bims-pideca Biomed News
on Class IA PI3K signalling in development and cancer
Issue of 2021–09–26
thirteen papers selected by
Ralitsa Radostinova Madsen, University College London
  1. Phosphoproteomics identifies PI3K inhibitor-selective adaptive responses in pancreatic cancer cell therapy and resistance.
  2. KARATE: PKA-induced KRAS4B-RHOA-mTORC2 supercomplex phosphorylates AKT in insulin signaling and glucose homeostasis.
  3. Topical Application of the PI3Kβ-Selective Small Molecule Inhibitor TGX-221 Is an Effective Treatment Option for Experimental Epidermolysis Bullosa Acquisita.
  4. Interleukin-6 mediates PSAT1 expression and serine metabolism in TSC2-deficient cells.
  5. RTK-dependent inducible degradation of mutant PI3Kα drives GDC-0077 (Inavolisib) efficacy.
  6. Dissecting the biology of mTORC1 beyond rapamycin.
  7. A PTEN variant uncouples longevity from impaired fitness in Caenorhabditis elegans with reduced insulin/IGF-1 signaling.
  8. Reconstructing aspects of human embryogenesis with pluripotent stem cells.
  9. Inositol serves as a natural inhibitor of mitochondrial fission by directly targeting AMPK.
  10. Integrated safety analysis of umbralisib, a dual PI3Kδ/CK1ε inhibitor, in relapsed/refractory lymphoid malignancies.
  11. Editorial overview: How cells extract information from environmental cues.
  12. The enigma of phosphoinositides and their derivatives: Their role in regulation of subcellular compartment morphology.
  13. Moonlighting functions of metabolic enzymes and metabolites in cancer.
  1. Mol Cancer Ther. 2021 Sep 22. pii: molcanther.0981.2020. [Epub ahead of print]
    Phosphoproteomics identifies PI3K inhibitor-selective adaptive responses in pancreatic cancer cell therapy and resistance.
    Celia Cintas, Thibault Douche, Zahra Dantes, Emmanuelle Mouton-Barbosa, Marie-Pierre Bousquet, Coralie Cayron, Nicole Therville, Frédéric Pont, Fernanda Ramos-Delgado, Camille Guyon, Barbara H Garmy-Susini, Paola Cappello, Odile Burlet-Schiltz, Emilio Hirsch, Anne Gomez-Brouchet, Benoît Thibault, Maximilian Reichert, Julie Guillermet-Guibert.
      The PI3K pathway is highly active in human cancers. The four class I isoforms of PI3K are activated by distinct mechanisms leading to a common downstream signaling. Their downstream redundancy is thought to be responsible for treatment failures of PI3K inhibitors. We challenged this concept, by mapping the differential phosphoproteome evolution in response to PI3K inhibitors with different isoform selectivity patterns in pancreatic cancer, a disease currently without effective therapy. In this cancer, the PI3K signal was shown to control cell proliferation. We compared the effects of LY294002 that inhibit with equal potency all class I isoenzymes and downstream mTOR with the action of inhibitors with higher isoform-selectivity towards PI3Kα, PI3Kβ or PI3Kγ (namely A66, TGX-221 and AS-252424). A bioinformatics global pathway analysis of phosphoproteomics data allowed us to identify common and specific signals activated by PI3K inhibitors supported by the biological data. AS-252424 was the most effective treatment and induced apoptotic pathway activation as well as the highest changes in global phosphorylation-regulated cell signal. However, AS-252424 treatment induced re-activation of Akt, therefore decreasing the treatment outcome on cell survival. Reversely, AS-252424 and A66 combination treatment prevented p-Akt reactivation and led to synergistic action in cell lines and patient organoids. The combination of clinically approved a-selective BYL-719 with γ-selective IPI-549 was more efficient than single molecule treatment on xenograft growth. Mapping unique adaptive signaling responses to isoform-selective PI3K inhibition will help to design better combinative treatments that prevent the induction of selective compensatory signals.
    DOI:  https://doi.org/10.1158/1535-7163.MCT-20-0981
  2. Mol Cell. 2021 Sep 14. pii: S1097-2765(21)00735-8. [Epub ahead of print]
    KARATE: PKA-induced KRAS4B-RHOA-mTORC2 supercomplex phosphorylates AKT in insulin signaling and glucose homeostasis.
    Hiroshi Senoo, Daisuke Murata, May Wai, Kenta Arai, Wakiko Iwata, Hiromi Sesaki, Miho Iijima.
      AKT is a serine/threonine kinase that plays an important role in metabolism, cell growth, and cytoskeletal dynamics. AKT is activated by two kinases, PDK1 and mTORC2. Although the regulation of PDK1 is well understood, the mechanism that controls mTORC2 is unknown. Here, by investigating insulin receptor signaling in human cells and biochemical reconstitution, we found that insulin induces the activation of mTORC2 toward AKT by assembling a supercomplex with KRAS4B and RHOA GTPases, termed KARATE (KRAS4B-RHOA-mTORC2 Ensemble). Insulin-induced KARATE assembly is controlled via phosphorylation of GTP-bound KRAS4B at S181 and GDP-bound RHOA at S188 by protein kinase A. By developing a KARATE inhibitor, we demonstrate that KRAS4B-RHOA interaction drives KARATE formation. In adipocytes, KARATE controls insulin-dependent translocation of the glucose transporter GLUT4 to the plasma membrane for glucose uptake. Thus, our work reveals a fundamental mechanism that activates mTORC2 toward AKT in insulin-regulated glucose homeostasis.
    Keywords:  AKT; KRAS GTPase; PKA; RHOA GTPase; insulin; mTORC2
    DOI:  https://doi.org/10.1016/j.molcel.2021.09.001
  3. Front Med (Lausanne). 2021 ;8 713312
    Topical Application of the PI3Kβ-Selective Small Molecule Inhibitor TGX-221 Is an Effective Treatment Option for Experimental Epidermolysis Bullosa Acquisita.
    Hannah Zillikens, Anika Kasprick, Colin Osterloh, Natalie Gross, Michael Radziewitz, Cindy Hass, Veronika Hartmann, Martina Behnen-Härer, Nancy Ernst, Katharina Boch, Gestur Vidarsson, Remco Visser, Tamás Laskay, Xinhua Yu, Frank Petersen, Ralf J Ludwig, Katja Bieber.
      Class I phosphoinositide 3-kinases (PI3K) have been implemented in pathogenesis of experimental epidermolysis bullosa acquisita (EBA), an autoimmune skin disease caused by type VII collagen (COL7) autoantibodies. Mechanistically, inhibition of specific PI3K isoforms, namely PI3Kβ or PI3Kδ, impaired immune complex (IC)-induced neutrophil activation, a key prerequisite for EBA pathogenesis. Data unrelated to EBA showed that neutrophil activation is also modulated by PI3Kα and γ, but their impact on the EBA has, so far, remained elusive. To address this and to identify potential therapeutic targets, we evaluated the impact of a panel of PI3K isoform-selective inhibitors (PI3Ki) on neutrophil function in vitro, and in pre-clinical EBA mouse models. We document that distinctive, and EBA pathogenesis-related activation-induced neutrophil in vitro functions depend on distinctive PI3K isoforms. When mice were treated with the different PI3Ki, selective blockade of PI3Kα (alpelisib), PI3Kγ (AS-604850), or PI3Kβ (TGX-221) impaired clinical disease manifestation. When applied topically, only TGX-221 impaired induction of experimental EBA. Ultimately, multiplex kinase activity profiling in the presence of disease-modifying PI3Ki identified unique signatures of different PI3K isoform-selective inhibitors on the kinome of IC-activated human neutrophils. Collectively, we here identify topical PI3Kβ inhibition as a potential therapeutic target for the treatment of EBA.
    Keywords:  PI3K; bullous skin diseases; immune-complex induced autoimmunity; neutrophils; signaling
    DOI:  https://doi.org/10.3389/fmed.2021.713312
  4. Proc Natl Acad Sci U S A. 2021 09 28. pii: e2101268118. [Epub ahead of print]118(39):
    Interleukin-6 mediates PSAT1 expression and serine metabolism in TSC2-deficient cells.
    Ji Wang, Harilaos Filippakis, Thomas Hougard, Heng Du, Chenyang Ye, Heng-Jia Liu, Long Zhang, Khadijah Hindi, Shefali Bagwe, Julie Nijmeh, John M Asara, Wei Shi, Souheil El-Chemaly, Elizabeth P Henske, Hilaire C Lam.
      Tuberous sclerosis complex (TSC) and lymphangioleiomyomatosis (LAM) are caused by aberrant mechanistic Target of Rapamycin Complex 1 (mTORC1) activation due to loss of either TSC1 or TSC2 Cytokine profiling of TSC2-deficient LAM patient-derived cells revealed striking up-regulation of Interleukin-6 (IL-6). LAM patient plasma contained increased circulating IL-6 compared with healthy controls, and TSC2-deficient cells showed up-regulation of IL-6 transcription and secretion compared to wild-type cells. IL-6 blockade repressed the proliferation and migration of TSC2-deficient cells and reduced oxygen consumption and extracellular acidification. U-13C glucose tracing revealed that IL-6 knockout reduced 3-phosphoserine and serine production in TSC2-deficient cells, implicating IL-6 in de novo serine metabolism. IL-6 knockout reduced expression of phosphoserine aminotransferase 1 (PSAT1), an essential enzyme in serine biosynthesis. Importantly, recombinant IL-6 treatment rescued PSAT1 expression in the TSC2-deficient, IL-6 knockout clones selectively and had no effect on wild-type cells. Treatment with anti-IL-6 (αIL-6) antibody similarly reduced cell proliferation and migration and reduced renal tumors in Tsc2 +/- mice while reducing PSAT1 expression. These data reveal a mechanism through which IL-6 regulates serine biosynthesis, with potential relevance to the therapy of tumors with mTORC1 hyperactivity.
    Keywords:  interleukin 6; lymphangioleiomyomatosis; mTORC1; phosphoserine aminotransferase 1 (PSAT1); tuberous sclerosis complex
    DOI:  https://doi.org/10.1073/pnas.2101268118
  5. Cancer Discov. 2021 Sep 20. pii: candisc.0072.2021. [Epub ahead of print]
    RTK-dependent inducible degradation of mutant PI3Kα drives GDC-0077 (Inavolisib) efficacy.
    Kyung W Song, Kyle A Edgar, Emily J Hanan, Marc Hafner, Jason Oeh, Mark Merchant, Deepak Sampath, Michelle A Nannini, Rebecca Hong, Lilian Phu, William F Forrest, Eric Stawiski, Stephen Schmidt, Nicholas Endres, Jane Guan, Jeffrey J Wallin, Jonathan Cheong, Emile G Plise, Gail D Lewis Phillips, Laurent Salphati, Timothy P Heffron, Alan G Olivero, Shiva Malek, Steven T Staben, Donald S Kirkpatrick, Anwesha Dey, Lori S Friedman.
      PIK3CA is one of the most frequently mutated oncogenes; the p110α protein it encodes plays a central role in tumor cell proliferation. Small molecule inhibitors targeting the PI3K p110α catalytic subunit have entered clinical trials, with early-phase GDC-0077 studies showing anti-tumor activity and a manageable safety profile in patients with PIK3CA-mutant breast cancer. However, preclinical studies have shown that PI3K pathway inhibition releases negative feedback and activates receptor tyrosine kinase signaling, reengaging the pathway and attenuating drug activity. Here we discover that GDC-0077 and taselisib more potently inhibit mutant PI3K pathway signaling and cell viability through unique HER2-dependent mutant p110a degradation. Both are more effective than other PI3K inhibitors at maintaining prolonged pathway suppression. This study establishes a new strategy for identifying inhibitors that specifically target mutant tumors by selective degradation of the mutant oncoprotein and provide a strong rationale for pursuing PI3Kα degraders in patients with HER2-positive breast cancer.
    DOI:  https://doi.org/10.1158/2159-8290.CD-21-0072
  6. Sci Signal. 2021 Sep 21. 14(701): eabe0161
    Dissecting the biology of mTORC1 beyond rapamycin.
    Guang Yang, Deanne Francis, James R Krycer, Mark Larance, Ziyang Zhang, Chris J Novotny, Alexis Diaz-Vegas, Kevan M Shokat, David E James.
      [Figure: see text].
    DOI:  https://doi.org/10.1126/scisignal.abe0161
  7. Nat Commun. 2021 Sep 24. 12(1): 5631
    A PTEN variant uncouples longevity from impaired fitness in Caenorhabditis elegans with reduced insulin/IGF-1 signaling.
    Hae-Eun H Park, Wooseon Hwang, Seokjin Ham, Eunah Kim, Ozlem Altintas, Sangsoon Park, Heehwa G Son, Yujin Lee, Dongyeop Lee, Won Do Heo, Seung-Jae V Lee.
      Insulin/IGF-1 signaling (IIS) regulates various physiological aspects in numerous species. In Caenorhabditis elegans, mutations in the daf-2/insulin/IGF-1 receptor dramatically increase lifespan and immunity, but generally impair motility, growth, and reproduction. Whether these pleiotropic effects can be dissociated at a specific step in insulin/IGF-1 signaling pathway remains unknown. Through performing a mutagenesis screen, we identified a missense mutation daf-18(yh1) that alters a cysteine to tyrosine in DAF-18/PTEN phosphatase, which maintained the long lifespan and enhanced immunity, while improving the reduced motility in adult daf-2 mutants. We showed that the daf-18(yh1) mutation decreased the lipid phosphatase activity of DAF-18/PTEN, while retaining a partial protein tyrosine phosphatase activity. We found that daf-18(yh1) maintained the partial activity of DAF-16/FOXO but restricted the detrimental upregulation of SKN-1/NRF2, contributing to beneficial physiological traits in daf-2 mutants. Our work provides important insights into how one evolutionarily conserved component, PTEN, can coordinate animal health and longevity.
    DOI:  https://doi.org/10.1038/s41467-021-25920-w
  8. Nat Commun. 2021 Sep 21. 12(1): 5550
    Reconstructing aspects of human embryogenesis with pluripotent stem cells.
    Berna Sozen, Victoria Jorgensen, Bailey A T Weatherbee, Sisi Chen, Meng Zhu, Magdalena Zernicka-Goetz.
      Understanding human development is of fundamental biological and clinical importance. Despite its significance, mechanisms behind human embryogenesis remain largely unknown. Here, we attempt to model human early embryo development with expanded pluripotent stem cells (EPSCs) in 3-dimensions. We define a protocol that allows us to generate self-organizing cystic structures from human EPSCs that display some hallmarks of human early embryogenesis. These structures mimic polarization and cavitation characteristic of pre-implantation development leading to blastocyst morphology formation and the transition to post-implantation-like organization upon extended culture. Single-cell RNA sequencing of these structures reveals subsets of cells bearing some resemblance to epiblast, hypoblast and trophectoderm lineages. Nevertheless, significant divergences from natural blastocysts persist in some key markers, and signalling pathways point towards ways in which morphology and transcriptional-level cell identities may diverge in stem cell models of the embryo. Thus, this stem cell platform provides insights into the design of stem cell models of embryogenesis.
    DOI:  https://doi.org/10.1038/s41467-021-25853-4
  9. Mol Cell. 2021 Sep 16. pii: S1097-2765(21)00692-4. [Epub ahead of print]81(18): 3803-3819.e7
    Inositol serves as a natural inhibitor of mitochondrial fission by directly targeting AMPK.
    Che-Chia Hsu, Xian Zhang, Guihua Wang, Weina Zhang, Zhen Cai, Bo-Syong Pan, Haiwei Gu, Chuan Xu, Guoxiang Jin, Xiangshang Xu, Rajesh Kumar Manne, Yan Jin, Wei Yan, Jingwei Shao, Tingjin Chen, Emily Lin, Amit Ketkar, Robert Eoff, Zhi-Gang Xu, Zhong-Zhu Chen, Hong-Yu Li, Hui-Kuan Lin.
      Mitochondrial dynamics regulated by mitochondrial fusion and fission maintain mitochondrial functions, whose alterations underline various human diseases. Here, we show that inositol is a critical metabolite directly restricting AMPK-dependent mitochondrial fission independently of its classical mode as a precursor for phosphoinositide generation. Inositol decline by IMPA1/2 deficiency elicits AMPK activation and mitochondrial fission without affecting ATP level, whereas inositol accumulation prevents AMPK-dependent mitochondrial fission. Metabolic stress or mitochondrial damage causes inositol decline in cells and mice to elicit AMPK-dependent mitochondrial fission. Inositol directly binds to AMPKγ and competes with AMP for AMPKγ binding, leading to restriction of AMPK activation and mitochondrial fission. Our study suggests that the AMP/inositol ratio is a critical determinant for AMPK activation and establishes a model in which AMPK activation requires inositol decline to release AMPKγ for AMP binding. Hence, AMPK is an inositol sensor, whose inactivation by inositol serves as a mechanism to restrict mitochondrial fission.
    Keywords:  AMP; AMPK; IMPA1; energy stress; glucose deprivation; inosiotl sensor; inositol; inositol/AMP ratio; mitochondrial fission; mitocondrial dynamics
    DOI:  https://doi.org/10.1016/j.molcel.2021.08.025
  10. Blood Adv. 2021 Sep 21. pii: bloodadvances.2021005132. [Epub ahead of print]
    Integrated safety analysis of umbralisib, a dual PI3Kδ/CK1ε inhibitor, in relapsed/refractory lymphoid malignancies.
    Matthew S Davids, Owen A O'Connor, Wojciech Jurczak, Felipe Samaniego, Timothy S Fenske, Pier Luigi Zinzani, Manish R Patel, Nilanjan Ghosh, Bruce D Cheson, Enrico Derenzini, Danielle M Brander, James A Reeves, Wanda Knopinska-Posluszny, John N Allan, Tycel Phillips, Paolo F Caimi, Ewa Lech-Maranda, John M Burke, Richy Agajanian, Ruth Pettengell, Lori A Leslie, Chan Y Cheah, Gustavo Fonseca, James H Essell, Julio C Chavez, John M Pagel, Jeff P Sharman, Yanzhi Hsu, Hari P Miskin, Peter Sportelli, Michael S Weiss, Ian W Flinn.
      Phosphoinositide 3-kinase-delta (PI3Kδ) inhibitors are active in lymphoid malignancies, though associated toxicities can limit their use. Umbralisib is a dual inhibitor of PI3Kδ and casein kinase-1ε (CK1ε). This study analyzed integrated comprehensive toxicity data from 4 open-label, phase 1 and 2 studies that included 371 adult patients (median age, 67 years) with relapsed/refractory non-Hodgkin lymphoma (follicular lymphoma [n = 147]; marginal zone lymphoma [n = 82]; diffuse large B-cell lymphoma/mantle cell lymphoma [n = 74]; chronic lymphocytic leukemia [n = 43]; and other [n = 25]) who were treated with recommended phase 2 dose of umbralisib 800 mg or higher once daily. At data cutoff, median duration of umbralisib treatment was 5.9 months (range, 0.1-75.1), and 107 patients (28.8%) received umbralisib for ≥12 months. Any-grade treatment-emergent adverse events (TEAEs) occurred in 366/371 patients (98.7%), with the most frequent being diarrhea (52.3%), nausea (41.5%), and fatigue (31.8%). Grade ≥3 TEAEs occurred in 189/371 of patients (50.9%), including neutropenia (11.3%), diarrhea (7.3%), and increased aminotransferases (5.7%). Treatment-emergent serious AEs occurred in 95/371 patients (25.6%). AEs of special interest were limited and included pneumonia (29/371 [7.8%]), noninfectious colitis (9/371 [2.4%]), and pneumonitis (4/371 [1.1%]). AEs led to discontinuation of umbralisib in 51 patients (13.7%). Four patients (1.1%) died due to AEs, none of which were deemed related to umbralisib. No cumulative toxicities were reported. The favorable long-term tolerability profile and low rates of immune-mediated toxicities support the potential use of umbralisib for the benefit of a broad population of patients with lymphoid malignancies.
    DOI:  https://doi.org/10.1182/bloodadvances.2021005132
  11. Curr Opin Cell Biol. 2021 Sep 15. pii: S0955-0674(21)00098-3. [Epub ahead of print]
    Editorial overview: How cells extract information from environmental cues.
    Danijela Matic Vignjevic, Robert H Insall.
      
    DOI:  https://doi.org/10.1016/j.ceb.2021.08.002
  12. Biochim Biophys Acta Biomembr. 2021 Sep 18. pii: S0005-2736(21)00228-5. [Epub ahead of print] 183780
    The enigma of phosphoinositides and their derivatives: Their role in regulation of subcellular compartment morphology.
    Banafshé Larijani, Lior Pytowski, David J Vaux.
      The general segregation of a molecular class, lipids, from the pathways of cellular communication, via endo-membranes, has resulted in the over-simplification and misconceptions in deciphering cell signalling mechanisms. Mechanisms in signal transduction and protein activation require targeting of proteins to membranous compartments with a specific localised morphology and dynamics that are dependent on their lipid composition. Many posttranslational events define cellular behaviours and without the active role of membranous compartments these events lead to various dysregulations of the signalling pathways. We summarise the key findings, using tools such as the rapalogue dimerisation, in the structural roles and signalling of the inter-related phosphoinositide lipids and their derivative, diacylglycerol, in the regulation of nuclear envelope biogenesis and other subcellular compartments such as the nucleoplasmic reticulum.
    Keywords:  CLEM; Membrane fusion; Nuclear envelope; Nucleoplasmic reticula; Phosphoinositides; Rapalogue dimerisation tool
    DOI:  https://doi.org/10.1016/j.bbamem.2021.183780
  13. Mol Cell. 2021 Sep 16. pii: S1097-2765(21)00698-5. [Epub ahead of print]81(18): 3760-3774
    Moonlighting functions of metabolic enzymes and metabolites in cancer.
    Chaoyun Pan, Bo Li, M Celeste Simon.
      The growing field of tumor metabolism has greatly expanded our knowledge of metabolic reprogramming in cancer. Apart from their established roles, various metabolic enzymes and metabolites harbor non-canonical ("moonlighting") functions to support malignant transformation. In this article, we intend to review the current understanding of moonlighting functions of metabolic enzymes and related metabolites broadly existing in cancer cells by dissecting each major metabolic pathway and its regulation of cellular behaviors. Understanding these non-canonical functions may broaden the horizon of the cancer metabolism field and uncover novel therapeutic vulnerabilities in cancer.
    DOI:  https://doi.org/10.1016/j.molcel.2021.08.031
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