Cell death by autophagy: facts and apparent artefacts (original) (raw)

• Kerr JF, Wyllie AH, Currie AR . Apoptosis: a basic biological phenomenon with wide-ranging implications in tissue kinetics. Br J Cancer 1972; 26: 239–257.
  CAS PubMed PubMed Central Google Scholar
• Galluzzi L, Vitale I, Abrams JM, Alnemri ES, Baehrecke EH, Blagosklonny MV et al. Molecular definitions of cell death subroutines: recommendations of the Nomenclature Committee on Cell Death 2012. Cell Death Differ 2011; e-pub ahead of print 15 July 2011; doi:10.1038/cdd.2011.96.
  Article Google Scholar
• Kumar S . Caspase function in programmed cell death. Cell Death Differ 2007; 14: 32–43.
  Article CAS PubMed Google Scholar
• Yang Z, Klionsky DJ . Eaten alive: a history of macroautophagy. Nat Cell Biol 2010; 12: 814–822.
  Article CAS PubMed PubMed Central Google Scholar
• Mizushima N, Levine B, Cuervo AM, Klionsky DJ . Autophagy fights disease through cellular self-digestion. Nature 2008; 451: 1069–1075.
  Article CAS PubMed PubMed Central Google Scholar
• Kroemer G, Levine B . Autophagic cell death: the story of a misnomer. Nat Rev Mol Cell Biol 2008; 9: 1004–1010.
  Article CAS PubMed PubMed Central Google Scholar
• Chen Y, Klionsky DJ . The regulation of autophagy – unanswered questions. J Cell Sci 2011; 124: 161–170.
  Article CAS PubMed Google Scholar
• Chang YY, Neufeld TP . Autophagy takes flight in Drosophila. FEBS Lett 2010; 584: 1342–1349.
  Article CAS PubMed PubMed Central Google Scholar
• Yang Z, Klionsky DJ . Mammalian autophagy: core molecular machinery and signaling regulation. Curr Opin Cell Biol 2010; 22: 124–131.
  Article CAS PubMed Google Scholar
• McPhee CK, Baehrecke EH . Autophagy in Drosophila melanogaster. Biochim Biophys Acta 2009; 1793: 1452–1460.
  Article CAS PubMed PubMed Central Google Scholar
• Neufeld TP . TOR-dependent control of autophagy: biting the hand that feeds. Curr Opin Cell Biol 2010; 22: 157–168.
  Article CAS PubMed Google Scholar
• Melendez A, Neufeld TP . The cell biology of autophagy in metazoans: a developing story. Development 2008; 135: 2347–2360.
  Article CAS PubMed Google Scholar
• Berry DL, Baehrecke EH . Growth arrest and autophagy are required for salivary gland cell degradation in Drosophila. Cell 2007; 131: 1137–1148.
  Article CAS PubMed PubMed Central Google Scholar
• Gump JM, Thorburn A . Autophagy and apoptosis: what is the connection? Trends Cell Biol 2011; 21: 387–392.
  Article CAS PubMed PubMed Central Google Scholar
• Eisenberg-Lerner A, Bialik S, Simon HU, Kimchi A . Life and death partners: apoptosis, autophagy and the cross-talk between them. Cell Death Differ 2009; 16: 966–975.
  Article CAS PubMed Google Scholar
• Shen HM, Codogno P . Autophagic cell death: Loch Ness monster or endangered species? Autophagy 2011; 7: 457–465.
  Article CAS PubMed Google Scholar
• Klionsky DJ, Abeliovich H, Agostinis P, Agrawal DK, Aliev G, Askew DS et al. Guidelines for the use and interpretation of assays for monitoring autophagy in higher eukaryotes. Autophagy 2008; 4: 151–175.
  Article CAS PubMed Google Scholar
• Kepp O, Galluzzi L, Lipinski M, Yuan J, Kroemer G . Cell death assays for drug discovery. Nat Rev Drug Discov 2011; 10: 221–237.
  Article CAS PubMed Google Scholar
• Shen S, Kepp O, Michaud M, Martins I, Minoux H, Metivier D et al. Association and dissociation of autophagy, apoptosis and necrosis by systematic chemical study. Oncogene 2011; e-pub ahead of print 16 May 2011; doi:10.1038/onc.2011.168.
  Article CAS PubMed Google Scholar
• van Doorn WG, Beers EP, Dangl JL, Franklin-Tong VE, Gallois P, Hara-Nishimura I et al. Morphological classification of plant cell deaths. Cell Death Differ 2011; 18: 1241–1246.
  Article CAS PubMed PubMed Central Google Scholar
• Kwon SI, Cho HJ, Jung JH, Yoshimoto K, Shirasu K, Park OK . The Rab GTPase RabG3b functions in autophagy and contributes to tracheary element differentiation in Arabidopsis. Plant J 2010; 64: 151–164.
  CAS PubMed Google Scholar
• Kwon SI, Cho HJ, Park OK . Role of Arabidopsis RabG3b and autophagy in tracheary element differentiation. Autophagy 2010; 6: 1187–1189.
  Article CAS PubMed Google Scholar
• Giusti C, Tresse E, Luciani MF, Golstein P . Autophagic cell death: analysis in Dictyostelium. Biochim Biophys Acta 2009; 1793: 1422–1431.
  Article CAS PubMed Google Scholar
• Luciani MF, Giusti C, Harms B, Oshima Y, Kikuchi H, Kubohara Y et al. Atg1 allows second-signaled autophagic cell death in Dictyostelium. Autophagy 2011; 7: 501–508.
  Article CAS PubMed Google Scholar
• Kumar S, Cakouros D . Transcriptional control of the core cell-death machinery. Trends Biochem Sci 2004; 29: 193–199.
  Article CAS PubMed Google Scholar
• Lee CY, Cooksey BA, Baehrecke EH . Steroid regulation of midgut cell death during Drosophila development. Dev Biol 2002; 250: 101–111.
  Article CAS PubMed Google Scholar
• Jiang C, Baehrecke EH, Thummel CS . Steroid regulated programmed cell death during Drosophila metamorphosis. Development 1997; 124: 4673–4683.
  CAS PubMed Google Scholar
• Lee CY, Simon CR, Woodard CT, Baehrecke EH . Genetic mechanism for the stage- and tissue-specific regulation of steroid triggered programmed cell death in Drosophila. Dev Biol 2002; 252: 138–148.
  Article CAS PubMed Google Scholar
• Dorstyn L, Colussi PA, Quinn LM, Richardson H, Kumar S . DRONC, an ecdysone-inducible Drosophila caspase. Proc Natl Acad Sci USA 1999; 96: 4307–4312.
  Article CAS PubMed PubMed Central Google Scholar
• Cakouros D, Daish T, Martin D, Baehrecke EH, Kumar S . Ecdysone-induced expression of the caspase DRONC during hormone-dependent programmed cell death in Drosophila is regulated by Broad-Complex. J Cell Biol 2002; 157: 985–995.
  Article CAS PubMed PubMed Central Google Scholar
• Cakouros D, Daish TJ, Kumar S . Ecdysone receptor directly binds the promoter of the Drosophila caspase dronc, regulating its expression in specific tissues. J Cell Biol 2004; 165: 631–640.
  Article CAS PubMed PubMed Central Google Scholar
• Kilpatrick ZE, Cakouros D, Kumar S . Ecdysone-mediated upregulation of the effector caspase DRICE is required for hormone-dependent apoptosis in Drosophila cells. J Biol Chem 2005; 280: 11981–11986.
  Article CAS PubMed Google Scholar
• Lee CY, Baehrecke EH . Steroid regulation of autophagic programmed cell death during development. Development 2001; 128: 1443–1455.
  CAS PubMed Google Scholar
• Lee CY, Clough EA, Yellon P, Teslovich TM, Stephan DA, Baehrecke EH . Genome-wide analyses of steroid- and radiation-triggered programmed cell death in Drosophila. Curr Biol 2003; 13: 350–357.
  Article CAS PubMed Google Scholar
• Baehrecke EH . Autophagic programmed cell death in Drosophila. Cell Death Differ 2003; 10: 940–945.
  Article CAS PubMed Google Scholar
• Martin DN, Baehrecke EH . Caspases function in autophagic programmed cell death in Drosophila. Development 2004; 131: 275–284.
  Article CAS PubMed Google Scholar
• Daish TJ, Mills K, Kumar S . Drosophila caspase DRONC is required for specific developmental cell death pathways and stress-induced apoptosis. Dev Cell 2004; 7: 909–915.
  Article CAS PubMed Google Scholar
• Mills K, Daish T, Harvey KF, Pfleger CM, Hariharan IK, Kumar S . The Drosophila melanogaster Apaf-1 homologue ARK is required for most, but not all, programmed cell death. J Cell Biol 2006; 172: 809–815.
  Article CAS PubMed PubMed Central Google Scholar
• Scott RC, Juhasz G, Neufeld TP . Direct induction of autophagy by Atg1 inhibits cell growth and induces apoptotic cell death. Curr Biol 2007; 17: 1–11.
  Article CAS PubMed PubMed Central Google Scholar
• McPhee CK, Logan MA, Freeman MR, Baehrecke EH . Activation of autophagy during cell death requires the engulfment receptor Draper. Nature 2010; 465: 1093–1096.
  Article CAS PubMed PubMed Central Google Scholar
• McPhee CK, Baehrecke EH . The engulfment receptor Draper is required for autophagy during cell death. Autophagy 2010; 6: 1192–1193.
  Article PubMed PubMed Central Google Scholar
• Denton D, Shravage B, Simin R, Mills K, Berry DL, Baehrecke EH et al. Autophagy, not apoptosis, is essential for midgut cell death in Drosophila. Curr Biol 2009; 19: 1741–1746.
  Article CAS PubMed PubMed Central Google Scholar
• Denton D, Shravage B, Simin R, Baehrecke EH, Kumar S . Larval midgut destruction in Drosophila: not dependent on caspases but suppressed by the loss of autophagy. Autophagy 2010; 6: 163–165.
  Article PubMed Google Scholar
• Dutta S, Baehrecke EH . Warts is required for PI3K-regulated growth arrest, autophagy, and autophagic cell death in Drosophila. Curr Biol 2008; 18: 1466–1475.
  Article CAS PubMed PubMed Central Google Scholar
• Hou YC, Chittaranjan S, Barbosa SG, McCall K, Gorski SM . Effector caspase Dcp-1 and IAP protein Bruce regulate starvation-induced autophagy during Drosophila melanogaster oogenesis. J Cell Biol 2008; 182: 1127–1139.
  Article CAS PubMed PubMed Central Google Scholar
• Nezis IP, Lamark T, Velentzas AD, Rusten TE, Bjorkoy G, Johansen T et al. Cell death during Drosophila melanogaster early oogenesis is mediated through autophagy. Autophagy 2009; 5: 298–302.
  Article CAS PubMed Google Scholar
• Nezis IP, Shravage BV, Sagona AP, Johansen T, Baehrecke EH, Stenmark H . Autophagy as a trigger for cell death: autophagic degradation of inhibitor of apoptosis dBruce controls DNA fragmentation during late oogenesis in Drosophila. Autophagy 2010; 6: 1214–1215.
  Article PubMed PubMed Central Google Scholar
• Barth JM, Szabad J, Hafen E, Kohler K . Autophagy in Drosophila ovaries is induced by starvation and is required for oogenesis. Cell Death Differ 2011; 18: 915–924.
  Article CAS PubMed Google Scholar
• Mohseni N, McMillan SC, Chaudhary R, Mok J, Reed BH . Autophagy promotes caspase-dependent cell death during Drosophila development. Autophagy 2009; 5: 329–338.
  Article CAS PubMed Google Scholar
• Kuma A, Hatano M, Matsui M, Yamamoto A, Nakaya H, Yoshimori T et al. The role of autophagy during the early neonatal starvation period. Nature 2004; 432: 1032–1036.
  Article CAS PubMed Google Scholar
• Qu X, Zou Z, Sun Q, Luby-Phelps K, Cheng P, Hogan RN et al. Autophagy gene-dependent clearance of apoptotic cells during embryonic development. Cell 2007; 128: 931–946.
  Article CAS PubMed Google Scholar
• Komatsu M, Waguri S, Ueno T, Iwata J, Murata S, Tanida I et al. Impairment of starvation-induced and constitutive autophagy in Atg7-deficient mice. J Cell Biol 2005; 169: 425–434.
  Article CAS PubMed PubMed Central Google Scholar
• Yue Z, Jin S, Yang C, Levine AJ, Heintz N . Beclin 1, an autophagy gene essential for early embryonic development, is a haploinsufficient tumor suppressor. Proc Natl Acad Sci USA 2003; 100: 15077–15082.
  Article CAS PubMed PubMed Central Google Scholar
• Shimizu S, Kanaseki T, Mizushima N, Mizuta T, Arakawa-Kobayashi S, Thompson CB et al. Role of Bcl-2 family proteins in a non-apoptotic programmed cell death dependent on autophagy genes. Nat Cell Biol 2004; 6: 1221–1228.
  Article CAS PubMed Google Scholar
• Shimizu S, Konishi A, Nishida Y, Mizuta T, Nishina H, Yamamoto A et al. Involvement of JNK in the regulation of autophagic cell death. Oncogene 2010; 29: 2070–2082.
  Article CAS PubMed Google Scholar
• Yu L, Alva A, Su H, Dutt P, Freundt E, Welsh S et al. Regulation of an ATG7–beclin 1 program of autophagic cell death by caspase-8. Science 2004; 304: 1500–1502.
  Article CAS PubMed Google Scholar
• Laane E, Tamm KP, Buentke E, Ito K, Kharaziha P, Oscarsson J et al. Cell death induced by dexamethasone in lymphoid leukemia is mediated through initiation of autophagy. Cell Death Differ 2009; 16: 1018–1029.
  Article CAS PubMed Google Scholar
• Grander D, Kharaziha P, Laane E, Pokrovskaja K, Panaretakis T . Autophagy as the main means of cytotoxicity by glucocorticoids in hematological malignancies. Autophagy 2009; 5: 1198–1200.
  Article CAS PubMed Google Scholar
• Zhao Y, Yang J, Liao W, Liu X, Zhang H, Wang S et al. Cytosolic FoxO1 is essential for the induction of autophagy and tumour suppressor activity. Nat Cell Biol 2010; 12: 665–675.
  Article CAS PubMed Google Scholar
• Elgendy M, Sheridan C, Brumatti G, Martin SJ . Oncogenic Ras-induced expression of Noxa and Beclin-1 promotes autophagic cell death and limits clonogenic survival. Mol Cell 2011; 42: 23–35.
  Article CAS PubMed Google Scholar
• Byun JY, Kim MJ, Yoon CH, Cha H, Yoon G, Lee SJ . Oncogenic Ras signals through activation of both phosphoinositide 3-kinase and Rac1 to induce c-Jun NH2-terminal kinase-mediated, caspase-independent cell death. Mol Cancer Res 2009; 7: 1534–1542.
  Article CAS PubMed Google Scholar
• Byun JY, Yoon CH, An S, Park IC, Kang CM, Kim MJ et al. The Rac1/MKK7/JNK pathway signals upregulation of Atg5 and subsequent autophagic cell death in response to oncogenic Ras. Carcinogenesis 2009; 30: 1880–1888.
  Article CAS PubMed Google Scholar
• Guo JY, Chen HY, Mathew R, Fan J, Strohecker AM, Karsli-Uzunbas G et al. Activated Ras requires autophagy to maintain oxidative metabolism and tumorigenesis. Genes Dev 2011; 25: 460–470.
  Article CAS PubMed PubMed Central Google Scholar
• Lock R, Roy S, Kenific CM, Su JS, Salas E, Ronen SM et al. Autophagy facilitates glycolysis during Ras-mediated oncogenic transformation. Mol Biol Cell 2011; 22: 165–178.
  Article CAS PubMed PubMed Central Google Scholar
• Kim JH, Kim HY, Lee YK, Yoon YS, Xu WG, Yoon JK et al. Involvement of mitophagy in oncogenic K-Ras-induced transformation: overcoming a cellular energy deficit from glucose deficiency. Autophagy 2011; 7: 1187–1198.
  Article CAS PubMed PubMed Central Google Scholar
• Kim MJ, Woo SJ, Yoon CH, Lee JS, An S, Choi YH et al. Involvement of autophagy in oncogenic K-Ras-induced malignant cell transformation. J Biol Chem 2011; 286: 12924–12932.
  Article CAS PubMed PubMed Central Google Scholar
• Yang S, Wang X, Contino G, Liesa M, Sahin E, Ying H et al. Pancreatic cancers require autophagy for tumor growth. Genes Dev 2011; 25: 717–729.
  Article CAS PubMed PubMed Central Google Scholar
• Rubinsztein DC, Gestwicki JE, Murphy LO, Klionsky DJ . Potential therapeutic applications of autophagy. Nat Rev Drug Discov 2007; 6: 304–312.
  Article CAS PubMed Google Scholar
• Hara T, Nakamura K, Matsui M, Yamamoto A, Nakahara Y, Suzuki-Migishima R et al. Suppression of basal autophagy in neural cells causes neurodegenerative disease in mice. Nature 2006; 441: 885–889.
  Article CAS PubMed Google Scholar
• Komatsu M, Waguri S, Chiba T, Murata S, Iwata J, Tanida I et al. Loss of autophagy in the central nervous system causes neurodegeneration in mice. Nature 2006; 441: 880–884.
  Article CAS PubMed Google Scholar
• Komatsu M, Wang QJ, Holstein GR, Friedrich Jr VL, Iwata J, Kominami E et al. Essential role for autophagy protein Atg7 in the maintenance of axonal homeostasis and the prevention of axonal degeneration. Proc Natl Acad Sci USA 2007; 104: 14489–14494.
  Article CAS PubMed PubMed Central Google Scholar
• Yu SW, Baek SH, Brennan RT, Bradley CJ, Park SK, Lee YS et al. Autophagic death of adult hippocampal neural stem cells following insulin withdrawal. Stem Cells 2008; 26: 2602–2610.
  Article CAS PubMed Google Scholar
• Baek SH, Kim EK, Goudreau JL, Lookingland KJ, Kim SW, Yu SW . Insulin withdrawal-induced cell death in adult hippocampal neural stem cells as a model of autophagic cell death. Autophagy 2009; 5: 277–279.
  Article CAS PubMed Google Scholar
• Radoshevich L, Murrow L, Chen N, Fernandez E, Roy S, Fung C et al. ATG12 conjugation to ATG3 regulates mitochondrial homeostasis and cell death. Cell 2010; 142: 590–600.
  Article CAS PubMed PubMed Central Google Scholar
• Erdelyi P, Borsos E, Takacs-Vellai K, Kovacs T, Kovacs AL, Sigmond T et al. Shared developmental roles and transcriptional control of autophagy and apoptosis in Caenorhabditis elegans. J Cell Sci 2011; 124: 1510–1518.
  Article CAS PubMed PubMed Central Google Scholar