bims-pideca Biomed News
on Class IA PI3K signalling in development and cancer
Issue of 2025–08–24
eight papers selected by
Ralitsa Radostinova Madsen, MRC-PPU
  1. Fluctuation structure predicts genome-wide perturbation outcomes.
  2. Phosphatidylinositol-4,5-bisphosphate 3-kinase (PI3K) inhibitors reduce vascular inflammation in vitro and in vivo.
  3. ONE-STEP tagging: a versatile method for rapid site-specific integration by simultaneous reagent delivery.
  4. Structural Insights into the Development of Inhibitors Against Cancer-Specific Mutations of PI3Kα.
  5. Viral insulin/IGF-like peptides inhibit IGF-1 receptor signaling to enhance viral replication.
  6. Phosphoproteome-derived peptide libraries for deep specificity profiling of phosphatases and phospholyases.
  7. Using R, Seurat, and CellChat to Analyze a Single-Cell Transcriptomics Dataset of Mouse Skin Wound Healing.
  8. High-throughput profiling of chemical-induced gene expression across 93,644 perturbations.
  1. Res Sq. 2025 Aug 12. pii: rs.3.rs-7304871. [Epub ahead of print]
    Fluctuation structure predicts genome-wide perturbation outcomes.
    Yogesh Goyal, Benjamin Kuznets-Speck, Leon Schwartz, Hanxiao Sun, Madeline Melzer, Nitu Kumari, Benjamin Haley, Ekta Prashnani, Suriyanarayanan Vaikuntanathan.
      Pooled single-cell perturbation screens represent powerful experimental platforms for functional genomics, yet interpreting these rich datasets for meaningful biological conclusions remains challenging. Most current methods fall at one of two extremes: either opaque deep learning models that obscure biological meaning, or simplified frameworks that treat genes as isolated units. As such, these approaches overlook a crucial insight: gene co-fluctuations in unperturbed cellular states can be harnessed to model perturbation responses. Here we present CIPHER (Covariance Inference for Perturbation and High-dimensional Expression Response), a conceptual framework leveraging linear response theory from statistical physics to predict transcriptome-wide perturbation outcomes using gene co-fluctuations in unperturbed cells. We validated CIPHER on synthetic regulatory networks before applying it to 11 large-scale single-cell perturbation datasets covering 4,234 perturbations and over 1.36M cells. CIPHER robustly recapitulated genome-wide responses to single and double perturbations by exploiting baseline gene covariance structure. Importantly, eliminating gene-gene covariances, while retaining gene-intrinsic variances, reduced model performance by 11-fold, demonstrating the rich information stored within baseline fluctuation structures. Moreover, gene-gene correlations transferred successfully across independent studies of the same cell type, revealing stereotypic fluctuation structures. Furthermore, CIPHER outperformed conventional differential expression metrics in identifying true perturbations while providing uncertainty-aware effect size estimates through Bayesian inference. Finally, most genome-wide responses propagated through the covariance matrix along approximately three independent and global gene modules. CIPHER underscores the importance of theoretically-grounded models in capturing complex biological responses, highlighting fundamental design principles encoded in cellular fluctuation patterns.
    DOI:  https://doi.org/10.21203/rs.3.rs-7304871/v1
  2. Br J Pharmacol. 2025 Aug 18.
    Phosphatidylinositol-4,5-bisphosphate 3-kinase (PI3K) inhibitors reduce vascular inflammation in vitro and in vivo.
    Hiba Chaudhry, Ali A Zarban, Silvia Cellone Trevelin, Xenia Kodji, Camilla Cerutti, Xiaoqing Xiong, Fulye Argunhan, Ajay M Shah, Anne J Ridley, Susan D Brain.
       BACKGROUND AND PURPOSE: Endothelial cells play central roles in increasing vascular permeability and leukocyte recruitment. Therapeutic approaches for treating endothelial cell barrier dysfunction to reduce unwanted fluid accumulation in tissues are limited. Phosphatidylinositol-4,5-bisphosphate 3-kinase (PI3K) enzymes are implicated in signalling inflammatory endothelial permeability and leukocyte recruitment. We investigated the ability of PI3K inhibitors to influence cutaneous oedema formation and neutrophil accumulation.
    EXPERIMENTAL APPROACH: We used cultured endothelial cells to determine the effects of inflammatory mediators on permeability and vascular leakage, and a murine model of vascular inflammation in mouse skin in vivo. The effects of inflammatory mediators that induce vascular leakage and neutrophil accumulation (TNFα, IL-1β and C5a) were examined, with the neuropeptides substance P and α-CGRP used as controls. The ability of PI3K inhibitors to modulate inflammatory responses was studied.
    KEY RESULTS: A broad spectrum PI3K inhibitor (PI-103) and a selective inhibitor of the class 1A p110α catalytic subunit (BYL-719/alpelisib) inhibited endothelial morphological changes and permeability induced by TNFα and IL-1β in vitro. In vivo, oedema and neutrophil accumulation induced by TNFα and IL-1β, but not by the complement fragment C5a, is inhibited by BYL-719, whereas PI-103 blocks effects of all three mediators. Neither influences the acute oedema formation induced by neuropeptides.
    CONCLUSIONS AND IMPLICATIONS: Selective p110α inhibition of vascular inflammation may provide a novel therapeutic pathway for limiting adverse tissue swelling. Moreover, the limited effect of BYL-719 on C5a-mediated responses implies that this innate component of the immune response will continue to provide essential defence activity during p110α blockade.
    Keywords:  endothelial cell; inflammation; neutrophil; oedema formation; phosphoinositide‐3 kinase inhibitors
    DOI:  https://doi.org/10.1111/bph.70152
  3. Nucleic Acids Res. 2025 Aug 11. pii: gkaf809. [Epub ahead of print]53(15):
    ONE-STEP tagging: a versatile method for rapid site-specific integration by simultaneous reagent delivery.
    Valentina Migliori, Michaela B Bruntraeger, Ivan S Gyulev, Florence Lichou, Thomas Burgold, Daniel P Gitterman, Sho Iwama, Andrew L Trinh, Sam J Washer, Carla P Jones, Gosia Trynka, Andrew R Bassett.
      We present a novel, versatile genome editing method termed ONE-STEP tagging, which combines CRISPR-Cas9-mediated targeting with Bxb1 integrase-based site-specific integration for efficient, precise, and scalable protein tagging. Applied in human-induced pluripotent stem cells (hiPSCs), cancer cells and primary T cells, this system enables rapid generation of endogenously tagged proteins. By enhancing the nuclear localization signal of the catalytically superior eeBxb1 integrase and co-delivering a DNA-PK inhibitor, we achieved up to ∼90% integration efficiency at the ACTR10 locus in hiPSCs. ONE-STEP tagging is robust across loci and cell types and supports large DNA cargo integration, with efficiencies reaching 16.6% for a 14.4 kb construct. The method also enables multiplexed tagging of multiple proteins within the same cell and simultaneous CRISPR-based editing at secondary loci, such as gene knockouts or homology-directed repair. Importantly, we demonstrate successful application in primary T cells by targeting the T cell receptor locus while simultaneously knocking out B2M, a key step towards generating immune-evasive, off-the-shelf chimeric antigen receptor T cells. Additionally, we introduce a dual-cassette version of the method compatible with universal donor plasmids, allowing use of entirely off-the-shelf reagents. Together, these advances establish ONE-STEP tagging as a powerful tool for both basic and therapeutic genome engineering.
    DOI:  https://doi.org/10.1093/nar/gkaf809
  4. Annu Rev Pharmacol Toxicol. 2025 Aug 19.
    Structural Insights into the Development of Inhibitors Against Cancer-Specific Mutations of PI3Kα.
    Xiao Liu, Yanyan Chen, Wei Han, Yan Chen, Wenbo Feng, Qingtong Zhou, Ming-Wei Wang.
      Phosphoinositide 3-kinase alpha (PI3Kα) is a pivotal regulator of cell growth, proliferation, and survival. Dysregulation of the PI3K/AKT/mTOR pathway, driven predominantly by PIK3CA mutations (e.g., H1047R, E542K, and E545K), is a hallmark of many cancers. Advances in structural, biochemical, and computational studies have elucidated mutation-specific conformational changes of PI3Kα. While early pan- and isoform-selective PI3K inhibitors (alpelisib) show clinical utility, their intrinsic toxicity and resistance to treatment persist. Recent breakthroughs include the emergence of allosteric inhibitors (RLY-2608 and STX-478) that exploit mutation-induced cryptic pockets to achieve mutant selectivity as well as covalent inhibitors and degraders (inavolisib) that enhance specificity, aiming at decoupling antitumor activity from metabolic dysfunction. This review synthesizes current progress in PI3Kα inhibitor development, emphasizing structural characteristics, clinical challenges, and emerging strategies. Addressing challenges to increase mutant selectivity, exploring conformational modulation, uncovering new mechanisms of action, and implementing personalized therapies are key future directions for PI3Kα-targeted drug discovery.
    DOI:  https://doi.org/10.1146/annurev-pharmtox-082924-022724
  5. Cell Rep. 2025 Aug 12. pii: S2211-1247(25)00920-9. [Epub ahead of print] 116149
    Viral insulin/IGF-like peptides inhibit IGF-1 receptor signaling to enhance viral replication.
    Aurelien Chuard, Kalaimagal Nesarajah, Khadija Danazumi, Kaitlin Reiners, Fa Zhang, Lev Levintov, Marta Lubos, Lenka Žáková, Rachel Ruggera, Sarah McMenamin, Harish Vashisth, Jiří Jiráček, Richard Dimarchi, Emrah Altindis.
      The insulin/insulin growth factor (IGF) system plays a central role in regulating metabolism and growth. We identified viral insulin/IGF1-like peptides (VILPs) in Iridoviridae and investigated their role in host-virus interactions. Using grouper iridovirus (GIV) on grouper and zebrafish cells, we show that VILPs are early viral genes and are secreted during infection. VILPs activate insulin receptor (IR) and IGF-1 receptor (IGF1R) phosphorylation and stimulate the phosphatidylinositol 3-kinase (PI3K) pathway. GIV-VILP present in the supernatants of infected cells triggers dose- and time-dependent signaling through selective interaction with IGF1R. Functionally, IR inhibition suppresses GIV replication, whereas IGF1R inhibition enhances it, and IGF-1 stimulation reduces replication. During infection, GIV-VILP competes with IGF-1, attenuating IGF1R signaling and reducing proliferation. Transcriptome analysis confirms negative regulation of cell cycle pathways. Using a zebrafish infection model, we demonstrate VILP expression and IGF-1 signaling inhibition. Our findings reveal a viral mimicry mechanism that modulates host IGF-1 signaling to promote viral replication.
    Keywords:  CP: Metabolism; CP: Microbiology; IGF-1; IGF1R inhibition; VILP; grouper iridovirus; insulin; mimicry; zebrafish
    DOI:  https://doi.org/10.1016/j.celrep.2025.116149
  6. bioRxiv. 2025 Aug 13. pii: 2025.08.12.669978. [Epub ahead of print]
    Phosphoproteome-derived peptide libraries for deep specificity profiling of phosphatases and phospholyases.
    Katarzyna Radziwon, Laura A Campbell, Lauren E Mazurkiewicz, Sopo Jalalishvili, Izabelle Eppinger, Aanika Parikh, Amy M Weeks.
      Protein phosphorylation is dynamically regulated by the opposing activities of phosphowriter enzymes (kinases) and phosphoeraser enzymes (phosphatases and phospholyases). While significant progress has been made toward defining the sequences preferences of kinases, the selectivity of phosphoerasers has not been explored at scale. Here, we develop an experimental platform based on tandem mass spectrometry analysis of phosphoproteome-derived peptide libraries (PhosPropels) to map phosphoeraser activity across thousands of biologically relevant phosphosites. We extract positional residue preferences to rapidly define sequence motifs recognized by eight phosphoerasers spanning diverse species of origin, protein folds, and enzymatic mechanisms. Taking advantage of the throughput of our approach, we profiled 34 variants of the phosphothreonine lyase OspF from Shigella flexneri , uncovering an intrinsic preference for p38 and Erk MAP kinase activation loops and revealing the enzyme residues that influence its selectivity for phosphothreonine. Our results establish a general method for linking phosphorylation sites to the enzymes that remove them, providing a means to dissect a key component of cellular regulatory networks.
    DOI:  https://doi.org/10.1101/2025.08.12.669978
  7. J Vis Exp. 2025 Aug 01.
    Using R, Seurat, and CellChat to Analyze a Single-Cell Transcriptomics Dataset of Mouse Skin Wound Healing.
    Shalyn Keiser, Nichole Botello, Ethan Cruz, Mateusz S Wietecha.
      The process of wound healing is regulated by complex interactions between different cell types across space and time. Through the profiling of individual cells within their complex environment, single-cell transcriptomics methods enable the investigation of cellular heterogeneity, cell communication networks, and cell-cell interactions involved in the wound healing process. However, many single-cell analysis tools are run within a computer coding environment, and their more widespread use by wound healing scientists is thwarted by the apparent lack of bioinformatics expertise. Therefore, a step-by-step workflow is presented showing how to use a graphical coding environment called RStudio to perform a basic single-cell analysis of a temporal mouse excisional skin wound healing dataset. This visual and guided protocol will enable scientists with no bioinformatics background to download a previously published wound healing dataset, perform critical quality control steps, run a standard single-cell analysis workflow including dataset visualizations and cell type annotations using Seurat, run cell subtype analyses, run module scoring analyses, run cell-cell interaction analyses using CellChat, and perform integrative analyses of multiple datasets using Seurat. Narrative explanations are provided for each step in the protocol and graphical results from every line of code are presented to safely guide the user through the workflow. The goal of this visual introduction to a single-cell analysis pipeline is to enable more wound healing scientists to use bioinformatics tools directly in their own laboratories in order to facilitate deeper analyses of their own single-cell datasets as well as more widespread re-analyses of previously published single-cell datasets.
    DOI:  https://doi.org/10.3791/67266
  8. Nat Methods. 2025 Aug 18.
    High-throughput profiling of chemical-induced gene expression across 93,644 perturbations.
    Lei Xiang, Yumei Wang, Wei Shao, Qingzhou Li, Xiankuo Yu, Mingming Wei, Yu Gui, Shengrong Li, Pan Qin, Chao Hu, Guochen Zhang, Xianwen Zhang, Jiawen Wang, Yingying Li, Jun An, Yan Luo, Yile Liao, Jinghong Deng, Xinran Tai, Richard Y Xu, Lijun Huang, Dale Guo, Guanbin Zhang, Zhi Xie, Yun Deng, Junquan Xu, Dong Wang.
      In this Resource, we present an extensive dataset of chemical-induced gene signatures (CIGS), encompassing expression patterns of 3,407 genes regulating key biological processes in 2 human cell lines exposed to 13,221 compounds across 93,664 perturbations. This dataset encompasses 319,045,108 gene expression events, generated through 2 high-throughput technologies: the previously documented high-throughput sequencing-based high-throughput screening (HTS2) and the newly developed highly multiplexed and parallel sequencing (HiMAP-seq). Our results show that HiMAP-seq is comparable to RNA sequencing, but can profile the expression of thousands of genes across thousands of samples in one single test by utilizing a pooled-sample strategy. We further illustrate CIGS's utility in elucidating the mechanism of action of unannotated small molecules, like ligustroflavone and 2,4-dihydroxybenzaldehyde, and to identify perturbation-induced cell states, such as those resistant to ferroptosis. The full dataset is publicly accessible at https://cigs.iomicscloud.com/ .
    DOI:  https://doi.org/10.1038/s41592-025-02781-5
This page is being maintained by Thomas Krichel. It was last updated on 2025‒08‒24 at 10:33.