cancer susceptibility and tumour growth rate. Even modest genetic divergence, comparable with that found across human ancestry groups, can strikingly alter selection pressures during cancer development to shape both cancer risk and the trajectory of tumour evolution.
    DOI:  https://doi.org/10.1038/s41586-026-10821-z
  7. Cell Rep. 2026 Jul 24. pii: S2211-1247(26)00797-7. [Epub ahead of print]45(8): 117719
      Cancer cells acquire distinct metabolic and signaling dependencies driven by oncogenic mutations. Defining these mutation-specific liabilities can uncover therapeutic opportunities. Here, we identify dihydroorotate dehydrogenase (DHODH) as a selective metabolic dependency in PIK3CA-mutant colorectal cancer (CRC). DHODH sustains WDR77 O-GlcNAcylation and protein stability by promoting the generation of uridine diphosphate (UDP)-N-acetylglucosamine (UDP-GlcNAc), thereby maintaining PI3K-AKT signaling. Genetic or pharmacological inhibition of DHODH reduces WDR77 protein abundance, decreases phosphorylated AKT, and impairs cancer cell self-renewal and tumor initiation. Uridine supplementation restores WDR77 and AKT signaling, whereas O-GlcNAc transferase (OGT) depletion abrogates this rescue, establishing a UDP-dependent mechanism linking pyrimidine metabolism to signaling maintenance. Treatment with the DHODH inhibitor HL6 recapitulates the genetic phenotypes and suppresses tumor growth in xenograft, orthotopic, and patient-derived CRC models. This study demonstrates that the metabolic regulation of protein stability represents a critical mechanism underlying oncogene-specific dependencies in CRC.
    Keywords:  CP: cancer; DHODH; O-GlcNAcylation; PIK3CA mutation; cancer stemness; colorectal cancer
    DOI:  https://doi.org/10.1016/j.celrep.2026.117719
  8. iScience. 2026 Jul 17. 29(7): 116627
      Translation elongation is highly sensitive to amino acid availability, with deprivation causing ribosome pausing at cognate codons, suppression of the mammalian target of rapamycin (mTORC1) signaling pathway, and GCN2-mediated phosphorylation of eIF2α. However, cell-type heterogeneity in these responses remains unclear. Integrating ribosome profiling datasets across over ten human cell lines and multiple starvation conditions, we uncover translational resistance in breast cancer cells specifically under leucine and glutamine deprivation. Unlike non-breast cancer cells, breast cancer cells maintain ribosome occupancy on mRNAs with a 5' terminal oligopyrimidine tract (5'TOP mRNAs), indicating sustained mTORC1 activity, and exhibit attenuated codon-specific pausing. GCN2-eIF2α pathway activation varies among breast cancer lines. Downregulation of the cystine/glutamate transporter SLC7A11 correlates with this resistance, and its overexpression restores sensitivity by reducing S6K phosphorylation while enhancing eIF2α phosphorylation. Our findings reveal that breast cancer cells adaptively reshape translation regulation to withstand amino acid starvation, highlighting a potential metabolic vulnerability.
    Keywords:  amino acid starvation; mTORC1; ribosome profiling; sensitivity; translation elongation
    DOI:  https://doi.org/10.1016/j.isci.2026.116627
  9. Cell Metab. 2026 Jul 21. pii: S1550-4131(26)00274-3. [Epub ahead of print]
      Systemic metabolic homeostasis maintains circulating nutrient concentrations within physiological ranges. Insulin is central to this process, lowering circulating levels of glucose, lactate, free fatty acids, and ketones. Yet how the simultaneous homeostasis of these nutrients is achieved remains unclear. Here, we develop a differential equation model of fasting metabolic homeostasis. Grounded in mass action kinetics, this multi-nutrient model reveals how a fixed energy demand naturally leads to competition between major circulating nutrients for oxidation ("competitive catabolism"). Perturbative nutrient infusions confirm this emergent behavior. The multi-nutrient model predicts that insulin promotes fasting glucose homeostasis primarily indirectly by slowing lipolysis. It further identifies a physiological circuit by which obesity causes insulin resistance: increased fat mass promotes lipolysis, releasing fatty acids into circulation that compete with glucose for oxidation, elevating glucose and thus insulin, which acts to restore proper lipid catabolic flux. Thus, quantitative modeling reveals a physiological homeostatic circuit through which obesity causes type 2 diabetes.
    Keywords:  competitive catabolism; differential equation modeling; hyperinsulinemia; insulin regulation; insulin resistance; mass action kinetics; metabolic homeostasis; nutrient competition; obesity; type 2 diabetes
    DOI:  https://doi.org/10.1016/j.cmet.2026.07.001
  10. Sci Adv. 2026 Jul 24. 12(30): eaec0131
      Rhythmic gene expression is essential to the daily organization of biological processes. While cycling transcriptomes are regulated by circadian clocks present in nearly every cell, accumulating evidence indicates that they can also be initiated by rhythmic food-driven systemic signals independently of circadian clocks. The underlying mechanisms remain however largely unknown. Here, we show that signaling through the nutrient-sensing kinase mechanistic target of rapamycin (mTOR) is both necessary and sufficient to mediate food-driven hepatic rhythmic gene expression, rhythmic regulation of the liver metabolome, and endoplasmic reticulum stress response. Acute inhibition of mTOR before the active phase desynchronizes the phase of mTOR-driven rhythmic genes without affecting clock-controlled rhythmic genes, indicating that alignment of rhythmic mTOR activity to the circadian cycle is critical for overt cycling transcriptomes. These findings may explain how misalignment between clock and systemic signals contributes to disease and underscore the use of mTOR inhibitors for resynchronizing system-driven rhythms and alleviating circadian rhythm disorders.
    DOI:  https://doi.org/10.1126/sciadv.aec0131
  11. Elife. 2026 Jul 20. pii: RP110034. [Epub ahead of print]15
      Gene regulation underpins development and is an intricate biological process involving transcription, typically at promoters within accessible chromatin. To understand cell-type-specific regulatory networks, the ability to capture both transcription and chromatin accessibility simultaneously is crucial. However, joint measurements are technically challenging and current methodologies still face adoption challenges. Here, we present easySHARE-seq, an improvement on SHARE-seq for the simultaneous measurement of ATAC- and RNA-seq in single cells. We address several limitations of the previous method by improving the barcode and streamlining the protocol. As a result, easySHARE-seq libraries have a usable sequence of up to 300 bp (+200 bp increase), making it suitable for, e.g., investigation of allele-specific signals or variant discovery. Furthermore, easySHARE-seq libraries do not require a dedicated sequencing run thus saving costs. We applied easySHARE-seq to murine liver nuclei and recovered 19,664 nuclei with joint chromatin and expression profiles. By benchmarking against other combinatorial indexing-based techniques, we showed that we can recover over 1.5-fold more transcripts per cell while retaining high scalability and low cost. To showcase our method, we identified cell types, exploited the multiomic measurements to link cis-regulatory elements to their target genes and investigated liver-specific micro-scale changes. We conclude that easySHARE-seq improves upon previous methods and can produce high-quality multiomic datasets. We expect it to be applicable to a wide range of study designs.
    Keywords:  developmental biology; genetics; genomics; hepatocytes; human; liver; liver sinusoidal endothelial cells; mouse
    DOI:  https://doi.org/10.7554/eLife.110034
  12. PLoS Biol. 2026 Jul;24(7): e3003888
      New technologies have generated huge volumes of biological data, much of which is underutilized. AI-assisted data reanalysis could drive the next era of biological discovery, but realizing its full potential requires standards, validation, and responsible use.
    DOI:  https://doi.org/10.1371/journal.pbio.3003888
  13. Nat Methods. 2026 Jul 24.
    Scverse Community
      Highly multiplexed immunofluorescence imaging visualizes and quantifies protein levels at single-cell resolution in intact tissues at low cost and high scalability. Analysis of these data involves multiple steps with many method and parameter choices that must be adapted to the data and analytical objectives. There is an unmet need for a toolbox that offers flexible end-to-end coverage of the workflow. Here we present 'spatialproteomics', a Python package that addresses these challenges. Spatialproteomics enables the processing and analysis of large imaging data, including steps such as segmentation, image processing and cell-type classification, while synchronizing shared coordinates across data modalities. We demonstrate spatialproteomics on images of reactive lymph nodes and B cell non-Hodgkin lymphomas from 132 patients. We showcase an end-to-end analysis from raw images to statistical characterization of how cell type composition and spatial distribution vary across indolent and aggressive lymphomas. Furthermore, we show how spatialproteomics can process Gigapixel whole-slide images.
    DOI:  https://doi.org/10.1038/s41592-026-03155-1
  14. Sci Adv. 2026 Jul 24. 12(30): eaea9826
      Sphingosine-1-phosphate (S1P) is a key mediator in the cardiovascular system with controversial effects on coagulation. We hypothesized that S1P reduces platelet adhesion and thrombus formation by up-regulating endothelial thrombomodulin (TM), an antithrombotic protein. S1P increased endothelial TM expression via S1P receptor 1 and phosphoinositide 3-kinase signaling. S1P reduced platelet adhesion on endothelial cells in flow-chamber experiments. In the absence of endothelial cells, S1P did not affect platelet activation. In mice, S1P enhanced endothelial TM expression and decreased in vivo arterial thrombus formation but did not change bleeding time. Conversely, sphingosine kinase 1-deficient mice with low S1P concentrations showed reduced endothelial TM expression and enhanced thrombus formation, reversible by TM treatment. In line with this, in an all-comer cohort of 74 patients with cardiovascular disease, higher S1P concentrations were associated with lower circulating thrombin concentrations. In conclusion, S1P inhibited thrombus formation in an endothelium- and TM-dependent manner. This might be a therapeutic target in prevention of thrombus formation without enhancing bleeding risk.
    DOI:  https://doi.org/10.1126/sciadv.aea9826
  15. Genes Dev. 2026 Jul 23.
      Misfolded protein accumulation in the endoplasmic reticulum (ER) perturbs cellular homeostasis, causing pathological ER stress. While a transcriptional response is paramount for the unfolded protein response (UPR), which counters ER protein stress, multiple UPR-linked mRNAs are posttranscriptionally regulated. However, the mechanisms mediating this regulation remain unclear. Here, we reveal specific interactions between the conserved RNA-binding protein IGF2BP3 and transcripts encoding UPR effectors. During ER stress, IGF2BP3 destabilizes many of its target transcripts, including UPR effectors. Mechanistically, ER stress enhances IGF2BP3's association with the mRNA decapping complex and the ER stress sensor RNase IRE1, which correlates with a shift toward mRNA destabilization. Unexpectedly, prolonged depletion of IGF2BP3 inhibits the UPR via decreased transcription of UPR target genes. Together, our findings suggest that IGF2BP3 contributes to proteostasis during ER stress through a dual mechanism: directly promoting mRNA degradation to reduce translation and folding burden and indirectly supporting transcriptional activation of the UPR.
    Keywords:  IGF2BP3; IRE1; RNA-binding proteins; endoplasmic reticulum; mRNA decapping complex; posttranscriptional regulation; unfolded protein response
    DOI:  https://doi.org/10.1101/gad.353291.125
  16. Pediatr Dermatol. 2026 Jul 23.
      Dermatologists play a central role in the diagnosis and medical management of vascular anomalies. Currently, vascular anomalies are categorized into vascular tumors and vascular malformations. The latest designations for the numerous types of vascular lesions are delineated in the International Society for the Study of Vascular Anomalies website (www.issva.org). The arenas for the therapy for hemangiomas, the most common vascular tumor, have been studied extensively and have been recognized as standard of care by the Society for Pediatric Dermatology, the American Academy of Dermatology and the American Academy of Pediatrics. Options for hemangioma treatment include systemic beta-blockers such as propranolol, atenolol, and nadolol, and the topical beta-blocker timolol. Vascular malformations and overgrowth syndromes encompass a separate set of treatment regimens. Recent pharmacological and technological advances in the medical management of vascular anomalies have decreased the need for surgery in many patients while also leading to improved outcomes and quality of life. This review will guide the dermatologist through the current medical treatment landscape for vascular malformations.
    Keywords:  PIK3CA; alpelisib; miransertib; overgrowth syndromes; sirolimus; sotorasib; trametinib; vascular anomalies; vascular malformations
    DOI:  https://doi.org/10.1111/pde.70302
  17. bioRxiv. 2026 Jun 23. pii: 2026.06.20.733393. [Epub ahead of print]
      Mechanical forces from blood flow are essential for production of hematopoietic stem and progenitor cells (HSPCs) during embryogenesis, but the molecular mechanisms by which hemodynamic cues are sensed and orchestrate endothelial-to-hematopoietic (EHT) transition remain incompletely defined. We previously identified YAP mechanotransduction as a key integrator of physical forces with EHT. Here we show that hemodynamic forces can activate YAP signaling via the mechanoresponsive ion channel Piezo1 in human iPSC-derived hemogenic endothelium (HE) and zebrafish embryos. Investigation of the Piezo1/YAP axis revealed shared and unique roles of YAP and its paralogue TAZ in EHT. Mechanistically, we find a requirement for the Tead DNA-binding co-factor in YAP/TAZ-dependent control of HSPC number, and note that TAZ uniquely augments transcriptional output of the hematopoietic master regulator Runx1 via direct protein-protein interactions. By comprehensive scRNA-sequencing of YAP/TAZ gain-of-function (GOF) and yap-deficient cells from zebrafish, we reveal that YAP/TAZ promotes HSC production by positively regulating gene programs for hematopoietic self-renewal, cell cycle, and glycolysis-to-oxidative phosphorylation switching, while preventing reversion to endothelial identity. Importantly, comparison of GOF transcriptomes and functional analyses suggest decoupling of metabolic/proliferative and endothelial gene regulatory modules between YAP and TAZ: while either can functionally compensate for loss of the other in EHT, indiscriminate overactivation of TAZ enhances an endothelial program over pro-hematopoietic fate, ultimately blunting progression of HSPC production. Given that hemodynamic cues are integrated simultaneously by arterial and HE cells in embryonic vessels in which EHT occurs, these findings have strong implications for strategies designed to introduce biomechanical cues to in vitro hematopoietic differentiation systems to drive HSC production.
    DOI:  https://doi.org/10.64898/2026.06.20.733393