Skip to main content

Part of the book series: Methods in Molecular Biology ((MIMB,volume 648))

Abstract

Autophagy is a cellular quality control process by which cytoplasmic constituents including proteins, protein aggregates, organelles, and invading pathogens can be delivered to lysosomes for degradation. Autophagy is activated in response to changes in the internal status of the cell and/or changes in the extracellular environment. It is therefore essential for the maintenance of cellular homeostasis and for an efficient response to cellular stresses. As such autophagy has been implicated either in the pathogenesis, or response to a wide variety of diseases, bacterial, and viral infections, and ageing.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Protocol
USD 49.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 89.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 119.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 169.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  1. Huang J, Klionsky DJ (2007) Autophagy and human disease. Cell Cycle 6:1837–1849

    Article  PubMed  CAS  Google Scholar 

  2. Eskelinen EL, Saftig P (2009) Autophagy: A lysosomal degradation pathway with a central role in health and disease. Biochim Biophys Acta 1793:664–673

    Article  PubMed  CAS  Google Scholar 

  3. Levine B, Kroemer G (2008) Autophagy in the pathogenesis of disease. Cell 132:27–42

    Article  PubMed  CAS  Google Scholar 

  4. Kundu M, Thompson CB (2008) Autophagy: Basic principles and relevance to disease. Annu Rev Pathol 3:427–455

    Article  PubMed  CAS  Google Scholar 

  5. Colombo MI (2007) Autophagy: A pathogen driven process. IUBMB Life 59:238–242

    Article  PubMed  CAS  Google Scholar 

  6. Mizushima N, Klionsky DJ (2007) Protein turnover via autophagy: Implications for metabolism. Annu Rev Nutr 27:19–40

    Article  PubMed  CAS  Google Scholar 

  7. Cecconi F, Levine B (2008) The role of autophagy in mammalian development: Cell makeover rather than cell death. Dev Cell 15:344–357

    Article  PubMed  CAS  Google Scholar 

  8. Hussey S, Terebiznik MR, Jones NL (2008) Autophagy: Healthy eating and self digestion for gastroenterologists. J Pediatr Gastroenterol Nutr 46:496–506

    Article  PubMed  Google Scholar 

  9. Mizushima N, Levine B, Cuervo AM, Klionsky DJ (2008) Autophagy fights disease through cellular self-digestion. Nature 451:1069–1075

    Article  PubMed  CAS  Google Scholar 

  10. Uchiyama Y, Shibata M, Koike M, Yoshimura K, Sasaki M (2008) Autophagy-physiology and pathophysiology. Histochem Cell Biol 129:407–420

    Article  PubMed  CAS  Google Scholar 

  11. van der Vaart A, Mari M, Reggiori F (2008) A picky eater: Exploring the mechanisms of selective autophagy in human pathologies. Traffic 9:281–289

    Article  PubMed  Google Scholar 

  12. Yin XM, Ding WX, Gao W (2008) Autophagy in the liver. Hepatology 47:1773–1785

    Article  PubMed  CAS  Google Scholar 

  13. Yu L, Strandberg L, Leonardo MJ (2008) The selectivity of autophagy and its role in cell death and survival. Autophagy 4:567–573

    PubMed  Google Scholar 

  14. Todde V, Veenhuis M, van der Klei IJ (2009) Autophagy: Principles and significance in health and disease. Biochim Biophys Acta 1792:3–13

    Article  PubMed  CAS  Google Scholar 

  15. Axe EL, Walker SA, Manifava M, Chandra P, Roderick HL, Habermann A, Griffiths G, Ktistakis NT (2008) Autophagosome formation from membrane compartments enriched in phosphatidylinositol 3-phosphate and dynamically connected to the endoplasmic reticulum. J Cell Biol 182:685–701

    Article  PubMed  CAS  Google Scholar 

  16. Klionsky DJ (2007) Autophagy: From phenomenology to molecular understanding in less than a decade. Nat Rev Mol Cell Biol 8:931–937

    Article  PubMed  CAS  Google Scholar 

  17. Xie Z, Klionsky DJ (2007) Autophagosome formation: Core machinery and adaptations. Nat Cell Biol 9:1102–1109

    Article  PubMed  CAS  Google Scholar 

  18. Meijer WH, van der Klei IJ, Veenhuis M, Kiel JA (2007) ATG genes involved in non-selective autophagy are conserved from yeast to man, but the selective Cvt and pexophagy pathways also require organism-specific genes. Autophagy 3:106–116

    PubMed  CAS  Google Scholar 

  19. Yorimitsu T, Klionsky DJ (2005) Autophagy: Molecular machinery for self-eating. Cell Death Differ 12(Suppl 2):1542–1552

    Article  PubMed  CAS  Google Scholar 

  20. Suzuki K, Ohsumi Y (2007) Molecular machinery of autophagosome formation in yeast, Saccharomyces cerevisiae. FEBS Lett 581:2156–2161

    Article  PubMed  CAS  Google Scholar 

  21. Yang YP, Liang ZQ, Gu ZL, Qin ZH (2005) Molecular mechanism and regulation of autophagy. Acta Pharmacol Sin 26:1421–1434

    Article  PubMed  CAS  Google Scholar 

  22. Wullschleger S, Loewith R, Hall MN (2006) TOR signaling in growth and metabolism. Cell 124:471–484

    Article  PubMed  CAS  Google Scholar 

  23. Nicklin P, Bergman P, Zhang B, Triantafellow E, Wang H, Nyfeler B, Yang H, Hild M, Kung C, Wilson C, Myer VE, MacKeigan JP, Porter JA, Wang YK, Cantley LC, Finan PM, Murphy LO (2009) Bidirectional transport of amino acids regulates mTOR and autophagy. Cell 136:521–534

    Article  PubMed  CAS  Google Scholar 

  24. Kadowaki M, Karim MR, Carpi A, Miotto G (2006) Nutrient control of macroautophagy in mammalian cells. Mol Aspects Med 27:426–443

    Article  PubMed  CAS  Google Scholar 

  25. Meijer AJ, Codogno P (2006) Signalling and autophagy regulation in health, aging and disease. Mol Aspects Med 27:411–425

    Article  PubMed  CAS  Google Scholar 

  26. Dunn WA Jr, Cregg JM, Kiel JA, van der Klei IJ, Oku M, Sakai Y, Sibirny AA, Stasyk OV, Veenhuis M (2005) Pexophagy: The selective autophagy of peroxisomes. Autophagy 1:75–83

    Article  PubMed  CAS  Google Scholar 

  27. Krick R, Muehe Y, Prick T, Bremer S, Schlotterhose P, Eskelinen EL, Millen J, Goldfarb DS, Thumm M (2008) Piecemeal microautophagy of the nucleus requires the core macroautophagy genes. Mol Biol Cell 19:4492–4505

    Article  PubMed  CAS  Google Scholar 

  28. Kiššová I, Salin B, Schaeffer J, Bhatia S, Manon S, Camougrand N (2007) Selective and non-selective autophagic degradation of mitochondria in yeast. Autophagy 3:329–336

    PubMed  Google Scholar 

  29. Dubouloz F, Deloche O, Wanke V, Cameroni E, De Virgilio C (2005) The TOR and EGO protein complexes orchestrate microautophagy in yeast. Mol Cell 19:15–26

    Article  PubMed  CAS  Google Scholar 

  30. Uttenweiler A, Schwarz H, Neumann H, Mayer A (2007) The vacuolar transporter chaperone (VTC) complex is required for microautophagy. Mol Biol Cell 18:166–175

    Article  PubMed  CAS  Google Scholar 

  31. Kaushik S, Cuervo AM (2008) Chaperone-mediated autophagy. Meth Mol Biol 445:227–244

    Article  CAS  Google Scholar 

  32. Liang XH, Jackson S, Seaman M, Brown K, Kempkes B, Hibshoosh H, Levine B (1999) Induction of autophagy and inhibition of tumorigenesis by beclin 1. Nature 402:672–676

    Article  PubMed  CAS  Google Scholar 

  33. Jin S (2006) Autophagy, mitochondrial quality control, and oncogenesis. Autophagy 2:80–84

    PubMed  CAS  Google Scholar 

  34. Mathew R, Karantza-Wadsworth V, White E (2007) Role of autophagy in cancer. Nat Rev Cancer 7:961–967

    Article  PubMed  CAS  Google Scholar 

  35. Kroemer G, Levine B (2008) Autophagic cell death: The story of a misnomer. Nat Rev Mol Cell Biol 9:1004–1010

    Article  PubMed  CAS  Google Scholar 

  36. Bialik S, Kimchi A (2008) Autophagy and tumor suppression: Recent advances in understanding the link between autophagic cell death pathways and tumor development. Adv Exp Med Biol 615:177–200

    Article  PubMed  CAS  Google Scholar 

  37. Komatsu M, Waguri S, Chiba T, Murata S, Iwata J, Tanida I, Ueno T, Koike M, Uchiyama Y, Kominami E, Tanaka K (2006) Loss of autophagy in the central nervous system causes neurodegeneration in mice. Nature 441:880–884

    Article  PubMed  CAS  Google Scholar 

  38. Hara T, Nakamura K, Matsui M, Yamamoto A, Nakahara Y, Suzuki Migishima R, Yokoyama M, Mishima K, Saito I, Okano H, Mizushima N (2006) Suppression of basal autophagy in neural cells causes neurodegenerative disease in mice. Nature 441:885–889

    Article  PubMed  CAS  Google Scholar 

  39. Ventruti A, Cuervo AM (2007) Autophagy and neurodegeneration. Curr Neurol Neurosci Rep 7:443–451

    Article  PubMed  CAS  Google Scholar 

  40. Winslow AR, Rubinsztein DC (2008) Autophagy in neurodegeneration and development. Biochim Biophys Acta 1782:723–729

    Article  PubMed  CAS  Google Scholar 

  41. Yu WH, Cuervo AM, Kumar A, Peterhoff CM, Schmidt SD, Lee JH, Mohan PS, Mercken M, Farmery MR, Tjernberg LO, Jiang Y, Duff K, Uchiyama Y, Näslund J, Mathews PM, Cataldo AM, Nixon RA (2005) Macroautophagy-a novel Beta-amyloid peptide-generating pathway activated in Alzheimer’s disease. J Cell Biol 171:87–98

    Article  PubMed  CAS  Google Scholar 

  42. Koike M, Shibata M, Tadakoshi M, Gotoh K, Komatsu M, Waguri S, Kawahara N, Kuida K, Nagata S, Kominami E, Tanaka K, Uchiyama Y (2008) Inhibition of autophagy prevents hippocampal pyramidal neuron death after hypoxic-ischemic injury. Am J Pathol 172:454–469

    Article  PubMed  CAS  Google Scholar 

  43. Yue Z, Friedman L, Komatsu M, Tanaka K (2009) The cellular pathways of neuronal autophagy and their implication in neurodegenerative diseases. Biochim Biophys Acta 1793:1496–1507

    Google Scholar 

  44. Williams A, Jahreiss L, Sarkar S, Saiki S, Menzies FM, Ravikumar B, Rubinsztein DC (2006) Aggregate-prone proteins are cleared from the cytosol by autophagy: Therapeutic implications. Curr Top Dev Biol 76:89–101

    Article  PubMed  CAS  Google Scholar 

  45. Nishino I (2003) Autophagic vacuolar myopathies. Curr Neurol Neurosci Rep 3:64–69

    Article  PubMed  Google Scholar 

  46. Nishino I, Fu J, Tanji K, Yamada T, Shimojo S, Koori T, Mora M, Riggs JE, Oh SJ, Koga Y, Sue CM, Yamamoto A, Murakami N, Shanske S, Byrne E, Bonilla E, Nonaka I, DiMauro S, Hirano M (2000) Primary LAMP-2 deficiency causes X-linked vacuolar cardiomyopathy and myopathy (Danon disease). Nature 406:906–910

    Article  PubMed  CAS  Google Scholar 

  47. Martinet W, Knaapen MW, Kockx MM, De Meyer GR (2007) Autophagy in cardiovascular disease. Trends Mol Med 13:482–491

    Article  PubMed  CAS  Google Scholar 

  48. Nakai A, Yamaguchi O, Takeda T, Higuchi Y, Hikoso S, Taniike M, Omiya S, Mizote I, Matsumura Y, Asahi M, Nishida K, Hori M, Mizushima N, Otsu K (2007) The role of autophagy in cardiomyocytes in the basal state and in response to hemodynamic stress. Nat Med 13:619–624

    Article  PubMed  CAS  Google Scholar 

  49. Martinet W, De Meyer GR (2009) Autophagy in atherosclerosis: A cell survival and death phenomenon with therapeutic potential. Circ Res 104:304–317

    Article  PubMed  CAS  Google Scholar 

  50. Gannagé M, Münz C (2009) Macroauto­phagy in immunity and tolerance. Traffic 10:616–620

    Google Scholar 

  51. Münz C (2009) Enhancing immunity through autophagy. Annu Rev Immunol 27:423–449

    Article  PubMed  Google Scholar 

  52. Levine B, Deretic V (2007) Unveiling the roles of autophagy in innate and adaptive immunity. Nat Rev Immunol 7:767–777

    Article  PubMed  CAS  Google Scholar 

  53. Orvedahl A, Levine B (2009) Eating the enemy within: Autophagy in infectious diseases. Cell Death Differ 16:57–69

    Article  PubMed  CAS  Google Scholar 

  54. Hampe J, Franke A, Rosenstiel P, Till A, Teuber M, Huse K, Albrecht M, Mayr G, De La Vega FM, Briggs J, Günther S, Prescott NJ, Onnie CM, Häsler R, Sipos B, Fölsch UR, Lengauer T, Platzer M, Mathew CG, Krawczak M, Schreiber S (2007) A genome-wide association scan of nonsynonymous SNPs identifies a susceptibility variant for Crohn disease in ATG16L1. Nat Genet 39:207–211

    Article  PubMed  CAS  Google Scholar 

  55. Massey DC, Parkes M (2007) Genome-wide association scanning highlights two autophagy genes, ATG16L1 and IRGM, as being significantly associated with Crohn’s disease. Autophagy 3:649–651

    PubMed  CAS  Google Scholar 

  56. Kuballa P, Huett A, Rioux JD, Daly MJ, Xavier RJ (2008) Impaired autophagy of an intracellular pathogen induced by a Crohn’s disease associated ATG16L1 variant. PLoS ONE 3:e3391

    Article  PubMed  Google Scholar 

  57. Zhang H, Massey D, Tremelling M, Parkes M (2008) Genetics of inflammatory bowel disease: Clues to pathogenesis. Br Med Bull 87:17–30

    Article  PubMed  CAS  Google Scholar 

  58. Meijer AJ, Codogno P (2008) Autophagy: A sweet process in diabetes. Cell Metab 8:275–276

    Article  PubMed  CAS  Google Scholar 

  59. Codogno P, Meijer AJ (2005) Autophagy and signaling: Their role in cell survival and cell death. Cell Death Differ 12(Suppl 2):1509–1518

    Article  PubMed  CAS  Google Scholar 

  60. Russell SJ, Kahn CR (2007) Endocrine regulation of ageing. Nat Rev Mol Cell Biol 8:681–91

    Article  PubMed  CAS  Google Scholar 

  61. Kaniuk NA, Kiraly M, Bates H, Vranic M, Volchuk A, Brumell JH (2007) Ubiquitinated-protein aggregates form in pancreatic beta-cells during diabetes-induced oxidative stress and are regulated by autophagy. Diabetes 56:930–939

    Article  PubMed  CAS  Google Scholar 

  62. Jung HS, Chung KW, Won Kim J, Kim J, Komatsu M, Tanaka K, Nguyen YH, Kang TM, Yoon KH, Kim JW, Jeong YT, Han MS, Lee MK, Kim KW, Shin J, Lee MS (2008) Loss of autophagy diminishes pancreatic beta cell mass and function with resultant hyperglycemia. Cell Metab 8:318–324

    Article  PubMed  CAS  Google Scholar 

  63. Ebato C, Uchida T, Arakawa M, Komatsu M, Ueno T, Komiya K, Azuma K, Hirose T, Tanaka K, Kominami E, Kawamori R, Fujitani Y, Watada H (2008) Autophagy is important in islet homeostasis and compensatory increase of beta cell mass in response to high-fat diet. Cell Metab 8:325–332

    Article  PubMed  CAS  Google Scholar 

  64. Cuervo AM (2004) Autophagy: In sickness and in health. Trends Cell Biol 14:70–77

    Article  PubMed  Google Scholar 

  65. Yen WL, Klionsky DJ (2008) How to live long and prosper: Autophagy, mitochondria, and aging. Physiology (Bethesda) 23:248–262

    Article  CAS  Google Scholar 

  66. Cuervo AM (2008) Autophagy and aging: Keeping that old broom working. Trends Genet 24:604–612

    Article  PubMed  CAS  Google Scholar 

  67. Rubinsztein DC, Gestwicki JE, Murphy LO, Klionsky DJ (2007) Potential therapeutic applications of autophagy. Nat Rev Drug Discov 6:304–312

    Article  PubMed  CAS  Google Scholar 

Download references

Acknowledgments

We apologise to investigators whose important original contributions have not been cited; where possible we have chosen to cite recent reviews in which details of such contributions can be found.

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Rodney J. Devenish .

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2010 Springer Science+Business Media, LLC

About this protocol

Cite this protocol

Mijaljica, D., Prescott, M., Devenish, R.J. (2010). Autophagy in Disease. In: Bross, P., Gregersen, N. (eds) Protein Misfolding and Cellular Stress in Disease and Aging. Methods in Molecular Biology, vol 648. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-60761-756-3_5

Download citation

  • DOI: https://doi.org/10.1007/978-1-60761-756-3_5

  • Published:

  • Publisher Name: Humana Press, Totowa, NJ

  • Print ISBN: 978-1-60761-755-6

  • Online ISBN: 978-1-60761-756-3

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics