Abstract
Autophagy is a homeostatic process that enables eukaryotic cells to deliver cytoplasmic constituents for lysosomal degradation, to recycle nutrients and to survive during starvation. In addition to these primordial functions, autophagy has emerged as a key mechanism in orchestrating innate and adaptive immune responses to intracellular pathogens. Autophagy restricts viral infections as well as replication of intracellular bacteria and parasites and delivers pathogenic determinants for TLR stimulation and for MHC class II presentation to the adaptive immune system. Apart from its role in defense against pathogens, autophagy-mediated presentation of self-antigens in the steady state could have a crucial role in the induction and maintenance of CD4+ T-cell tolerance. This review describes the mechanisms by which the immune system utilizes autophagic degradation of cytoplasmic material to regulate adaptive immune responses.
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Abbreviations
- CMA:
-
chaperone-mediated autophagy
- Atg:
-
autophagy-related gene
- TLR:
-
Toll-like receptor
- TNF:
-
tumor necrosis factor
- MHC:
-
major histocompatibility complex
- DRiPs:
-
defective ribosomal products
- TAP:
-
transporter associated with antigen processing
- Ii:
-
invariant chain
- CLIP:
-
class II-associated Ii peptide
- APC:
-
antigen-presenting cell
- MIIC:
-
MHC class II containing compartment
- HLA:
-
human leukocyte antigen
- DC:
-
dendritic cell
- EBV:
-
Epstein–Barr virus
- LAMP:
-
lysosome-associated membrane protein
References
Ciechanover A, Finley D, Varshavsky A . Ubiquitin dependence of selective protein degradation demonstrated in the mammalian cell cycle mutant ts85. Cell 1984; 37: 57–66.
De Duve C, Wattiaux R . Functions of lysosomes. Annu Rev Physiol 1966; 28: 435–492.
Henell F, Berkenstam A, Ahlberg J, Glaumann H . Degradation of short- and long-lived proteins in perfused liver and in isolated autophagic vacuoles – lysosomes. Exp Mol Pathol 1987; 46: 1–14.
Mizushima N, Levine B, Cuervo AM, Klionsky DJ . Autophagy fights disease through cellular self-digestion. Nature 2008; 451: 1069–1075.
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.
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.
Lünemann JD, Schmidt J, Schmid D, Barthel K, Wrede A, Dalakas MC et al. Beta-amyloid is a substrate of autophagy in sporadic inclusion body myositis. Ann Neurol 2007; 61: 476–483.
Martinez-Vicente M, Cuervo AM . Autophagy and neurodegeneration: when the cleaning crew goes on strike. Lancet Neurol 2007; 6: 352–361.
Cuervo AM, Dice JF . A receptor for the selective uptake and degradation of proteins by lysosomes. Science 1996; 273: 501–503.
Cuervo AM, Dice JF . Unique properties of lamp2a compared to other lamp2 isoforms. J Cell Sci 2000; 113 (Part 24): 4441–4450.
Agarraberes FA, Dice JF . A molecular chaperone complex at the lysosomal membrane is required for protein translocation. J Cell Sci 2001; 114 (Part 13): 2491–2499.
Fengsrud M, Erichsen ES, Berg TO, Raiborg C, Seglen PO . Ultrastructural characterization of the delimiting membranes of isolated autophagosomes and amphisomes by freeze-fracture electron microscopy. Eur J Cell Biol 2000; 79: 871–882.
Stromhaug PE, Berg TO, Fengsrud M, Seglen PO . Purification and characterization of autophagosomes from rat hepatocytes. Biochem J 1998; 335 (Part 2): 217–224.
Ohsumi Y . Molecular dissection of autophagy: two ubiquitin-like systems. Nat Rev Mol Cell Biol 2001; 2: 211–216.
Mizushima N, Klionsky DJ . Protein turnover via autophagy: implications for metabolism. Annu Rev Nutr 2007; 27: 19–40.
Klionsky DJ . Autophagy: from phenomenology to molecular understanding in less than a decade. Nat Rev Mol Cell Biol 2007; 8: 931–937.
Kabeya Y, Mizushima N, Ueno T, Yamamoto A, Kirisako T, Noda T et al. LC3, a mammalian homologue of yeast Apg8p, is localized in autophagosome membranes after processing. EMBO J 2000; 19: 5720–5728.
Tanida I, Minematsu-Ikeguchi N, Ueno T, Kominami E . Lysosomal turnover, but not a cellular level, of endogenous LC3 is a marker for autophagy. Autophagy 2005; 1: 84–91.
Schmid D, Pypaert M, Münz C . Antigen-loading compartments for major histocompatibility complex class II molecules continuously receive input from autophagosomes. Immunity 2007; 26: 79–92.
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.
Nakagawa I, Amano A, Mizushima N, Yamamoto A, Yamaguchi H, Kamimoto T et al. Autophagy defends cells against invading group A Streptococcus. Science 2004; 306: 1037–1040.
Gutierrez MG, Master SS, Singh SB, Taylor GA, Colombo MI, Deretic V . Autophagy is a defense mechanism inhibiting BCG and Mycobacterium tuberculosis survival in infected macrophages. Cell 2004; 119: 753–766.
Singh SB, Davis AS, Taylor GA, Deretic V . Human IRGM induces autophagy to eliminate intracellular mycobacteria. Science 2006; 313: 1438–1441.
Lee HK, Lund JM, Ramanathan B, Mizushima N, Iwasaki A . Autophagy-dependent viral recognition by plasmacytoid dendritic cells. Science 2007; 315: 1398–1401.
Xu Y, Jagannath C, Liu XD, Sharafkhaneh A, Kolodziejska KE, Eissa NT . Toll-like receptor 4 is a sensor for autophagy associated with innate immunity. Immunity 2007; 27: 135–144.
Delgado MA, Elmaoued RA, Davis AS, Kyei G, Deretic V . Toll-like receptors control autophagy. EMBO J 2008; 27: 1110–1121.
Orvedahl A, Alexander D, Talloczy Z, Sun Q, Wei Y, Zhang W et al. HSV-1 ICP34.5 confers neurovirulence by targeting the Beclin 1 autophagy protein. Cell Host Microbe 2007; 1: 23–35.
Talloczy Z, Jiang W, Virgin HWt, Leib DA, Scheuner D, Kaufman RJ et al. Regulation of starvation- and virus-induced autophagy by the eIF2alpha kinase signaling pathway. Proc Natl Acad Sci USA 2002; 99: 190–195.
Taylor GA, Feng CG, Sher A . p47 GTPases: regulators of immunity to intracellular pathogens. Nat Rev Immunol 2004; 4: 100–109.
Djavaheri-Mergny M, Amelotti M, Mathieu J, Besancon F, Bauvy C, Souquere S et al. NF-kappaB activation represses tumor necrosis factor-alpha-induced autophagy. J Biol Chem 2006; 281: 30373–30382.
Mills KR, Reginato M, Debnath J, Queenan B, Brugge JS . Tumor necrosis factor-related apoptosis-inducing ligand (TRAIL) is required for induction of autophagy during lumen formation in vitro. Proc Natl Acad Sci USA 2004; 101: 3438–3443.
Thorburn J, Moore F, Rao A, Barclay WW, Thomas LR, Grant KW et al. Selective inactivation of a Fas-associated death domain protein (FADD)-dependent apoptosis and autophagy pathway in immortal epithelial cells. Mol Biol Cell 2005; 16: 1189–1199.
Andrade RM, Wessendarp M, Gubbels MJ, Striepen B, Subauste CS . CD40 induces macrophage anti-Toxoplasma gondii activity by triggering autophagy-dependent fusion of pathogen-containing vacuoles and lysosomes. J Clin Invest 2006; 116: 2366–2377.
Zwart W, Griekspoor A, Kuijl C, Marsman M, van Rheenen J, Janssen H et al. Spatial separation of HLA-DM/HLA-DR interactions within MIIC and phagosome-induced immune escape. Immunity 2005; 22: 221–233.
Brazil MI, Weiss S, Stockinger B . Excessive degradation of intracellular protein in macrophages prevents presentation in the context of major histocompatibility complex class II molecules. Eur J Immunol 1997; 27: 1506–1514.
Dengjel J, Schoor O, Fischer R, Reich M, Kraus M, Muller M et al. Autophagy promotes MHC class II presentation of peptides from intracellular source proteins. Proc Natl Acad Sci USA 2005; 102: 7922–7927.
Dorfel D, Appel S, Grunebach F, Weck MM, Muller MR, Heine A et al. Processing and presentation of HLA class I and II epitopes by dendritic cells after transfection with in vitro-transcribed MUC1 RNA. Blood 2005; 105: 3199–3205.
Nimmerjahn F, Milosevic S, Behrends U, Jaffee EM, Pardoll DM, Bornkamm GW et al. Major histocompatibility complex class II-restricted presentation of a cytosolic antigen by autophagy. Eur J Immunol 2003; 33: 1250–1259.
Paludan C, Schmid D, Landthaler M, Vockerodt M, Kube D, Tuschl T et al. Endogenous MHC class II processing of a viral nuclear antigen after autophagy. Science 2005; 307: 593–596.
Zhou D, Li P, Lin Y, Lott JM, Hislop AD, Canaday DH et al. Lamp-2a facilitates MHC class II presentation of cytoplasmic antigens. Immunity 2005; 22: 571–581.
Kroemer G, Jaattela M . Lysosomes and autophagy in cell death control. Nat Rev Cancer 2005; 5: 886–897.
Wang Y, Singh R, Massey AC, Kane SS, Kaushik S, Grant T et al. Loss of macroautophagy promotes or prevents fibroblast apoptosis depending on the death stimulus. J Biol Chem 2008; 283: 4766–4777.
Pua HH, Dzhagalov I, Chuck M, Mizushima N, He YW . A critical role for the autophagy gene Atg5 in T cell survival and proliferation. J Exp Med 2007; 204: 25–31.
Li C, Capan E, Zhao Y, Zhao J, Stolz D, Watkins SC et al. Autophagy is induced in CD4+ T cells and important for the growth factor-withdrawal cell death. J Immunol 2006; 177: 5163–5168.
Espert L, Denizot M, Grimaldi M, Robert-Hebmann V, Gay B, Varbanov M et al. Autophagy is involved in T cell death after binding of HIV-1 envelope proteins to CXCR4. J Clin Invest 2006; 116: 2161–2172.
Miller BC, Zhao Z, Stephenson LM, Cadwell K, Pua HH, Lee HK et al. The autophagy gene ATG5 plays an essential role in B lymphocyte development. Autophagy 2008; 4: 309–314.
Jacobson S, Sekaly RP, Jacobson CL, McFarland HF, Long EO . HLA class II-restricted presentation of cytoplasmic measles virus antigens to cytotoxic T cells. J Virol 1989; 63: 1756–1762.
Jaraquemada D, Marti M, Long EO . An endogenous processing pathway in vaccinia virus-infected cells for presentation of cytoplasmic antigens to class II-restricted T cells. J Exp Med 1990; 72: 947–954.
Nuchtern JG, Biddison WE, Klausner RD . Class II MHC molecules can use the endogenous pathway of antigen presentation. Nature 1990; 343: 74–76.
Gueguen M, Long EO . Presentation of a cytosolic antigen by major histocompatibility complex class II molecules requires a long-lived form of the antigen. Proc Natl Acad Sci USA 1996; 93: 14692–14697.
Aichinger G, Karlsson L, Jackson MR, Vestberg M, Vaughan JH, Teyton L et al. Major histocompatibility complex class II-dependent unfolding, transport, and degradation of endogenous proteins. J Biol Chem 1997; 272: 29127–29136.
Malnati MS, Marti M, LaVaute T, Jaraquemada D, Biddison W, DeMars R et al. Processing pathways for presentation of cytosolic antigen to MHC class II-restricted T cells. Nature 1992; 357: 702–704.
Chen M, Shirai M, Liu Z, Arichi T, Takahashi H, Nishioka M . Efficient class II major histocompatibility complex presentation of endogenously synthesized hepatitis C virus core protein by Epstein-Barr virus-transformed B-lymphoblastoid cell lines to CD4+ T cells. J Virol 1998; 72: 8301–8308.
Lich JD, Elliott JF, Blum JS . Cytoplasmic processing is a prerequisite for presentation of an endogenous antigen by major histocompatibility complex class II proteins. J Exp Med 2000; 191: 1513–1524.
Dongre AR, Kovats S, deRoos P, McCormack AL, Nakagawa T, Paharkova-Vatchkova V et al. In vivo MHC class II presentation of cytosolic proteins revealed by rapid automated tandem mass spectrometry and functional analyses. Eur J Immunol 2001; 31: 1485–1494.
Suri A, Walters JJ, Rohrs HW, Gross ML, Unanue ER . First signature of islet beta-cell-derived naturally processed peptides selected by diabetogenic class II MHC molecules. J Immunol 2008; 180: 3849–3856.
Bonifaz LC, Arzate S, Moreno J . Endogenous and exogenous forms of the same antigen are processed from different pools to bind MHC class II molecules in endocytic compartments. Eur J Immunol 1999; 29: 119–131.
Qi L, Rojas JM, Ostrand-Rosenberg S . Tumor cells present MHC class II-restricted nuclear and mitochondrial antigens and are the predominant antigen presenting cells in vivo. J Immunol 2000; 165: 5451–5461.
Mukherjee P, Dani A, Bhatia S, Singh N, Rudensky AY, George A et al. Efficient presentation of both cytosolic and endogenous transmembrane protein antigens on MHC class II is dependent on cytoplasmic proteolysis. J Immunol 2001; 167: 2632–2641.
Oukka M, Cohen-Tannoudji M, Tanaka Y, Babinet C, Kosmatopoulos K . Medullary thymic epithelial cells induce tolerance to intracellular proteins. J Immunol 1996; 156: 968–975.
Oukka M, Colucci-Guyon E, Tran PL, Cohen-Tannoudji M, Babinet C, Lotteau V et al. CD4 T cell tolerance to nuclear proteins induced by medullary thymic epithelium. Immunity 1996; 4: 545–553.
Dani A, Chaudhry A, Mukherjee P, Rajagopal D, Bhatia S, George A et al. The pathway for MHCII-mediated presentation of endogenous proteins involves peptide transport to the endo-lysosomal compartment. J Cell Sci 2004; 117 (Part 18): 4219–4230.
Weiss S, Bogen B . MHC class II-restricted presentation of intracellular antigen. Cell 1991; 64: 767–776.
Wang RF, Wang X, Atwood AC, Topalian SL, Rosenberg SA . Cloning genes encoding MHC class II-restricted antigens: mutated CDC27 as a tumor antigen. Science 1999; 284: 1351–1354.
Rammensee H, Bachmann J, Emmerich NP, Bachor OA, Stevanovic S . SYFPEITHI: database for MHC ligands and peptide motifs. Immunogenetics 1999; 50: 213–219.
Chicz RM, Urban RG, Gorga JC, Vignali DA, Lane WS, Strominger JL . Specificity and promiscuity among naturally processed peptides bound to HLA-DR alleles. J Exp Med 1993; 178: 27–47.
Friede T, Gnau V, Jung G, Keilholz W, Stevanovic S, Rammensee HG . Natural ligand motifs of closely related HLA-DR4 molecules predict features of rheumatoid arthritis associated peptides. Biochim Biophys Acta 1996; 1316: 85–101.
Aniento F, Roche E, Cuervo AM, Knecht E . Uptake and degradation of glyceraldehyde-3-phosphate dehydrogenase by rat liver lysosomes. J Biol Chem 1993; 268: 10463–10470.
Münz C, Bickham KL, Subklewe M, Tsang ML, Chahroudi A, Kurilla MG et al. Human CD4+ T lymphocytes consistently respond to the latent Epstein-Barr virus nuclear antigen EBNA1. J Exp Med 2000; 191: 1649–1660.
Starr TK, Jameson SC, Hogquist KA . Positive and negative selection of T cells. Annu Rev Immunol 2003; 21: 139–176.
Steinman RM, Hawiger D, Nussenzweig MC . Tolerogenic dendritic cells. Annu Rev Immunol 2003; 21: 685–711.
Lee JW, Epardaud M, Sun J, Becker JE, Cheng AC, Yonekura AR et al. Peripheral antigen display by lymph node stroma promotes T cell tolerance to intestinal self. Nat Immunol 2007; 8: 181–190.
Mizushima N, Yamamoto A, Matsui M, Yoshimori T, Ohsumi Y . In vivo analysis of autophagy in response to nutrient starvation using transgenic mice expressing a fluorescent autophagosome marker. Mol Biol Cell 2004; 15: 1101–1111.
Hampe J, Franke A, Rosenstiel P, Till A, Teuber M, Huse K et al. A genome-wide association scan of nonsynonymous SNPs identifies a susceptibility variant for Crohn disease in ATG16L1. Nat Genet 2007; 39: 207–211.
Rioux JD, Xavier RJ, Taylor KD, Silverberg MS, Goyette P, Huett A et al. Genome-wide association study identifies new susceptibility loci for Crohn's disease and implicates autophagy in disease pathogenesis. Nat Genet 2007; 39: 596–604.
Prescott NJ, Fisher SA, Franke A, Hampe J, Onnie CM, Soars D et al. A nonsynonymous SNP in ATG16L1 predisposes to ileal Crohn's disease and is independent of CARD15 and IBD5. Gastroenterology 2007; 132: 1665–1671.
Parkes M, Barrett JC, Prescott NJ, Tremelling M, Anderson CA, Fisher SA et al. Sequence variants in the autophagy gene IRGM and multiple other replicating loci contribute to Crohn's disease susceptibility. Nat Genet 2007; 39: 830–832.
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.
Bratton DL, Henson PM . Autoimmunity and apoptosis: refusing to go quietly. Nat Med 2005; 11: 26–27.
Acknowledgements
JDL is a recipient of the Dana Foundation and Irvington Institute's Human Immunology Fellowship from the Cancer Research Institute and is supported by a Pilot Grant from the National Multiple Sclerosis Society (PP1145) and an Institutional Clinical and Translational Science Pilot and Collaborative Project Grant (to the Rockefeller University Hospital). CM is supported by the Dana Foundation's Neuroimmunology program, the Arnold and Mabel Beckman Foundation, the Alexandrine and Alexander Sinsheimer Foundation, the Burroughs Wellcome Fund, the Starr Foundation, the National Cancer Institute (R01CA108609 and R01CA101741), the National Institute of Allergy and Infectious Diseases (RFP-NIH-NIAID-DAIDS-BAA-06-19), the Foundation for the National Institutes of Health (Grand Challenges in Global Health), and an Institutional Clinical and Translational Science Award (to the Rockefeller University Hospital).
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Lünemann, J., Münz, C. Autophagy in CD4+ T-cell immunity and tolerance. Cell Death Differ 16, 79–86 (2009). https://doi.org/10.1038/cdd.2008.113
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