A system to identify inhibitors of mTOR signaling using high-resolution growth analysis in Saccharomyces cerevisiae

Mitchell B. Lee1, Daniel T. Carr1, Michael G. Kiflezghi1,2, Yan Ting Zhao1, Deborah B. Kim1, Socheata Thon1, Margarete D. Moore1, Mary Ann K. Li1, Matt Kaeberlein1
1Department of Pathology, University of Washington, Seattle, USA
2Molecular Medicine and Mechanisms of Disease (M3D) Program, University of Washington, Seattle, USA

Tóm tắt

The mechanistic target of rapamycin (mTOR) is a central regulator of growth and proliferation and mTOR inhibition is a promising therapy for a variety of diseases and disorders. Inhibition of mTOR complex I (mTORC1) with rapamycin delays aging and increases healthy longevity in laboratory animals and is used clinically at high doses to prevent organ transplant rejection and to treat some forms of cancer. Clinical use of rapamycin is associated with several unwanted side effects, however, and several strategies are being taken to identify mTORC1 inhibitors with fewer side effects. We describe here a yeast-based growth assay that can be used to screen for novel inhibitors of mTORC1. By testing compounds using a wild-type strain and isogenic cells lacking either TOR1 or FPR1, we can resolve not only whether a compound is an inhibitor of mTORC1 but also whether the inhibitor acts through a mechanism similar to rapamycin by binding Fpr1. Using this assay, we show that rapamycin derivatives behave similarly to rapamycin, while caffeine and the ATP competitive inhibitors Torin 1 and GSK2126458 are mTORC1 inhibitors in yeast that act independently of Fpr1. Some mTOR inhibitors in mammalian cells do not inhibit mTORC1 in yeast, and several nutraceutical compounds were not found to specifically inhibit mTOR but resulted in a general inhibition of yeast growth. Our screening method holds promise as a means of effectively assaying drug libraries for mTOR-inhibitory molecules in vivo that may be adapted as novel treatments to fight diseases and extend healthy longevity.

Từ khóa


Tài liệu tham khảo

Anastasius N, Boston S, Lacey M, Storing N, Whitehead SA (2009) Evidence that low-dose, long-term genistein treatment inhibits oestradiol-stimulated growth in MCF-7 cells by down-regulation of the PI3-kinase/Akt signalling pathway. J Steroid Biochem Mol Biol 116(1–2):50–55 Anisimov VN et al (2011) Rapamycin increases lifespan and inhibits spontaneous tumorigenesis in inbred female mice. Cell Cycle 10(24):4230–4236 Beaupere C et al (2017) CAN1 arginine permease deficiency extends yeast replicative lifespan via translational activation of stress response genes. Cell Rep 18(8):1884–1892 Beevers CS, Li F, Liu L, Huang S (2006) Curcumin inhibits the mammalian target of rapamycin-mediated signaling pathways in cancer cells. Int J Cancer 119(4):757–764 Beevers CS et al (2009) Curcumin disrupts the mammalian target of rapamycin-raptor complex. Cancer Res 69(3):1000–1008 Benton BM, Zang JH, Thorner J (1994) A novel FK506- and rapamycin-binding protein (FPR3 gene product) in the yeast Saccharomyces cerevisiae is a proline rotamase localized to the nucleolus. J Cell Biol 127(3):623–639 Beretta L, Gingras AC, Svitkin YV, Hall MN, Sonenberg N (1996) Rapamycin blocks the phosphorylation of 4E-BP1 and inhibits cap-dependent initiation of translation. EMBO J 15(3):658–664 Bitto A et al (2016) Transient rapamycin treatment can increase lifespan and healthspan in middle-aged mice. elife 5:e16351 Bjedov I et al (2010) Mechanisms of life span extension by rapamycin in the fruit fly Drosophila melanogaster. Cell Metab 11(1):35–46 Blagosklonny MV (2010) Increasing healthy lifespan by suppressing aging in our lifetime: preliminary proposal. Cell Cycle 9(24):4788–4794 Bridi JC et al (2015) Lifespan extension induced by caffeine in Caenorhabditis elegans is partially dependent on adenosine signaling. Front Aging Neurosci 7:220 Brito PM et al (2009) Resveratrol inhibits the mTOR mitogenic signaling evoked by oxidized LDL in smooth muscle cells. Atherosclerosis 205(1):126–134 Burtner CR, Murakami CJ, Kennedy BK, Kaeberlein M (2009) A molecular mechanism of chronological aging in yeast. Cell Cycle 8(8):1256–1270 Chen C, Liu Y, Zheng P (2009) mTOR regulation and therapeutic rejuvenation of aging hematopoietic stem cells. Sci Signal 2(98):ra75 Chresta CM et al (2010) AZD8055 is a potent, selective, and orally bioavailable ATP-competitive mammalian target of rapamycin kinase inhibitor with in vitro and in vivo antitumor activity. Cancer Res 70(1):288–298 Dai DF et al (2014) Altered proteome turnover and remodeling by short-term caloric restriction or rapamycin rejuvenate the aging heart. Aging Cell 13(3):529–539 Delaney JR et al (2013) Stress profiling of longevity mutants identifies Afg3 as a mitochondrial determinant of cytoplasmic mRNA translation and aging. Aging Cell 12(1):156–166 Fabrizio P, Pozza F, Pletcher SD, Gendron CM, Longo VD (2001) Regulation of longevity and stress resistance by Sch9 in yeast. Science 292(5515):288–290 Fan X et al (2015) Berberine alleviates ox-LDL induced inflammatory factors by up-regulation of autophagy via AMPK/mTOR signaling pathway. J Transl Med 13:92 Fay JC, Benavides JA (2005) Evidence for domesticated and wild populations of Saccharomyces cerevisiae. PLoS Genet 1(1):66–71 Flynn JM et al (2013) Late-life rapamycin treatment reverses age-related heart dysfunction. Aging Cell 12(5):851–862 Folkes AJ et al (2008) The identification of 2-(1H-indazol-4-yl)-6-(4-methanesulfonyl-piperazin-1-ylmethyl)-4-morpholin-4-yl-t hieno[3,2-d]pyrimidine (GDC-0941) as a potent, selective, orally bioavailable inhibitor of class I PI3 kinase for the treatment of cancer. J Med Chem 51(18):5522–5532 Halloran J et al (2012) Chronic inhibition of mammalian target of rapamycin by rapamycin modulates cognitive and non-cognitive components of behavior throughout lifespan in mice. Neuroscience 223:102–113 Harrison DE et al (2009) Rapamycin fed late in life extends lifespan in genetically heterogeneous mice. Nature 460(7253):392–395 Heitman J, Movva NR, Hall MN (1991) Targets for cell cycle arrest by the immunosuppressant rapamycin in yeast. Science 253(5022):905–909 Helliwell SB et al (1994) TOR1 and TOR2 are structurally and functionally similar but not identical phosphatidylinositol kinase homologues in yeast. Mol Biol Cell 5(1):105–118 Jacinto E et al (2004) Mammalian TOR complex 2 controls the actin cytoskeleton and is rapamycin insensitive. Nat Cell Biol 6(11):1122–1128 Je Y, Giovannucci E (2014) Coffee consumption and total mortality: a meta-analysis of twenty prospective cohort studies. Br J Nutr 111(7):1162–1173 Jiang L, Jin Y, Wang H, Jiang Y, Dong J (2014) Glucosamine protects nucleus pulposus cells and induces autophagy via the mTOR-dependent pathway. J Orthop Res 32(11):1532–1542 Johnson SC, Rabinovitch PS, Kaeberlein M (2013a) mTOR is a key modulator of ageing and age-related disease. Nature 493(7432):338–345 Johnson SC, Martin GM, Rabinovitch PS, Kaeberlein M (2013b) Preserving youth: does rapamycin deliver? Sci Transl Med 5(211):211fs240 Johnson SC, Sangesland M, Kaeberlein M, Rabinovitch PS (2015) Modulating mTOR in aging and health. Interdiscip Top Gerontol 40:107–127 Kaeberlein M (2010) Lessons on longevity from budding yeast. Nature 464(7288):513–519 Kaeberlein M (2013) mTOR inhibition: from aging to autism and beyond. Scientifica (Cairo) 2013:849186 Kaeberlein M et al (2005a) Regulation of yeast replicative life span by TOR and Sch9 in response to nutrients. Science 310(5751):1193–1196 Kaeberlein M et al (2005b) Substrate-specific activation of sirtuins by resveratrol. J Biol Chem 280(17):17038–17045 Kaeberlein M, Rabinovitch PS, Martin GM (2015) Healthy aging: the ultimate preventative medicine. Science 350(6265):1191–1193 Kaeberlein M, Creevy KE, Promislow DE (2016) The dog aging project: translational geroscience in companion animals. Mamm Genome 27(7–8):279–288 Knight SD et al (2010) Discovery of GSK2126458, a highly potent inhibitor of PI3K and the mammalian target of rapamycin. ACS Med Chem Lett 1(1):39–43 Kunz J et al (1993) Target of rapamycin in yeast, TOR2, is an essential phosphatidylinositol kinase homolog required for G1 progression. Cell 73(3):585–596 Lamming DW et al (2012) Rapamycin-induced insulin resistance is mediated by mTORC2 loss and uncoupled from longevity. Science 335(6076):1638–1643 Li Z, Dungan CM, Carrier B, Rideout TC, Williamson DL (2014) Alpha-lipoic acid supplementation reduces mTORC1 signaling in skeletal muscle from high fat fed, obese Zucker rats. Lipids 49(12):1193–1201 Liti G et al (2009) Population genomics of domestic and wild yeasts. Nature 458(7236):337–341 Liu M et al (2010) Resveratrol inhibits mTOR signaling by promoting the interaction between mTOR and DEPTOR. J Biol Chem 285(47):36387–36394 Liu Q et al (2012) Selective ATP-competitive inhibitors of TOR suppress rapamycin-insensitive function of TORC2 in Saccharomyces cerevisiae. ACS Chem Biol 7(6):982–987 Loewith R et al (2002) Two TOR complexes, only one of which is rapamycin sensitive, have distinct roles in cell growth control. Mol Cell 10(3):457–468 Loftfield E et al (2015) Association of coffee consumption with overall and cause-specific mortality in a large US prospective cohort study. Am J Epidemiol 182(12):1010–1022 Longo VD, Shadel GS, Kaeberlein M, Kennedy B (2012) Replicative and chronological aging in Saccharomyces cerevisiae. Cell Metab 16(1):18–31 Lorenz MC, Heitman J (1995) TOR mutations confer rapamycin resistance by preventing interaction with FKBP12-rapamycin. J Biol Chem 270(46):27531–27537 Lu Q et al (2015) Quercetin inhibits the mTORC1/p70S6K signaling-mediated renal tubular epithelial-mesenchymal transition and renal fibrosis in diabetic nephropathy. Pharmacol Res 99:237–247 Majumder S et al (2012) Lifelong rapamycin administration ameliorates age-dependent cognitive deficits by reducing IL-1beta and enhancing NMDA signaling. Aging Cell 11(2):326–335 Mannick JB et al (2014) mTOR inhibition improves immune function in the elderly. Sci Transl Med 6(268):268ra179 McCormick MA et al (2015) A comprehensive analysis of replicative lifespan in 4,698 single-gene deletion strains uncovers conserved mechanisms of aging. Cell Metab 22(5):895–906 Meng FD et al (2015) Synergistic effects of snail and quercetin on renal cell carcinoma Caki-2 by altering AKT/mTOR/ERK1/2 signaling pathways. Int J Clin Exp Pathol 8(6):6157–6168 Murakami C & Kaeberlein M (2009) Quantifying yeast chronological life span by outgrowth of aged cells. J Vis Exp. doi:10.3791/1156 Murakami CJ, Burtner CR, Kennedy BK, Kaeberlein M (2008) A method for high-throughput quantitative analysis of yeast chronological life span. J Gerontol A Biol Sci Med Sci 63(2):113–121 Murakami CJ, Wall V, Basisty N, Kaeberlein M (2011) Composition and acidification of the culture medium influences chronological aging similarly in vineyard and laboratory yeast. PLoS One 6(9):e24530 Neff F et al (2013) Rapamycin extends murine lifespan but has limited effects on aging. J Clin Invest 123(8):3272–3291 O'Donnell JS, Massi D, Teng MWL, & Mandala M (2017) PI3K-AKT-mTOR inhibition in cancer immunotherapy, redux. Semin Cancer Biol. doi:10.1016/j.semcancer.2017.04.015 Olsen B, Murakami CJ, Kaeberlein M (2010) YODA: software to facilitate high-throughput analysis of chronological life span, growth rate, and survival in budding yeast. BMC Bioinformatics 11:141 Park D et al (2016) Resveratrol induces autophagy by directly inhibiting mTOR through ATP competition. Sci Rep 6:21772 Popovich IG et al (2014) Lifespan extension and cancer prevention in HER-2/neu transgenic mice treated with low intermittent doses of rapamycin. Cancer Biol Ther 15(5):586–592 Powers RW 3rd, Kaeberlein M, Caldwell SD, Kennedy BK, Fields S (2006) Extension of chronological life span in yeast by decreased TOR pathway signaling. Genes Dev 20(2):174–184 Rallis C, Codlin S, Bahler J (2013) TORC1 signaling inhibition by rapamycin and caffeine affect lifespan, global gene expression, and cell proliferation of fission yeast. Aging Cell 12(4):563–573 Reinke A, Chen JC, Aronova S, Powers T (2006) Caffeine targets TOR complex I and provides evidence for a regulatory link between the FRB and kinase domains of Tor1p. J Biol Chem 281(42):31616–31626 Robida-Stubbs S et al (2012) TOR signaling and rapamycin influence longevity by regulating SKN-1/Nrf and DAF-16/FoxO. Cell Metab 15(5):713–724 Saiki S et al (2011) Caffeine induces apoptosis by enhancement of autophagy via PI3K/Akt/mTOR/p70S6K inhibition. Autophagy 7(2):176–187 Saxton RA, Sabatini DM (2017) mTOR signaling in growth, metabolism, and disease. Cell 168(6):960–976 Steffen KK et al (2008) Yeast life span extension by depletion of 60s ribosomal subunits is mediated by Gcn4. Cell 133(2):292–302 Sutphin GL, Bishop E, Yanos ME, Moller RM, Kaeberlein M (2012) Caffeine extends life span, improves healthspan, and delays age-associated pathology in Caenorhabditis elegans. Longev Healthspan 1:9 Tillu DV et al (2012) Resveratrol engages AMPK to attenuate ERK and mTOR signaling in sensory neurons and inhibits incision-induced acute and chronic pain. Mol Pain 8:5 Urfer SR et al (2017a) A randomized controlled trial to establish effects of short-term rapamycin treatment in 24 middle-aged companion dogs. Geroscience 39(2):117–127 Urfer SR et al (2017b) Asymptomatic heart valve dysfunction in healthy middle-aged companion dogs and its implications for cardiac aging. Geroscience 39(1):43–50 Van Aller GS et al (2011) Epigallocatechin gallate (EGCG), a major component of green tea, is a dual phosphoinositide-3-kinase/mTOR inhibitor. Biochem Biophys Res Commun 406(2):194–199 Wanke V et al (2008) Caffeine extends yeast lifespan by targeting TORC1. Mol Microbiol 69(1):277–285 Wiczk A, Hofman D, Konopa G, Herman-Antosiewicz A (2012) Sulforaphane, a cruciferous vegetable-derived isothiocyanate, inhibits protein synthesis in human prostate cancer cells. Biochim Biophys Acta 1823(8):1295–1305 Winzeler EA et al (1999) Functional characterization of the S. cerevisiae genome by gene deletion and parallel analysis. Science 285(5429):901–906 Wu TJ et al (2015) Identification of a non-gatekeeper hot spot for drug-resistant mutations in mTOR kinase. Cell Rep 11(3):446–459 Wullschleger S, Loewith R, Hall MN (2006) TOR signaling in growth and metabolism. Cell 124(3):471–484 Xie R et al (2012) Alpha-lipoic acid pre- and post-treatments provide protection against in vitro ischemia-reperfusion injury in cerebral endothelial cells via Akt/mTOR signaling. Brain Res 1482:81–90 Zhang Q et al (2006) Green tea extract and (−)-epigallocatechin-3-gallate inhibit mast cell-stimulated type I collagen expression in keloid fibroblasts via blocking PI-3K/AkT signaling pathways. J Invest Dermatol 126(12):2607–2613