bims-pideca Biomed News
on Class IA PI3K signalling in development and cancer
Issue of 2023–12–10
sixteen papers selected by
Ralitsa Radostinova Madsen, MRC-PPU
  1. mTOR takes charge: Relaying uncharged tRNA levels by mTOR ubiquitination.
  2. Protocol for screening cellular outputs activated by optogenetically controlled temporal PI3K signaling activation patterns.
  3. FDA approves first-in-class AKT inhibitor.
  4. How developmental cell atlases inform stem cell embryo models.
  5. An enzyme that selectively S-nitrosylates proteins to regulate insulin signaling.
  6. Death by a thousand cuts through kinase inhibitor combinations that maximize selectivity and enable rational multitargeting.
  7. scPipe: an extended preprocessing pipeline for comprehensive single-cell ATAC-Seq data integration in R/Bioconductor.
  8. A unified approach to dissecting biphasic responses in cell signalling.
  9. A biotin targeting chimera (BioTAC) system to map small molecule interactomes in situ.
  10. kallisto, bustools, and kb-python for quantifying bulk, single-cell, and single-nucleus RNA-seq.
  11. Thrombomodulin Regulates PTEN/AKT Signaling Axis in Endothelial Cells.
  12. A human embryonic limb cell atlas resolved in space and time.
  13. One-Hour Phosphoproteome Analysis with the Orbitrap Astral Mass Spectrometer.
  14. Hsf1 and the molecular chaperone Hsp90 support a 'rewiring stress response' leading to an adaptive cell size increase in chronic stress.
  15. A reversible epigenetic memory of inflammatory injury controls lineage plasticity and tumor initiation in the mouse pancreas.
  16. High-capacity sample multiplexing for single cell chromatin accessibility profiling.
  1. Cell Metab. 2023 Dec 05. pii: S1550-4131(23)00417-5. [Epub ahead of print]35(12): 2097-2099
    mTOR takes charge: Relaying uncharged tRNA levels by mTOR ubiquitination.
    Estela Jacinto.
      Nutrient availability is conveyed to the mechanistic target of rapamycin (mTOR), which couples metabolic processes with cell growth and proliferation. How mTOR itself is modulated by amino acid levels remains poorly understood. Ge and colleagues now demonstrate that broad sensing of uncharged tRNAs by GCN2/FBXO22 inactivates mTOR complex 1 (mTORC1) via mTOR ubiquitination.
    DOI:  https://doi.org/10.1016/j.cmet.2023.11.006
  2. STAR Protoc. 2023 Oct 27. pii: S2666-1667(23)00589-0. [Epub ahead of print]4(4): 102622
    Protocol for screening cellular outputs activated by optogenetically controlled temporal PI3K signaling activation patterns.
    Yoshibumi Ueda, Shohei Matsushita, Mitsugu Suzuki, Takeaki Ozawa.
      PI3K signaling elicits distinct outputs in response to different patterns of extracellular stimulation. Here, we present a protocol for screening cellular outputs activated by optogenetically controlled temporal PI3K signaling activation patterns in 96-well plates. We describe steps for establishing PPAP2-stable cells, probe expression, and blue light irradiation. We then detail procedures for analysis of translation activity. This protocol can be applied for purposes, such as examining the effect of PI3K signaling on the efficacy of anticancer drugs. For complete details on the use and execution of this protocol, please refer to Ueda et al. (2022).1.
    Keywords:  Cancer; Cell Biology; Cell Membrane
    DOI:  https://doi.org/10.1016/j.xpro.2023.102622
  3. Nat Rev Drug Discov. 2023 Dec 04.
    FDA approves first-in-class AKT inhibitor.
    Asher Mullard.
      
    DOI:  https://doi.org/10.1038/d41573-023-00202-w
  4. Nat Methods. 2023 Dec 06.
    How developmental cell atlases inform stem cell embryo models.
    Muzlifah Haniffa, Aidan Maartens, Sarah A Teichmann.
      
    DOI:  https://doi.org/10.1038/s41592-023-02072-x
  5. Cell. 2023 Nov 30. pii: S0092-8674(23)01226-6. [Epub ahead of print]
    An enzyme that selectively S-nitrosylates proteins to regulate insulin signaling.
    Hua-Lin Zhou, Zachary W Grimmett, Nicholas M Venetos, Colin T Stomberski, Zhaoxia Qian, Precious J McLaughlin, Puneet K Bansal, Rongli Zhang, James D Reynolds, Richard T Premont, Jonathan S Stamler.
      Acyl-coenzyme A (acyl-CoA) species are cofactors for numerous enzymes that acylate thousands of proteins. Here, we describe an enzyme that uses S-nitroso-CoA (SNO-CoA) as its cofactor to S-nitrosylate multiple proteins (SNO-CoA-assisted nitrosylase, SCAN). Separate domains in SCAN mediate SNO-CoA and substrate binding, allowing SCAN to selectively catalyze SNO transfer from SNO-CoA to SCAN to multiple protein targets, including the insulin receptor (INSR) and insulin receptor substrate 1 (IRS1). Insulin-stimulated S-nitrosylation of INSR/IRS1 by SCAN reduces insulin signaling physiologically, whereas increased SCAN activity in obesity causes INSR/IRS1 hypernitrosylation and insulin resistance. SCAN-deficient mice are thus protected from diabetes. In human skeletal muscle and adipose tissue, SCAN expression increases with body mass index and correlates with INSR S-nitrosylation. S-nitrosylation by SCAN/SNO-CoA thus defines a new enzyme class, a unique mode of receptor tyrosine kinase regulation, and a revised paradigm for NO function in physiology and disease.
    Keywords:  S-nitrosylation, nitric oxide, redox signaling, posttranslational modification, diabetes, nitrosylase, insulin receptor
    DOI:  https://doi.org/10.1016/j.cell.2023.11.009
  6. Elife. 2023 Dec 04. pii: e86189. [Epub ahead of print]12
    Death by a thousand cuts through kinase inhibitor combinations that maximize selectivity and enable rational multitargeting.
    Ian R Outhwaite, Sukrit Singh, Benedict-Tilman Berger, Stefan Knapp, John D Chodera, Markus A Seeliger.
      Kinase inhibitors are successful therapeutics in the treatment of cancers and autoimmune diseases and are useful tools in biomedical research. However, the high sequence and structural conservation of the catalytic kinase domain complicates the development of selective kinase inhibitors. Inhibition of off-target kinases makes it difficult to study the mechanism of inhibitors in biological systems. Current efforts focus on the development of inhibitors with improved selectivity. Here, we present an alternative solution to this problem by combining inhibitors with divergent off-target effects. We develop a multicompound-multitarget scoring (MMS) method that combines inhibitors to maximize target inhibition and to minimize off-target inhibition. Additionally, this framework enables optimization of inhibitor combinations for multiple on-targets. Using MMS with published kinase inhibitor datasets we determine potent inhibitor combinations for target kinases with better selectivity than the most selective single inhibitor and validate the predicted effect and selectivity of inhibitor combinations using in vitro and in cellulo techniques. MMS greatly enhances selectivity in rational multitargeting applications. The MMS framework is generalizable to other non-kinase biological targets where compound selectivity is a challenge and diverse compound libraries are available.
    Keywords:  biochemistry; chemical biology; computational biology; none; systems biology
    DOI:  https://doi.org/10.7554/eLife.86189
  7. NAR Genom Bioinform. 2023 Dec;5(4): lqad105
    scPipe: an extended preprocessing pipeline for comprehensive single-cell ATAC-Seq data integration in R/Bioconductor.
    Shanika L Amarasinghe, Phil Yang, Oliver Voogd, Haoyu Yang, Mei R M Du, Shian Su, Daniel V Brown, Jafar S Jabbari, Rory Bowden, Matthew E Ritchie.
      scPipe is a flexible R/Bioconductor package originally developed to analyse platform-independent single-cell RNA-Seq data. To expand its preprocessing capability to accommodate new single-cell technologies, we further developed scPipe to handle single-cell ATAC-Seq and multi-modal (RNA-Seq and ATAC-Seq) data. After executing multiple data cleaning steps to remove duplicated reads, low abundance features and cells of poor quality, a SingleCellExperiment object is created that contains a sparse count matrix with features of interest in the rows and cells in the columns. Quality control information (e.g. counts per cell, features per cell, total number of fragments, fraction of fragments per peak) and any relevant feature annotations are stored as metadata. We demonstrate that scPipe can efficiently identify 'true' cells and provides flexibility for the user to fine-tune the quality control thresholds using various feature and cell-based metrics collected during data preprocessing. Researchers can then take advantage of various downstream single-cell tools available in Bioconductor for further analysis of scATAC-Seq data such as dimensionality reduction, clustering, motif enrichment, differential accessibility and cis-regulatory network analysis. The scPipe package enables a complete beginning-to-end pipeline for single-cell ATAC-Seq and RNA-Seq data analysis in R.
    DOI:  https://doi.org/10.1093/nargab/lqad105
  8. Elife. 2023 Dec 06. pii: e86520. [Epub ahead of print]12
    A unified approach to dissecting biphasic responses in cell signalling.
    Vaidhiswaran Ramesh, J Krishnan.
      Biphasic responses are encountered at all levels in biological systems. At the cellular level, biphasic dose-responses are widely encountered in cell signalling and post-translational modification systems and represent safeguards against over-activation or overexpression of species. In this paper we provide a unified theoretical synthesis of biphasic responses in cell signalling systems, by assessing signalling systems ranging from basic biochemical building blocks to canonical network structures to well-characterized exemplars on one hand, and examining different types of doses on the other. By using analytical and computational approaches applied to a range of systems across levels (described by broadly employed models) we reveal (i) design principles enabling the presence of biphasic responses, including in almost all instances, an explicit characterization of the parameter space (ii) structural factors which preclude the possibility of biphasic responses (iii) different combinations of the presence or absence of enzyme-biphasic and substrate-biphasic responses, representing safeguards against overactivation and overexpression respectively (iv) the possibility of broadly robust biphasic responses (v) the complete alteration of signalling behaviour in a network due to biphasic interactions between species (biphasic regulation) (vi) the propensity of different co-existing biphasic responses in the Erk signalling network. These results both individually and in totality have a number of important consequences for systems and synthetic biology.
    Keywords:  none; physics of living systems
    DOI:  https://doi.org/10.7554/eLife.86520
  9. Nat Commun. 2023 Dec 04. 14(1): 8016
    A biotin targeting chimera (BioTAC) system to map small molecule interactomes in situ.
    Andrew J Tao, Jiewei Jiang, Gillian E Gadbois, Pavitra Goyal, Bridget T Boyle, Elizabeth J Mumby, Samuel A Myers, Justin G English, Fleur M Ferguson.
      Understanding how small molecules bind to specific protein complexes in living cells is critical to understanding their mechanism-of-action. Unbiased chemical biology strategies for direct readout of protein interactome remodelling by small molecules would provide advantages over target-focused approaches, including the ability to detect previously unknown ligand targets and complexes. However, there are few current methods for unbiased profiling of small molecule interactomes. To address this, we envisioned a technology that would combine the sensitivity and live-cell compatibility of proximity labelling coupled to mass spectrometry, with the specificity and unbiased nature of chemoproteomics. In this manuscript, we describe the BioTAC system, a small-molecule guided proximity labelling platform that can rapidly identify both direct and complexed small molecule binding proteins. We benchmark the system against µMap, photoaffinity labelling, affinity purification coupled to mass spectrometry and proximity labelling coupled to mass spectrometry datasets. We also apply the BioTAC system to provide interactome maps of Trametinib and analogues. The BioTAC system overcomes a limitation of current approaches and supports identification of both inhibitor bound and molecular glue bound complexes.
    DOI:  https://doi.org/10.1038/s41467-023-43507-5
  10. bioRxiv. 2023 Nov 22. pii: 2023.11.21.568164. [Epub ahead of print]
    kallisto, bustools, and kb-python for quantifying bulk, single-cell, and single-nucleus RNA-seq.
    Delaney K Sullivan, Kyung Hoi Joseph Min, Kristján Eldjárn Hjörleifsson, Laura Luebbert, Guillaume Holley, Lambda Moses, Johan Gustafsson, Nicolas L Bray, Harold Pimentel, A Sina Booeshaghi, Páll Melsted, Lior Pachter.
      The term "RNA-seq" refers to a collection of assays based on sequencing experiments that involve quantifying RNA species from bulk tissue, from single cells, or from single nuclei. The kallisto, bustools, and kb-python programs are free, open-source software tools for performing this analysis that together can produce gene expression quantification from raw sequencing reads. The quantifications can be individualized for multiple cells, multiple samples, or both. Additionally, these tools allow gene expression values to be classified as originating from nascent RNA species or mature RNA species, making this workflow amenable to both cell-based and nucleus-based assays. This protocol describes in detail how to use kallisto and bustools in conjunction with a wrapper, kb-python, to preprocess RNA-seq data.
    DOI:  https://doi.org/10.1101/2023.11.21.568164
  11. Arterioscler Thromb Vasc Biol. 2023 Dec 07.
    Thrombomodulin Regulates PTEN/AKT Signaling Axis in Endothelial Cells.
    Hemant Giri, Indranil Biswas, Alireza R Rezaie.
       BACKGROUND: We recently demonstrated that deletion of thrombomodulin gene from endothelial cells results in upregulation of proinflammatory phenotype. In this study, we investigated the molecular basis for the altered phenotype in thrombomodulin-deficient (TM-/-) cells.
    METHODS: Different constructs containing deletions or mutations in the cytoplasmic domain of thrombomodulin were prepared and introduced to TM-/- cells. The phenotype of cells expressing different derivatives of thrombomodulin and tissue samples of thrombomodulin-knockout mice were analyzed for expression of distinct regulatory genes in established signaling assays.
    RESULTS: The phosphatase and tensin homolog were phosphorylated and its recruitment to the plasma membrane was impaired in TM-/- cells, leading to hyperactivation of AKT (protein kinase B) and phosphorylation-dependent nuclear exclusion of the transcription factor, forkhead box O1. The proliferative/migratory properties of TM-/- cells were enhanced, and cells exhibited hypersensitivity to stimulation by angiopoietin 1 and vascular endothelial growth factor. Reexpression of wild-type thrombomodulin in TM-/- cells normalized the cellular phenotype; however, thrombomodulin lacking its cytoplasmic domain failed to restore the normal phenotype in TM-/- cells. Increased basal permeability and loss of VE-cadherin were restored to normal levels by reexpression of wild-type thrombomodulin but not by a thrombomodulin construct lacking its cytoplasmic domain. A thrombomodulin cytoplasmic domain deletion mutant containing 3-membrane-proximal Arg-Lys-Lys residues restored the barrier-permeability function of TM-/- cells. Enhanced phosphatase and tensin homolog phosphorylation and activation of AKT and mTORC1 (mammalian target of rapamycin complex 1) were also observed in the liver of thrombomodulin-KO mice.
    CONCLUSIONS: These results suggest that the cytoplasmic domain of thrombomodulin interacts with the actin cytoskeleton and plays a crucial role in regulation of phosphatase and tensin homolog/AKT signaling in endothelial cells.
    Keywords:  endothelial cells; phenotype; signaling; thrombomodulin; upregulation
    DOI:  https://doi.org/10.1161/ATVBAHA.123.320000
  12. Nature. 2023 Dec 06.
    A human embryonic limb cell atlas resolved in space and time.
    Bao Zhang, Peng He, John E G Lawrence, Shuaiyu Wang, Elizabeth Tuck, Brian A Williams, Kenny Roberts, Vitalii Kleshchevnikov, Lira Mamanova, Liam Bolt, Krzysztof Polanski, Tong Li, Rasa Elmentaite, Eirini S Fasouli, Martin Prete, Xiaoling He, Nadav Yayon, Yixi Fu, Hao Yang, Chen Liang, Hui Zhang, Raphael Blain, Alain Chedotal, David R FitzPatrick, Helen Firth, Andrew Dean, Omer Ali Bayraktar, John C Marioni, Roger A Barker, Mekayla A Storer, Barbara J Wold, Hongbo Zhang, Sarah A Teichmann.
      Human limbs emerge during the fourth post-conception week as mesenchymal buds, which develop into fully formed limbs over the subsequent months1. This process is orchestrated by numerous temporally and spatially restricted gene expression programmes, making congenital alterations in phenotype common2. Decades of work with model organisms have defined the fundamental mechanisms underlying vertebrate limb development, but an in-depth characterization of this process in humans has yet to be performed. Here we detail human embryonic limb development across space and time using single-cell and spatial transcriptomics. We demonstrate extensive diversification of cells from a few multipotent progenitors to myriad differentiated cell states, including several novel cell populations. We uncover two waves of human muscle development, each characterized by different cell states regulated by separate gene expression programmes, and identify musculin (MSC) as a key transcriptional repressor maintaining muscle stem cell identity. Through assembly of multiple anatomically continuous spatial transcriptomic samples using VisiumStitcher, we map cells across a sagittal section of a whole fetal hindlimb. We reveal a clear anatomical segregation between genes linked to brachydactyly and polysyndactyly, and uncover transcriptionally and spatially distinct populations of the mesenchyme in the autopod. Finally, we perform single-cell RNA sequencing on mouse embryonic limbs to facilitate cross-species developmental comparison, finding substantial homology between the two species.
    DOI:  https://doi.org/10.1038/s41586-023-06806-x
  13. bioRxiv. 2023 Nov 21. pii: 2023.11.21.568149. [Epub ahead of print]
    One-Hour Phosphoproteome Analysis with the Orbitrap Astral Mass Spectrometer.
    Noah M Lancaster, Pavel Sinitcyn, Patrick Forny, Trenton M Peters-Clarke, Caroline Fecher, Andrew J Smith, Evgenia Shishkova, Tabiwang N Arrey, Anna Pashkova, Margaret Lea Robinson, Nicholas Arp, Jing Fan, Juli Hansen, Andrea Galmozzi, Lia R Serrano, Michael S Westphall, Hamish Stewart, Christian Hock, Eugen Damoc, David J Pagliarini, Vlad Zabrouskov, Joshua J Coon.
      As a key mechanism for cellular signal transduction, protein phosphorylation plays critical roles in myriad cellular processes. This modification, however, is highly dynamic and occurs at sub-stoichiometric levels. Mass spectrometry is an essential tool for studying this modification on a global scale; however, the technology's impact suffers from four main limitations: need for site localization, dynamic range, reproducibility, and throughput. Here we describe the use of a novel mass spectrometer (Orbitrap Astral) coupled with data-independent acquisition (DIA) to achieve detection of close to 40,000 unique phosphorylation sites within one hour of analysis. We applied this approach to generate a phosphoproteome atlas of the mouse. Altogether, we detected 81,120 unique phosphorylation sites within 12 hours of measurement. With this unique dataset, we examine the sequence and structural context of protein phosphorylation. Finally, we highlight the discovery potential of this resource with multiple examples of novel phosphorylation events relevant to mitochondrial and brain biology.
    DOI:  https://doi.org/10.1101/2023.11.21.568149
  14. Elife. 2023 Dec 07. pii: RP88658. [Epub ahead of print]12
    Hsf1 and the molecular chaperone Hsp90 support a 'rewiring stress response' leading to an adaptive cell size increase in chronic stress.
    Samarpan Maiti, Kaushik Bhattacharya, Diana Wider, Dina Hany, Olesya Panasenko, Lilia Bernasconi, Nicolas Hulo, Didier Picard.
      Cells are exposed to a wide variety of internal and external stresses. Although many studies have focused on cellular responses to acute and severe stresses, little is known about how cellular systems adapt to sublethal chronic stresses. Using mammalian cells in culture, we discovered that they adapt to chronic mild stresses of up to two weeks, notably proteotoxic stresses such as heat, by increasing their size and translation, thereby scaling the amount of total protein. These adaptations render them more resilient to persistent and subsequent stresses. We demonstrate that Hsf1, well known for its role in acute stress responses, is required for the cell size increase, and that the molecular chaperone Hsp90 is essential for coupling the cell size increase to augmented translation. We term this translational reprogramming the 'rewiring stress response', and propose that this protective process of chronic stress adaptation contributes to the increase in size as cells get older, and that its failure promotes aging.
    Keywords:  aging; cell biology; cytoplasmic density; human; proteostasis; senescence; stress adaptation; translation
    DOI:  https://doi.org/10.7554/eLife.88658
  15. Dev Cell. 2023 Nov 30. pii: S1534-5807(23)00583-X. [Epub ahead of print]
    A reversible epigenetic memory of inflammatory injury controls lineage plasticity and tumor initiation in the mouse pancreas.
    David J Falvo, Adrien Grimont, Paul Zumbo, William B Fall, Julie L Yang, Alexa Osterhoudt, Grace Pan, Andre F Rendeiro, Yinuo Meng, John E Wilkinson, Friederike Dündar, Olivier Elemento, Rhonda K Yantiss, Erika Hissong, Richard Koche, Doron Betel, Rohit Chandwani.
      Inflammation is essential to the disruption of tissue homeostasis and can destabilize the identity of lineage-committed epithelial cells. Here, we employ lineage-traced mouse models, single-cell transcriptomic and chromatin analyses, and CUT&TAG to identify an epigenetic memory of inflammatory injury in the pancreatic acinar cell compartment. Despite resolution of pancreatitis, our data show that acinar cells fail to return to their molecular baseline, with retention of elevated chromatin accessibility and H3K4me1 at metaplasia genes, such that memory represents an incomplete cell fate decision. In vivo, we find this epigenetic memory controls lineage plasticity, with diminished metaplasia in response to a second insult but increased tumorigenesis with an oncogenic Kras mutation. The lowered threshold for oncogenic transformation, in turn, can be restored by blockade of MAPK signaling. Together, we define the chromatin dynamics, molecular encoding, and recall of a prolonged epigenetic memory of inflammatory injury that impacts future responses but remains reversible.
    Keywords:  ATAC-seq; CUT&TAG; cell fate; epigenetic memory; inflammatory injury; lineage plasticity; pancreatic cancer; pancreatitis; single-cell RNA sequencing; tumorigenesis
    DOI:  https://doi.org/10.1016/j.devcel.2023.11.008
  16. BMC Genomics. 2023 Dec 04. 24(1): 737
    High-capacity sample multiplexing for single cell chromatin accessibility profiling.
    Gregory T Booth, Riza M Daza, Sanjay R Srivatsan, José L McFaline-Figueroa, Rula Green Gladden, Andrew C Mullen, Scott N Furlan, Jay Shendure, Cole Trapnell.
      Single-cell chromatin accessibility has emerged as a powerful means of understanding the epigenetic landscape of diverse tissues and cell types, but profiling cells from many independent specimens is challenging and costly. Here we describe a novel approach, sciPlex-ATAC-seq, which uses unmodified DNA oligos as sample-specific nuclear labels, enabling the concurrent profiling of chromatin accessibility within single nuclei from virtually unlimited specimens or experimental conditions. We first demonstrate our method with a chemical epigenomics screen, in which we identify drug-altered distal regulatory sites predictive of compound- and dose-dependent effects on transcription. We then analyze cell type-specific chromatin changes in PBMCs from multiple donors responding to synthetic and allogeneic immune stimulation. We quantify stimulation-altered immune cell compositions and isolate the unique effects of allogeneic stimulation on chromatin accessibility specific to T-lymphocytes. Finally, we observe that impaired global chromatin decondensation often coincides with chemical inhibition of allogeneic T-cell activation.
    Keywords:  Chromatin; Genomics; Perturbation; Screening; Sequencing; Single-cell
    DOI:  https://doi.org/10.1186/s12864-023-09832-1
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