Autophagy: A Lysosome-Dependent Process with Implications in Cellular Redox Homeostasis and Human Disease

Abstract

Significance: Autophagy, a lysosome-dependent homeostatic process inherent to cells and tissues, has emerging significance in the pathogenesis of human disease. This process enables the degradation and turnover of cytoplasmic substrates via membrane-dependent sequestration in autophagic vesicles (autophagosomes) and subsequent lysosomal delivery of cargo. Recent Advances: Selective forms of autophagy can target specific substrates (e.g., organelles, protein aggregates, and lipids) for processing. Autophagy is highly regulated by oxidative stress, including exposure to altered oxygen tension, by direct and indirect mechanisms, and contributes to inducible defenses against oxidative stress. Mitochondrial autophagy (mitophagy) plays a critical role in the oxidative stress response, through maintenance of mitochondrial integrity.

Critical issues: Autophagy can impact a number of vital cellular processes including inflammation and adaptive immunity, host defense, lipid metabolism and storage, mitochondrial homeostasis, and clearance of aggregated proteins, all which may be of significance in human disease. Autophagy can exert both maladaptive and adaptive roles in disease pathogenesis, which may also be influenced by autophagy impairment. This review highlights the essential roles of autophagy in human diseases, with a focus on diseases in which oxidative stress or inflammation play key roles, including human lung, liver, kidney and heart diseases, metabolic diseases, and diseases of the cardiovascular and neural systems.

Future directions: Investigations that further elucidate the complex role of autophagy in the pathogenesis of disease will facilitate targeting this pathway for therapies in specific diseases.

Keywords: autophagy; lysosome; mitophagy; oxidative stress; selective autophagy.

FIG. 1.

Molecular regulation of autophagy. The autophagy pathway progresses through a series of sequential steps: (A) Initiation (formation of the isolation membrane) (upper panel). Growth factors or nutrient signals stimulate mTORC1, whereas starvation, ROS, or hyperoxia inhibit mTORC1 activity. mTORC1 inhibition leads to activation of ULK1. ULK1 resides in a macromolecular complex containing various regulatory proteins: FIP200, ATG13, and ATG101. Formation of the isolation membrane requires the Beclin 1 macromolecular complex, which includes VPS34/PIK3C3, p150/Vps15, and ATG14L. ULK1 positively regulates autophagy by activating Beclin1 via phosphorylation of Beclin1 or ATG14L. UVRAG can exchange for ATG14L. AMBRA-1 positively whereas BCL2 negatively regulates the Beclin1 complex. Bif-1 acts as a positive whereas Rubicon acts as a negative regulator of Beclin1–UVRAG complex. VPS34 activity generates PI3P, which promotes the formation of the isolation membrane. ATG9 also facilitates lipid recruitment to the nascent autophagosome membrane. (B) Elongation and maturation of the phagophore to form autophagosomes (lower panel). PI3P recruits regulatory proteins, including DFCP1 and WIPI, to the phagophore. The elongation of the phagophore involves two ubiquitin-like conjugation systems: (i) ATG5–ATG12 conjugation system. ATG12 is conjugated to ATG5 by ATG7 (E1 ubiquitin activating enzyme-like) and Atg10 (E2 ubiquitin-conjugase-like) enzymes. ATG5–ATG12 complex associates with Atg16L1 with the assistance of VAMP7. (ii) LC3/ATG8 conjugation system, ATG4B endopeptidase cleaves pro-LC3 to generate LC3B-I. Conjugation of PE with LC3-I is catalyzed by Atg7 (E1-like) and Atg3 (E2-like) activities. Both conjugation systems are involved in autophagosome formation. Rab7 in its GTP bound form also regulates the maturation of autophagosome. The HOPS-tethering complex that includes VPS33A and VPS16 promotes autophagosome–lysosome fusion through interaction with the autophagosomal Qa-SNARE, syntaxin-17 (STX-17). STX-17 is localized on the outer membrane of the mature autophagosome, interacts with ATG14L and SNAP29. The SNARE complex involved in autophagosome–lysosome fusion is composed of STX-17, SNAP29, and VAMP8. LAMP-2A helps in recruitment of STX-17. The fusion results in cargo degradation by lysosomal acid hydrolases and recycling of nutrients through lysosomal efflux permeases. AMBRA-1, autophagy/Beclin 1 regulator; ATG, autophagy-related; Bif-1, Bax-interacting factor-1; DFCP1, double FYVE-containing protein-1; ER, endoplasmic reticulum; FIP200, focal adhesion kinase family interacting protein of 200 kDa; HOPS, homotypic fusion and protein sorting; LAMP-2A, lysosome-associated membrane protein-2A; LC3B, microtubule-associated protein-1 light chain 3B; mTOR, mechanistic/mammalian target of rapamycin; mTORC1, mTOR complex 1; PE, phosphatidylethanolamine; PI3P, phosphatidylinositol-3-phosphate; PIK3C3, phosphatidylinositol 3-kinase Class III; ROS, reactive oxygen species; Rubicon, run-domain Beclin-1 interacting and cysteine-rich containing protein; SNARE, soluble N-ethylmaleimide-sensitive factor attachment receptor; STX-17, syntaxin-17; ULK1, unc-51-like autophagy activating kinase-1; UVRAG, ultraviolet radiation resistance-associated gene protein; VPS, vacuolar protein sorting; WIPI, WD-repeat protein interacting with phosphoinositides. To see this illustration in color, the reader is referred to the web version of this article at www.liebertpub.com/ars

FIG. 2.

Signaling pathways and cross talk between autophagy, apoptosis, and necroptosis. Autophagy is a cellular homeostatic program associated with cell survival, which can interact with the major programmed cell death pathways (i.e., apoptosis and necroptosis). Both autophagy and apoptosis can be triggered in response to cellular stress or nutrient deprivation. Apoptosis is activated by extrinsic signals (e.g., binding of TNF-α, FASL, or TRAIL to the death receptor) or intrinsic stimuli (e.g., BH3-only protein-induced release of Cyt c by mitochondria). Internalization of TNF-α by the death receptor (TNFR1) stimulates the formation of the cytoplasmic DISC and subsequent activation of caspase 8. DISC formation involves recruitment of FADD, TRADD, and RIP1. Caspase 8 plays a critical role in both apoptosis and necroptosis. Caspase 8 cleaves Bid into t-Bid and promotes apoptosome formation by activation of caspase 7 and caspase 3. In addition, intrinsic stimuli induce MOMP and release of apoptotic mediators including Cyt c, which promotes caspase 9-dependent activation of caspase 7 and caspase 3. These signaling events culminate in DNA fragmentation associated with apoptosis. The cross talk between apoptosis and autophagy includes inhibition of Beclin 1 by apoptotic proteins Bcl-2 and Bcl-XL. The cleaved c-terminal portion of Beclin 1 triggers apoptotic signaling events in mitochondria. The proteolytic cleavage of caspase 8 from the complex containing RIP1, RIP3, TRADD, and FADD induces the formation of the RIP1–RIP3 necrosome complex. This complex phosphorylates (activates) mixed lineage kinase domain-like protein (MLKL) and promotes necroptosis. The relationship between autophagy and necroptosis remains incompletely understood. SIRT2 (orthologues of silent information regulator) promotes RIP1–RIP3 complex formation by deacetylation of RIP1. However, in response to oxidative stress, the transcription factor FOXO1 dissociates from SIRT2 and, in its acetylated form, stimulates autophagy through binding to ATG7. Cyt c, cytochrome c; DISC, death-inducing signaling complex; FADD, FAS-associated protein with death domain; MOMP, mitochondrial outer membrane permeabilization; RIP, receptor-interacting protein; SIRT2, Sirtuin 2; TNF-α, tumor necrosis factor-alpha; TNFR1, TNF receptor 1; TRADD, TNFR1-associated death domain protein . To see this illustration in color, the reader is referred to the web version of this article at www.liebertpub.com/ars

FIG. 3.

Selective autophagy mediates the removal of dysfunctional or superfluous organelles, protein aggregates, accumulated glycogen, lipid droplets, or defective ribosomes, and contributes in maintaining cellular quality control, organelle function, and promotes cell survival under oxidative stress conditions. Mitophagy exerts protective functions in various diseases by removing dysfunctional mitochondria and suppressing mtROS-induced mtDNA damage. Aggrephagy removes aggregates of oxidized or misfolded proteins, and its impairment leading to the accumulation of protein aggregates has been implicated in disorders such as neurodegenerative diseases. Lipophagy removes lipid droplets, and its impairment has been associated with diseases such as atherosclerosis and hepatic steatosis. Glycophagy degrades accumulated glycogen, which is potentially important in diabetes. Xenophagy assists in immune responses by promoting clearance of foreign pathogens such as bacteria and viruses. ERphagy removes aggregate-prone proteins from the ER membrane. ERphagy may limit unfolded protein-induced ER stress responses. Pexophagy suppresses peroxisomal ROS production by recycling damaged peroxisomes. Ribophagy assists in the removal of nonfunctional ribosomes. Inflammasomophagy involves targeted destruction of inflammasomes either through binding of p62 to the ubiquitylated ASC subunit or via recognition of Nod like receptor protein−1 (NLRP1) or NLRP3 by TRIM20. TRIM20 promotes autophagy by recruiting ULK1, Beclin1, and ATG8 complexes. Nucleophagy involves autophagy-mediated degradation of nucleus or its components. The LC3/Atg8 conjugation system binds and degrades nuclear lamina protein lamin B1 during tumorigenic stress, such as by activated oncogenes. Ferritinophagy may contribute to the maintenance of iron homeostasis by shuttling of iron-bound ferritin to the lysosome for recycling. ASC, apoptosis-associated speck-like protein containing caspase-recruitment domain; ER, endoplasmic reticulum; mtDNA, mitochondrial DNA; mtROS, mitochondria-derived reactive oxygen species; NLRP, Nod like receptor protein; p62, sequestosome; TRIM20, tripartite motif-containing 20; UB, ubiquitin. To see this illustration in color, the reader is referred to the web version of this article at www.liebertpub.com/ars

FIG. 4.

Mechanisms of mitochondrial autophagy (mitophagy). Mitophagy can proceed via PINK1/Parkin-dependent and independent pathways. In the PINK1/Parkin-dependent pathway, healthy mitochondria permit PINK1 (a serine/threonine kinase) into the IMM via TOM and TIM-23 proteins. The matrix metalloprotease of mitochondria cleaves the MTS of PINK1. However, during severe oxidative stress, impaired mitochondria with declining mitochondrial membrane potential fail to import PINK1 into the IMM. Under these conditions, PINK1 associates with TOM and accumulates on the OMM. PINK1 promotes the recruitment and activation of Parkin from the cytoplasm to the OMM. Parkin ubiquitinates various OMM proteins (e.g., mitofusin 1 and mitofusin 2, VDAC, and Miro). Subsequently, p62, a cargo adaptor protein, recognizes and binds to the ubiquitinated OMM proteins. Finally, p62 binds with LC3B and promotes autophagosome formation. PINK1/Parkin-independent mitophagy involves interaction of LC3B with OMM proteins: FUNDC1, Nix/Bnip3L, and Bnip3 through the LIR. This results in removal of mitochondria through mitophagy. Bnip3, Bcl-2/adenovirus E1B 19 kDa-interacting protein-3; FUNDC1, FUN14 domain containing 1; IMM, inner mitochondrial membrane; LIR, LC3-interacting region; MTS, mitochondral targeting signal; Nix/Bnip3L, NIP3-like protein X; OMM, outer mitochondrial membrane; PINK1, phosphatase and tensin homologue deleted in chromosome 10 (PTEN)-induced putative kinase 1; TIM, translocase of inner membrane; TOM, translocase of outer membrane; VDAC, voltage-dependent anion channel. To see this illustration in color, the reader is referred to the web version of this article at www.liebertpub.com/ars

FIG. 5.

Interaction of autophagy with the Nrf2-mediated antioxidant response. Under basal conditions, Nrf2 is bound to its repressor, the E3 ubiquitin ligase adaptor protein, Keap1. Keap1 promotes Nrf2 ubiquitylation and proteasomal-mediated degradation. During oxidative stress, increases in autophagic flux promote p62-mediated sequestration and degradation of Keap1. Keap1 can also be degraded by oxidation of its thiol group. Nrf2 that dissociates from Keap1 remains activated and translocates to the nucleus, where it binds with small MAF (musculoaponeurotic-fibrosarcoma virus) proteins. The heterodimer of Nrf2–MAF binds to the promoter regions of target genes via the antioxidant response element and positively regulates gene transcription. In addition to regulation of antioxidant genes, Nrf2 may regulate the transcription of p62, a protein involved in cargo recognition. Keap1, Kelch-like ECH-associated protein 1; Nrf2, nuclear factor erythroid 2-related factor 2. To see this illustration in color, the reader is referred to the web version of this article at www.liebertpub.com/ars

FIG. 6.

Autophagy in human diseases. Autophagy plays a complex role in a growing number of human diseases. Scheme of organ-specific pathologies is shown in which alterations in autophagy are discussed in this review, including diseases of the brain, heart, lung, liver, kidney, and pancreas. Both protective and pathogenic roles for autophagy have been proposed in these diseases. Autophagy may modulate disease pathogenesis through selective pathways, which include the preservation of mitochondrial homeostasis through mitophagy, the clearance of aggregated or mutant proteins through aggrephagy, the clearance of cellular substrates such as collagen or glycogen, and the clearance of pathogenic bacteria or viruses through xenophagy. To see this illustration in color, the reader is referred to the web version of this article at www.liebertpub.com/ars