Autophagy Function and Regulation in Kidney Disease

Abstract

Autophagy is a dynamic process by which intracellular damaged macromolecules and organelles are degraded and recycled for the synthesis of new cellular components. Basal autophagy in the kidney acts as a quality control system and is vital for cellular metabolic and organelle homeostasis. Under pathological conditions, autophagy facilitates cellular adaptation; however, activation of autophagy in response to renal injury may be insufficient to provide protection, especially under dysregulated conditions. Kidney-specific deletion of Atg genes in mice has consistently demonstrated worsened acute kidney injury (AKI) outcomes supporting the notion of a pro-survival role of autophagy. Recent studies have also begun to unfold the role of autophagy in progressive renal disease and subsequent fibrosis. Autophagy also influences tubular cell death in renal injury. In this review, we reported the current understanding of autophagy regulation and its role in the pathogenesis of renal injury. In particular, the classic mammalian target of rapamycin (mTOR)-dependent signaling pathway and other mTOR-independent alternative signaling pathways of autophagy regulation were described. Finally, we summarized the impact of autophagy activation on different forms of cell death, including apoptosis and regulated necrosis, associated with the pathophysiology of renal injury. Understanding the regulatory mechanisms of autophagy would identify important targets for therapeutic approaches.

Keywords: AMPK; acute kidney injury; apoptosis; autophagy; chronic kidney disease; diabetic nephropathy; mTORC1; regulated necrosis; renal fibrosis.

Figure 2

(A): Ca²⁺-calpain, cAMP- exchange protein directly activated by cAMP (Epac)- phosphoinositide-specific phospholipase C-ε (PLC-ε)-inositol phosphate 3 (IP₃)_, and inositol signaling pathways of autophagy regulation. Calpains cleave α-subunit of G-protein (Gsα) to from active Gsα (Gsα_a). Gsα_a enhances adenyl cyclase activity to generate cAMP. The cAMP also regulates autophagy via a cAMP-Epac-PLC-ε-IP₃ pathway to generate Ins (1,4,5) P3 (IP₃), which inhibits autophagy in an mTOR-independent manner. Also, calpains activated by cytosolic calcium cleave autophagy proteins ATG5^38,39 and beclin-1³⁸ that can inactivate autophagy. (B): mTORC1-independent regulation of autophagy. TFEB-mediated autophagy induction: In response to renal IR injury, TFEB is translocated to the nucleus and induces lysosomal biogenesis and autophagy. Forkhead box O3 (FoxO3)-mediated autophagy induction: FoxO3 induces activation of TFEB, which upon translocation to the nucleus, transactivates autophagy genes. Also, FoxO3 induces FoxO1, which in association with Rab 7, facilitates the fusion of the lysosome to the autophagosome. Also, janus kinase (JNK), tether containing a UBX domain for GLUT4 (TUG), death-associated protein kinase (DAPK), and p38 regulate autophagy, as shown in the figure.

Figure 1

mTORC1-dependent and mTORC1-independent regulation of autophagy activation: Suppression of mTORC1 and induction of adenosine monophosphate activated protein kinase (AMPK) promote Unc-51 like autophagy activating kinase (ULK1) complex [ULK1, Atg13, focal adhesion kinase family interacting protein of 200 kD (FIP200), and Atg101] activation at the pre-autophagosomal assembly site (the certain domain of the ER) and initiates the autophagy process. Active ULK1 complex regulates the activity of the class III phosphatidylinositol (PtdIns) 3-kinase complex (including Beclin-1, Atg14(L)/barkor, Vps15, Vps34, and Ambra1) that generates phosphatidylinositol 3-phosphate (PI3P) rich domain. PI3P and PI3P-binding proteins (double FYVE domain-containing protein 1 (DFCP-1) and WIPI proteins) participate in the nucleation and associated membrane dynamics of the phagophore structure, the site of nucleation. Atg9 positive vesicles, that traffic from Golgi and endosomes and regulated by ULK1 complex, contribute to the formation of omegosomes and phagophores. Expansion and maturation of autophagosome from the phagophore structure require two ubiquitin-like conjugation systems that produce Atg12-Atg5-Atg16 oligomeric complex (Atg16 L1 complex) and lipidation of microtubule-associated protein 1A/1B-light chain 3 (LC3) (mammalian homolog of yeast Atg8) with phosphatidyl-ethanolamine (PE). WIPI upon binding to PI3P recruits Atg16 L1 complex to PI3P initiation sites. Atg12-Atg5 of the Atg L1 complex is then involved as an E3-like enzyme for the formation of the lipidated form of LC3. Once the autophagosome is produced, it then fuses with the lysosome to form autolysosome, and subsequently, the lysosomal hydrolases degrade the sequestered cargo. mTORC1 positively regulates protein synthesis, nucleotide synthesis, lipid synthesis, and mitochondrial biogenesis, as shown in the figure. mTORC1-independent alternative pathways negatively regulate autophagy.

Figure 3

(A) Binding of tumor necrosis factor α (TNFα) with TNF receptor activates the receptor, which recruits TNFR1-associated death domain protein (TRADD). TRADD can recruit several binding partners, including shown in Table 2. Receptor-interacting serine/threonine-protein kinase 1 (RIPK1) and inhibitor of apoptosis proteins (cIAP) are involved in different downstream signaling pathways, including NF-κB activation, apoptosis, and necroptosis. TNFR-associated factor 2 (TRAF 2) binds to its cytoplasmic death domain. TRADD has several protein-binding partners and participates in different signaling pathways, including NF-κB, apoptosis, necrosis, and mitogen-activated protein (MAP) kinase activation. The N-terminal domain of TRADD interacts with the C-terminal domain of TRAF2 and recruits TRAF2 to TNFR1 for activation of the NF-κB pathway. E3 ubiquitin ligases cIAP1/cIAP2 polyubiquitinate (Ub–Ub) RIP1 that promotes the recruitment of inhibitor of nuclear factor kappa-B kinase (IKK) complex and TAK1, for NF-κB activation. In the absence of cIAP1 or deubiquitination of RIPK1 by cylindromatosis (CYLD), a K63-specific deubiquitinating enzyme (DUB) mediates the deubiquitination of RIP1 to facilitate the formation of complex II (IIa and Iib), which is dissociated from the receptor when TNFR is internalized. cFLIP, RIP1, FADD, and caspase-8 form cytosolic complex IIa to activate the caspase cascade and induce apoptosis. Active caspase 8 also cleaves and inactivates RIPK1 and RIPK2. When a caspase-8 activity is compromised by cFLIPs, vFLIP, or zVAD fmk, RIPK1 interacts with RIPK3 in a “necrosome” complex. RIP3 upon activation phosphorylates MLKL, and this promotes oligomerization of MLKL, resulting in its insertion in the plasma membrane to execute necroptosis. (B) Molecular interactions between necroptosis and autophagy show the involvement of cellular FLICE (FADD-like IL-1β converting enzyme) inhibitory protein (cFLIP), caspase-8, and Atg3. cFLIPs promotes necrosome assembly and subsequent necroptosis by inhibiting caspase-8; cFLIPL prevents its assembly by activation of caspase 8 that cleave RIP1 in the complex. cFLIPL can suppress autophagy by preventing Atg3 from converting LC3 to LC3-II.