bims-pideca Biomed News
on Class IA PI3K signalling in development and cancer
Issue of 2025–11–09
twelve papers selected by
Ralitsa Radostinova Madsen, MRC-PPU
  1. Protocol to rapidly verify silent gene reporter in human pluripotent stem cells using CRISPR activation.
  2. Activity and dynamics of p110α are not differentially modulated by regulatory subunit isoforms.
  3. Pharmacological SHIP2 blockade enhances sensitivity to standard and targeted cancer therapies.
  4. Chemical compensation to mechanical loss in cell mechanosensation.
  5. TRIM21 and OTUD6A orchestrate AKT K27-linked atypical ubiquitination to modulate cancer chemoresistance.
  6. Cell signaling meets gene transcription.
  7. Lysosomal and mTORC1 signaling dysregulation underpin the pathology of spastic paraplegia type 80.
  8. Site-specific DNA insertion into the human genome with engineered recombinases.
  9. Aging represses oncogenic KRAS-driven lung tumorigenesis and alters tumor suppression.
  10. Squidiff: predicting cellular development and responses to perturbations using a diffusion model.
  11. Drugmakers share data to feed voracious foundation models.
  12. A novel paradigm for single-cell annotation in stem cell research.
  1. STAR Protoc. 2025 Oct 25. pii: S2666-1667(25)00570-2. [Epub ahead of print]6(4): 104164
    Protocol to rapidly verify silent gene reporter in human pluripotent stem cells using CRISPR activation.
    Youjun Wu, Aaron Zhong, Bernny Ramirez, Su Su Wai, Ting Zhou.
      Validating human pluripotent stem cell (hPSC) reporters targeting silent genes typically requires inducing gene expression through cell state transitions, which can be time consuming and complex. Here, we present a rapid workflow to verify reporter knockins at unexpressed loci in hPSCs using CRISPR-mediated transcriptional activation (CRISPRa). We detail steps for designing and cloning single-guide RNA (sgRNA), delivery of CRISPRa into reporter cells, and detection of reporter gene. In this protocol, we illustrate this process using KLF17-GFP reporter hPSCs. For complete details on the use and execution of this protocol, please refer to Wu et al.1.
    Keywords:  CRISPR; Stem Cells; Tissue Engineering
    DOI:  https://doi.org/10.1016/j.xpro.2025.104164
  2. Adv Biol Regul. 2025 Nov 04. pii: S2212-4926(25)00055-7. [Epub ahead of print] 101128
    Activity and dynamics of p110α are not differentially modulated by regulatory subunit isoforms.
    Isobel Barlow-Busch, Emma E Walsh, Hunter G Nyvall, John E Burke.
      Class IA phosophoinositide kinases (PI3Ks) are master regulators of growth, metabolism, and immunity. The class IA PI3Ks are a heterodimer composed of a p110 catalytic subunit and one of five possible regulatory subunits (p85α, p85β, p55γ, p55α, p50α). The regulatory subunit plays critical roles in stability, inhibition, and activation of the p110 catalytic subunit. The p110α catalytic subunit frequently contains activating mutations in human cancer, with many of these mutations altering the interaction between catalytic and regulatory subunits. It has been found that different regulatory subunits play unique roles in human disease, but it is unknown how these different subunits regulate p110α. Here, using a synergy of biochemical assays and hydrogen deuterium exchange mass spectrometry (HDX-MS) we examined how the five different regulatory subunits inhibit, activate, and interact with the p110α catalytic subunit. We find that there are no significant differences in lipid kinase activity or in membrane recruitment between the different heterodimer complexes. HDX-MS in the presence and absence of an activating phosphopeptide also showed only minor conformational differences between different regulatory subunit complexes. Overall, our work reveals that the different regulatory subunits interact with and inhibit p110α in a similar fashion at a molecular level.
    DOI:  https://doi.org/10.1016/j.jbior.2025.101128
  3. Adv Biol Regul. 2025 Nov 04. pii: S2212-4926(25)00057-0. [Epub ahead of print] 101130
    Pharmacological SHIP2 blockade enhances sensitivity to standard and targeted cancer therapies.
    Nadia Gillet, Cyril Bodart, Benjamin Beck.
      Esophageal squamous cell carcinoma (eSCC) is an aggressive malignancy with poor prognosis and limited therapeutic options. The phosphoinositide 3-kinase (PI3K)/AKT pathway is frequently activated in eSCC, but clinical use of PI3K or AKT inhibitors is restricted by toxicity and compensatory signaling. SHIP2, an inositol 5-phosphatase encoded by INPPL1, modulates this pathway by converting PI(3,4,5)P3 to PI(3,4)P2, thereby regulating AKT activation. We previously identified INPPL1 amplification as recurrent in eSCC and demonstrated that SHIP2 inhibition suppresses tumor growth and synergizes with PLK1 inhibition. Here, we extend these findings and show that SHIP2-PLK1 synergy is not confined to eSCC but is also observed in multiple colorectal cancer cell lines, revealing a conserved vulnerability across tumor types. Mechanistic analyses demonstrate that this synergy depends on PI3K/AKT signaling, with SHIP2 inhibition producing stronger effects than direct PI3K blockade, suggesting additional regulatory functions beyond canonical PI3K control. Furthermore, SHIP2 inhibition enhances the cytotoxic activity of standard chemotherapies, including 5-fluorouracil and paclitaxel, in eSCC cells. Importantly, these effects occur at sub-cytotoxic drug concentrations, indicating potential therapeutic benefit with reduced toxicity. Collectively, our results identify SHIP2 as a central regulator of the PI3K/AKT axis in eSCC and colorectal cancer and highlight its value as a combinatorial target. SHIP2 inhibition represents a promising strategy to potentiate existing chemotherapies and targeted agents, opening new avenues for the treatment of refractory gastrointestinal cancers.
    Keywords:  Chemotherapy; Phosphatase; Phosphoinosititides; Squamous cell carcinoma; Synergy
    DOI:  https://doi.org/10.1016/j.jbior.2025.101130
  4. Proc Natl Acad Sci U S A. 2025 Nov 11. 122(45): e2507935122
    Chemical compensation to mechanical loss in cell mechanosensation.
    Qin Ni, Zhuoxu Ge, Anindya Sen, Yufei Wu, Jinyu Fu, Alice Amitrano, Nitish Srivastava, Konstantinos Konstantopoulos, Sean X Sun.
      Mammalian cells sense and respond to environmental changes using a complex and intelligent system that integrates chemical and mechanical signals. The transduction of mechanical cues into chemical changes modulates cell physiology, allowing a cell to adapt to its microenvironment. Understanding how the chemical and mechanical regulatory modules interact is crucial for elucidating mechanisms of mechanosensation and cellular homeostasis. In this study, we find that cells exhibit nonmonotonic changes in cell volume and intracellular pH when subjected to physical stimuli and varying degrees of actomyosin cytoskeleton disruption. We find that these nonmonotonic responses are mediated by a chemical compensation mechanism, where the attenuation of actomyosin activity stimulates the activity of PI3K/Akt pathway. This, in turn, activates sodium-hydrogen exchanger 1 (NHE1), resulting in elevated intracellular pH and increased cell volume. Furthermore, we identify a competitive interaction between the PI3K/Akt and MAPK/ERK pathways-two major regulators of cell proliferation and motility. This competition modulates the chemical compensation based on the relative activities of these pathways. Our mathematical modeling reveals the network structure that is essential for establishing the nonmonotonic response. Interestingly, this regulatory system is altered in HT1080 fibrosarcoma, highlighting a potential mechanistic divergence in cancer cells in contrast to their normal-like counterpart, such as NIH 3T3 and HFF-1 fibroblasts. Overall, our work reveals a compensatory mechanism between chemical and mechanical signals, providing an infrastructure to elucidate the integrated mechanochemical response to environmental stimuli.
    Keywords:  PI3K signaling; biophysical modeling; cell volume; cytoskeleton; mechanosensation
    DOI:  https://doi.org/10.1073/pnas.2507935122
  5. Nat Struct Mol Biol. 2025 Nov 04.
    TRIM21 and OTUD6A orchestrate AKT K27-linked atypical ubiquitination to modulate cancer chemoresistance.
    Qiwei Jiang, Peipei Song, Shuishen Zhang, Qin Ren, Meiyan Zhu, Jiawei Ge, Lang Bu, Wei Chen, Xueji Wu, Shiyao Han, Yaqing Su, Lei Wang, Wei Xie, Chao Cheng, Zhenwei Peng, Jianping Guo.
      Ubiquitination regulates various physiological and pathological processes. However, the impact of atypical AKT ubiquitination and its potential role in tumorigenesis remain unclear. Here we show that AKT is modified by K27-linked ubiquitination by the E3 ubiquitin ligase TRIM21, a process antagonized by the deubiquitinase OTUD6A. As such, TRIM21 acts as a tumor suppressor by repressing AKT activity, whereas OTUD6A counteracts AKT suppression. Mechanistically, TRIM21-mediated AKT ubiquitination disrupts SKP2-mediated or TRAF6-mediated K63 ubiquitination, thereby blocking AKT membrane localization and its kinase activity. Upon activation in response to amino acids, S6K1 directly phosphorylates and inactivates OTUD6A, enabling a negative feedback loop regulating AKT activity in a deubiquitination-dependent manner. In agreement with this model, Otud6a deficiency reduces lung tumorigenesis in a KrasG12D-driven lung cancer mouse model and TRIM21 induction alleviates hyperactive AKT-induced tumor growth in vivo. Thus, our findings unveil a fine-tuned regulation of AKT through atypical ubiquitination and suggest the strategy for combating AKT-driven cancers by targeting the TRIM21-OTUD6A axis.
    DOI:  https://doi.org/10.1038/s41594-025-01697-0
  6. Science. 2025 Nov 06. 390(6773): 568-569
    Cell signaling meets gene transcription.
    Richard Young.
      Receptor tyrosine kinases directly regulate RNA polymerase II in the nucleus.
    DOI:  https://doi.org/10.1126/science.aec1434
  7. Nat Commun. 2025 Nov 07. 16(1): 9833
    Lysosomal and mTORC1 signaling dysregulation underpin the pathology of spastic paraplegia type 80.
    Yiqiang Zhi, Tongtong Zhang, Danping Lu, Shuhuai Lin, Huizhen Su, Yupei Wu, Qiyuan Chang, Shuyuan Wang, Chenning Lv, Honggao Fu, Li-Yu Chen, Wan-Jin Chen, Ning Wang, Zhifei Fu, Xiang Lin, Dan Xu.
      Endosomal sorting complex required for transport (ESCRT) is the major membrane remodeling complex, closely associated with endolysosomal repair and hereditary spastic paraplegias (HSP) diseases. Loss of function mutations in the ESCRT-I component UBAP1 causes a rare type of HSP (spastic paraplegia 80, SPG80), while the underlying pathological mechanism is unclear. Here, we found that UBAP1 but not SPG80 causing mutant was efficiently recruited to damaged lysosomes and mediated lysosome recovery. Loss of UBAP1 results in dysfunction of lysosomes, disconnecting mTOR localization on lysosomes, leading to cytoplasmic mTORC1 activation and TFEB dephosphorylation, as confirmed in vitro and in vivo models. Administration of rapamycin, a specific inhibitor of mTORC1, enhances mTOR lysosomal localization and TFEB phosphorylation. This pharmacological intervention effectively attenuated disease progression and restored lysosomal homeostasis in Ubap1 deficiency mice. Our findings reveal UBAP1's role in lysosome regulation and suggest rapamycin may benefit patients with HSP and other motor neuron disorders.
    DOI:  https://doi.org/10.1038/s41467-025-64800-5
  8. Nat Biotechnol. 2025 Nov 06.
    Site-specific DNA insertion into the human genome with engineered recombinases.
    Alison Fanton, Liam J Bartie, Juliana Q Martins, Vincent Q Tran, Laine Goudy, Courtney Kernick, Matthew G Durrant, Jingyi Wei, Zev Armour-Garb, April Pawluk, Silvana Konermann, Alexander Marson, Luke A Gilbert, Theodore L Roth, Patrick D Hsu.
      Insertions of large DNA sequences into the genome are broadly enabling for research and therapeutic applications. Large serine recombinases (LSRs) can mediate direct, site-specific genomic integration of multi-kilobase DNA sequences without a pre-installed landing pad, albeit with low insertion rates and high off-target activity. Here we present an engineering roadmap for jointly optimizing their DNA recombination efficiency and specificity. We combine directed evolution, structural analysis and computational models to rapidly identify additive mutational combinations. We further enhance performance through donor DNA optimization and dCas9 fusions, enabling simultaneous target and donor recruitment. Our top engineered LSR variants, superDn29-dCas9, goldDn29-dCas9 and hifiDn29-dCas9, achieve up to 53% integration efficiency and 97% genome-wide specificity at an endogenous human locus and effectively integrate large DNA cargoes up to 12 kb for stable expression in non-dividing cells, stem cells and primary human T cells. Rational engineering of DNA recombinases enables precise and efficient single-step genome insertion for diverse applications across gene and cell therapies.
    DOI:  https://doi.org/10.1038/s41587-025-02895-3
  9. Nat Aging. 2025 Nov 04.
    Aging represses oncogenic KRAS-driven lung tumorigenesis and alters tumor suppression.
    Emily G Shuldiner, Saswati Karmakar, Min K Tsai, Jess D Hebert, Yuning J Tang, Laura Andrejka, Maggie R Robertson, Minwei Wang, Colin R Detrick, Hongchen Cai, Rui Tang, Christian A Kunder, David M Feldser, Dmitri A Petrov, Monte M Winslow.
      Most cancers are diagnosed in people over 60 years of age, but little is known about how age impacts tumorigenesis. While aging is accompanied by mutation accumulation (widely understood to contribute to cancer risk) it is associated with numerous other cellular and molecular changes likely to impact tumorigenesis. Moreover, cancer incidence decreases in the oldest part of the population, suggesting that very old age may reduce carcinogenesis. Here we show that aging represses oncogenic KRAS-driven tumor initiation and growth in genetically engineered mouse models of human lung cancer. Moreover, aging dampens the impact of inactivating many tumor suppressor genes with the impact of inactivating PTEN, a negative regulator of the PI3K-AKT pathway, weakened disproportionately. Single-cell transcriptomic analysis revealed that neoplastic cells in aged mice retain age-related transcriptomic changes, showing that the impact of age persists through oncogenic transformation. Furthermore, the consequences of PTEN inactivation were strikingly age-dependent, with PTEN deficiency reducing signatures of aging in cancer cells and the tumor microenvironment. Our findings underscore the interconnectedness of the pathways involved in aging and tumorigenesis and document tumor-suppressive effects of aging that may contribute to the deceleration in cancer incidence with age.
    DOI:  https://doi.org/10.1038/s43587-025-00986-z
  10. Nat Methods. 2025 Nov 03.
    Squidiff: predicting cellular development and responses to perturbations using a diffusion model.
    Siyu He, Yuefei Zhu, Daniel Naveed Tavakol, Haotian Ye, Yeh-Hsing Lao, Zixian Zhu, Cong Xu, Shradha Chauhan, Guy Garty, Raju Tomer, Gordana Vunjak-Novakovic, James Zou, Elham Azizi, Kam W Leong.
      Single-cell sequencing has revolutionized our understanding of cellular heterogeneity and responses to environmental stimuli. However, mapping transcriptomic changes across diverse cell types in response to various stimuli and elucidating underlying disease mechanisms remains challenging. Here we present Squidiff, a diffusion model-based generative framework that predicts transcriptomic changes across diverse cell types in response to environmental changes. We demonstrate the robustness of Squidiff across cell differentiation, gene perturbation and drug response prediction. Through continuous denoising and semantic feature integration, Squidiff learns transient cell states and predicts high-resolution transcriptomic landscapes over time and conditions. Furthermore, we applied Squidiff to model blood vessel organoid development and cellular responses to neutron irradiation and growth factors. Our results demonstrate that Squidiff enables in silico screening of molecular landscapes and cellular state transitions, facilitating rapid hypothesis generation and providing valuable insights into the regulatory principles of cell fate decisions.
    DOI:  https://doi.org/10.1038/s41592-025-02877-y
  11. Nat Biotechnol. 2025 Nov 06.
    Drugmakers share data to feed voracious foundation models.
    Andrew Marshall.
      
    DOI:  https://doi.org/10.1038/s41587-025-02901-8
  12. Stem Cell Reports. 2025 Nov 06. pii: S2213-6711(25)00311-X. [Epub ahead of print] 102707
    A novel paradigm for single-cell annotation in stem cell research.
    Trevor Atkeson, Sean B Wilson, Elias R Ruiz-Morales, Melissa H Little, Roser Vento-Tormo, Drew Neavin, Joseph E Powell.
      Stem cell-derived models are a powerful tool for studying biology and are increasingly paving the way for cell-based therapies. However, understanding precisely which cell types are present and how closely they recapitulate in vivo cells remains challenging. Single-cell genomics, coupled with annotation methods, provides a framework for evaluating the congruence of stem cells with in vivo biology. Here, we explore approaches to cell annotation and discuss the challenges of implementing these methods in stem cell-derived models. We provide recommendations for the application of these methods, as well as our vision for the future of stem cell annotation using cell manifolds.
    Keywords:  AI; cell annotation; cellular genomics; hPSCs; single cell
    DOI:  https://doi.org/10.1016/j.stemcr.2025.102707
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