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  • Review Article
  • Published:

Autophagy in the liver: functions in health and disease

Key Points

  • Autophagy was first discovered in rodent liver tissues in 1960s, and early studies of autophagy in liver tissues and hepatocytes revealed regulation via hormones and amino acids

  • In the 1990s, autophagy-related genes essential for autophagosome formation were identified, advancing our understanding of the molecular mechanisms of autophagy as well as its physiological roles

  • Catabolism of glycogen granules, lipid droplets and proteins through autophagy has an effect on hepatocyte metabolic pathways including glycogenolysis, gluconeogenesis and β-oxidation

  • Hepatic metabolic processes mediated by autophagy are regulated by a series of transcription factors including CREB, TFEB, PPARα and NRF2

  • Impaired liver autophagy caused by HCV and HBV infection and lipid toxicity is closely related to the pathogenesis of liver diseases such as NAFLD and hepatocellular carcinoma

  • Pharmacological enhancement of autophagy attenuates clinical symptoms of α1-antitrypsin deficiency, a conformational liver disease

Abstract

The concept of macroautophagy was established in 1963, soon after the discovery of lysosomes in rat liver. Over the 50 years since, studies of liver autophagy have produced many important findings. The liver is rich in lysosomes and possesses high levels of metabolic-stress-induced autophagy, which is precisely regulated by concentrations of hormones and amino acids. Liver autophagy provides starved cells with amino acids, glucose and free fatty acids for use in energy production and synthesis of new macromolecules, and also controls the quality and quantity of organelles such as mitochondria. Although the efforts of early investigators contributed markedly to our current knowledge of autophagy, the identification of autophagy-related genes represented a revolutionary breakthrough in our understanding of the physiological roles of autophagy in the liver. A growing body of evidence has shown that liver autophagy contributes to basic hepatic functions, including glycogenolysis, gluconeogenesis and β-oxidation, through selective turnover of specific cargos controlled by a series of transcription factors. In this Review, we outline the history of liver autophagy study, and then describe the roles of autophagy in hepatic metabolism under healthy and disease conditions, including the involvement of autophagy in α1-antitrypsin deficiency, NAFLD, hepatocellular carcinoma and viral hepatitis.

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Figure 1: Autophagic pathways.
Figure 2: Autophagosome formation in mammalian cells.
Figure 3: Selective autophagy related to liver metabolism.
Figure 4: Amino-acid-dependent mTORC1 activation.
Figure 5: Spatiotemporal regulation of hepatic autophagy.

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References

  1. Appelmans, F., Wattiaux, R. & De Duve, C. Tissue fractionation studies. 5. The association of acid phosphatase with a special class of cytoplasmic granules in rat liver. Biochem. J. 59, 438–445 (1955).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  2. De Duve, C., Pressman, B. C., Gianetto, R., Wattiaux, R. & Appelmans, F. Tissue fractionation studies. 6. Intracellular distribution patterns of enzymes in rat-liver tissue. Biochem. J. 60, 604–617 (1955).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  3. Beaufay, H., Bendall, D. S., Baudhun, P., Wattiaux, R. & De Duve, C. Tissue fractionation studies. 13. Analysis of mitochondrial fractions from rat liver by density-gradient centrifuging. Biochem. J. 73, 628–637 (1959).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  4. Novikoff, A. B., Beaufay, H. & De Duve, C. Electron microscopy of lysosomerich fractions from rat liver. J. Biophys. Biochem. Cytol. 2, 179–184 (1956).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  5. Essner, E. & Novikoff, A. B. Localization of acid phosphatase activity in hepatic lysosomes by means of electron microscopy. J. Biophys. Biochem. Cytol. 9, 773–784 (1961).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  6. Straus, W. Rapid cytochemical identification of phagosomes in various tissues of the rat and their differentiation from mitochondria by the peroxidase method. J. Biophys. Biochem. Cytol. 5, 193–204 (1959).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  7. Straus, W. Cytochemical observations on the relationship between lysosomes and phagosomes in kidney and liver by combined staining for acid phosphatase and intravenously injected horseradish peroxidase. J. Cell Biol. 20, 497–507 (1964).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  8. Clark, S. L. Jr. Cellular differentiation in the kidneys of newborn mice studies with the electron microscope. J. Biophys. Biochem. Cytol. 3, 349–362 (1957).

    Article  PubMed  PubMed Central  Google Scholar 

  9. Novikoff, A. B. The proximal tubule cell in experimental hydronephrosis. J. Biophys. Biochem. Cytol. 6, 136–138 (1959).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  10. Ashford, T. P. & Porter, K. R. Cytoplasmic components in hepatic cell lysosomes. J. Cell Biol. 12, 198–202 (1962).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  11. Novikoff, A. B. & Essner, E. Cytolysomes and mitochondrial degeneration. J. Cell Biol. 15, 140–146 (1962).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  12. Moe, H. & Behnke, O. Cytoplasmic bodies containing mitochondria, ribosomes, and rough surfaced endoplasmic membranes in the epithelium of the small intestine of newborn rats. J. Cell Biol. 13, 168–171 (1962).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  13. Hruban, Z., Spargo, B., Swift, H., Wissler, R. W. & Kleinfeld, R. G. Focal cytoplasmic degradation. Am. J. Pathol. 42, 657–683 (1963).

    CAS  PubMed  PubMed Central  Google Scholar 

  14. Miller, L. L. Glucagon: a protein catabolic hormone in the isolated perfused rat liver. Nature 185, 248 (1960).

    Article  CAS  PubMed  Google Scholar 

  15. De Duve, C. The lysosome. Sci. Am. 208, 64–72 (1963).

    Article  CAS  PubMed  Google Scholar 

  16. De Duve, C. & Wattiaux, R. Functions of lysosomes. Annu. Rev. Physiol. 28, 435–492 (1966).

    Article  CAS  PubMed  Google Scholar 

  17. Mizushima, N., Levine, B., Cuervo, A. M. & Klionsky, D. J. Autophagy fights disease through cellular self-digestion. Nature 451, 1069–1075 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  18. Arstila, A. U. & Trump, B. F. Studies on cellular autophagocytosis. The formation of autophagic vacuoles in the liver after glucagon administration. Am. J. Pathol. 53, 687–733 (1968).

    CAS  PubMed  PubMed Central  Google Scholar 

  19. Ericsson, J. L. Studies on induced cellular autophagy. II. Characterization of the membranes bordering autophagosomes in parenchymal liver cells. Exp. Cell Res. 56, 393–405 (1969).

    Article  CAS  PubMed  Google Scholar 

  20. Furuno, K. et al. Immunocytochemical study of the surrounding envelope of autophagic vacuoles in cultured rat hepatocytes. Exp. Cell Res. 189, 261–268 (1990).

    Article  CAS  PubMed  Google Scholar 

  21. Dunn, W. A. Jr. Studies on the mechanisms of autophagy: formation of the autophagic vacuole. J. Cell Biol. 110, 1923–1933 (1990).

    Article  PubMed  Google Scholar 

  22. Masaki, R., Yamamoto, A. & Tashiro, Y. Cytochrome P-450 and NADPH-cytochrome P-450 reductase are degraded in the autolysosomes in rat liver. J. Cell Biol. 104, 1207–1215 (1987).

    Article  CAS  PubMed  Google Scholar 

  23. Locke, M. & Sykes, A. K. The role of the Golgi complex in the isolation and digestion of organelles. Tissue Cell 7, 143–158 (1975).

    Article  CAS  PubMed  Google Scholar 

  24. Yamamoto, A., Masaki, R. & Tashiro, Y. Characterization of the isolation membranes and the limiting membranes of autophagosomes in rat hepatocytes by lectin cytochemistry. J. Histochem. Cytochem. 38, 573–580 (1990).

    Article  CAS  PubMed  Google Scholar 

  25. Seglen, P. O., Gordon, P. B. & Holen, I. Non-selective autophagy. Semin. Cell Biol. 1, 441–448 (1990).

    CAS  PubMed  Google Scholar 

  26. Rez, G. & Meldolesi, J. Freeze-fracture of drug-induced autophagocytosis in the mouse exocrine pancreas. Lab. Invest. 43, 269–277 (1980).

    CAS  PubMed  Google Scholar 

  27. Baba, M., Takeshige, K., Baba, N. & Ohsumi, Y. Ultrastructural analysis of the autophagic process in yeast: detection of autophagosomes and their characterization. J. Cell Biol. 124, 903–913 (1994).

    Article  CAS  PubMed  Google Scholar 

  28. Tsukada, M. & Ohsumi, Y. Isolation and characterization of autophagy-defective mutants of Saccharomyces cerevisiae. FEBS Lett. 333, 169–174 (1993).

    Article  CAS  PubMed  Google Scholar 

  29. Thumm, M. et al. Isolation of autophagocytosis mutants of Saccharomyces cerevisiae. FEBS Lett. 349, 275–280 (1994).

    Article  CAS  PubMed  Google Scholar 

  30. Harding, T. M., Hefner-Gravink, A., Thumm, M. & Klionsky, D. J. Genetic and phenotypic overlap between autophagy and the cytoplasm to vacuole protein targeting pathway. J. Biol. Chem. 271, 17621–17624 (1996).

    Article  CAS  PubMed  Google Scholar 

  31. Klionsky, D. J. et al. A unified nomenclature for yeast autophagy-related genes. Dev. Cell 5, 539–545 (2003).

    Article  CAS  PubMed  Google Scholar 

  32. Ravikumar, B., Moreau, K., Jahreiss, L., Puri, C. & Rubinsztein, D. C. Plasma membrane contributes to the formation of pre-autophagosomal structures. Nat. Cell Biol. 12, 747–757 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  33. Yla-Anttila, P., Vihinen, H., Jokitalo, E. & Eskelinen, E. L. 3D tomography reveals connections between the phagophore and endoplasmic reticulum. Autophagy 5, 1180–1185 (2009).

    Article  PubMed  Google Scholar 

  34. Hayashi-Nishino, M. et al. A subdomain of the endoplasmic reticulum forms a cradle for autophagosome formation. Nat. Cell Biol. 11, 1433–1437 (2009).

    Article  CAS  PubMed  Google Scholar 

  35. Hamasaki, M. et al. Autophagosomes form at ER–mitochondria contact sites. Nature 495, 389–393 (2013).

    Article  CAS  PubMed  Google Scholar 

  36. Yen, W. L. et al. The conserved oligomeric Golgi complex is involved in double-membrane vesicle formation during autophagy. J. Cell Biol. 188, 101–114 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  37. Schneider, J. L. & Cuervo, A. M. Liver autophagy: much more than just taking out the trash. Nat. Rev. Gastroenterol. Hepatol. 11, 187–200 (2014).

    Article  PubMed  Google Scholar 

  38. Nakatogawa, H., Suzuki, K., Kamada, Y. & Ohsumi, Y. Dynamics and diversity in autophagy mechanisms: lessons from yeast. Nat. Rev. Mol. Cell Biol. 10, 458–467 (2009).

    Article  CAS  PubMed  Google Scholar 

  39. Mizushima, N., Yoshimori, T. & Ohsumi, Y. The role of Atg proteins in autophagosome formation. Annu. Rev. Cell Dev. Biol. 27, 107–132 (2011).

    Article  CAS  PubMed  Google Scholar 

  40. Meley, D. et al. AMP-activated protein kinase and the regulation of autophagic proteolysis. J. Biol. Chem. 281, 34870–34879 (2006).

    Article  CAS  PubMed  Google Scholar 

  41. Kim, J., Kundu, M., Viollet, B. & Guan, K. L. AMPK and mTOR regulate autophagy through direct phosphorylation of Ulk1. Nat. Cell Biol. 13, 132–141 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  42. Noda, T. & Ohsumi, Y. Tor, a phosphatidylinositol kinase homologue, controls autophagy in yeast. J. Biol. Chem. 273, 3963–3966 (1998).

    Article  CAS  PubMed  Google Scholar 

  43. Kamada, Y. et al. Tor-mediated induction of autophagy via an Apg1 protein kinase complex. J. Cell Biol. 150, 1507–1513 (2000).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  44. Hosokawa, N. et al. Nutrient-dependent mTORC1 association with the ULK1–Atg13–FIP200 complex required for autophagy. Mol. Biol. Cell 20, 1981–1991 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  45. Jung, C. H. et al. ULK–Atg13–FIP200 complexes mediate mTOR signaling to the autophagy machinery. Mol. Biol. Cell 20, 1992–2003 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  46. Itakura, E., Kishi-Itakura, C. & Mizushima, N. The hairpin-type tail-anchored SNARE syntaxin 17 targets to autophagosomes for fusion with endosomes/lysosomes. Cell 151, 1256–1269 (2012).

    Article  CAS  PubMed  Google Scholar 

  47. Diao, J. et al. ATG14 promotes membrane tethering and fusion of autophagosomes to endolysosomes. Nature 520, 563–566 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  48. McEwan, D. G. et al. PLEKHM1 regulates autophagosome–lysosome fusion through HOPS complex and LC3/GABARAP proteins. Mol. Cell 57, 39–54 (2015).

    Article  CAS  PubMed  Google Scholar 

  49. Khaminets, A., Behl, C. & Dikic, I. Ubiquitin-dependent and independent signals in selective autophagy. Trends Cell Biol. 26, 6–16 (2016).

    Article  CAS  PubMed  Google Scholar 

  50. Rogov, V., Dotsch, V., Johansen, T. & Kirkin, V. Interactions between autophagy receptors and ubiquitin-like proteins form the molecular basis for selective autophagy. Mol. Cell 53, 167–178 (2014).

    Article  CAS  PubMed  Google Scholar 

  51. Fujita, N. et al. Recruitment of the autophagic machinery to endosomes during infection is mediated by ubiquitin. J. Cell Biol. 203, 115–128 (2013).

    Article  PubMed  PubMed Central  Google Scholar 

  52. Lazarou, M. et al. The ubiquitin kinase PINK1 recruits autophagy receptors to induce mitophagy. Nature 524, 309–314 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  53. Koyano, F. et al. Ubiquitin is phosphorylated by PINK1 to activate parkin. Nature 510, 162–166 (2014).

    Article  CAS  PubMed  Google Scholar 

  54. Kane, L. A. et al. PINK1 phosphorylates ubiquitin to activate Parkin E3 ubiquitin ligase activity. J. Cell Biol. 205, 143–153 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  55. Bingol, B. et al. The mitochondrial deubiquitinase USP30 opposes parkin-mediated mitophagy. Nature 510, 370–375 (2014).

    Article  CAS  PubMed  Google Scholar 

  56. Heo, J. M., Ordureau, A., Paulo, J. A., Rinehart, J. & Harper, J. W. The PINK1–PARKIN mitochondrial ubiquitylation pathway drives a program of OPTN/NDP52 recruitment and TBK1 activation to promote mitophagy. Mol. Cell 60, 7–20 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  57. Richter, B. et al. Phosphorylation of OPTN by TBK1 enhances its binding to Ub chains and promotes selective autophagy of damaged mitochondria. Proc. Natl Acad. Sci. USA 113, 4039–4044 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  58. Tripathi, D. N. & Walker, C. L. The peroxisome as a cell signaling organelle. Curr. Opin. Cell Biol. 39, 109–112 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  59. Till, A., Lakhani, R., Burnett, S. F. & Subramani, S. Pexophagy: the selective degradation of peroxisomes. Int. J. Cell Biol. 2012, 512721 (2012).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  60. Kim, P. K., Hailey, D. W., Mullen, R. T. & Lippincott-Schwartz, J. Ubiquitin signals autophagic degradation of cytosolic proteins and peroxisomes. Proc. Natl Acad. Sci. USA 105, 20567–20574 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  61. Iwata, J. et al. Excess peroxisomes are degraded by autophagic machinery in mammals. J. Biol. Chem. 281, 4035–4041 (2006).

    Article  CAS  PubMed  Google Scholar 

  62. Watters, D. et al. Localization of a portion of extranuclear ATM to peroxisomes. J. Biol. Chem. 274, 34277–34282 (1999).

    Article  CAS  PubMed  Google Scholar 

  63. Zhang, J. et al. ATM functions at the peroxisome to induce pexophagy in response to ROS. Nat. Cell Biol. 17, 1259–1269 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  64. Tripathi, D. N. et al. Reactive nitrogen species regulate autophagy through ATM–AMPK–TSC2-mediated suppression of mTORC1. Proc. Natl Acad. Sci. USA 110, E2950–E2957 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  65. Walter, K. M. et al. Hif-2α promotes degradation of mammalian peroxisomes by selective autophagy. Cell Metab. 20, 882–897 (2014).

    Article  CAS  PubMed  Google Scholar 

  66. Deosaran, E. et al. NBR1 acts as an autophagy receptor for peroxisomes. J. Cell Sci. 126, 939–952 (2013).

    CAS  PubMed  Google Scholar 

  67. Singh, R. et al. Autophagy regulates lipid metabolism. Nature 458, 1131–1135 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  68. Martinez-Lopez, N. & Singh, R. Autophagy and lipid droplets in the liver. Annu. Rev. Nutr. 35, 215–237 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  69. Kaushik, S. et al. Autophagy in hypothalamic AgRP neurons regulates food intake and energy balance. Cell Metab. 14, 173–183 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  70. Coupe, B. et al. Loss of autophagy in pro-opiomelanocortin neurons perturbs axon growth and causes metabolic dysregulation. Cell Metab. 15, 247–255 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  71. Kaushik, S. & Cuervo, A. M. Degradation of lipid droplet-associated proteins by chaperone-mediated autophagy facilitates lipolysis. Nat. Cell Biol. 17, 759–770 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  72. Martinez-Lopez, N. et al. Autophagy in the CNS and periphery coordinate lipophagy and lipolysis in the brown adipose tissue and liver. Cell Metab. 23, 113–127 (2016).

    Article  CAS  PubMed  Google Scholar 

  73. Jiang, S. et al. Starch binding domain-containing protein 1/genethonin 1 is a novel participant in glycogen metabolism. J. Biol. Chem. 285, 34960–34971 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  74. Jiang, S., Wells, C. D. & Roach, P. J. Starch-binding domain-containing protein 1 (Stbd1) and glycogen metabolism: identification of the Atg8 family interacting motif (AIM) in Stbd1 required for interaction with GABARAPL1. Biochem. Biophys. Res. Commun. 413, 420–425 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  75. Zhu, Y., Zhang, M., Kelly, A. R. & Cheng, A. The carbohydrate-binding domain of overexpressed STBD1 is important for its stability and protein-protein interactions. Biosci. Rep. 34, e00117 (2014).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  76. Sun, T., Yi, H., Yang, C., Kishnani, P. S. & Sun, B. Starch Binding Domain-containing Protein 1 Plays a Dominant Role in Glycogen Transport to Lysosomes in Liver. J. Biol. Chem. 291, 16479–16484 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  77. Komatsu, M. et al. The selective autophagy substrate p62 activates the stress responsive transcription factor Nrf2 through inactivation of Keap1. Nat. Cell Biol. 12, 213–223 (2010).

    Article  CAS  PubMed  Google Scholar 

  78. Jain, A. et al. p62/SQSTM1 is a target gene for transcription factor NRF2 and creates a positive feedback loop by inducing antioxidant response element-driven gene transcription. J. Biol. Chem. 285, 22576–22591 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  79. Lau, A. et al. A noncanonical mechanism of Nrf2 activation by autophagy deficiency: direct interaction between Keap1 and p62. Mol. Cell. Biol. 30, 3275–3285 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  80. Taguchi, K. et al. Keap1 degradation by autophagy for the maintenance of redox homeostasis. Proc. Natl Acad. Sci. USA 109, 13561–13566 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  81. Ichimura, Y. et al. Phosphorylation of p62 activates the Keap1–Nrf2 pathway during selective autophagy. Mol. Cell 51, 618–631 (2013).

    Article  CAS  PubMed  Google Scholar 

  82. Bae, S. H. et al. Sestrins activate Nrf2 by promoting p62-dependent autophagic degradation of Keap1 and prevent oxidative liver damage. Cell Metab. 17, 73–84 (2013).

    Article  CAS  PubMed  Google Scholar 

  83. Ro, S. H. et al. Sestrin2 promotes Unc-51-like kinase 1 mediated phosphorylation of p62/sequestosome-1. FEBS J. 281, 3816–3827 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  84. Pfeifer, U. Inverted diurnal rhythm of cellular autophagy in liver cells of rats fed a single daily meal. Virchows Arch. B Cell Pathol. 10, 1–3 (1972).

    Article  CAS  PubMed  Google Scholar 

  85. Eng, C. H., Yu, K., Lucas, J., White, E. & Abraham, R. T. Ammonia derived from glutaminolysis is a diffusible regulator of autophagy. Sci. Signal. 3, ra31 (2010).

    PubMed  Google Scholar 

  86. Cheong, H., Lindsten, T., Wu, J., Lu, C. & Thompson, C. B. Ammonia-induced autophagy is independent of ULK1/ULK2 kinases. Proc. Natl Acad. Sci. USA 108, 11121–11126 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  87. Pfeifer, U. Inhibition by insulin of the formation of autophagic vacuoles in rat liver. A morphometric approach to the kinetics of intracellular degradation by autophagy. J. Cell Biol. 78, 152–167 (1978).

    Article  CAS  PubMed  Google Scholar 

  88. Blommaart, E. F., Luiken, J. J., Blommaart, P. J., van Woerkom, G. M. & Meijer, A. J. Phosphorylation of ribosomal protein S6 is inhibitory for autophagy in isolated rat hepatocytes. J. Biol. Chem. 270, 2320–2326 (1995).

    Article  CAS  PubMed  Google Scholar 

  89. Petiot, A., Ogier-Denis, E., Blommaart, E. F., Meijer, A. J. & Codogno, P. Distinct classes of phosphatidylinositol 3′-kinases are involved in signaling pathways that control macroautophagy in HT-29 cells. J. Biol. Chem. 275, 992–998 (2000).

    Article  CAS  PubMed  Google Scholar 

  90. Naito, T., Kuma, A. & Mizushima, N. Differential contribution of insulin and amino acids to the mTORC1-autophagy pathway in the liver and muscle. J. Biol. Chem. 288, 21074–21081 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  91. Cahill, G. F. Starvation in Man. N. Engl. J. Med. 282, 668–675 (1970).

    Article  CAS  PubMed  Google Scholar 

  92. Mortimore, G. E. & Schworer, C. M. Induction of autophagy by amino-acid deprivation in perfused rat liver. Nature 270, 174–176 (1977).

    Article  CAS  PubMed  Google Scholar 

  93. Schworer, C. M., Shiffer, K. A. & Mortimore, G. E. Quantitative relationship between autophagy and proteolysis during graded amino acid deprivation in perfused rat liver. J. Biol. Chem. 256, 7652–7658 (1981).

    Article  CAS  PubMed  Google Scholar 

  94. Poso, A. R., Wert, J. J. Jr & Mortimore, G. E. Multifunctional control of amino acids of deprivation-induced proteolysis in liver: role of leucine. J. Biol. Chem. 257, 12114–12120 (1982).

    Article  CAS  PubMed  Google Scholar 

  95. Mortimore, G. E., Hutson, N. J. & Surmacz, C. A. Quantitative correlation between proteolysis and macro- and microautophagy in mouse hepatocytes during starvation and refeeding. Proc. Natl Acad. Sci. USA 80, 2179–2183 (1983).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  96. Seglen, P. O., Gordon, P. B. & Poli, A. Amino acid inhibition of the autophagic/lysosomal pathway of protein degradation in isolated rat hepatocytes. Biochim. Biophys. Acta 630, 103–118 (1980).

    Article  CAS  PubMed  Google Scholar 

  97. Kovacs, A. L., Grinde, B. & Seglen, P. O. Inhibition of autophagic vacuole formation and protein degradation by amino acids in isolated hepatocytes. Exp. Cell Res. 133, 431–436 (1981).

    Article  CAS  PubMed  Google Scholar 

  98. Bar-Peled, L. & Sabatini, D. M. Regulation of mTORC1 by amino acids. Trends Cell Biol. 24, 400–406 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  99. Hara, K. et al. Amino acid sufficiency and mTOR regulate p70 S6 kinase and eIF-4E BP1 through a common effector mechanism. J. Biol. Chem. 273, 14484–14494 (1998).

    Article  CAS  PubMed  Google Scholar 

  100. Nicklin, P. et al. Bidirectional transport of amino acids regulates mTOR and autophagy. Cell 136, 521–534 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  101. Wolfson, R. L. et al. Sestrin2 is a leucine sensor for the mTORC1 pathway. Science 351, 43–48 (2016).

    Article  CAS  PubMed  Google Scholar 

  102. Chantranupong, L. et al. The CASTOR proteins are arginine sensors for the mTORC1 pathway. Cell 165, 153–164 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  103. Han, J. M. et al. Leucyl-tRNA synthetase is an intracellular leucine sensor for the mTORC1-signaling pathway. Cell 149, 410–424 (2012).

    Article  CAS  PubMed  Google Scholar 

  104. Duran, R. V. et al. Glutaminolysis activates Rag–mTORC1 signaling. Mol. Cell 47, 349–358 (2012).

    Article  CAS  PubMed  Google Scholar 

  105. Sener, A. & Malaisse, W. J. L-Leucine and a nonmetabolized analogue activate pancreatic islet glutamate dehydrogenase. Nature 288, 187–189 (1980).

    Article  CAS  PubMed  Google Scholar 

  106. Rebsamen, M. et al. SLC38A9 is a component of the lysosomal amino acid sensing machinery that controls mTORC1. Nature 519, 477–481 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  107. Wang, S. et al. Lysosomal amino acid transporter SLC38A9 signals arginine sufficiency to mTORC1. Science 347, 188–194 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  108. Jung, J., Genau, H. M. & Behrends, C. Amino acid-dependent mTORC1 regulation by the lysosomal membrane protein SLC38A9. Mol. Cell. Biol. 35, 2479–2494 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  109. Deter, R. L. & De Duve, C. Influence of glucagon, an inducer of cellular autophagy, on some physical properties of rat liver lysosomes. J. Cell Biol. 33, 437–449 (1967).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  110. Deter, R. L., Baudhuin, P. & De Duve, C. Participation of lysosomes in cellular autophagy induced in rat liver by glucagon. J. Cell Biol. 35, C11–C16 (1967).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  111. Deter, R. L. Quantitative characterization of dense body, autophagic vacuole, and acid phosphatase-bearing particle populations during the early phases of glucagon-induced autophagy in rat liver. J. Cell Biol. 48, 473–489 (1971).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  112. Shelburne, J. D., Arstila, A. U. & Trump, B. F. Studies on cellular autophagocytosis. Cyclic AMP- and dibutyryl cyclic AMP-stimulated autophagy in rat liver. Am. J. Pathol. 72, 521–540 (1973).

    CAS  PubMed  PubMed Central  Google Scholar 

  113. Adeva-Andany, M. M., Gonzalez-Lucan, M., Donapetry-Garcia, C., Fernandez-Fernandez, C. & Ameneiros-Rodriguez, E. Glycogen metabolism in humans. BBA Clin. 5, 85–100 (2016).

    Article  PubMed  PubMed Central  Google Scholar 

  114. Devos, P. & Hers, H. G. Random, presumably hydrolytic, and lysosomal glycogenolysis in the livers of rats treated with phlorizin and of newborn rats. Biochem. J. 192, 177–181 (1980).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  115. Schiaffino, S., Mammucari, C. & Sandri, M. The role of autophagy in neonatal tissues: just a response to amino acid starvation? Autophagy 4, 727–730 (2008).

    Article  CAS  PubMed  Google Scholar 

  116. Gonzalez, G. A. & Montminy, M. R. Cyclic AMP stimulates somatostatin gene transcription by phosphorylation of CREB at serine 133. Cell 59, 675–680 (1989).

    Article  CAS  PubMed  Google Scholar 

  117. Koo, S. H. et al. The CREB coactivator TORC2 is a key regulator of fasting glucose metabolism. Nature 437, 1109–1111 (2005).

    Article  CAS  PubMed  Google Scholar 

  118. Screaton, R. A. et al. The CREB coactivator TORC2 functions as a calcium- and cAMP-sensitive coincidence detector. Cell 119, 61–74 (2004).

    Article  CAS  PubMed  Google Scholar 

  119. Herzig, S. et al. CREB regulates hepatic gluconeogenesis through the coactivator PGC-1. Nature 413, 179–183 (2001).

    Article  CAS  PubMed  Google Scholar 

  120. Widlund, H. R. & Fisher, D. E. Microphthalamia-associated transcription factor: a critical regulator of pigment cell development and survival. Oncogene 22, 3035–3041 (2003).

    Article  CAS  PubMed  Google Scholar 

  121. Settembre, C. et al. TFEB links autophagy to lysosomal biogenesis. Science 332, 1429–1433 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  122. O'Rourke, E. J. & Ruvkun, G. MXL-3 and HLH-30 transcriptionally link lipolysis and autophagy to nutrient availability. Nat. Cell Biol. 15, 668–676 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  123. Lapierre, L. R. et al. The TFEB orthologue HLH-30 regulates autophagy and modulates longevity in Caenorhabditis elegans. Nat. Commun. 4, 2267 (2013).

    Article  CAS  PubMed  Google Scholar 

  124. Settembre, C. et al. TFEB controls cellular lipid metabolism through a starvation-induced autoregulatory loop. Nat. Cell Biol. 15, 647–658 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  125. Martina, J. A., Chen, Y., Gucek, M. & Puertollano, R. MTORC1 functions as a transcriptional regulator of autophagy by preventing nuclear transport of TFEB. Autophagy 8, 903–914 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  126. Roczniak-Ferguson, A. et al. The transcription factor TFEB links mTORC1 signaling to transcriptional control of lysosome homeostasis. Sci. Signal. 5, ra42 (2012).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  127. Settembre, C. et al. A lysosome-to-nucleus signalling mechanism senses and regulates the lysosome via mTOR and TFEB. EMBO J. 31, 1095–1108 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  128. Sengupta, S., Peterson, T. R., Laplante, M., Oh, S. & Sabatini, D. M. mTORC1 controls fasting-induced ketogenesis and its modulation by ageing. Nature 468, 1100–1104 (2010).

    Article  CAS  PubMed  Google Scholar 

  129. Liu, Y. et al. A fasting inducible switch modulates gluconeogenesis via activator/coactivator exchange. Nature 456, 269–273 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  130. Zhao, Y. et al. Cytosolic FoxO1 is essential for the induction of autophagy and tumour suppressor activity. Nat. Cell Biol. 12, 665–675 (2010).

    Article  CAS  PubMed  Google Scholar 

  131. Liu, H. Y. et al. Hepatic autophagy is suppressed in the presence of insulin resistance and hyperinsulinemia: inhibition of FoxO1-dependent expression of key autophagy genes by insulin. J. Biol. Chem. 284, 31484–31492 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  132. Xiong, X., Tao, R., DePinho, R. A. & Dong, X. C. The autophagy-related gene 14 (Atg14) is regulated by forkhead box O transcription factors and circadian rhythms and plays a critical role in hepatic autophagy and lipid metabolism. J. Biol. Chem. 287, 39107–39114 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  133. Lee, I. H. et al. A role for the NAD-dependent deacetylase Sirt1 in the regulation of autophagy. Proc. Natl Acad. Sci. USA 105, 3374–3379 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  134. Ezaki, J. et al. Liver autophagy contributes to the maintenance of blood glucose and amino acid levels. Autophagy 7, 727–736 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  135. Lum, J. J. et al. Growth factor regulation of autophagy and cell survival in the absence of apoptosis. Cell 120, 237–248 (2005).

    Article  CAS  PubMed  Google Scholar 

  136. Tsukamoto, S. et al. Autophagy is essential for preimplantation development of mouse embryos. Science 321, 117–120 (2008).

    Article  CAS  PubMed  Google Scholar 

  137. Onodera, J. & Ohsumi, Y. Autophagy is required for maintenance of amino acid levels and protein synthesis under nitrogen starvation. J. Biol. Chem. 280, 31582–31586 (2005).

    Article  CAS  PubMed  Google Scholar 

  138. Suzuki, S. W., Onodera, J. & Ohsumi, Y. Starvation induced cell death in autophagy-defective yeast mutants is caused by mitochondria dysfunction. PLoS ONE 6, e17412 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  139. Reczek, C. R. & Chandel, N. S. ROS-dependent signal transduction. Curr. Opin. Cell Biol. 33, 8–13 (2015).

    Article  CAS  PubMed  Google Scholar 

  140. Cardaci, S., Filomeni, G. & Ciriolo, M. R. Redox implications of AMPK-mediated signal transduction beyond energetic clues. J. Cell Sci. 125, 2115–2125 (2012).

    CAS  PubMed  Google Scholar 

  141. Filomeni, G., Desideri, E., Cardaci, S., Rotilio, G. & Ciriolo, M. R. Under the ROS...thiol network is the principal suspect for autophagy commitment. Autophagy 6, 999–1005 (2010).

    Article  CAS  PubMed  Google Scholar 

  142. Scherz-Shouval, R. et al. Reactive oxygen species are essential for autophagy and specifically regulate the activity of Atg4. EMBO J. 26, 1749–1760 (2007).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  143. Hayes, J. D. & McMahon, M. NRF2 and KEAP1 mutations: permanent activation of an adaptive response in cancer. Trends Biochem. Sci. 34, 176–188 (2009).

    Article  CAS  PubMed  Google Scholar 

  144. Taguchi, K., Motohashi, H. & Yamamoto, M. Molecular mechanisms of the Keap1–Nrf2 pathway in stress response and cancer evolution. Genes Cells 16, 123–140 (2011).

    Article  CAS  PubMed  Google Scholar 

  145. Vittorini, S. et al. The age-related accumulation of protein carbonyl in rat liver correlates with the age-related decline in liver proteolytic activities. J. Gerontol. A Biol. Sci. Med. Sci. 54, B318–B323 (1999).

    Article  CAS  PubMed  Google Scholar 

  146. Cavallini, G., Donati, A., Gori, Z., Pollera, M. & Bergamini, E. The protection of rat liver autophagic proteolysis from the age-related decline co-varies with the duration of anti-ageing food restriction. Exp. Gerontol. 36, 497–506 (2001).

    Article  CAS  PubMed  Google Scholar 

  147. Donati, A. et al. Age-related changes in the regulation of autophagic proteolysis in rat isolated hepatocytes. J. Gerontol. A Biol. Sci. Med. Sci. 56, B288–B293 (2001).

    Article  CAS  PubMed  Google Scholar 

  148. Uddin, M. N., Nishio, N., Ito, S., Suzuki, H. & Isobe, K. Autophagic activity in thymus and liver during aging. Age (Dordr.) 34, 75–85 (2012).

    Article  Google Scholar 

  149. Stoller, J. K. & Aboussouan, L. S. A review of α1-antitrypsin deficiency. Am. J. Respir. Crit. Care Med. 185, 246–259 (2012).

    Article  CAS  PubMed  Google Scholar 

  150. Carlson, J. A. et al. Multiple tissues express alpha 1-antitrypsin in transgenic mice and man. J. Clin. Invest. 82, 26–36 (1988).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  151. Carlson, J. A. et al. Accumulation of PiZ α1-antitrypsin causes liver damage in transgenic mice. J. Clin. Invest. 83, 1183–1190 (1989).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  152. Qu, D., Teckman, J. H., Omura, S. & Perlmutter, D. H. Degradation of a mutant secretory protein, alpha1-antitrypsin Z, in the endoplasmic reticulum requires proteasome activity. J. Biol Chem. 271, 22791–22795 (1996).

    Article  CAS  PubMed  Google Scholar 

  153. Teckman, J. H. et al. The proteasome participates in degradation of mutant alpha 1-antitrypsin Z in the endoplasmic reticulum of hepatoma-derived hepatocytes. J Biol. Chem. 276, 44865–44872 (2001).

    Article  CAS  PubMed  Google Scholar 

  154. Teckman, J. H. & Perlmutter, D. H. Retention of mutant α1-antitrypsin Z in endoplasmic reticulum is associated with an autophagic response. Am. J. Physiol. Gastrointest. Liver Physiol. 279, G961–G974 (2000).

    Article  CAS  PubMed  Google Scholar 

  155. Kamimoto, T. et al. Intracellular inclusions containing mutant α1-antitrypsin Z are propagated in the absence of autophagic activity. J. Biol. Chem. 281, 4467–4476 (2006).

    Article  CAS  PubMed  Google Scholar 

  156. Pastore, N. et al. Gene transfer of master autophagy regulator TFEB results in clearance of toxic protein and correction of hepatic disease in alpha-1-anti-trypsin deficiency. EMBO Mol. Med. 5, 397–412 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  157. Hidvegi, T. et al. An autophagy-enhancing drug promotes degradation of mutant α1-antitrypsin Z and reduces hepatic fibrosis. Science 329, 229–232 (2010).

    Article  CAS  PubMed  Google Scholar 

  158. US National Library of Medicine. Carbamazepine in Severe Liver Disease Due to Alpha-1 Antitrypsin Deficiency. ClinicalTrials.gov [online], (2016).

  159. Li, J. et al. Fluphenazine reduces proteotoxicity in C. elegans and mammalian models of alpha-1-antitrypsin deficiency. PLoS ONE 9, e87260 (2014).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  160. Mochida, K. et al. Receptor-mediated selective autophagy degrades the endoplasmic reticulum and the nucleus. Nature 522, 359–362 (2015).

    Article  CAS  PubMed  Google Scholar 

  161. Khaminets, A. et al. Regulation of endoplasmic reticulum turnover by selective autophagy. Nature 522, 354–358 (2015).

    Article  CAS  PubMed  Google Scholar 

  162. Fumagalli, F. et al. Translocon component Sec62 acts in endoplasmic reticulum turnover during stress recovery. Nat. Cell Biol. 18, 1173–1184 (2016).

    Article  CAS  PubMed  Google Scholar 

  163. Sveger, T. Liver disease in alpha1-antitrypsin deficiency detected by screening of 200,000 infants. N. Engl. J. Med. 294, 1316–1321 (1976).

    Article  CAS  PubMed  Google Scholar 

  164. Piitulainen, E., Carlson, J., Ohlsson, K. & Sveger, T. α1-antitrypsin deficiency in 26-year-old subjects: lung, liver, and protease/protease inhibitor studies. Chest 128, 2076–2081 (2005).

    Article  CAS  PubMed  Google Scholar 

  165. Zatloukal, K. et al. p62 Is a common component of cytoplasmic inclusions in protein aggregation diseases. Am. J. Pathol. 160, 255–263 (2002).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  166. Zatloukal, K. et al. From Mallory to Mallory–Denk bodies: what, how and why? Exp. Cell Res. 313, 2033–2049 (2007).

    Article  CAS  PubMed  Google Scholar 

  167. Aishima, S. et al. p62+ hyaline inclusions in intrahepatic cholangiocarcinoma associated with viral hepatitis or alcoholic liver disease. Am. J. Clin. Pathol. 134, 457–465 (2010).

    Article  PubMed  Google Scholar 

  168. Fukuo, Y. et al. Abnormality of autophagic function and cathepsin expression in the liver from patients with non-alcoholic fatty liver disease. Hepatol. Res. 44, 1026–1036 (2014).

    Article  CAS  PubMed  Google Scholar 

  169. Gonzalez-Rodriguez, A. et al. Impaired autophagic flux is associated with increased endoplasmic reticulum stress during the development of NAFLD. Cell Death Dis. 5, e1179 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  170. Liu, B. et al. Hepatitis B virus stimulates G6PD expression through HBx-mediated Nrf2 activation. Cell Death Dis. 6, e1980 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  171. Wang, S., Pacher, P., De Lisle, R. C., Huang, H. & Ding, W. X. A mechanistic review of cell death in alcohol-induced liver injury. Alcohol. Clin. Exp. Res. 40, 1215–1223 (2016).

    Article  PubMed  PubMed Central  Google Scholar 

  172. Ding, W. X. et al. Autophagy reduces acute ethanol-induced hepatotoxicity and steatosis in mice. Gastroenterology 139, 1740–1752 (2010).

    Article  CAS  PubMed  Google Scholar 

  173. Eid, N., Ito, Y., Maemura, K. & Otsuki, Y. Elevated autophagic sequestration of mitochondria and lipid droplets in steatotic hepatocytes of chronic ethanol-treated rats: an immunohistochemical and electron microscopic study. J. Mol. Histol 44, 311–326 (2013).

    Article  CAS  PubMed  Google Scholar 

  174. Kharbanda, K. K., McVicker, D. L., Zetterman, R. K. & Donohue, T. M. Jr. Ethanol consumption alters trafficking of lysosomal enzymes and affects the processing of procathepsin L in rat liver. Biochim. Biophys. Acta 1291, 45–52 (1996).

    Article  PubMed  Google Scholar 

  175. Kharbanda, K. K., McVicker, D. L., Zetterman, R. K., MacDonald, R. G. & Donohue, T. M. Jr. Flow cytometric analysis of vesicular pH in rat hepatocytes after ethanol administration. Hepatology 26, 929–934 (1997).

    Article  CAS  PubMed  Google Scholar 

  176. Stumptner, C., Omary, M. B., Fickert, P., Denk, H. & Zatloukal, K. Hepatocyte cytokeratins are hyperphosphorylated at multiple sites in human alcoholic hepatitis and in a mallory body mouse model. Am. J. Pathol. 156, 77–90 (2000).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  177. Sir, D. et al. The early autophagic pathway is activated by hepatitis B virus and required for viral DNA replication. Proc. Natl Acad. Sci. USA 107, 4383–4388 (2010).

    Article  PubMed  PubMed Central  Google Scholar 

  178. Li, J. et al. Subversion of cellular autophagy machinery by hepatitis B virus for viral envelopment. J. Virol. 85, 6319–6333 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  179. Tian, Y., Sir, D., Kuo, C. F., Ann, D. K. & Ou, J. H. Autophagy required for hepatitis B virus replication in transgenic mice. J. Virol. 85, 13453–13456 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  180. Luo, M. X. et al. Autophagy mediates HBx-induced nuclear factor-κB activation and release of IL-6, IL-8, and CXCL2 in hepatocytes. J. Cell. Physiol. 230, 2382–2389 (2015).

    Article  CAS  PubMed  Google Scholar 

  181. Liu, B. et al. Hepatitis B virus X protein inhibits autophagic degradation by impairing lysosomal maturation. Autophagy 10, 416–430 (2014).

    Article  CAS  PubMed  Google Scholar 

  182. Tanida, I. et al. Knockdown of autophagy-related gene decreases the production of infectious hepatitis C virus particles. Autophagy 5, 937–945 (2009).

    Article  CAS  PubMed  Google Scholar 

  183. Dreux, M., Gastaminza, P., Wieland, S. F. & Chisari, F. V. The autophagy machinery is required to initiate hepatitis C virus replication. Proc. Natl Acad. Sci. USA 106, 14046–14051 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  184. Guevin, C. et al. Autophagy protein ATG5 interacts transiently with the hepatitis C virus RNA polymerase (NS5B) early during infection. Virology 405, 1–7 (2010).

    Article  CAS  PubMed  Google Scholar 

  185. Sir, D. et al. Replication of hepatitis C virus RNA on autophagosomal membranes. J. Biol. Chem. 287, 18036–18043 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  186. Ferraris, P., Blanchard, E. & Roingeard, P. Ultrastructural and biochemical analyses of hepatitis C virus-associated host cell membranes. J. Gen. Virol. 91, 2230–2237 (2010).

    Article  CAS  PubMed  Google Scholar 

  187. Rautou, P. E. et al. Changes in autophagic response in patients with chronic hepatitis C virus infection. Am. J. Pathol. 178, 2708–2715 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  188. Farrell, G. C. & Larter, C. Z. Nonalcoholic fatty liver disease: from steatosis to cirrhosis. Hepatology 43, 99–112 (2006).

    Article  CAS  Google Scholar 

  189. Brenner, C., Galluzzi, L., Kepp, O. & Kroemer, G. Decoding cell death signals in liver inflammation. J. Hepatol. 59, 583–594 (2013).

    Article  CAS  PubMed  Google Scholar 

  190. Yoon, H. & Cha, B. S. Pathogenesis and therapeutic approaches for non-alcoholic fatty liver disease. World J. Hepatol. 6, 800–811 (2014).

    Article  PubMed  PubMed Central  Google Scholar 

  191. Yang, L., Li, P., Fu, S., Calay, E. S. & Hotamisligil, G. S. Defective hepatic autophagy in obesity promotes ER stress and causes insulin resistance. Cell Metab. 11, 467–478 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  192. Park, H. W. et al. Pharmacological correction of obesity-induced autophagy arrest using calcium channel blockers. Nat. Commun. 5, 4834 (2014).

    Article  CAS  PubMed  Google Scholar 

  193. Lin, C. W. et al. Pharmacological promotion of autophagy alleviates steatosis and injury in alcoholic and non-alcoholic fatty liver conditions in mice. J. Hepatol. 58, 993–999 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  194. Sinha, R. A. et al. Caffeine stimulates hepatic lipid metabolism by the autophagy–lysosomal pathway in mice. Hepatology 59, 1366–1380 (2014).

    Article  CAS  PubMed  Google Scholar 

  195. Sun, L. et al. Hydrogen sulfide reduces serum triglyceride by activating liver autophagy via the AMPK–mTOR pathway. Am. J. Physiol. Endocrinol. Metab. 309, E925–E935 (2015).

    Article  CAS  PubMed  Google Scholar 

  196. Harada, M., Hanada, S., Toivola, D. M., Ghori, N. & Omary, M. B. Autophagy activation by rapamycin eliminates mouse Mallory–Denk bodies and blocks their proteasome inhibitor-mediated formation. Hepatology 47, 2026–2035 (2008).

    Article  CAS  PubMed  Google Scholar 

  197. Friedman, S. L. Mechanisms of hepatic fibrogenesis. Gastroenterology 134, 1655–1669 (2008).

    Article  CAS  PubMed  Google Scholar 

  198. Hernandez-Gea, V. et al. Autophagy releases lipid that promotes fibrogenesis by activated hepatic stellate cells in mice and in human tissues. Gastroenterology 142, 938–946 (2012).

    Article  PubMed  Google Scholar 

  199. White, E. The role for autophagy in cancer. J. Clin. Invest. 125, 42–46 (2015).

    Article  PubMed  PubMed Central  Google Scholar 

  200. Rao, S. et al. A dual role for autophagy in a murine model of lung cancer. Nat. Commun. 5, 3056 (2014).

    Article  CAS  PubMed  Google Scholar 

  201. Guo, J. Y. et al. Autophagy suppresses progression of K-ras-induced lung tumors to oncocytomas and maintains lipid homeostasis. Genes Dev. 27, 1447–1461 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  202. Jiang, P. & Mizushima, N. Autophagy and human diseases. Cell Res. 24, 69–79 (2014).

    Article  CAS  PubMed  Google Scholar 

  203. Zhi, X. & Zhong, Q. Autophagy in cancer. F1000Prime Rep. 7, 18 (2015).

    Article  PubMed  PubMed Central  Google Scholar 

  204. Rosenfeldt, M. T. et al. p53 status determines the role of autophagy in pancreatic tumour development. Nature 504, 296–300 (2013).

    Article  CAS  PubMed  Google Scholar 

  205. Inami, Y. et al. Persistent activation of Nrf2 through p62 in hepatocellular carcinoma cells. J. Cell Biol. 193, 275–284 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  206. Takamura, A. et al. Autophagy-deficient mice develop multiple liver tumors. Genes Dev. 25, 795–800 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  207. Qu, X. et al. Promotion of tumorigenesis by heterozygous disruption of the beclin 1 autophagy gene. J. Clin. Invest. 112, 1809–1820 (2003).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  208. Yue, Z., Jin, S., Yang, C., Levine, A. J. & Heintz, N. Beclin 1, an autophagy gene essential for early embryonic development, is a haploinsufficient tumor suppressor. Proc. Natl Acad. Sci. USA 100, 15077–15082 (2003).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  209. Ni, H. M. et al. Nrf2 promotes the development of fibrosis and tumorigenesis in mice with defective hepatic autophagy. J. Hepatol. 61, 617–625 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  210. Li, L. et al. SQSTM1 is a pathogenic target of 5q copy number gains in kidney cancer. Cancer Cell 24, 738–750 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  211. Ling, J. et al. KrasG12D-induced IKK2/β/NF-κB activation by IL-1α and p62 feedforward loops is required for development of pancreatic ductal adenocarcinoma. Cancer Cell 21, 105–120 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  212. Duran, A. et al. The signaling adaptor p62 is an important NF-κB mediator in tumorigenesis. Cancer Cell 13, 343–354 (2008).

    Article  CAS  PubMed  Google Scholar 

  213. Gjyshi, O. et al. Kaposi's sarcoma-associated herpesvirus induces Nrf2 activation in latently infected endothelial cells through SQSTM1 phosphorylation and interaction with polyubiquitinated Keap1. J. Virol. 89, 2268–2286 (2015).

    Article  CAS  PubMed  Google Scholar 

  214. Russell, R. C., Yuan, H. X. & Guan, K. L. Autophagy regulation by nutrient signaling. Cell Res. 24, 42–57 (2014).

    Article  CAS  PubMed  Google Scholar 

  215. Kenerson, H. L., Subramanian, S., McIntyre, R., Kazami, M. & Yeung, R. S. Livers with constitutive mTORC1 activity resist steatosis independent of feedback suppression of Akt. PLoS ONE 10, e0117000 (2015).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  216. Kenerson, H. L. et al. Akt and mTORC1 have different roles during liver tumorigenesis in mice. Gastroenterology 144, 1055–1065 (2013).

    Article  CAS  PubMed  Google Scholar 

  217. Sporn, M. B. & Liby, K. T. NRF2 and cancer: the good, the bad and the importance of context. Nat. Rev. Cancer 12, 564–571 (2012).

    Article  CAS  PubMed  Google Scholar 

  218. Totoki, Y. et al. Trans-ancestry mutational landscape of hepatocellular carcinoma genomes. Nat. Genet. 46, 1267–1273 (2014).

    Article  CAS  PubMed  Google Scholar 

  219. Cancer Genome Atlas Research Network. Comprehensive genomic characterization of squamous cell lung cancers. Nature 489, 519–525 (2012).

  220. Adam, J. et al. Renal cyst formation in Fh1-deficient mice is independent of the Hif/Phd pathway: roles for fumarate in KEAP1 succination and Nrf2 signaling. Cancer Cell 20, 524–537 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  221. Ooi, A. et al. An antioxidant response phenotype shared between hereditary and sporadic type 2 papillary renal cell carcinoma. Cancer Cell 20, 511–523 (2011).

    Article  CAS  PubMed  Google Scholar 

  222. Mitsuishi, Y. et al. Nrf2 redirects glucose and glutamine into anabolic pathways in metabolic reprogramming. Cancer Cell 22, 66–79 (2012).

    Article  CAS  PubMed  Google Scholar 

  223. Saito, T. et al. p62/Sqstm1 promotes malignancy of HCV-positive hepatocellular carcinoma through Nrf2-dependent metabolic reprogramming. Nat. Commun. 7, 12030 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  224. Umemura, A. et al. p62, upregulated during preneoplasia, induces hepatocellular carcinogenesis by maintaining survival of stressed HCC-initiating cells. Cancer Cell 29, 935–948 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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Acknowledgements

We apologize to authors whose work could not be cited because of space limitations. M.K. is supported by a Grant-in-Aid for Scientific Research on Innovative Areas (25111006 and 25111001), a Grant-in-Aid for Scientific Research (A) (26253019) and the Japan Society for the Promotion of Science (an A3 Foresight Program). M.K. and T.U. are both supported by the Takeda Science Foundation.

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Ueno, T., Komatsu, M. Autophagy in the liver: functions in health and disease. Nat Rev Gastroenterol Hepatol 14, 170–184 (2017). https://doi.org/10.1038/nrgastro.2016.185

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