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PI3K isoforms in cell signalling and vesicle trafficking

Abstract

PI3Ks are a family of lipid kinases that phosphorylate intracellular inositol lipids to regulate signalling and intracellular vesicular traffic. Mammals have eight isoforms of PI3K, divided into three classes. The class I PI3Ks generate 3-phosphoinositide lipids, which directly activate signal transduction pathways. In addition to being frequently genetically activated in cancer, similar mutations in class I PI3Ks have now also been found in a human non-malignant overgrowth syndrome and a primary immune disorder that predisposes to lymphoma. The class II and class III PI3Ks are regulators of membrane traffic along the endocytic route, in endosomal recycling and autophagy, with an often indirect effect on cell signalling. Here, we summarize current knowledge of the different PI3K classes and isoforms, focusing on recently uncovered biological functions and the mechanisms by which these kinases are activated. Deeper insight into the PI3K isoforms will undoubtedly continue to contribute to a better understanding of fundamental cell biological processes and, ultimately, of human disease.

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References

  1. 1.

    Herman, P. K. & Emr, S. D. Characterization of VPS34, a gene required for vacuolar protein sorting and vacuole segregation in Saccharomyces cerevisiae. Mol. Cell. Biol. 10, 6742–6754 (1990).

  2. 2.

    Balla, T. Phosphoinositides: tiny lipids with giant impact on cell regulation. Physiol. Rev. 93, 1019–1137 (2013).

  3. 3.

    Schink, K. O., Tan, K.-W. & Stenmark, H. Phosphoinositides in control of membrane dynamics. Annu. Rev. Cell Dev. Biol. 32, 143–171 (2016).

  4. 4.

    Zvelebil, M. J. et al. Structural and functional diversity of phosphoinositide 3-kinases. Philos. Trans. R. Soc. B 351, 217–223 (1996).

  5. 5.

    MacDougall, L. K., Domin, J. & Waterfield, M. D. A family of phosphoinositide 3-kinases in Drosophila identifies a new mediator of signal transduction. Curr. Biol. 5, 1404–1415 (1995).

  6. 6.

    Vanhaesebroeck, B., Leevers, S. J., Panayotou, G. & Waterfield, M. D. Phosphoinositide 3-kinases: a conserved family of signal transducers. Trends Biochem. Sci. 22, 267–272 (1997).

  7. 7.

    Domin, J. & Waterfield, M. D. Using structure to define the function of phosphoinositide 3-kinase family members. FEBS Lett. 410, 91–95 (1997).

  8. 8.

    Vanhaesebroeck, B., Ali, K., Bilancio, A., Geering, B. & Foukas, L. C. Signalling by PI3K isoforms: insights from gene-targeted mice. Trends Biochem. Sci. 30, 194–204 (2005).

  9. 9.

    Gulluni, F. et al. Mitotic spindle assembly and genomic stability in breast cancer require PI3K-C2α scaffolding function. Cancer Cell 32, 444–459 (2017).This study provides the first evidence for a scaffolding function of a class II PI3K that is independent of its catalytic activity.

  10. 10.

    Devereaux, K. et al. Regulation of mammalian autophagy by class II and III PI 3-kinases through PI3P synthesis. PLOS ONE 8, e76405 (2013).

  11. 11.

    Hirsch, E., Braccini, L., Ciraolo, E., Morello, F. & Perino, A. Twice upon a time: PI3K’s secret double life exposed. Trends Biochem. Sci. 34, 244–248 (2009).

  12. 12.

    Burke, J. E. Structural basis for regulation of phosphoinositide kinases and their involvement in human disease. Mol. Cell 71, 653–673 (2018).

  13. 13.

    Burke, J. E. & Williams, R. L. Synergy in activating class I PI3Ks. Trends Biochem. Sci. 40, 88–100 (2015).

  14. 14.

    Dornan, G. L. & Burke, J. E. Molecular mechanisms of human disease mediated by oncogenic and primary immunodeficiency mutations in class IA phosphoinositide 3-kinases. Front. Immunol. 9, 575 (2018).

  15. 15.

    Fruman, D. A. et al. The PI3K pathway in human disease. Cell 170, 605–635 (2017).

  16. 16.

    Vanhaesebroeck, B., Whitehead, M. A. & Pineiro, R. Molecules in medicine mini-review: isoforms of PI3K in biology and disease. J. Mol. Med. 94, 5–11 (2016).

  17. 17.

    Hawkins, P. T. & Stephens, L. R. PI3K signalling in inflammation. Biochim. Biophys. Acta 1851, 882–897 (2015).

  18. 18.

    Stark, A. K., Sriskantharajah, S., Hessel, E. M. & Okkenhaug, K. PI3K inhibitors in inflammation, autoimmunity and cancer. Curr. Opin. Pharmacol. 23, 82–91 (2015).

  19. 19.

    Fruman, D. A. & Rommel, C. PI3K and cancer: lessons, challenges and opportunities. Nat. Rev. Drug Discov. 13, 140–156 (2014).

  20. 20.

    Thorpe, L. M., Yuzugullu, H. & Zhao, J. J. PI3K in cancer: divergent roles of isoforms, modes of activation and therapeutic targeting. Nat. Rev. Cancer 15, 7–24 (2015).

  21. 21.

    Janku, F., Yap, T. A. & Meric-Bernstam, F. Targeting the PI3K pathway in cancer: are we making headway? Nat. Rev. Clin. Oncol. 15, 273–291 (2018).

  22. 22.

    Mayer, I. A. & Arteaga, C. L. The PI3K/AKT pathway as a target for cancer treatment. Annu. Rev. Med. 67, 11–28 (2016).

  23. 23.

    Tsolakos, N. et al. Quantitation of class IA PI3Ks in mice reveals p110-free-p85s and isoform-selective subunit associations and recruitment to receptors. Proc. Natl Acad. Sci. USA 115, 12176–12181 (2018).This study provides an in-depth quantitative assessment of the endogenous levels of the class IA PI3K catalytic and regulatory subunits in mouse tissues and cells and their interaction with each other and with receptors under basal and stimulated conditions.

  24. 24.

    Vadas, O. et al. Molecular determinants of PI3Kγ-mediated activation downstream of G-protein-coupled receptors (GPCRs). Proc. Natl Acad. Sci. USA 110, 18862–18867 (2013).

  25. 25.

    Fritsch, R. & Downward, J. SnapShot: class I PI3K isoform signaling. Cell 154, 940–940 (2013).

  26. 26.

    Fritsch, R. et al. RAS and RHO families of GTPases directly regulate distinct phosphoinositide 3-kinase isoforms. Cell 153, 1050–1063 (2013).

  27. 27.

    Dbouk, H. A. et al. G protein-coupled receptor-mediated activation of p110β by Gβγ is required for cellular transformation and invasiveness. Sci. Signal. 5, ra89 (2012).

  28. 28.

    Salamon, R. S. et al. Identification of the Rab5 binding site in p110β: assays for PI3Kβ binding to Rab5. Methods Mol. Biol. 1298, 271–281 (2015).

  29. 29.

    Bresnick, A. R. & Backer, J. M. PI3Kβ — a versatile transducer for GPCR, RTK and small GTPase signaling. Endocrinology 160, 536–555 (2019).

  30. 30.

    Malek, M. et al. PTEN regulates PI(3,4)P2 signaling downstream of class I PI3K. Mol. Cell 68, 566–580 (2017).This study demonstrates that PTEN is not only a lipid phosphatase for PtdIns(3,4,5)P 3 as was previously thought but also uses PtdIns(3,4)P 2 as a substrate to convert it into PtdIns4P.

  31. 31.

    Lee, Y. R., Chen, M. & Pandolfi, P. P. The functions and regulation of the PTEN tumour suppressor: new modes and prospects. Nat. Rev. Mol. Cell. Biol. 19, 547–562 (2018).

  32. 32.

    Costa, C. & Hirsch, E. in Current Topics in Microbiology and Immunology (eds Rommel, C., Vanhaesebroeck, B. & Vogt, P.) 171–181 (Springer, 2010).

  33. 33.

    Ito, Y., Hart, J. R. & Vogt, P. K. Isoform-specific activities of the regulatory subunits of phosphatidylinositol 3-kinases — potentially novel therapeutic targets. Expert Opin. Ther. Targets 22, 869–877 (2018).

  34. 34.

    Takiar, V., Ip, C. K., Gao, M., Mills, G. B. & Cheung, L. W. Neomorphic mutations create therapeutic challenges in cancer. Oncogene 36, 1607–1618 (2017).

  35. 35.

    Marshall, J. D. S., Whitecross, D. E., Mellor, P. & Anderson, D. H. Impact of p85α alterations in cancer. Biomolecules 9, 29 (2019).

  36. 36.

    Vanhaesebroeck, B., Guillermet-Guibert, J., Graupera, M. & Bilanges, B. The emerging mechanisms of isoform-specific PI3K signalling. Nat. Rev. Mol. Cell. Biol. 11, 329–341 (2010).

  37. 37.

    Li, H. & Marshall, A. J. Phosphatidylinositol (3,4) bisphosphate-specific phosphatases and effector proteins: a distinct branch of PI3K signaling. Cell. Signal. 27, 1789–1798 (2015).

  38. 38.

    Hawkins, P. T. & Stephens, L. R. Emerging evidence of signalling roles for PI(3,4)P2 in class I and II PI3K-regulated pathways. Biochem. Soc. Trans. 44, 307–314 (2016).

  39. 39.

    Isakoff, S. J. et al. Identification and analysis of PH domain-containing targets of phosphatidylinositol 3-kinase using a novel in vivo assay in yeast. EMBO J. 17, 5374–5387 (1998).

  40. 40.

    Zhang, P., Wang, Y., Sesaki, H. & Iijima, M. Proteomic identification of phosphatidylinositol (3,4,5) triphosphate-binding proteins in Dictyostelium discoideum. Proc. Natl Acad. Sci. USA 107, 11829–11834 (2010).

  41. 41.

    Park, W. S. et al. Comprehensive identification of PIP3-regulated PH domains from C. elegans to H. sapiens by model prediction and live imaging. Mol. Cell 30, 381–392 (2008).

  42. 42.

    Krugmann, S. et al. Identification of ARAP3, a novel PI3K effector regulating both Arf and Rho GTPases, by selective capture on phosphoinositide affinity matrices. Mol. Cell 9, 95–108 (2002).

  43. 43.

    Chen, C. L., Wang, Y., Sesaki, H. & Iijima, M. Myosin I links PIP3 signaling to remodeling of the actin cytoskeleton in chemotaxis. Sci. Signal. 5, ra10 (2012).

  44. 44.

    Plantard, L. et al. PtdIns(3,4,5)P3 is a regulator of myosin-X localization and filopodia formation. J. Cell Sci. 123, 3525–3534 (2010).

  45. 45.

    Manning, B. D. & Toker, A. AKT/PKB signaling: navigating the network. Cell 169, 381–405 (2017).

  46. 46.

    Lien, E. C., Dibble, C. C. & Toker, A. PI3K signaling in cancer: beyond AKT. Curr. Opin. Cell Biol. 45, 62–71 (2017).

  47. 47.

    Dansen, T. B. & Burgering, B. M. Unravelling the tumor-suppressive functions of FOXO proteins. Trends Cell Biol. 18, 421–429 (2008).

  48. 48.

    Hornsveld, M., Dansen, T. B., Derksen, P. W. & Burgering, B. M. T. Re-evaluating the role of FOXOs in cancer. Semin. Cancer Biol. 50, 90–100 (2018).

  49. 49.

    Hedrick, S. M., Hess Michelini, R., Doedens, A. L., Goldrath, A. W. & Stone, E. L. FOXO transcription factors throughout T cell biology. Nat. Rev. Immunol. 12, 649–661 (2012).

  50. 50.

    Luo, C. T. & Li, M. O. Foxo transcription factors in T cell biology and tumor immunity. Semin. Cancer Biol. 50, 13–20 (2018).

  51. 51.

    Dummler, B. & Hemmings, B. A. Physiological roles of PKB/Akt isoforms in development and disease. Biochem. Soc. Trans. 35, 231–235 (2007).

  52. 52.

    Toker, A. & Marmiroli, S. Signaling specificity in the Akt pathway in biology and disease. Adv. Biol. Regul. 55, 28–38 (2014).

  53. 53.

    Chin, Y. R. & Toker, A. The actin-bundling protein palladin is an Akt1-specific substrate that regulates breast cancer cell migration. Mol. Cell 38, 333–344 (2010).This is one of the first reports of AKT isoform substrate specificity in cells.

  54. 54.

    Liu, S. L. et al. Quantitative lipid imaging reveals a new signaling function of phosphatidylinositol-3,4-bisphophate: isoform- and site-specific activation of Akt. Mol. Cell 71, 1092–1104 (2018).This study provides a molecular mechanism, based on AKT-isoform-selective endocytosis, for AKT isoform substrate specificity in cells.

  55. 55.

    Li Chew, C. et al. In vivo role of INPP4B in tumor and metastasis suppression through regulation of PI3K–AKT signaling at endosomes. Cancer Discov. 5, 740–751 (2015).

  56. 56.

    Walz, H. A. et al. Isoform-specific regulation of Akt signaling by the endosomal protein WDFY2. J. Biol. Chem. 285, 14101–14108 (2010).

  57. 57.

    Braccini, L. et al. PI3K-C2γ is a Rab5 effector selectively controlling endosomal Akt2 activation downstream of insulin signalling. Nat. Commun. 6, 7400–7400 (2015).This is the first description of a role of the liver-specific class II isoform PI3KC2γ, based on endosomal PtdIns(3,4)P 2 production.

  58. 58.

    Cho, H. et al. Insulin resistance and a diabetes mellitus-like syndrome in mice lacking the protein kinase Akt2 (PKBβ). Science 292, 1728–1731 (2001).

  59. 59.

    Choi, S. et al. Agonist-stimulated phosphatidylinositol-3,4,5-trisphosphate generation by scaffolded phosphoinositide kinases. Nat. Cell Biol. 18, 1324–1335 (2016).

  60. 60.

    Foukas, L. C. et al. Critical role for the p110α phosphoinositide-3-OH kinase in growth and metabolic regulation. Nature 441, 366–370 (2006).

  61. 61.

    Knight, Z. A. et al. A pharmacological map of the PI3-K family defines a role for p110α in insulin signaling. Cell 125, 733–747 (2006).

  62. 62.

    Nylander, S. et al. Human target validation of phosphoinositide 3-kinase (PI3K)β: effects on platelets and insulin sensitivity, using AZD6482 a novel PI3Kβ inhibitor. J. Thromb. Haemost. 10, 2127–2136 (2012).

  63. 63.

    Mateo, J. et al. A first-time-in-human study of GSK2636771, a phosphoinositide 3 kinase beta-selective inhibitor, in patients with advanced solid tumors. Clin. Cancer Res. 23, 5981–5992 (2017).

  64. 64.

    Graupera, M. et al. Angiogenesis selectively requires the p110α isoform of PI3K to control endothelial cell migration. Nature 453, 662–666 (2008).

  65. 65.

    Ciraolo, E. et al. Essential role of the p110β subunit of phosphoinositide 3-OH kinase in male fertility. Mol. Biol. Cell 21, 704–711 (2010).

  66. 66.

    Guillermet-Guibert, J. et al. Novel role for p110β PI 3-kinase in male fertility through regulation of androgen receptor activity in Sertoli cells. PLOS Genet. 11, e1005304 (2015).

  67. 67.

    Gratacap, M. P. et al. Regulation and roles of PI3Kβ, a major actor in platelet signaling and functions. Adv. Enzyme Regul. 51, 106–116 (2011).

  68. 68.

    So, L. & Fruman, D. A. PI3K signalling in B- and T-lymphocytes: new developments and therapeutic advances. Biochem. J. 442, 465–481 (2012).

  69. 69.

    Ruckle, T., Schwarz, M. K. & Rommel, C. PI3Kγ inhibition: towards an ‘aspirin of the 21st century’? Nat. Rev. Drug Discov. 5, 903–918 (2006).

  70. 70.

    Perino, A. et al. Integrating cardiac PIP3 and cAMP signaling through a PKA anchoring function of p110γ. Mol. Cell 42, 84–95 (2011).

  71. 71.

    Damilano, F. et al. Distinct effects of leukocyte and cardiac phosphoinositide 3-kinase γ activity in pressure overload-induced cardiac failure. Circulation 123, 391–399 (2011).

  72. 72.

    Eickholt, B. J. et al. Control of axonal growth and regeneration of sensory neurons by the p110δ PI 3-kinase. PLOS ONE 2, e869 (2007).

  73. 73.

    Law, A. J. et al. Neuregulin 1–ErbB4–PI3K signaling in schizophrenia and phosphoinositide 3-kinase-p110δ inhibition as a potential therapeutic strategy. Proc. Natl Acad. Sci. USA 109, 12165–12170 (2012).

  74. 74.

    Bartok, B., Hammaker, D. & Firestein, G. S. Phosphoinositide 3-kinase δ regulates migration and invasion of synoviocytes in rheumatoid arthritis. J. Immunol. 192, 2063–2070 (2014).

  75. 75.

    Whitehead, M. A., Bombardieri, M., Pitzalis, C. & Vanhaesebroeck, B. Isoform-selective induction of human p110δ PI3K expression by TNFα: identification of a new and inducible PIK3CD promoter. Biochem. J. 443, 857–867 (2012).

  76. 76.

    Sawyer, C. et al. Regulation of breast cancer cell chemotaxis by the phosphoinositide 3-kinase p110δ. Cancer Res. 63, 1667–1675 (2003).

  77. 77.

    Goulielmaki, E. et al. Pharmacological inactivation of the PI3K p110δ prevents breast tumour progression by targeting cancer cells and macrophages. Cell Death Dis. 9, 678 (2018).

  78. 78.

    Ko, E. et al. PI3Kδ is a new therapeutic target in hepatocellular carcinoma. Hepatology 68, 2285–2300 (2018).

  79. 79.

    Yue, D. & Sun, X. Idelalisib promotes Bim-dependent apoptosis through AKT/FoxO3a in hepatocellular carcinoma. Cell Death Dis. 9, 935 (2018).

  80. 80.

    Papakonstanti, E. A. et al. Distinct roles of class IA PI3K isoforms in primary and immortalised macrophages. J. Cell Sci. 121, 4124–4133 (2008).

  81. 81.

    Foukas, L. C., Berenjeno, I. M., Gray, A., Khwaja, A. & Vanhaesebroeck, B. Activity of any class IA PI3K isoform can sustain cell proliferation and survival. Proc. Natl Acad. Sci. USA 107, 11381–11386 (2010).

  82. 82.

    Arafeh, R. & Samuels, Y. PIK3CA in cancer: the past 30 years. >Semin. Cancer Biol. https://doi.org/10.1016/j.semcancer.2019.02.002 (2019).

  83. 83.

    Burke, J. E., Perisic, O., Masson, G. R., Vadas, O. & Williams, R. L. Oncogenic mutations mimic and enhance dynamic events in the natural activation of phosphoinositide 3-kinase p110α (PIK3CA). Proc. Natl Acad. Sci. USA 109, 15259–15264 (2012).This study provides an in-depth assessment of how cancer-associated mutations in PIK3CA affect the biochemical characteristics of the p110α–p85α complex.

  84. 84.

    Oda, K., Stokoe, D., Taketani, Y. & McCormick, F. High frequency of coexistent mutations of PIK3CA and PTEN genes in endometrial carcinoma. Cancer Res. 65, 10669–10673 (2005).

  85. 85.

    Madsen, R. R. et al. Oncogenic PIK3CA promotes cellular stemness in an allele dose-dependent manner. Proc. Natl Acad. Sci. USA 116, 8380–8389 (2019). This study shows that homozygous but not heterozygous mutation of PIK3CA induces broad biological effects in human induced pluripotent stem cells, and provides evidence that many PIK3CA -mutant tumours either show homozygous mutation in this gene or carry additional activating genetic lesions in the PI3K pathway.

  86. 86.

    Hyman, D. M. et al. AKT inhibition in solid tumors with AKT1 mutations. J. Clin. Oncol. 35, 2251–2259 (2017).

  87. 87.

    Berenjeno, I. M. et al. Oncogenic PIK3CA induces centrosome amplification and tolerance to genome doubling. Nat. Commun. 8, 1773 (2017).

  88. 88.

    Gerstung, M. et al. The evolutionary history of 2,658 cancers. Preprint at bioRxiv https://www.biorxiv.org/content/10.1101/161562v3 (2019).

  89. 89.

    Jamal-Hanjani, M. et al. Tracking the evolution of non-small-cell lung cancer. N. Engl. J. Med. 376, 2109–2121 (2017).

  90. 90.

    Morris, J. Z., Tissenbaum, H. A. & Ruvkun, G. A phosphatidylinositol-3-OH kinase family member regulating longevity and diapause in Caenorhabditis elegans. Nature 382, 536–539 (1996).

  91. 91.

    Bosch, A. et al. PI3K inhibition results in enhanced estrogen receptor function and dependence in hormone receptor-positive breast cancer. Sci. Transl. Med. 7, 283ra51 (2015).

  92. 92.

    Toska, E. et al. PI3K pathway regulates ER-dependent transcription in breast cancer through the epigenetic regulator KMT2D. Science 355, 1324–1330 (2017).The studies reported in Bosch et al. (2015) and Toska et al. (2017) uncover mechanisms of how PIK3CA mutation modulates oestrogen hormone responsiveness in breast cancer cell lines, and together with other studies form the basis of the ongoing phase III trials of PI3Kα inhibitors with hormone therapy.

  93. 93.

    Koren, S. & Bentires-Alj, M. Tackling resistance to PI3K inhibition by targeting the epigenome. Cancer Cell 31, 616–618 (2017).

  94. 94.

    Carver, B. S. et al. Reciprocal feedback regulation of PI3K and androgen receptor signaling in PTEN-deficient prostate cancer. Cancer Cell 19, 575–586 (2011).

  95. 95.

    Zhu, Q. et al. Phosphoinositide 3-OH kinase p85α and p110β are essential for androgen receptor transactivation and tumor progression in prostate cancers. Oncogene 27, 4569–4579 (2008).

  96. 96.

    Jiang, X., Chen, S., Asara, J. M. & Balk, S. P. Phosphoinositide 3-kinase pathway activation in phosphate and tensin homolog (PTEN)-deficient prostate cancer cells is independent of receptor tyrosine kinases and mediated by the p110β and p110δ catalytic subunits. J. Biol. Chem. 285, 14980–14989 (2010).

  97. 97.

    Marques, R. B. et al. High efficacy of combination therapy using PI3K/AKT inhibitors with androgen deprivation in prostate cancer preclinical models. Eur. Urol. 67, 1177–1185 (2015).

  98. 98.

    Rinnerthaler, G., Gampenrieder, S. P. & Greil, R. ASCO 2018 highlights: metastatic breast cancer. Memo 11, 276–279 (2018).

  99. 99.

    Kaneda, M. M. et al. PI3Kγ is a molecular switch that controls immune suppression. Nature 539, 437–442 (2016).

  100. 100.

    De Henau, O. et al. Overcoming resistance to checkpoint blockade therapy by targeting PI3Kγ in myeloid cells. Nature 539, 443–447 (2016).

  101. 101.

    Ali, K. et al. Inactivation of PI(3)K p110δ breaks regulatory T cell-mediated immune tolerance to cancer. Nature 510, 407–411 (2014).The studies reported in Kaneda et al. (2016), De Henau et al. (2016) and Ali et al. (2014) demonstrate the potential of drugs targeting leukocyte-expressed PI3Kγ and PI3Kδ in cancer immunotherapy.

  102. 102.

    Abu-Eid, R. et al. Selective inhibition of regulatory T cells by targeting the PI3K–Akt pathway. Cancer Immunol. Res. 2, 1080–1089 (2014).

  103. 103.

    Ahmad, S. et al. Differential PI3Kδ signaling in CD4+ T cell subsets enables selective targeting of T regulatory cells to enhance cancer immunotherapy. Cancer Res. 77, 1892–1904 (2017).

  104. 104.

    Lu, X. et al. Effective combinatorial immunotherapy for castration-resistant prostate cancer. Nature 543, 728–732 (2017).

  105. 105.

    Okkenhaug, K., Graupera, M. & Vanhaesebroeck, B. Targeting PI3K in cancer: impact on tumor cells, their protective stroma, angiogenesis, and immunotherapy. Cancer Discov. 6, 1090–1105 (2016).

  106. 106.

    Burger, J. A. & Wiestner, A. Targeting B cell receptor signalling in cancer: preclinical and clinical advances. Nat. Rev. Cancer 18, 148–167 (2018).

  107. 107.

    Brown, J. R. The PI3K pathway: clinical inhibition in chronic lymphocytic leukemia. Semin. Oncol. 43, 260–264 (2016).

  108. 108.

    Ho, L. K., Liu, D., Rozycka, M., Brown, R. A. & Fry, M. J. Identification of four novel human phosphoinositide 3-kinases defines a multi-isoform subfamily. Biochem. Biophys. Res. Commun. 235, 130–137 (1997).

  109. 109.

    Falasca, M. et al. The role of phosphoinositide 3-kinase C2α in insulin signaling. J. Biol. Chem. 282, 28226–28236 (2007).

  110. 110.

    Leibiger, B. et al. Insulin-feedback via PI3K-C2α activated PKBα/Akt1 is required for glucose-stimulated insulin secretion. FASEB J. 24, 1824–1837 (2010).

  111. 111.

    Maffucci, T. et al. Class II phosphoinositide 3-kinase defines a novel signaling pathway in cell migration. J. Cell Biol. 169, 789–799 (2005).

  112. 112.

    Bridges, D. et al. Phosphatidylinositol 3,5-bisphosphate plays a role in the activation and subcellular localization of mechanistic target of rapamycin 1. Mol. Biol. Cell 23, 2955–2962 (2012).

  113. 113.

    Marat, A. L. & Haucke, V. Phosphatidylinositol 3-phosphates—at the interface between cell signalling and membrane traffic. EMBO J. 35, 561–579 (2016).

  114. 114.

    Gulluni, F., De Santis, M. C., Margaria, J. P., Martini, M. & Hirsch, E. Class II PI3K functions in cell biology and disease. Trends Cell Biol. 29, 339–359 (2019).

  115. 115.

    Wang, H. et al. Autoregulation of class II alpha PI3K activity by its lipid-binding PX-C2 domain module. Mol. Cell 71, 343–351 (2018).This is the first description of a regulatory mechanism for a class II PI3K.

  116. 116.

    Gaidarov, I., Smith, M. E., Domin, J. & Keen, J. H. The class II phosphoinositide 3-kinase C2α is activated by clathrin and regulates clathrin-mediated membrane trafficking. Mol. Cell 7, 443–449 (2001).

  117. 117.

    Posor, Y. et al. Spatiotemporal control of endocytosis by phosphatidylinositol-3, 4-bisphosphate. Nature 499, 233–237 (2013).This study provided evidence of PtdIns(3,4)P 2 formation by a class II PI3K and how this regulates clathrin-mediated endocytosis.

  118. 118.

    Stahelin, R. V. et al. Structural and membrane binding analysis of the Phox homology domain of phosphoinositide 3-kinase-C2α. J. Biol. Chem. 281, 39396–39406 (2006).

  119. 119.

    Chen, K. E., Tillu, V. A., Chandra, M. & Collins, B. M. Molecular basis for membrane recruitment by the PX and C2 domains of class II phosphoinositide 3-kinase-C2α. Structure 26, 1–14 (2018).

  120. 120.

    Pirola, L. et al. Activation loop sequences confer substrate specificity to phosphoinositide 3-kinase α (PI3Kα). Functions of lipid kinase-deficient PI3Kα in signaling. J. Biol. Chem. 276, 21544–21554 (2001).

  121. 121.

    Goulden, B. D. et al. A high-avidity biosensor reveals plasma membrane PI(3,4)P2 is predominantly a class I PI3K signaling product. J. Cell Biol. 218, 1066–1079 (2018).

  122. 122.

    Laketa, V. et al. Membrane-permeant phosphoinositide derivatives as modulators of growth factor signaling and neurite outgrowth. Chem. Biol. 16, 1190–1196 (2009).

  123. 123.

    Marat, A. L. et al. mTORC1 activity repression by late endosomal phosphatidylinositol 3,4-bisphosphate. Science 356, 968–968 (2017).This study reveals a new link between class II PI3Ks and mTORC1 regulation.

  124. 124.

    Campa, C. C. et al. Rab11 activity and PtdIns(3)P turnover removes recycling cargo from endosomes. Nat. Chem. Biol. 14, 801–810 (2018).

  125. 125.

    Franco, I. et al. PI3K class II α controls spatially restricted endosomal PtdIns3P and Rab11 activation to promote primary cilium function. Dev. Cell 28, 647–658 (2014).

  126. 126.

    Campa, C. C., Franco, I. & Hirsch, E. PI3K-C2α: one enzyme for two products coupling vesicle trafficking and signal transduction. FEBS Lett. 589, 1552–1558 (2015).

  127. 127.

    Nakatsu, F. et al. PtdIns4P synthesis by PI4KIIIα at the plasma membrane and its impact on plasma membrane identity. J. Cell Biol. 199, 1003–1016 (2012).

  128. 128.

    Hammond, G. R. V. et al. PI4P and PI(4,5)P2 are essential but independent lipid determinants of membrane identity. Science 727, 2–6 (2012).

  129. 129.

    Saheki, Y. et al. Control of plasma membrane lipid homeostasis by the extended synaptotagmins. Nat. Cell Biol. 18, 504–515 (2016).

  130. 130.

    Booth, D. G., Hood, F. E., Prior, I. A. & Royle, S. J. A. TACC3/ch-TOG/clathrin complex stabilises kinetochore fibres by inter-microtubule bridging. EMBO J. 30, 906–919 (2011).

  131. 131.

    Jean, S., Cox, S., Schmidt, E. J., Robinson, F. L. & Kiger, A. Sbf/MTMR13 coordinates PI(3)P and Rab21 regulation in endocytic control of cellular remodeling. Mol. Biol. Cell 23, 2723–2740 (2012).

  132. 132.

    Hauswirth, A. G. et al. A postsynaptic PI3K-cII dependent signaling controller for presynaptic homeostatic plasticity. eLife 7, e31535 (2018).

  133. 133.

    Velichkova, M. et al. Drosophila Mtm and class II PI3K coregulate a PI(3)P pool with cortical and endolysosomal functions. J. Cell Biol. 190, 407–425 (2010).

  134. 134.

    Posor, Y., Eichhorn-Grünig, M. & Haucke, V. Phosphoinositides in endocytosis. Biochim. Biophys. Acta 1851, 794–804 (2014).

  135. 135.

    Schöneberg, J. et al. Lipid-mediated PX-BAR domain recruitment couples local membrane constriction to endocytic vesicle fission. Nat. Commun. 8, 15873 (2017).

  136. 136.

    Almeida-Souza, L. et al. A flat BAR protein promotes actin polymerization at the base of clathrin-coated pits. Cell 174, 325–337 (2018).

  137. 137.

    He, K. et al. Dynamics of phosphoinositide conversion in clathrin-mediated endocytic traffic. Nature 552, 410–414 (2017).

  138. 138.

    Aki, S., Yoshioka, K., Okamoto, Y., Takuwa, N. & Takuwa, Y. Phosphatidylinositol 3-kinase class II α-isoform PI3K-C2α is required for transforming growth factor β-induced Smad signaling in endothelial cells. J. Biol. Chem. 290, 6086–6105 (2015).

  139. 139.

    Alliouachene, S. et al. Inactivation of the class II PI3K-C2β potentiates insulin signaling and sensitivity. Cell Rep. 13, 1881–1894 (2015).

  140. 140.

    Korolchuk, V. I. et al. Lysosomal positioning coordinates cellular nutrient responses. Nat. Cell Biol. 13, 453–460 (2011).

  141. 141.

    Katso, R. M. et al. Phosphoinositide 3-kinase C2β regulates cytoskeletal organization and cell migration via Rac-dependent mechanisms. Mol. Biol. Cell 17, 3729–3744 (2006).

  142. 142.

    Domin, J. et al. The class II phosphoinositide 3-kinase PI3K-C2β regulates cell migration by a PtdIns(3)P dependent mechanism. J. Cell. Physiol. 205, 452–462 (2005).

  143. 143.

    Yoshioka, K. et al. Endothelial PI3K-C2α, a class II PI3K, has an essential role in angiogenesis and vascular barrier function. Nat. Med. 18, 1560–1569 (2012).This study demonstrated that homozygous knockout of Pik3c2a in mice causes embryonic lethality as a consequence of impaired angiogenesis.

  144. 144.

    Biswas, K. et al. Essential role of class II phosphatidylinositol-3-kinase-C2α in sphingosine 1-phosphate receptor-1-mediated signaling and migration in endothelial cells. J. Biol. Chem. 288, 2325–2339 (2013).

  145. 145.

    Kalaidzidis, I. et al. APPL endosomes are not obligatory endocytic intermediates but act as stable cargo-sorting compartments. J. Cell Biol. 211, 123–144 (2015).

  146. 146.

    Zoncu, R. et al. A phosphoinositide switch controls the maturation and signaling properties of APPL endosomes. Cell 136, 1110–1121 (2009).

  147. 147.

    Cai, X. et al. Tripartite motif containing protein 27 negatively regulates CD4 T cells by ubiquitinating and inhibiting the class II PI3K-C2β. Proc. Natl Acad. Sci. USA 108, 20072–20077 (2011).

  148. 148.

    Srivastava, S. et al. The class II phosphatidylinositol 3 kinase C2β is required for the activation of the K+ channel KCa3.1 and CD4 T cells. Mol. Biol. Cell 20, 3783–3791 (2009).

  149. 149.

    Srivastava, S., Cai, X., Li, Z., Sun, Y. & Skolnik, E. Y. Phosphatidylinositol-3-kinase C2 and TRIM27 function to positively and negatively regulate IgE receptor activation of mast cells. Mol. Cell. Biol. 32, 3132–3139 (2012).

  150. 150.

    Srivastava, S., Li, Z. & Skolnik, E. Y. Phosphatidlyinositol-3-kinase C2 beta (PI3KC2β) is a potential new target to treat IgE mediated disease. PLOS ONE 12, e0183474 (2017).

  151. 151.

    Falasca, M. et al. Class II phosphoinositide 3-kinases as novel drug targets. J. Med. Chem. 60, 47–65 (2017).

  152. 152.

    Alliouachene, S. et al. Inactivation of class II PI3K-C2α induces leptin resistance, age-dependent insulin resistance and obesity in male mice. Diabetologia 59, 1503–1512 (2016).

  153. 153.

    Mountford, J. K. et al. The class II PI 3-kinase, PI3KC2α, links platelet internal membrane structure to shear-dependent adhesive function. Nat. Commun. 6, 6535 (2015).

  154. 154.

    Valet, C. et al. Essential role of class II PI3K-C2α in platelet membrane morphology. Blood 126, 1128–1138 (2015).

  155. 155.

    Tiosano, D. Mutations in PIK3C2A cause syndromic short stature, skeletal abnormalities, and cataracts associated with ciliary dysfunction. PLOS Genet. 15, e1008088 (2019).

  156. 156.

    Harada, K., Truong, A. B., Cai, T. & Khavari, P. A. The class II phosphoinositide 3-kinase C2β is not essential for epidermal differentiation. Mol. Cell. Biol. 25, 11122–11130 (2005).

  157. 157.

    Amoasii, L., Hnia, K. & Laporte, J. Myotubularin phosphoinositide phosphatases in human diseases. Curr. Top. Microbiol. Immunol. 362, 209–233 (2012).

  158. 158.

    Ketel, K. et al. A phosphoinositide conversion mechanism for exit from endosomes. Nature 529, 408–412 (2016).

  159. 159.

    Ribeiro, I., Yuan, L., Tanentzapf, G., Dowling, J. J. & Kiger, A. Phosphoinositide regulation of integrin trafficking required for muscle attachment and maintenance. PLOS Genet. 7, e1001295 (2011).

  160. 160.

    Sabha, N. et al. PIK3C2B inhibition improves function and prolongs survival in myotubular myopathy animal models. J. Clin. Invest. 126, 3613–3625 (2016).

  161. 161.

    Backer, J. The intricate regulation and complex functions of the class III phosphoinositide 3-kinase Vps34. Biochem. J. 473, 2251–2271 (2016).

  162. 162.

    Ktistakis, N. T. & Tooze, S. A. Digesting the expanding mechanisms of autophagy. Trends Cell Biol. 26, 624–635 (2016).

  163. 163.

    Stjepanovic, G., Baskaran, S., Lin, M. G. & Hurley, J. H. Unveiling the role of VPS34 kinase domain dynamics in regulation of the autophagic PI3K complex. Mol. Cell. Oncol. 4, e1367873 (2017).

  164. 164.

    Russell, R. C. et al. ULK1 induces autophagy by phosphorylating beclin-1 and activating VPS34 lipid kinase. Nat. Cell Biol. 15, 741–750 (2013).

  165. 165.

    Rostislavleva, K. et al. Structure and flexibility of the endosomal Vps34 complex reveals the basis of its function on membranes. Science 350, aac7365 (2015).This study reports on the crystal structure of the yeast Vps34 complex II and documents how Vps34 complexes adapt to membrane curvature.

  166. 166.

    Stjepanovic, G., Baskaran, S., Lin, M. G. & Hurley, J. H. Vps34 kinase domain dynamics regulate the autophagic PI 3-kinase complex. Mol. Cell 67, 528–534 (2017).This study reports on the series of conformational changes involved in the regulation of VPS34 lipid kinase activity.

  167. 167.

    Baskaran, S. et al. Architecture and dynamics of the autophagic phosphatidylinositol 3-kinase complex. eLife 3, e05115 (2014).

  168. 168.

    Ohashi, Y., Tremel, S. & Williams, R. L. VPS34 complexes from a structural perspective. J. Lipid Res. 60, 229–241 (2018).

  169. 169.

    Fan, W., Nassiri, A. & Zhong, Q. Autophagosome targeting and membrane curvature sensing by Barkor/Atg14(L). Proc. Natl Acad. Sci. USA 108, 7769–7774 (2011).This study reveals the requirement of the BATS domain of ATG14 for its localization to the autophagosome in vivo and for membrane association in vitro.

  170. 170.

    Miller, S. et al. Shaping development of autophagy inhibitors with the structure of the lipid kinase Vps34. Science 327, 1638–1642 (2010).This study was the first to unveil the structure of VPS34 (from D. melanogaster ), providing new insights into its catalytic mechanism and the binding of VPS34 inhibitors.

  171. 171.

    Bago, R. et al. Characterization of VPS34-IN1, a selective inhibitor of Vps34, reveals that the phosphatidylinositol 3-phosphate-binding SGK3 protein kinase is a downstream target of class III phosphoinositide 3-kinase. Biochem. J. 463, 413–427 (2014).

  172. 172.

    Dowdle, W. E. et al. Selective VPS34 inhibitor blocks autophagy and uncovers a role for NCOA4 in ferritin degradation and iron homeostasis in vivo. Nat. Cell Biol. 16, 1069–1079 (2014).

  173. 173.

    Ronan, B. et al. A highly potent and selective Vps34 inhibitor alters vesicle trafficking and autophagy. Nat. Chem. Biol. 10, 1013–1019 (2014).The studies reported in Bago et al. (2014), Dowdle et al. (2014) and Ronan et al. (2014) were the first to report highly selective VPS34 inhibitors.

  174. 174.

    Bilanges, B. et al. Vps34 PI 3-kinase inactivation enhances insulin sensitivity through reprogramming of mitochondrial metabolism. Nat. Commun. 8, 1804 (2017).

  175. 175.

    Honda, A. et al. Potent, selective, and orally bioavailable inhibitors of VPS34 provide chemical tools to modulate autophagy in vivo. ACS Med. Chem. Lett. 7, 72–76 (2016).

  176. 176.

    Pasquier, B. et al. Discovery of (2S)-8-[(3R)-3-methylmorpholin-4-yl]-1-(3-methyl-2-oxobutyl)-2-(trifluoromethyl)- 3,4-dihydro-2H-pyrimido[1,2-a]pyrimidin-6-one: a novel potent and selective inhibitor of Vps34 for the treatment of solid tumors. J. Med. Chem. 58, 376–400 (2015).

  177. 177.

    Malik, N. et al. Mechanism of activation of SGK3 by growth factors via the class 1 and class 3 PI3Ks. Biochem. J. 475, 117–135 (2018).

  178. 178.

    Bago, R. et al. The hVps34–SGK3 pathway alleviates sustained PI3K/Akt inhibition by stimulating mTORC1 and tumour growth. EMBO J. 35, 1902–1922 (2016).

  179. 179.

    Valet, C. et al. A dual role for the class III PI3K, Vps34, in platelet production and thrombus growth. Blood 130, 2032–2042 (2017).

  180. 180.

    Kim, J. et al. Differential regulation of distinct Vps34 complexes by AMPK in nutrient stress and autophagy. Cell 152, 290–303 (2013).

  181. 181.

    Nemazanyy, I. et al. Class III PI3K regulates organismal glucose homeostasis by providing negative feedback on hepatic insulin signalling. Nat. Commun. 6, 8283 (2015).

  182. 182.

    He, F. et al. Phosphatidylinositol-3-phosphate is light-regulated and essential for survival in retinal rods. Sci. Rep. 6, 26978 (2016).

  183. 183.

    Martinez, J. et al. Molecular characterization of LC3-associated phagocytosis reveals distinct roles for Rubicon, NOX2 and autophagy proteins. Nat. Cell Biol. 17, 893–906 (2015).

  184. 184.

    Gasser, J. A. et al. SGK3 mediates INPP4B-dependent PI3K signaling in breast cancer. Mol. Cell 56, 595–607 (2014).

  185. 185.

    Ebner, M., Sinkovics, B., Szczygiel, M., Ribeiro, D. W. & Yudushkin, I. Localization of mTORC2 activity inside cells. J. Cell Biol. 216, 343–353 (2017).

  186. 186.

    Tessier, M. & Woodgett, J. R. Role of the Phox homology domain and phosphorylation in activation of serum and glucocorticoid-regulated kinase-3. J. Biol. Chem. 281, 23978–23989 (2006).

  187. 187.

    Vasudevan, K. M. et al. AKT-independent signaling downstream of oncogenic PIK3CA mutations in human cancer. Cancer Cell 16, 21–32 (2009).

  188. 188.

    O’Farrell, F. et al. Class III phosphatidylinositol-3-OH kinase controls epithelial integrity through endosomal LKB1 regulation. Nat. Cell Biol. 19, 1412–1423 (2017).

  189. 189.

    Juhasz, G. et al. The class III PI(3)K Vps34 promotes autophagy and endocytosis but not TOR signaling in Drosophila. J. Cell Biol. 181, 655–666 (2008).

  190. 190.

    Yoon, M. S., Du, G., Backer, J. M., Frohman, M. A. & Chen, J. Class III PI-3-kinase activates phospholipase D in an amino acid-sensing mTORC1 pathway. J. Cell Biol. 195, 435–447 (2011).

  191. 191.

    Nobukuni, T. et al. Amino acids mediate mTOR/raptor signaling through activation of class 3 phosphatidylinositol 3OH-kinase. Proc. Natl Acad. Sci. USA 102, 14238–14243 (2005).

  192. 192.

    Gulati, P. et al. Amino acids activate mTOR complex 1 via Ca2+/CaM signaling to hVps34. Cell Metab. 7, 456–465 (2008).

  193. 193.

    Byfield, M. P., Murray, J. T. & Backer, J. M. hVps34 is a nutrient-regulated lipid kinase required for activation of p70 S6 kinase. J. Biol. Chem. 280, 33076–33082 (2005).The studies reported in Nobukuni et al. (2005) and Byfield et al. (2005) were the first to report a link between VPS34 and mTORC1.

  194. 194.

    Jaber, N. et al. Class III PI3K Vps34 plays an essential role in autophagy and in heart and liver function. Proc. Natl Acad. Sci. USA 109, 2003–2008 (2012).

  195. 195.

    Willinger, T. & Flavell, R. A. Canonical autophagy dependent on the class III phosphoinositide-3 kinase Vps34 is required for naive T cell homeostasis. Proc. Natl Acad. Sci. USA 109, 8670–8675 (2012).

  196. 196.

    Zhou, X., Takatoh, J. & Wang, F. The mammalian class 3 PI3K (PIK3C3) is required for early embryogenesis and cell proliferation. PLOS ONE 6, e16358 (2011).

  197. 197.

    Kuma, A., Komatsu, M. & Mizushima, N. Autophagy-monitoring and autophagy-deficient mice. Autophagy 13, 1619–1628 (2017).

  198. 198.

    Rohatgi, R. A. et al. Beclin 1 regulates growth factor receptor signaling in breast cancer. Oncogene 34, 5352–5362 (2015).

  199. 199.

    Madsen, R. R., Vanhaesebroeck, B. & Semple, R. K. Cancer-associated PIK3CA mutations in overgrowth disorders. Trends Mol. Med. 24, 856–870 (2018).

  200. 200.

    Dyczynski, M. et al. Targeting autophagy by small molecule inhibitors of vacuolar protein sorting 34 (Vps34) improves the sensitivity of breast cancer cells to sunitinib. Cancer Lett. 435, 32–43 (2018).

  201. 201.

    Liu, X. et al. Simultaneous inhibition of Vps34 kinase would enhance PI3Kδ inhibitor cytotoxicity in the B cell malignancies. Oncotarget 7, 53515–53525 (2016).

  202. 202.

    Levy, J. M. M., Towers, C. G. & Thorburn, A. Targeting autophagy in cancer. Nat. Rev. Cancer 17, 528–542 (2017).

  203. 203.

    Saxton, R. A. & Sabatini, D. M. mTOR signaling in growth, metabolism, and disease. Cell 169, 361–371 (2017).

  204. 204.

    Castillo, S. D., Baselga, E. & Graupera, M. PIK3CA mutations in vascular malformations. Curr. Opin. Hematol. 26, 170–178 (2019).

  205. 205.

    Hare, L. M. et al. Heterozygous expression of the oncogenic Pik3caH1047R mutation during murine development results in fatal embryonic and extraembryonic defects. Dev. Biol. 404, 14–26 (2015).

  206. 206.

    Venot, Q. et al. Targeted therapy in patients with PIK3CA-related overgrowth syndrome. Nature 558, 540–546 (2018).This clinical study shows that treatment with a low dose of a PI3Kα-selective inhibitor is well tolerated in human patients with PIK3CA -related overgrowth spectrum, reduces aberrant tissue overgrowth and leads to clinical benefit.

  207. 207.

    Semple, R. K. & Vanhaesebroeck, B. Lessons for cancer drug treatment from tackling a non-cancerous overgrowth syndrome. Nature 558, 523–525 (2018).

  208. 208.

    Rozengurt, E., Soares, H. P. & Sinnet-Smith, J. Suppression of feedback loops mediated by PI3K/mTOR induces multiple overactivation of compensatory pathways: an unintended consequence leading to drug resistance. Mol. Cancer Ther. 13, 2477–2488 (2014).

  209. 209.

    Hollander, M. C., Blumenthal, G. M. & Dennis, P. A. PTEN loss in the continuum of common cancers, rare syndromes and mouse models. Nat. Rev. Cancer 11, 289–301 (2011).

  210. 210.

    Yehia, L. & Eng, C. One gene, many endocrine and metabolic syndromes: PTEN-opathies and precision medicine. Endocr. Relat. Cancer 25, T121–T140 (2018).

  211. 211.

    Keppler-Noreuil, K. M., Parker, V. E., Darling, T. N. & Martinez-Agosto, J. A. Somatic overgrowth disorders of the PI3K/AKT/mTOR pathway and therapeutic strategies. Am. J. Med. Genet. C 172, 402–421 (2016).

  212. 212.

    Zak, M., Ledbetter, M. & Maertens, P. Infantile Lhermitte–Duclos disease treated successfully with rapamycin. J. Child Neurol. 32, 322–326 (2017).

  213. 213.

    Marsh, D. J. et al. Rapamycin treatment for a child with germline PTEN mutation. Nat. Clin. Pract. Oncol. 5, 357–361 (2008).

  214. 214.

    Angulo, I. et al. Phosphoinositide 3-kinase delta gene mutation predisposes to respiratory infection and airway damage. Science 342, 866–871 (2013).

  215. 215.

    Lucas, C. L. et al. Dominant-activating germline mutations in the gene encoding the PI(3)K catalytic subunit p110delta result in T cell senescence and human immunodeficiency. Nat. Immunol. 15, 88–97 (2014).

  216. 216.

    Lucas, C. L., Chandra, A., Nejentsev, S., Condliffe, A. M. & Okkenhaug, K. PI3Kdelta and primary immunodeficiencies. Nat. Rev. Immunol. 16, 702–714 (2016).

  217. 217.

    Michalovich, D. & Nejentsev, S. Activated PI3 kinase delta syndrome: from genetics to therapy. Front. Immunol. 9, 369 (2018).

  218. 218.

    Coulter, T. I. et al. Clinical spectrum and features of activated phosphoinositide 3-kinase delta syndrome: a large patient cohort study. J. Allergy Clin. Immunol. 139, 597–606 (2017).

  219. 219.

    Rao, V. K. et al. Effective “activated PI3Kdelta syndrome”-targeted therapy with the PI3Kdelta inhibitor leniolisib. Blood 130, 2307–2316 (2017).

  220. 220.

    Gwinn, D. M. et al. AMPK phosphorylation of raptor mediates a metabolic checkpoint. Mol. Cell 30, 214–226 (2008).

  221. 221.

    Yoon, M. S. et al. Rapid mitogenic regulation of the mTORC1 inhibitor, DEPTOR, by phosphatidic acid. Mol. Cell 58, 549–556 (2015).

  222. 222.

    Raiborg, C. et al. Repeated ER–endosome contacts promote endosome translocation and neurite outgrowth. Nature 520, 234–238 (2015).

  223. 223.

    Hong, Z. et al. PtdIns3P controls mTORC1 signaling through lysosomal positioning. J. Cell Biol. 216, 4217–4233 (2017).

  224. 224.

    Liang, C. et al. Beclin1-binding UVRAG targets the class C Vps complex to coordinate autophagosome maturation and endocytic trafficking. Nat. Cell Biol. 10, 776–787 (2008).

  225. 225.

    Sun, Q., Westphal, W., Wong, K. N., Tan, I. & Zhong, Q. Rubicon controls endosome maturation as a Rab7 effector. Proc. Natl Acad. Sci. USA 107, 19338–19343 (2010).

  226. 226.

    Sun, Q. et al. The RUN domain of rubicon is important for hVps34 binding, lipid kinase inhibition, and autophagy suppression. J. Biol. Chem. 286, 185–191 (2011).

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Acknowledgements

Work in the laboratory of B.V. is supported by PTEN Research, Cancer Research UK (C23338/A25722), the UK Biotechnology and Biological Sciences Research Council (BB/I007806/1, BB/M013278/1 and BB/R017972/1) and the UK NIHR University College London Hospitals Biomedical Research Centre. Y.P. has been supported by a long-term EMBO fellowship (ALTF 1227-2014) and an EU Marie Skłodowska-Curie fellowship (656778). The authors thank R. Madsen, M. Graupera and K. Okkenhaug for excellent feedback on the manuscript.

Reviewer information

Nature Reviews Molecular Cell Biology thanks V. Haucke, and other anonymous reviewer(s), for their contribution to the peer review of this work.

Author information

B.B., Y.P. and B.V. contributed equally to writing the article and to the review and editing of the manuscript before submission.

Competing interests

B.V. is a consultant for Karus Therapeutics (Oxford, UK), iOnctura (Geneva, Switzerland) and Venthera (Palo Alto, CA, USA) and has received speaker fees from Gilead. The other authors declare no conflict of interest.

Correspondence to Benoit Bilanges or York Posor or Bart Vanhaesebroeck.

Supplementary information

Supplementary information

Glossary

Phosphatidylinositol

A phospholipid with myo-inositol as its head group. The 3′-OH, 4′-OH and 5′-OH groups of the inositol ring can be reversibly phosphorylated, resulting in a total of seven lipid species, collectively referred to as phosphoinositides. PI3Ks phosphorylate the 3′ position of the inositol ring.

Autophagy

A cellular ‘self-eating’ process that involves breaking down subcellular components (for example, protein and damaged organelles) through the lysosomal pathway in response to nutrient depletion or stress. It is characterized by membrane trafficking events that sequester cytoplasmic material in double-membrane structures, called autophagosomes, followed by degradation and recycling of cellular components by the lysosome.

Small GTPases

GTP-binding proteins that bind to and hydrolyse GTP to GDP and are mostly active in the GTP-bound state. Most activities in cells are regulated to some extent by small GTPases.

C2 domain

A membrane-binding domain homologous to the C2 domain of protein kinase C with mostly only moderate lipid specificity. Some C2 domains associate with membranes in a Ca2+-dependent manner.

G protein-coupled receptors

Receptors that contain seven transmembrane helices. They activate heterotrimeric G proteins, which, in turn, regulate the function of various proteins.

Early endosomes

Membrane-bound intracellular vesicles marked by RAB5 and EEA1 and high levels of phosphatidylinositol 3-phosphate. Endocytic vesicles fuse with early endosomes and endocytic cargo is sorted for recycling or degradation. Early endosomes then mature into late endosomes.

AKT

A group of Ser/Thr-specific protein kinases, also known as protein kinase B, that are activated by PI3K.

Hormone therapy

Also known as endocrine therapy, this treatment interferes with hormone signalling in hormone receptor-positive cancers, such as some types of breast or prostate cancer.

Insulin receptor substrate proteins

Proteins that bind to the intracellular domains of activated receptors for insulin and cytokines. These adaptor proteins then engage with other downstream signalling molecules.

Neomorphic proteins

Proteins that, as a result of mutation, acquire new functions beyond their normal physiological roles.

Pleckstrin homology (PH) domains

Sequences of approximately 100 amino acids that can mediate specific binding to phosphoinositide lipids and are present in many signalling molecules. Only a minority of PH domains actually bind lipids, with the PH representing a conserved structural fold in proteins without necessarily a specific biological function.

GTPase-activating proteins

(GAPs). Proteins that inactivate small GTP-binding proteins, such as RAS and RHEB family members, by increasing their rate of GTP hydrolysis.

Guanine nucleotide exchange factors

Proteins that facilitate the exchange of GDP for GTP in the nucleotide-binding pocket of GTP-binding proteins.

PDK1

A Ser/Thr-specific protein kinase. It is a master kinase that is involved in the activation of many other Ser/Thr kinases belonging to the cAMP-dependent, cGMP-dependent protein kinase C (AGC) family of protein kinases, which includes AKT, protein kinase C and S6 kinase. It is now clear that the activation of PDK1 is not dependent on phosphoinositides, as its name would imply.

mTOR complex 2

(mTORC2). A multiprotein complex consisting of mTOR, rapamycin-insensitive companion of mTOR (Rictor), mammalian stress-activated protein kinase interacting protein 1 (mSIN1), protein observed with Rictor 1 (Protor 1), mammalian lethal with SEC13 protein 8 (mLST8) and DEP domain-containing mTOR-interacting protein (DEPTOR). mTORC2 is insensitive to short-term treatment with rapamycin. This complex phosphorylates AKT on Ser473 in its hydrophobic motif.

Forkhead box protein O

(FOXO). A transcription factor family characterized by a winged-helix DNA-binding motif and the forkhead domain. The mammalian FOXO family has four members: FOXO1, FOXO3, FOXO4 and FOXO6. They are involved in a wide range of cellular processes, such as metabolism, cell cycle arrest, stress resistance and apoptosis.

mTOR complex 1

(mTORC1). This complex controls metabolic processes in response to environmental cues, including nutrient and growth factor availability as well as stress. mTORC1 is a multiprotein complex consisting of mTOR, regulatory-associated protein of mTOR (Raptor), mammalian lethal with SEC13 protein 8 (mLST8; also known as GβL) and the negative regulators proline-rich AKT substrate of 40 kDa (PRAS40) and DEP domain-containing mTOR-interacting protein (DEPTOR) and is sensitive to rapamycin.

Clathrin-mediated endocytosis

The internalization of plasma membrane and receptors present therein into small vesicles that is mediated by a protein coat containing clathrin, adaptors and accessory proteins.

FYVE domain

A phosphatidylinositol 3-phosphate-binding domain of approximately 60–65 amino acids that is named after the four Cys-rich proteins — FAB1, YOTB (also known as ZK632.12), VAC1 and EEA1 — in which it has been found.

Paclitaxel

An anticancer agent that acts by stabilizing microtubules through binding to tubulin.

Regulatory T cells

A subset of T lymphocytes that are involved in the suppression of immune responses.

Nurse-like cells

A specialized subset of tumour-associated macrophages that regulate leukaemic cell functions.

Phox homology (PX) domain

A domain mediating lipid and protein interactions that consists of 100–130 amino acids and is defined by sequences that are found in two components of the phagocyte NADPH oxidase (phox) complex.

Late endosomes

Membrane-bound compartments late on the endocytic route just before fusion with the lysosome. Late endosomes are marked by RAB7 and other proteins also present on lysosomes, such as lysosome-associated membrane glycoproteins.

Kinetochore fibres

Bundles of spindle microtubules that attach to the kinetochore, a protein complex at the centromere of each chromosome.

Endosomal sorting and recycling

A process in which endocytosed cargo proteins are sorted in early endosomes for degradation in lysosomes, recycling to the plasma membrane or retrograde trafficking to the trans-Golgi network.

Haemocytes

The circulating blood cells that form the innate immune system in insects.

BAR domain

A membrane-curvature-inducing and membrane-curvature-sensing protein domain.

Dynamin

A large mechanochemical GTPase that assembles into a helical oligomer on highly curved membranes. GTP hydrolysis by dynamin is coupled to conformational changes that catalyse constriction and eventually fission of the underlying tubular membrane.

Sonic hedgehog

A key morphogen, that is, a secreted signalling molecule that acts along a local concentration gradient, which is crucial during vertebrate embryonic development.

Primary cilia

Solitary elongated protrusions of the plasma membrane supported by a microtubule-based axoneme of nine doublet microtubules anchored at the centriole. Primary cilia serve as sensory structures and specialized signalling platforms that are of particular importance in development.

RAB11

A small GTPase required for multiple steps during endocytic recycling, including the formation of vesicles travelling to and from the endocytic recycling compartment.

APPL1

An effector of the small GTPase RAB5 that operates as a scaffolding protein on endosomes, interacting with numerous signalling molecules, including receptor tyrosine kinases and AKT.

Thrombus

A blood clot formed in a blood vessel.

Phospholipase D1

A phosphodiesterase that hydrolyses phosphatidylcholine and other glycerophospholipids to generate phosphatidic acid and the free head group of the substrate lipid.

X-linked centronuclear myopathy

(XLCNM). Also called myotubular myopathy, a severe paediatric neuromuscular disorder causing muscle weakness.

Phagocytosis

A largely actin-driven form of endocytosis that serves to ingest large particles, such as cellular debris or whole microorganisms.

Macropinocytosis

An evolutionarily conserved endocytic pathway that allows internalization of extracellular fluid via large endocytic vesicles called macropinosomes.

Phagophore

Also called isolation membrane, a double-membrane cup-shaped structure that engulfs cytoplasmic material during autophagy. It is the precursor of the autophagosome.

BARA domain

β-α-Repeated, autophagy-specific domain.

BATS domain

Barkor/ATG14 autophagosome targeting domain, which binds to the autophagosome membrane via the hydrophobic surface of an intrinsic amphipathic α-helix.

Amphipathic helix

α-Helical sequence in which polar and charged amino acids are oriented to one side and hydrophobic ones are oriented to the other side. The lipophilic side dips into bent membranes displaying packing defects in the outer leaflet, thereby providing a means of sensing membrane curvature.

Autophagy cargo receptors

Receptors or adaptors that can recognize material or cargo destined for autophagic degradation and bind to a component of the forming autophagosomes.

LC3-associated phagocytosis-engaged phagosomes

Also known as LAPosomes, they are dead-cell-containing phagosomes that recruit the autophagy machinery and ultimately become LC3-associated phagosomes.

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Fig. 1: Substrate specificity and domain organization of the PI3K isoforms and their lipid products.
Fig. 2: Isoform-selective regulation of class I PI3Ks and AKT family members.
Fig. 3: Cell biological functions and activation of class II PI3K isoforms.
Fig. 4: Cell biological functions and activation of VPS34.