bims-pideca Biomed News
on Class IA PI3K signalling in development and cancer
Issue of 2021–06–20
twelve papers selected by
Ralitsa Radostinova Madsen, University College London
  1. PI3K inhibitors are finally coming of age.
  2. Targeted PI3K/AKT-hyperactivation induces cell death in chronic lymphocytic leukemia.
  3. AIMTOR, a BRET Biosensor for Live Recording of mTOR Activity in Cell Populations and Single Cells.
  4. Highly metastatic claudin-low mammary cancers can originate from luminal epithelial cells.
  5. A forecast for large-scale, predictive biology: Lessons from meteorology.
  6. Sensitive period for rescuing parvalbumin interneurons connectivity and social behavior deficits caused by TSC1 loss.
  7. Mapping the multiscale structure of biological systems.
  8. Evolutionary predictability of genetic versus nongenetic resistance to anticancer drugs in melanoma.
  9. BRN2 is a non-canonical melanoma tumor-suppressor.
  10. Applications of Organoids for Cancer Biology and Precision Medicine.
  11. Non-hotspot PIK3CA mutations are more frequent in CLOVES than in common or combined lymphatic malformations.
  12. Rigorous review and editorial oversight of clinical preprints.
  1. Nat Rev Drug Discov. 2021 Jun 14.
    PI3K inhibitors are finally coming of age.
    Bart Vanhaesebroeck, Matthew W D Perry, Jennifer R Brown, Fabrice André, Klaus Okkenhaug.
      Overactive phosphoinositide 3-kinase (PI3K) in cancer and immune dysregulation has spurred extensive efforts to develop therapeutic PI3K inhibitors. Although progress has been hampered by issues such as poor drug tolerance and drug resistance, several PI3K inhibitors have now received regulatory approval - the PI3Kα isoform-selective inhibitor alpelisib for the treatment of breast cancer and inhibitors mainly aimed at the leukocyte-enriched PI3Kδ in B cell malignancies. In addition to targeting cancer cell-intrinsic PI3K activity, emerging evidence highlights the potential of PI3K inhibitors in cancer immunotherapy. This Review summarizes key discoveries that aid the clinical translation of PI3Kα and PI3Kδ inhibitors, highlighting lessons learnt and future opportunities.
    DOI:  https://doi.org/10.1038/s41573-021-00209-1
  2. Nat Commun. 2021 06 10. 12(1): 3526
    Targeted PI3K/AKT-hyperactivation induces cell death in chronic lymphocytic leukemia.
    Veronika Ecker, Martina Stumpf, Lisa Brandmeier, Tanja Neumayer, Lisa Pfeuffer, Thomas Engleitner, Ingo Ringshausen, Nina Nelson, Manfred Jücker, Stefan Wanninger, Thorsten Zenz, Clemens Wendtner, Katrin Manske, Katja Steiger, Roland Rad, Markus Müschen, Jürgen Ruland, Maike Buchner.
      Current therapeutic approaches for chronic lymphocytic leukemia (CLL) focus on the suppression of oncogenic kinase signaling. Here, we test the hypothesis that targeted hyperactivation of the phosphatidylinositol-3-phosphate/AKT (PI3K/AKT)-signaling pathway may be leveraged to trigger CLL cell death. Though counterintuitive, our data show that genetic hyperactivation of PI3K/AKT-signaling or blocking the activity of the inhibitory phosphatase SH2-containing-inositol-5'-phosphatase-1 (SHIP1) induces acute cell death in CLL cells. Our mechanistic studies reveal that increased AKT activity upon inhibition of SHIP1 leads to increased mitochondrial respiration and causes excessive accumulation of reactive oxygen species (ROS), resulting in cell death in CLL with immunogenic features. Our results demonstrate that CLL cells critically depend on mechanisms to fine-tune PI3K/AKT activity, allowing sustained proliferation and survival but avoid ROS-induced cell death and suggest transient SHIP1-inhibition as an unexpectedly promising concept for CLL therapy.
    DOI:  https://doi.org/10.1038/s41467-021-23752-2
  3. Bio Protoc. 2021 Apr 20. 11(8): e3989
    AIMTOR, a BRET Biosensor for Live Recording of mTOR Activity in Cell Populations and Single Cells.
    Nathalie Bouquier, Enora Moutin, Julie Perroy, Vincent Ollendorff.
      Mammalian target of rapamycin (mTOR) controls many crucial cellular functions, including protein synthesis, cell size, energy metabolism, lysosome and mitochondria biogenesis, and autophagy. Consequently, deregulation of mTOR signaling plays a role in numerous pathological conditions such as cancer, metabolic disorders and neurological diseases. Developing new tools to monitor mTOR spatiotemporal activation is crucial to better understand its roles in physiological and pathological conditions. However, the most widely used method to report mTOR activity relies on the quantification of specific mTOR-phosphorylated substrates by western blot. This approach requires cellular lysate preparation, which restricts the quantification to a single time point. Here, we present a simple protocol to study mTOR activity in living cells in real time using AIMTOR, an intramolecular BRET-based (bioluminescence resonance energy transfer) biosensor that we recently designed ( Bouquier et al., 2020 ). We describe transfection of AIMTOR in the C2C12 cell line and procedures to monitor BRET in a cell population using a plate reader and in single cells by microscopy. Importantly, this protocol is transposable to any cell line and primary cells. In addition, several subcellular compartment-specific versions of AIMTOR have been developed, enabling compartmentalized assessment of mTOR activity. This protocol describes how to use the sensitive AIMTOR biosensor to investigate mTOR signaling dynamics in living cells. Graphic abstract: AIMTOR protocol overview from seeding cells to live BRET recording.
    Keywords:  BRET; Kinase activity; Living cells; Real time imaging; mTOR signaling; mTORC1 biosensor
    DOI:  https://doi.org/10.21769/BioProtoc.3989
  4. Nat Commun. 2021 Jun 18. 12(1): 3742
    Highly metastatic claudin-low mammary cancers can originate from luminal epithelial cells.
    Patrick D Rädler, Barbara L Wehde, Aleata A Triplett, Hridaya Shrestha, Jonathan H Shepherd, Adam D Pfefferle, Hallgeir Rui, Robert D Cardiff, Charles M Perou, Kay-Uwe Wagner.
      Claudin-low breast cancer represents an aggressive molecular subtype that is comprised of mostly triple-negative mammary tumor cells that possess stem cell-like and mesenchymal features. Little is known about the cellular origin and oncogenic drivers that promote claudin-low breast cancer. In this study, we show that persistent oncogenic RAS signaling causes highly metastatic triple-negative mammary tumors in mice. More importantly, the activation of endogenous mutant KRAS and expression of exogenous KRAS specifically in luminal epithelial cells in a continuous and differentiation stage-independent manner induces preneoplastic lesions that evolve into basal-like and claudin-low mammary cancers. Further investigations demonstrate that the continuous signaling of oncogenic RAS, as well as regulators of EMT, play a crucial role in the cellular plasticity and maintenance of the mesenchymal and stem cell characteristics of claudin-low mammary cancer cells.
    DOI:  https://doi.org/10.1038/s41467-021-23957-5
  5. Cell Syst. 2021 Jun 16. pii: S2405-4712(21)00200-3. [Epub ahead of print]12(6): 488-496
    A forecast for large-scale, predictive biology: Lessons from meteorology.
    Markus W Covert, Taryn E Gillies, Takamasa Kudo, Eran Agmon.
      Quantitative systems biology, in which predictive mathematical models are constructed to guide the design of experiments and predict experimental outcomes, is at an exciting transition point, where the foundational scientific principles are becoming established, but the impact is not yet global. The next steps necessary for mathematical modeling to transform biological research and applications, in the same way it has already transformed other fields, is not completely clear. The purpose of this perspective is to forecast possible answers to this question-what needs to happen next-by drawing on the experience gained in another field, specifically meteorology. We review here a number of lessons learned in weather prediction that are directly relevant to biological systems modeling, and that we believe can enable the same kinds of global impact in our field as atmospheric modeling makes today.
    Keywords:  computational biology; systems biology; whole-cell modeling
    DOI:  https://doi.org/10.1016/j.cels.2021.05.014
  6. Nat Commun. 2021 06 16. 12(1): 3653
    Sensitive period for rescuing parvalbumin interneurons connectivity and social behavior deficits caused by TSC1 loss.
    Clara A Amegandjin, Mayukh Choudhury, Vidya Jadhav, Josianne Nunes Carriço, Ariane Quintal, Martin Berryer, Marina Snapyan, Bidisha Chattopadhyaya, Armen Saghatelyan, Graziella Di Cristo.
      The Mechanistic Target Of Rapamycin Complex 1 (mTORC1) pathway controls several aspects of neuronal development. Mutations in regulators of mTORC1, such as Tsc1 and Tsc2, lead to neurodevelopmental disorders associated with autism, intellectual disabilities and epilepsy. The correct development of inhibitory interneurons is crucial for functional circuits. In particular, the axonal arborisation and synapse density of parvalbumin (PV)-positive GABAergic interneurons change in the postnatal brain. How and whether mTORC1 signaling affects PV cell development is unknown. Here, we show that Tsc1 haploinsufficiency causes a premature increase in terminal axonal branching and bouton density formed by mutant PV cells, followed by a loss of perisomatic innervation in adult mice. PV cell-restricted Tsc1 haploinsufficient and knockout mice show deficits in social behavior. Finally, we identify a sensitive period during the third postnatal week during which treatment with the mTOR inhibitor Rapamycin rescues deficits in both PV cell innervation and social behavior in adult conditional haploinsufficient mice. Our findings reveal a role of mTORC1 signaling in the regulation of the developmental time course and maintenance of cortical PV cell connectivity and support a mechanistic basis for the targeted rescue of autism-related behaviors in disorders associated with deregulated mTORC1 signaling.
    DOI:  https://doi.org/10.1038/s41467-021-23939-7
  7. Cell Syst. 2021 Jun 16. pii: S2405-4712(21)00198-8. [Epub ahead of print]12(6): 622-635
    Mapping the multiscale structure of biological systems.
    Leah V Schaffer, Trey Ideker.
      Biological systems are by nature multiscale, consisting of subsystems that factor into progressively smaller units in a deeply hierarchical structure. At any level of the hierarchy, an ever-increasing diversity of technologies can be applied to characterize the corresponding biological units and their relations, resulting in large networks of physical or functional proximities-e.g., proximities of amino acids within a protein, of proteins within a complex, or of cell types within a tissue. Here, we review general concepts and progress in using network proximity measures as a basis for creation of multiscale hierarchical maps of biological systems. We discuss the functionalization of these maps to create predictive models, including those useful in translation of genotype to phenotype, along with strategies for model visualization and challenges faced by multiscale modeling in the near future. Collectively, these approaches enable a unified hierarchical approach to biological data, with application from the molecular to the macroscopic.
    Keywords:  community detection; hierarchical models; multiscale; network biology; networks; structural biology; structure; systems biology
    DOI:  https://doi.org/10.1016/j.cels.2021.05.012
  8. Cancer Cell. 2021 Jun 07. pii: S1535-6108(21)00281-6. [Epub ahead of print]
    Evolutionary predictability of genetic versus nongenetic resistance to anticancer drugs in melanoma.
    Oskar Marin-Bejar, Aljosja Rogiers, Michael Dewaele, Julia Femel, Panagiotis Karras, Joanna Pozniak, Greet Bervoets, Nina Van Raemdonck, Dennis Pedri, Toon Swings, Jonas Demeulemeester, Sara Vander Borght, Stefan Lehnert, Francesca Bosisio, Joost J van den Oord, Isabelle Vanden Bempt, Diether Lambrechts, Thierry Voet, Oliver Bechter, Helen Rizos, Mitchell P Levesque, Eleonora Leucci, Amanda W Lund, Florian Rambow, Jean-Christophe Marine.
      Therapy resistance arises from heterogeneous drug-tolerant persister cells or minimal residual disease (MRD) through genetic and nongenetic mechanisms. A key question is whether specific molecular features of the MRD ecosystem determine which of these two distinct trajectories will eventually prevail. We show that, in melanoma exposed to mitogen-activated protein kinase therapeutics, emergence of a transient neural crest stem cell (NCSC) population in MRD concurs with the development of nongenetic resistance. This increase relies on a glial cell line-derived neurotrophic factor-dependent signaling cascade, which activates the AKT survival pathway in a focal adhesion kinase (FAK)-dependent manner. Ablation of the NCSC population through FAK inhibition delays relapse in patient-derived tumor xenografts. Strikingly, all tumors that ultimately escape this treatment exhibit resistance-conferring genetic alterations and increased sensitivity to extracellular signal-regulated kinase inhibition. These findings identify an approach that abrogates the nongenetic resistance trajectory in melanoma and demonstrate that the cellular composition of MRD deterministically imposes distinct drug resistance evolutionary paths.
    Keywords:  FAK signaling; cutaneous melanoma; minimal residual disease; neural crest stem cells; nongenetic reprogramming; patient-derived tumor xenografts; single-cell sequencing; therapy resistance
    DOI:  https://doi.org/10.1016/j.ccell.2021.05.015
  9. Nat Commun. 2021 06 17. 12(1): 3707
    BRN2 is a non-canonical melanoma tumor-suppressor.
    Michael Hamm, Pierre Sohier, Valérie Petit, Jérémy H Raymond, Véronique Delmas, Madeleine Le Coz, Franck Gesbert, Colin Kenny, Zackie Aktary, Marie Pouteaux, Florian Rambow, Alain Sarasin, Nisamanee Charoenchon, Alfonso Bellacosa, Luis Sanchez-Del-Campo, Laura Mosteo, Martin Lauss, Dies Meijer, Eirikur Steingrimsson, Göran B Jönsson, Robert A Cornell, Irwin Davidson, Colin R Goding, Lionel Larue.
      While the major drivers of melanoma initiation, including activation of NRAS/BRAF and loss of PTEN or CDKN2A, have been identified, the role of key transcription factors that impose altered transcriptional states in response to deregulated signaling is not well understood. The POU domain transcription factor BRN2 is a key regulator of melanoma invasion, yet its role in melanoma initiation remains unknown. Here, in a BrafV600E PtenF/+ context, we show that BRN2 haplo-insufficiency promotes melanoma initiation and metastasis. However, metastatic colonization is less efficient in the absence of Brn2. Mechanistically, BRN2 directly induces PTEN expression and in consequence represses PI3K signaling. Moreover, MITF, a BRN2 target, represses PTEN transcription. Collectively, our results suggest that on a PTEN heterozygous background somatic deletion of one BRN2 allele and temporal regulation of the other allele elicits melanoma initiation and progression.
    DOI:  https://doi.org/10.1038/s41467-021-23973-5
  10. Nat Cancer. 2020 Aug;1(8): 761-773
    Applications of Organoids for Cancer Biology and Precision Medicine.
    Yuan-Hung Lo, Kasper Karlsson, Calvin J Kuo.
      Organoid technologies enable the creation of in vitro physiologic systems that model tissues of origin more accurately than classical culture approaches. Seminal characteristics, including three-dimensional structure and recapitulation of self-renewal, differentiation, and disease pathology, render organoids eminently suited as hybrids that combine the experimental tractability of traditional 2D cell lines with cellular attributes of in vivo model systems. Here, we describe recent advances in this rapidly evolving field and their applications in cancer biology, clinical translation and precision medicine.
    DOI:  https://doi.org/10.1038/s43018-020-0102-y
  11. Orphanet J Rare Dis. 2021 Jun 10. 16(1): 267
    Non-hotspot PIK3CA mutations are more frequent in CLOVES than in common or combined lymphatic malformations.
    Pascal Brouillard, Matthieu J Schlögel, Nassim Homayun Sepehr, Raphaël Helaers, Angela Queisser, Elodie Fastré, Simon Boutry, Sandra Schmitz, Philippe Clapuyt, Frank Hammer, Anne Dompmartin, Annamaria Weitz-Tuoretmaa, Jussi Laranne, Louise Pasquesoone, Catheline Vilain, Laurence M Boon, Miikka Vikkula.
       BACKGROUND: Theragnostic management, treatment according to precise pathological molecular targets, requests to unravel patients' genotypes. We used targeted next-generation sequencing (NGS) or digital droplet polymerase chain reaction (ddPCR) to screen for somatic PIK3CA mutations on DNA extracted from resected lesional tissue or lymphatic endothelial cells (LECs) isolated from lesions. Our cohort (n = 143) was composed of unrelated patients suffering from a common lymphatic malformation (LM), a combined lymphatic malformation [lymphatico-venous malformation (LVM), capillaro-lymphatic malformation (CLM), capillaro-lymphatico-venous malformation (CLVM)], or a syndrome [CLVM with hypertrophy (Klippel-Trenaunay-Weber syndrome, KTS), congenital lipomatous overgrowth-vascular malformations-epidermal nevi -syndrome (CLOVES), unclassified PIK3CA-related overgrowth syndrome (PROS) or unclassified vascular (lymphatic) anomaly syndrome (UVA)].
    RESULTS: We identified a somatic PIK3CA mutation in resected lesions of 108 out of 143 patients (75.5%). The frequency of the variant allele ranged from 0.54 to 25.33% in tissues, and up to 47% in isolated endothelial cells. We detected a statistically significant difference in the distribution of mutations between patients with common and combined LM compared to the syndromes, but not with KTS. Moreover, the variant allele frequency was higher in the syndromes.
    CONCLUSIONS: Most patients with an common or combined lymphatic malformation with or without overgrowth harbour a somatic PIK3CA mutation. However, in about a quarter of patients, no such mutation was detected, suggesting the existence of (an)other cause(s). We detected a hotspot mutation more frequently in common and combined LMs compared to syndromic cases (CLOVES and PROS). Diagnostic genotyping should thus not be limited to PIK3CA hotspot mutations. Moreover, the higher mutant allele frequency in syndromes suggests a wider distribution in patients' tissues, facilitating detection. Clinical trials have demonstrated efficacy of Sirolimus and Alpelisib in treating patients with an LM or PROS. Genotyping might lead to an increase in efficacy, as treatments could be more targeted, and responses could vary depending on presence and type of PIK3CA-mutation.
    Keywords:  Allele; Epidemiology; Frequency; Gene; Isolated; Lymphatic malformation; Mutation; PI3K; Somatic; Theragnostic
    DOI:  https://doi.org/10.1186/s13023-021-01898-y
  12. Elife. 2021 Jun 16. pii: e67528. [Epub ahead of print]10
    Rigorous review and editorial oversight of clinical preprints.
    Mone Zaidi, Diane M Harper, Anna Akhmanova, Detlef Weigel, Timothy E Behrens, Michael B Eisen.
      Research in many different areas of medicine will benefit from new approaches to peer review and publishing.
    Keywords:  medicine; peer review; physician-scientists; preprints; public health
    DOI:  https://doi.org/10.7554/eLife.67528
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