bims-pideca Biomed News
on Class IA PI3K signalling in development and cancer
Issue of 2020–10–18
twelve papers selected by
Ralitsa Radostinova Madsen, University College London
  1. Inhibition of class I PI3K enhances chaperone-mediated autophagy.
  2. PI3K Driver Mutations: A Biophysical Membrane-Centric Perspective.
  3. The GATOR-Rag GTPase pathway inhibits mTORC1 activation by lysosome-derived amino acids.
  4. Pan-cancer analysis reveals TAp63-regulated oncogenic lncRNAs that promote cancer progression through AKT activation.
  5. Lactate Lights up PI3K Inhibitor Resistance in Breast Cancer.
  6. Palmitic acid negatively regulates tumor suppressor PTEN through T366 phosphorylation and protein degradation.
  7. PIK3CA mutation enrichment and quantitation from blood and tissue.
  8. Conserved Roles for Receptor Tyrosine Kinase Extracellular Regions in Regulating Receptor and Pathway Activity.
  9. Cardiovascular toxicity of PI3Kα inhibitors.
  10. Development and characterization of protein kinase B/AKT isoform-specific nanobodies.
  11. Control of Glucocorticoid Receptor Levels by PTEN Establishes a Failsafe Mechanism for Tumor Suppression.
  12. Lights and Shade of Next-Generation Pi3k Inhibitors in Chronic Lymphocytic Leukemia.
  1. J Cell Biol. 2020 Dec 07. pii: e202001031. [Epub ahead of print]219(12):
    Inhibition of class I PI3K enhances chaperone-mediated autophagy.
    S Joseph Endicott, Zachary J Ziemba, Logan J Beckmann, Dennis N Boynton, Richard A Miller.
      Chaperone-mediated autophagy (CMA) is the most selective form of lysosomal proteolysis, where individual peptides, recognized by a consensus motif, are translocated directly across the lysosomal membrane. CMA regulates the abundance of many disease-related proteins, with causative roles in neoplasia, neurodegeneration, hepatosteatosis, and other pathologies relevant to human health and aging. At the lysosomal membrane, CMA is inhibited by Akt-dependent phosphorylation of the CMA regulator GFAP. The INS-PI3K-PDPK1 pathway regulates Akt, but its role in CMA is unclear. Here, we report that inhibition of class I PI3K or PDPK1 activates CMA. In contrast, selective inhibition of class III PI3Ks does not activate CMA. Isolated liver lysosomes from mice treated with either of two orally bioavailable class I PI3K inhibitors, pictilisib or buparlisib, display elevated CMA activity, and decreased phosphorylation of lysosomal GFAP, with no change in macroautophagy. The findings of this study represent an important first step in repurposing class I PI3K inhibitors to modulate CMA in vivo.
    DOI:  https://doi.org/10.1083/jcb.202001031
  2. Cancer Res. 2020 Oct 12. pii: canres.0911.2020. [Epub ahead of print]
    PI3K Driver Mutations: A Biophysical Membrane-Centric Perspective.
    Mingzhen Zhang, Hyunbum Jang, Ruth Nussinov.
      Ras activates its effectors at the membrane. Active PI3Kα and its associated kinases/phosphatases assemble at membrane regions enriched in signaling lipids. By contrast, the Raf kinase domain extends into the cytoplasm and its assembly is away from the crowded membrane surface. Our structural membrane-centric outlook underscores the spatiotemporal principles of membrane and signaling lipids which helps clarify PI3Kα activation. Here we focus on mechanisms of activation driven by PI3Kα driver mutations, spotlighting the PI3Kα double (multiple) activating mutations. Single mutations can be potent, but double mutations are stronger: their combination is specific, a single strong driver cannot fully activate PI3K, and two weak drivers may or may not do so. By contrast, two strong drivers may successfully activate PI3K, where one, e.g. H1047R, modulates membrane interactions facilitating substrate binding at the active site (km) and the other, e.g. E542K and E545K, reduces the transition state barrier (ka), releasing autoinhibition by nSH2. Although mostly unidentified, weak drivers are expected to be common, so we ask here how common double mutations are likely to be and why PI3Kα with double mutations responds effectively to inhibitors. We provide a structural view of hotspot and weak driver mutations in PI3Kα activation, explain their mechanisms, compare these with mechanisms of Raf activation, and point to targeting cell-specific, chromatin-accessible, and parallel (or redundant) pathways to thwart the expected emergence of drug resistance. Collectively, our biophysical outlook delineates activation and highlights the challenges of drug resistance.
    DOI:  https://doi.org/10.1158/0008-5472.CAN-20-0911
  3. Science. 2020 Oct 16. 370(6514): 351-356
    The GATOR-Rag GTPase pathway inhibits mTORC1 activation by lysosome-derived amino acids.
    Geoffrey G Hesketh, Fotini Papazotos, Judy Pawling, Dushyandi Rajendran, James D R Knight, Sebastien Martinez, Mikko Taipale, Daniel Schramek, James W Dennis, Anne-Claude Gingras.
      The mechanistic target of rapamycin complex 1 (mTORC1) couples nutrient sufficiency to cell growth. mTORC1 is activated by exogenously acquired amino acids sensed through the GATOR-Rag guanosine triphosphatase (GTPase) pathway, or by amino acids derived through lysosomal degradation of protein by a poorly defined mechanism. Here, we revealed that amino acids derived from the degradation of protein (acquired through oncogenic Ras-driven macropinocytosis) activate mTORC1 by a Rag GTPase-independent mechanism. mTORC1 stimulation through this pathway required the HOPS complex and was negatively regulated by activation of the GATOR-Rag GTPase pathway. Therefore, distinct but functionally coordinated pathways control mTORC1 activity on late endocytic organelles in response to distinct sources of amino acids.
    DOI:  https://doi.org/10.1126/science.aaz0863
  4. Nat Commun. 2020 10 14. 11(1): 5156
    Pan-cancer analysis reveals TAp63-regulated oncogenic lncRNAs that promote cancer progression through AKT activation.
    Marco Napoli, Xiaobo Li, Hayley D Ackerman, Avani A Deshpande, Ivan Barannikov, Marlese A Pisegna, Isabelle Bedrosian, Jürgen Mitsch, Philip Quinlan, Alastair Thompson, Kimal Rajapakshe, Cristian Coarfa, Preethi H Gunaratne, Douglas C Marchion, Anthony M Magliocco, Kenneth Y Tsai, Elsa R Flores.
      The most frequent genetic alterations across multiple human cancers are mutations in TP53 and the activation of the PI3K/AKT pathway, two events crucial for cancer progression. Mutations in TP53 lead to the inhibition of the tumour and metastasis suppressor TAp63, a p53 family member. By performing a mouse-human cross species analysis between the TAp63 metastatic mammary adenocarcinoma mouse model and models of human breast cancer progression, we identified two TAp63-regulated oncogenic lncRNAs, TROLL-2 and TROLL-3. Further, using a pan-cancer analysis of human cancers and multiple mouse models of tumour progression, we revealed that these two lncRNAs induce the activation of AKT to promote cancer progression by regulating the nuclear to cytoplasmic translocation of their effector, WDR26, via the shuttling protein NOLC1. Our data provide preclinical rationale for the implementation of these lncRNAs and WDR26 as therapeutic targets for the treatment of human tumours dependent upon mutant TP53 and/or the PI3K/AKT pathway.
    DOI:  https://doi.org/10.1038/s41467-020-18973-w
  5. Cancer Cell. 2020 Oct 12. pii: S1535-6108(20)30485-2. [Epub ahead of print]38(4): 441-443
    Lactate Lights up PI3K Inhibitor Resistance in Breast Cancer.
    Alissandra L Hillis, Alex Toker.
      Predictive biomarkers can facilitate optimal patient selection for targeted cancer therapies. In this issue of Cancer Cell, Ros et al. show the utility of noninvasive metabolic imaging of labeled carbon transfer from pyruvate to lactate to detect early response and FOXM1-mediated resistance to PI3K inhibition in estrogen-receptor-positive breast cancer.
    DOI:  https://doi.org/10.1016/j.ccell.2020.09.011
  6. Cancer Lett. 2020 Oct 08. pii: S0304-3835(20)30506-1. [Epub ahead of print]
    Palmitic acid negatively regulates tumor suppressor PTEN through T366 phosphorylation and protein degradation.
    Dongmei Bai, Yong Wu, Poonamjot Deol, Yumiko Nobumori, Qi Zhou, Frances M Sladek, Xuan Liu.
      Chronic elevated free fatty (FFA) levels are linked to metabolic disorders and tumorigenesis. However, the molecular mechanism by which FFAs induce cancer remains poorly understood. Here, we show that the tumor suppressor PTEN protein levels were decreased in high fat diet (HFD) fed mice. As palmitic acid (PA, C16:0) showed a significant increase in the HFD fed mice, we further investigated its role in PTEN down regulation. Our studies revealed that exposure of cells to high doses of PA induced mTOR/S6K-mediated phosphorylation of PTEN at T366. The phosphorylation subsequently enhanced the interaction of PTEN with the E3 ubiquitin ligase WW domain-containing protein 2 (WWP2), which promoted polyubiquitination of PTEN and protein degradation. Consistent with PTEN degradation, exposure of cells to increased concentrations of PA also promoted PTEN-mediated AKT activation and cell proliferation. Significantly, a higher level of S6K activation, PTEN T366 phosphorylation, and AKT activation were also observed in the livers of the HFD fed mice. These results provide a molecular mechanism by which a HFD and elevated PA regulates cell proliferation through inactivation of tumor suppressor PTEN.
    Keywords:  PTEN; Palmitic acid; S6K; T366 phosphorylation; mTOR
    DOI:  https://doi.org/10.1016/j.canlet.2020.10.007
  7. Sci Rep. 2020 Oct 13. 10(1): 17082
    PIK3CA mutation enrichment and quantitation from blood and tissue.
    Ieva Keraite, Virginia Alvarez-Garcia, Isaac Garcia-Murillas, Matthew Beaney, Nicholas C Turner, Clare Bartos, Olga Oikonomidou, Maïwenn Kersaudy-Kerhoas, Nicholas R Leslie.
      PIK3CA is one of the two most frequently mutated genes in breast cancers, occurring in 30-40% of cases. Four frequent 'hotspot' PIK3CA mutations (E542K, E545K, H1047R and H1047L) account for 80-90% of all PIK3CA mutations in human malignancies and represent predictive biomarkers. Here we describe a PIK3CA mutation specific nuclease-based enrichment assay, which combined with a low-cost real-time qPCR detection method, enhances assay detection sensitivity from 5% for E542K and 10% for E545K to 0.6%, and from 5% for H1047R to 0.3%. Moreover, we present a novel flexible prediction method to calculate initial mutant allele frequency in tissue biopsy and blood samples with low mutant fraction. These advancements demonstrated a quick, accurate and simple detection and quantitation of PIK3CA mutations in two breast cancer cohorts (first cohort n = 22, second cohort n = 25). Hence this simple, versatile and informative workflow could be applicable for routine diagnostic testing where quantitative results are essential, e.g. disease monitoring subject to validation in a substantial future study.
    DOI:  https://doi.org/10.1038/s41598-020-74086-w
  8. Biochem J. 2020 Oct 12. pii: BCJ20200702. [Epub ahead of print]
    Conserved Roles for Receptor Tyrosine Kinase Extracellular Regions in Regulating Receptor and Pathway Activity.
    Monica Gonzalez-Magaldi, Jacqueline M McCabe, Haley N Cartwright, Ningze Sun, Daniel J Leahy.
      Receptor Tyrosine Kinases (RTKs) comprise a diverse group of cell-surface receptors that mediate key signaling events during animal development and are frequently activated in cancer.  We show here that deletion of the extracellular regions of 10 RTKs representing 7 RTK classes or their substitution with the dimeric immunoglobulin Fc region results in constitutive receptor phosphorylation but fails to result in phosphorylation of downstream signaling effectors Erk or Akt. Conversely, substitution of RTK extracellular regions with the extracellular region of the Epidermal Growth Factor Receptor (EGFR) results in increases in effector phosphorylation in response to EGF. These results indicate that the activation signal generated by the EGFR extracellular region is capable of activating at least 7 different RTK classes. Failure of phosphorylated Fc-RTK chimeras or RTKs with deleted extracellular regions to stimulate phosphorylation of downstream effectors indicates that either dimerization and receptor phosphorylation per se are insufficient to activate signaling or constitutive dimerization leads to pathway inhibition.
    Keywords:  epidermal growth factor receptor; receptor tyrosine kinases; signalling
    DOI:  https://doi.org/10.1042/BCJ20200702
  9. Clin Sci (Lond). 2020 Oct 16. 134(19): 2595-2622
    Cardiovascular toxicity of PI3Kα inhibitors.
    Chandu Sadasivan, Pavel Zhabyeyev, Dina Labib, James A White, D Ian Paterson, Gavin Y Oudit.
      The phosphoinositide 3-kinases (PI3Ks) are a family of intracellular lipid kinases that phosphorylate the 3'-hydroxyl group of inositol membrane lipids, resulting in the production of phosphatidylinositol 3,4,5-trisphosphate from phosphatidylinositol 4,5-bisphosphate. This results in downstream effects, including cell growth, proliferation, and migration. The heart expresses three PI3K class I enzyme isoforms (α, β, and γ), and these enzymes play a role in cardiac cellular survival, myocardial hypertrophy, myocardial contractility, excitation, and mechanotransduction. The PI3K pathway is associated with various disease processes but is particularly important to human cancers since many gain-of-function mutations in this pathway occur in various cancers. Despite the development, testing, and regulatory approval of PI3K inhibitors in recent years, there are still significant challenges when creating and utilizing these drugs, including concerns of adverse effects on the heart. There is a growing body of evidence from preclinical studies revealing that PI3Ks play a crucial cardioprotective role, and thus inhibition of this pathway could lead to cardiac dysfunction, electrical remodeling, vascular damage, and ultimately, cardiovascular disease. This review will focus on PI3Kα, including the mechanisms underlying the adverse cardiovascular effects resulting from PI3Kα inhibition and the potential clinical implications of treating patients with these drugs, such as increased arrhythmia burden, biventricular cardiac dysfunction, and impaired recovery from cardiotoxicity. Recommendations for future directions for preclinical and clinical work are made, highlighting the possible role of PI3Kα inhibition in the progression of cancer-related cachexia and female sex and pre-existing comorbidities as independent risk factors for cardiac abnormalities after cancer treatment.
    Keywords:  PI3Kα; cardiac arrhythmia; cardio-oncology; cardiotoxicity; chemotherapy; heart failure
    DOI:  https://doi.org/10.1042/CS20200302
  10. PLoS One. 2020 ;15(10): e0240554
    Development and characterization of protein kinase B/AKT isoform-specific nanobodies.
    Tijs Merckaert, Olivier Zwaenepoel, Kris Gevaert, Jan Gettemans.
      The serine/threonine protein kinase AKT is frequently over-activated in cancer and is associated with poor prognosis. As a central node in the PI3K/AKT/mTOR pathway, which regulates various processes considered to be hallmarks of cancer, this kinase has become a prime target for cancer therapy. However, AKT has proven to be a highly complex target as it comes in three isoforms (AKT1, AKT2 and AKT3) which are highly homologous, yet non-redundant. The isoform-specific functions of the AKT kinases can be dependent on context (i.e. different types of cancer) and even opposed to one another. To date, there is no isoform-specific inhibitor available and no alternative to genetic approaches to study the function of a single AKT isoform. We have developed and characterized nanobodies that specifically interact with the AKT1 or AKT2 isoforms. These new tools should enable future studies of AKT1 and AKT2 isoform-specific functions. Furthermore, for both isoforms we obtained a nanobody that interferes with the AKT-PIP3-interaction, an essential step in the activation of the kinase. The nanobodies characterized in this study are a new stepping stone towards unravelling AKT isoform-specific signalling.
    DOI:  https://doi.org/10.1371/journal.pone.0240554
  11. Mol Cell. 2020 Oct 15. pii: S1097-2765(20)30657-2. [Epub ahead of print]80(2): 279-295.e8
    Control of Glucocorticoid Receptor Levels by PTEN Establishes a Failsafe Mechanism for Tumor Suppression.
    Hon Yan K Yip, Annabel Chee, Ching-Seng Ang, Sung-Young Shin, Lisa M Ooms, Zainab Mohammadi, Wayne A Phillips, Roger J Daly, Timothy J Cole, Roderick T Bronson, Lan K Nguyen, Tony Tiganis, Robin M Hobbs, Catriona A McLean, Christina A Mitchell, Antonella Papa.
      The PTEN tumor suppressor controls cell death and survival by regulating functions of various molecular targets. While the role of PTEN lipid-phosphatase activity on PtdIns(3,4,5)P3 and inhibition of PI3K pathway is well characterized, the biological relevance of PTEN protein-phosphatase activity remains undefined. Here, using knockin (KI) mice harboring cancer-associated and functionally relevant missense mutations, we show that although loss of PTEN lipid-phosphatase function cooperates with oncogenic PI3K to promote rapid mammary tumorigenesis, the additional loss of PTEN protein-phosphatase activity triggered an extensive cell death response evident in early and advanced mammary tumors. Omics and drug-targeting studies revealed that PI3Ks act to reduce glucocorticoid receptor (GR) levels, which are rescued by loss of PTEN protein-phosphatase activity to restrain cell survival. Thus, we find that the dual regulation of GR by PI3K and PTEN functions as a rheostat that can be exploited for the treatment of PTEN loss-driven cancers.
    Keywords:  failsafe mechanism
    DOI:  https://doi.org/10.1016/j.molcel.2020.09.027
  12. Onco Targets Ther. 2020 ;13 9679-9688
    Lights and Shade of Next-Generation Pi3k Inhibitors in Chronic Lymphocytic Leukemia.
    Andrea Visentin, Federica Frezzato, Filippo Severin, Silvia Imbergamo, Stefano Pravato, Leila Romano Gargarella, Sabrina Manni, Serena Pizzo, Edoardo Ruggieri, Monica Facco, Anna Maria Brunati, Gianpietro Semenzato, Francesco Piazza, Livio Trentin.
      The treatment (i.e. therapy and management) of chronic lymphocytic leukemia (i.e. the disease) has been improved thanks to the introduction (i.e. approval) of kinase inhibitors during the last years. PI3K is one of the most important kinases at the crossroad to the B-cell receptor and cytokine receptor which play a key role in CLL cell survival, proliferation and migration. Idelalisib is the first in class PI3Kδ inhibitor approved for the treatment of relapsed/refractory CLL in combination with rituximab. Idelalisib activity in heavily treated patients is balanced by recurrent adverse events which limit its long-term use. These limitations prompt the investigation on novel PI3K inhibitors, also targeting different protein isoforms, and alternative schedule strategies. In this regard, duvelisib is the only PI3K γ and δ inhibitor approved as single agent for relapsed CLL. In this review, we will address novel insights on PI3K structure, isoforms, regulating signaling and the most updated data of next-generation PI3K inhibitors in CLL.
    Keywords:  PI3K inhibitor; chronic lymphocytic leukemia; copanlisib; duvelisib; umbralisib
    DOI:  https://doi.org/10.2147/OTT.S268899
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