Guidelines for the Use and Interpretation of Assays for Monitoring Autophagy (3rd edition)

Abstract

[EN] 3-MA, 3-methyladenine; ABC, avidin-biotin peroxidase complex; AIM, Atg8-family interacting motif; ALIS, aggresome-like induced structures; Ape1, aminopeptidase I; ARN, autophagy regulatory network; ASFV, African swine fever virus; Atg, autophagy-related; AV, autophagic vacuole; BDI, bright detail intensity; CASA, chaperone-assisted selective autophagy; CLEAR, coordinated lysosomal enhancement and regulation; CLEM, correlative light and electron microscopy; CMA, chaperone-mediated autophagy; cryo-SXT, cryo-soft X-ray tomography; Cvt, cytoplasm-to-vacuole targeting; DAMP, danger/damage-associated molecular pattern; DQ-BSA, dequenched bovine serum albumin; e-MI, endosomal microautophagy; EBSS, Earle¿s balanced salt solution; EM, electron microscopy; ER, endoplasmic reticulum; FACS, ¿uorescence-activated cell sorter; FRET, ¿uorescence resonance energy transfer; GAP, GTPase activating protein; GBP, guanylate binding protein; GFP, green ¿uorescent protein; HIV-1, human immunode¿ciency virus type 1; HKP, housekeeping protein; HSV-1, herpes simplex virus type 1; Hyp-PDT, hypericin-based photodynamic therapy; ICD, immunogenic cell death; IHC, immunohistochemistry; IMP, intramembrane particle; LAMP2, lysosomal-associated membrane protein 2; LAP, LC3-associated phagocytosis; LIR, LC3-interacting region; LN, late nucleophagy; MAP1LC3/LC3, microtubule associated protein 1 light chain 3; MDC, monodansylcadaverine; MEC, mammary epithelial cell; mRFP, monomeric red ¿uorescent protein; mtDNA, mitochondrial DNA; MTOR, mechanistic target of rapamycin (serine/threonine kinase); MVB, multivesicular body; NASH, nonalcoholic steatohepatitis; ncRNA, noncoding RNA; NET, neutrophil extracellular trap; NVJ, nucleus-vacuole junction; PAMP, pathogen-associated molecular pattern; PAS, phagophore assembly site; PDT, photodynamic therapy; PE, phosphatidylethanolamine; PI3K, phosphoinositide 3-kinase; PMN, piecemeal microautophagy of the nucleus; PMSF, phenylmethylsulfonyl¿uoride; POF, postovulatory follicle; PSSM, position-speci¿c scoring matrix; PtdIns3K, phosphatidylinositol 3-kinase; PtdIns3P, phosphatidylinositol 3-phosphate; PTM, posttranslational modi¿cation; PVM, parasitophorus vacuole membrane; qRT-PCR, quantitative real-time reverse transcription polymerase chain reaction; RBC, red blood cell; RCBs, Rubisco-containing bodies; Rluc, Renilla reniformis luciferase; ROS, reactive oxygen species; SD, standard deviation; SKL, serine-lysine-leucine (a peroxisome targeting signal); SOD, superoxide dismutase; TEM, transmission electron microscopy; tfLC3, tandem ¿uorescent LC3; TORC1, TOR complex I; TR-FRET, time-resolved ¿uorescence resonance energy transfer; TVA, tubulovesicular autophagosome; UPR, unfolded protein response; UPS, ubiquitin-proteasome system; V-ATPase, vacuolar-type HC-ATPase; xLIR, extended LIR-motif