bims-pideca Biomed News
on Class IA PI3K signalling in development and cancer
Issue of 2023–06–25
fifteen papers selected by
Ralitsa Radostinova Madsen, MRC-PPU
  1. Polydom/SVEP1 binds to Tie1 and promotes migration of lymphatic endothelial cells.
  2. Democratizing knowledge representation with BioCypher.
  3. Tuberous Sclerosis Complex cell-derived EVs have an altered protein cargo capable of regulating their microenvironment and have potential as disease biomarkers.
  4. A paradigm shift: AMPK negatively regulates ULK1 activity.
  5. MutSα and MutSβ as size-dependent cellular determinants for prime editing in human embryonic stem cells.
  6. Shedding light on stem cells: Optogenetics uncover the role of ERK dynamics in pluripotency.
  7. The effect of background noise and its removal on the analysis of single-cell expression data.
  8. CAJAL enables analysis and integration of single-cell morphological data using metric geometry.
  9. Sequential apoptotic and multiplexed proteomic evaluation of single cancer cells.
  10. A review of open-source image analysis tools for mammalian cell culture: algorithms, features and implementations.
  11. Predicting Mutations Generated by Cas9, Base Editing, and Prime Editing in Mammalian Cells.
  12. Oncogenic Ras deregulates cell-substrate interactions during mitotic rounding and respreading to alter cell division orientation.
  13. Loss of Macrophage mTORC2 Drives Atherosclerosis via FoxO1 and IL-1β Signaling.
  14. PE-STOP: A versatile tool for installing nonsense substitutions amenable for precise reversion.
  15. The computational capabilities of many-to-many protein interaction networks.
  1. J Cell Biol. 2023 Sep 04. pii: e202208047. [Epub ahead of print]222(9):
    Polydom/SVEP1 binds to Tie1 and promotes migration of lymphatic endothelial cells.
    Ryoko Sato-Nishiuchi, Masamichi Doiguchi, Nanami Morooka, Kiyotoshi Sekiguchi.
      Polydom is an extracellular matrix protein involved in lymphatic vessel development. Polydom-deficient mice die immediately after birth due to defects in lymphatic vessel remodeling, but the mechanism involved is poorly understood. Here, we report that Polydom directly binds to Tie1, an orphan receptor in the Angiopoietin-Tie axis, and facilitates migration of lymphatic endothelial cells (LECs) in a Tie1-dependent manner. Polydom-induced LEC migration is diminished by PI3K inhibitors but not by an ERK inhibitor, suggesting that the PI3K/Akt signaling pathway is involved in Polydom-induced LEC migration. In line with this possibility, Akt phosphorylation in LECs is enhanced by Polydom although no significant Tie1 phosphorylation is induced by Polydom. LECs also exhibited nuclear exclusion of Foxo1, a signaling event downstream of Akt activation, which was impaired in Polydom-deficient mice. These findings indicate that Polydom is a physiological ligand for Tie1 and participates in lymphatic vessel development through activation of the PI3K/Akt pathway.
    DOI:  https://doi.org/10.1083/jcb.202208047
  2. Nat Biotechnol. 2023 Jun 19.
    Democratizing knowledge representation with BioCypher.
    Sebastian Lobentanzer, Patrick Aloy, Jan Baumbach, Balazs Bohar, Vincent J Carey, Pornpimol Charoentong, Katharina Danhauser, Tunca Doğan, Johann Dreo, Ian Dunham, Elias Farr, Adrià Fernandez-Torras, Benjamin M Gyori, Michael Hartung, Charles Tapley Hoyt, Christoph Klein, Tamas Korcsmaros, Andreas Maier, Matthias Mann, David Ochoa, Elena Pareja-Lorente, Ferdinand Popp, Martin Preusse, Niklas Probul, Benno Schwikowski, Bünyamin Sen, Maximilian T Strauss, Denes Turei, Erva Ulusoy, Dagmar Waltemath, Judith A H Wodke, Julio Saez-Rodriguez.
      
    DOI:  https://doi.org/10.1038/s41587-023-01848-y
  3. J Extracell Vesicles. 2023 06;12(6): e12336
    Tuberous Sclerosis Complex cell-derived EVs have an altered protein cargo capable of regulating their microenvironment and have potential as disease biomarkers.
    Muireann Ní Bhaoighill, Juan M Falcón-Pérez, Félix Royo, Andrew R Tee, Jason P Webber, Elaine A Dunlop.
      Hyperactivation of mechanistic target of rapamycin complex 1 (mTORC1) is a feature of many solid tumours and is a key pathogenic driver in the inherited condition Tuberous Sclerosis Complex (TSC). Modulation of the tumour microenvironment by extracellular vesicles (EVs) is known to facilitate the development of various cancers. The role of EVs in modulating the tumour microenvironment and their impact on the development of TSC tumours, however, remains unclear. This study, therefore, focuses on the poorly defined contribution of EVs to tumour growth in TSC. We characterised EVs secreted from TSC2-deficient and TSC2-expressing cells and identified a distinct protein cargo in TSC2-deficient EVs, containing an enrichment of proteins thought to be involved in tumour-supporting signalling pathways. We show EVs from TSC2-deficient cells promote cell viability, proliferation and growth factor secretion from recipient fibroblasts within the tumour microenvironment. Rapalogs (mTORC1 inhibitors) are the current therapy for TSC tumours. Here, we demonstrate a previously unknown intercellular therapeutic effect of rapamycin in altering EV cargo and reducing capacity to promote cell proliferation in the tumour microenvironment. Furthermore, EV cargo proteins have the potential for clinical applications as TSC biomarkers, and we reveal three EV-associated proteins that are elevated in plasma from TSC patients compared to healthy donor plasma.
    Keywords:  TSC2; extracellular vesicles (EVs); fibroblasts; mTORC1; tuberous sclerosis complex (TSC); tumour microenvironment
    DOI:  https://doi.org/10.1002/jev2.12336
  4. Autophagy. 2023 Jun 20. 1-3
    A paradigm shift: AMPK negatively regulates ULK1 activity.
    Ji-Man Park, Do-Hyung Kim.
      In glucose-starved cells, macroautophagy (hereafter referred to as autophagy) is considered to serve as an energy-generating process contributing to cell survival. AMPK (adenosine monophosphate-activated protein kinase) is the primary cellular energy sensor that is activated during glucose starvation. According to the current paradigm in the field, AMPK promotes autophagy in response to energy deprivation by binding and phosphorylating ULK1 (UNC-51 like kinase 1), the protein kinase responsible for autophagy initiation. However, conflicting findings have been reported casting doubts about the current established model. In our recent study, we have thoroughly reevaluated the role of AMPK in autophagy. Contrary to the current paradigm, our study revealed that AMPK functions as a negative regulator of ULK1 activity. The study has elucidated the underlying mechanism and demonstrated the significance of the negative role in controlling autophagy and maintaining cellular resilience during energy depletion.Abbreviations: AMPK: adenosine monophosphate-activated protein kinase; ULK1: UNC-51 like kinase 1; MTORC1: mechanistic target of rapamycin complex 1; ATG14: autophagy-related protein 14; PIK3C3: phosphatidylinositol 3-kinase catalytic subunit type 3; ATP: adenosine triphosphate; VPS34: vacuolar protein sorting 34; BECN1: Beclin 1; AMPKα: AMPK catalytic subunit α; LKB1: liver kinase B1; PIK3R4: phosphatidylinositol 3-kinase regulatory subunit 4.
    Keywords:  AMPK; LKB1; MTORC1; ULK1; energy stress; glucose starvation
    DOI:  https://doi.org/10.1080/15548627.2023.2223465
  5. Mol Ther Nucleic Acids. 2023 Jun 13. 32 914-922
    MutSα and MutSβ as size-dependent cellular determinants for prime editing in human embryonic stem cells.
    Ju-Chan Park, Yun-Jeong Kim, Jun Hee Han, Dayeon Kim, Mihn Jeong Park, Jumee Kim, Hyeon-Ki Jang, Sangsu Bae, Hyuk-Jin Cha.
      Precise genome editing in human pluripotent stem cells (hPSCs) has potential applications in isogenic disease modeling and ex vivo stem cell therapy, necessitating diverse genome editing tools. However, unlike differentiated somatic cells, hPSCs have unique cellular properties that maintain genome integrity, which largely determine the overall efficiency of an editing tool. Considering the high demand for prime editors (PEs), it is imperative to characterize the key molecular determinants of PE outcomes in hPSCs. Through homozygous knockout (KO) of MMR pathway key proteins MSH2, MSH3, and MSH6, we reveal that MutSα and MutSβ determine PE efficiency in an editing size-dependent manner. Notably, MSH2 perturbation disrupted both MutSα and MutSβ complexes, dramatically escalating PE efficiency from base mispair to 10 bases, up to 50 folds. Similarly, impaired MutSα by MSH6 KO improved editing efficiency from single to three base pairs, while defective MutSβ by MSH3 KO heightened efficiency from three to 10 base pairs. Thus, the size-dependent effect of MutSα and MutSβ on prime editing implies that MMR is a vital PE efficiency determinant in hPSCs and highlights the distinct roles of MutSα and MutSβ in its outcome.
    Keywords:  DNA damage repair; MMR; MT: RNA/DNA editing;; MutSα; MutSβ; genome editing; human embryonic stem cells; human pluripotent stem cells; prime editor
    DOI:  https://doi.org/10.1016/j.omtn.2023.05.015
  6. Dev Cell. 2023 06 19. pii: S1534-5807(23)00249-6. [Epub ahead of print]58(12): 1005-1006
    Shedding light on stem cells: Optogenetics uncover the role of ERK dynamics in pluripotency.
    Adam A Moverley, Nicolas Plachta.
      In this issue of Developmental Cell, Arekatla et al. use optogenetic technologies to dissect the roles of ERK and AKT dynamics in pluripotency. They show how mouse embryonic stem cells can retain memory of signaling events controlling their fate.
    DOI:  https://doi.org/10.1016/j.devcel.2023.05.016
  7. Genome Biol. 2023 06 19. 24(1): 140
    The effect of background noise and its removal on the analysis of single-cell expression data.
    Philipp Janssen, Zane Kliesmete, Beate Vieth, Xian Adiconis, Sean Simmons, Jamie Marshall, Cristin McCabe, Holger Heyn, Joshua Z Levin, Wolfgang Enard, Ines Hellmann.
       BACKGROUND: In droplet-based single-cell and single-nucleus RNA-seq experiments, not all reads associated with one cell barcode originate from the encapsulated cell. Such background noise is attributed to spillage from cell-free ambient RNA or barcode swapping events.
    RESULTS: Here, we characterize this background noise exemplified by three scRNA-seq and two snRNA-seq replicates of mouse kidneys. For each experiment, cells from two mouse subspecies are pooled, allowing to identify cross-genotype contaminating molecules and thus profile background noise. Background noise is highly variable across replicates and cells, making up on average 3-35% of the total counts (UMIs) per cell and we find that noise levels are directly proportional to the specificity and detectability of marker genes. In search of the source of background noise, we find multiple lines of evidence that the majority of background molecules originates from ambient RNA. Finally, we use our genotype-based estimates to evaluate the performance of three methods (CellBender, DecontX, SoupX) that are designed to quantify and remove background noise. We find that CellBender provides the most precise estimates of background noise levels and also yields the highest improvement for marker gene detection. By contrast, clustering and classification of cells are fairly robust towards background noise and only small improvements can be achieved by background removal that may come at the cost of distortions in fine structure.
    CONCLUSIONS: Our findings help to better understand the extent, sources and impact of background noise in single-cell experiments and provide guidance on how to deal with it.
    Keywords:  (Gold) standard scRNA-seq data set; Ambient RNA; Background noise; Barcode swapping; Correction method comparison; Single-cell RNA-sequencing
    DOI:  https://doi.org/10.1186/s13059-023-02978-x
  8. Nat Commun. 2023 Jun 21. 14(1): 3672
    CAJAL enables analysis and integration of single-cell morphological data using metric geometry.
    Kiya W Govek, Patrick Nicodemus, Yuxuan Lin, Jake Crawford, Artur B Saturnino, Hannah Cui, Kristi Zoga, Michael P Hart, Pablo G Camara.
      High-resolution imaging has revolutionized the study of single cells in their spatial context. However, summarizing the great diversity of complex cell shapes found in tissues and inferring associations with other single-cell data remains a challenge. Here, we present CAJAL, a general computational framework for the analysis and integration of single-cell morphological data. By building upon metric geometry, CAJAL infers cell morphology latent spaces where distances between points indicate the amount of physical deformation required to change the morphology of one cell into that of another. We show that cell morphology spaces facilitate the integration of single-cell morphological data across technologies and the inference of relations with other data, such as single-cell transcriptomic data. We demonstrate the utility of CAJAL with several morphological datasets of neurons and glia and identify genes associated with neuronal plasticity in C. elegans. Our approach provides an effective strategy for integrating cell morphology data into single-cell omics analyses.
    DOI:  https://doi.org/10.1038/s41467-023-39424-2
  9. Sci Adv. 2023 Jun 23. 9(25): eadg4128
    Sequential apoptotic and multiplexed proteomic evaluation of single cancer cells.
    Emmalyn Lecky, Atreyi Mukherji, Rebecca German, Gabriella Antonellis, Jia-Ren Lin, Michael Yorsz, Kelley E McQueeney, Jeremy Ryan, Kimmie Ng, Ewa Sicinska, Peter K Sorger, Anthony Letai, Patrick D Bhola.
      A potential cause of cancer relapse is pretreatment chemoresistant subpopulations. Identifying targetable features of subpopulations that are poorly primed for therapy-induced cell death may improve cancer therapy. Here, we develop and validate real-time BH3 profiling, a live and functional single-cell measurement of pretreatment apoptotic sensitivity that occurs upstream of apoptotic protease activation. On the same single cells, we perform cyclic immunofluorescence, which enables multiplexed immunofluorescence of more than 30 proteins on the same cell. Using cultured cells and rapid ex vivo cultures of colon cancer patient-derived xenograft (PDX) models, we identify Bak as a univariate correlate of apoptotic priming, find that poorly primed subpopulations can correspond to specific stages of the cell cycle, and, in some PDX models, identify increased expression of Bcl-XL, Mcl-1, or Her2 in subpopulations that are poorly primed for apoptosis. Last, we generate and validate mathematical models of single-cell priming that describe how targetable proteins contribute to apoptotic priming.
    DOI:  https://doi.org/10.1126/sciadv.adg4128
  10. PeerJ Comput Sci. 2023 ;9 e1364
    A review of open-source image analysis tools for mammalian cell culture: algorithms, features and implementations.
    Hafizi Malik, Ahmad Syahrin Idris, Siti Fauziah Toha, Izyan Mohd Idris, Muhammad Fauzi Daud, Nur Liyana Azmi.
      Cell culture is undeniably important for multiple scientific applications, including pharmaceuticals, transplants, and cosmetics. However, cell culture involves multiple manual steps, such as regularly analyzing cell images for their health and morphology. Computer scientists have developed algorithms to automate cell imaging analysis, but they are not widely adopted by biologists, especially those lacking an interactive platform. To address the issue, we compile and review existing open-source cell image processing tools that provide interactive interfaces for management and prediction tasks. We highlight the prediction tools that can detect, segment, and track different mammalian cell morphologies across various image modalities and present a comparison of algorithms and unique features of these tools, whether they work locally or in the cloud. This would guide non-experts to determine which is best suited for their purposes and, developers to acknowledge what is worth further expansion. In addition, we provide a general discussion on potential implementations of the tools for a more extensive scope, which guides the reader to not restrict them to prediction tasks only. Finally, we conclude the article by stating new considerations for the development of interactive cell imaging tools and suggesting new directions for future research.
    Keywords:  Cell culture; Image analysis; Microscopy; Open-source
    DOI:  https://doi.org/10.7717/peerj-cs.1364
  11. CRISPR J. 2023 Jun 20.
    Predicting Mutations Generated by Cas9, Base Editing, and Prime Editing in Mammalian Cells.
    Juliane Weller, Ananth Pallaseni, Jonas Koeppel, Leopold Parts.
      The first fruits of the CRISPR-Cas revolution are starting to enter the clinic, with gene editing therapies offering solutions to previously incurable genetic diseases. The success of such applications hinges on control over the mutations that are generated, which are known to vary depending on the targeted locus. In this review, we present the current state of understanding and predicting CRISPR-Cas cutting, base editing, and prime editing outcomes in mammalian cells. We first provide an introduction to the basics of DNA repair and machine learning that the models rely on. We then overview the datasets and methods created for characterizing edits at scale, as well as the insights that have been derived from them. The predictions generated from these models serve as a foundation for designing efficient experiments across the broad contexts where these tools are applied.
    DOI:  https://doi.org/10.1089/crispr.2023.0016
  12. Curr Biol. 2023 Jun 13. pii: S0960-9822(23)00723-6. [Epub ahead of print]
    Oncogenic Ras deregulates cell-substrate interactions during mitotic rounding and respreading to alter cell division orientation.
    Sushila Ganguli, Tom Wyatt, Agata Nyga, Rachel H Lawson, Tim Meyer, Buzz Baum, Helen K Matthews.
      Oncogenic Ras has been shown to change the way cancer cells divide by increasing the forces generated during mitotic rounding. In this way, RasV12 enables cancer cells to divide across a wider range of mechanical environments than normal cells. Here, we identify a further role for oncogenic Ras-ERK signaling in division by showing that RasV12 expression alters the shape, division orientation, and respreading dynamics of cells as they exit mitosis. Many of these effects appear to result from the impact of RasV12 signaling on actomyosin contractility, because RasV12 induces the severing of retraction fibers that normally guide spindle positioning and provide a memory of the interphase cell shape. In support of this idea, the RasV12 phenotype is reversed by inhibition of actomyosin contractility and can be mimicked by the loss of cell-substrate adhesion during mitosis. Finally, we show that RasV12 activation also perturbs division orientation in cells cultured in 2D epithelial monolayers and 3D spheroids. Thus, the induction of oncogenic Ras-ERK signaling leads to rapid changes in division orientation that, along with the effects of RasV12 on cell growth and cell-cycle progression, are likely to disrupt epithelial tissue organization and contribute to cancer dissemination.
    Keywords:  MAPK signaling; actin cytoskeleton; cell division; division orientation; focal adhesions; mitosis; mitotic rounding; mitotic spindle
    DOI:  https://doi.org/10.1016/j.cub.2023.05.061
  13. Circ Res. 2023 Jun 23.
    Loss of Macrophage mTORC2 Drives Atherosclerosis via FoxO1 and IL-1β Signaling.
    Xiangyu Zhang, Trent D Evans, Sunny Chen, Ismail Sergin, Jeremiah Stitham, Se-Jin Jeong, Astrid Rodriguez-Velez, Yu-Sheng Yeh, Arick Park, In-Hyuk Jung, Abhinav Diwan, Joel D Schilling, Oren Rom, Arif Yurdagul, Slava Epelman, Jaehyung Cho, Irfan J Lodhi, Bettina Mittendorfer, Babak Razani.
       BACKGROUND: The mTOR (mechanistic target of rapamycin) pathway is a complex signaling cascade that regulates cellular growth, proliferation, metabolism, and survival. Although activation of mTOR signaling has been linked to atherosclerosis, its direct role in lesion progression and in plaque macrophages remains poorly understood. We previously demonstrated that mTORC1 (mTOR complex 1) activation promotes atherogenesis through inhibition of autophagy and increased apoptosis in macrophages.
    METHODS: Using macrophage-specific Rictor- and mTOR-deficient mice, we now dissect the distinct functions of mTORC2 pathways in atherogenesis.
    RESULTS: In contrast to the atheroprotective effect seen with blockade of macrophage mTORC1, macrophage-specific mTORC2-deficient mice exhibit an atherogenic phenotype, with larger, more complex lesions and increased cell death. In cultured macrophages, we show that mTORC2 signaling inhibits the FoxO1 (forkhead box protein O1) transcription factor, leading to suppression of proinflammatory pathways, especially the inflammasome/IL (interleukin)-1β response, a key mediator of vascular inflammation and atherosclerosis. In addition, administration of FoxO1 inhibitors efficiently rescued the proinflammatory response caused by mTORC2 deficiency both in vitro and in vivo. Interestingly, collective deletion of macrophage mTOR, which ablates mTORC1- and mTORC2-dependent pathways, leads to minimal change in plaque size or complexity, reflecting the balanced yet opposing roles of these signaling arms.
    CONCLUSIONS: Our data provide the first mechanistic details of macrophage mTOR signaling in atherosclerosis and suggest that therapeutic measures aimed at modulating mTOR need to account for its dichotomous functions.
    Keywords:  atherosclerosis; inflammation; interleukin; macrophage
    DOI:  https://doi.org/10.1161/CIRCRESAHA.122.321542
  14. J Biol Chem. 2023 Jun 19. pii: S0021-9258(23)01970-1. [Epub ahead of print] 104942
    PE-STOP: A versatile tool for installing nonsense substitutions amenable for precise reversion.
    Ziguo Song, Guiquan Zhang, Shuhong Huang, Yao Liu, Guanglei Li, Xianhui Zhou, Jiayuan Sun, Pengfei Gao, Yulin Chen, Xingxu Huang, Jianghuai Liu, Xiaolong Wang.
      The rapid advances in genome editing technologies have revolutionized the study of gene functions in cell or animal models. The recent generation of double-stranded DNA cleavage-independent base editors has been suitably adapted for interrogation of protein-coding genes on the basis of introducing premature stop codons or disabling the start codons. However, such versions of stop/start codon-oriented genetic tools still present limitations on their versatility, base-level precision and target specificity. Here we exploit a newly developed prime editor (PE) that differs from base editors by its adoption of a reverse transcriptase activity, which enables incorporation of various types of precise edits templated by a specialized prime editing guide RNA (pegRNA). Based on such a versatile platform, we established a prime editing-empowered method (PE-STOP) for installation of nonsense substitutions, providing a complementary approach to the present gene-targeting tools. PE-STOP is bioinformatically predicted to feature substantially expanded coverage in the genome space. In practice, PE-STOP introduces stop codons with good efficiencies in HEK293T and N2a cells (with medians of 29% [10 sites] and 25% [4 sites] editing efficiencies, respectively), while exhibiting minimal off-target effects and high on-target precision. Furthermore, given the fact that PE installs pegRNA-templated mutations, we introduce a unique strategy for precise genetic rescue of PE-STOP-dependent nonsense mutation via the same PE platform. Altogether, the present work demonstrates a versatile and specific tool for gene inactivation and for functional interrogation of nonsense mutations.
    Keywords:  PE-STOP; base editing; gene inactivation; nonsense mutation; off-target; prime editing; stop codon
    DOI:  https://doi.org/10.1016/j.jbc.2023.104942
  15. Cell Syst. 2023 Jun 21. pii: S2405-4712(23)00145-X. [Epub ahead of print]14(6): 430-446
    The computational capabilities of many-to-many protein interaction networks.
    Heidi E Klumpe, Jordi Garcia-Ojalvo, Michael B Elowitz, Yaron E Antebi.
      Many biological circuits comprise sets of protein variants that interact with one another in a many-to-many, or promiscuous, fashion. These architectures can provide powerful computational capabilities that are especially critical in multicellular organisms. Understanding the principles of biochemical computations in these circuits could allow more precise control of cellular behaviors. However, these systems are inherently difficult to analyze, due to their large number of interacting molecular components, partial redundancies, and cell context dependence. Here, we discuss recent experimental and theoretical advances that are beginning to reveal how promiscuous circuits compute, what roles those computations play in natural biological contexts, and how promiscuous architectures can be applied for the design of synthetic multicellular behaviors.
    Keywords:  biological circuit; biological computation; combinatorial protein interactions; molecular computation; promiscuous protein interactions; protein networks; signal transduction
    DOI:  https://doi.org/10.1016/j.cels.2023.05.001
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