1、Biological Functions of Autophagy Genes:A Disease PerspectiveBeth Levine1,2,3 and Guido Kroemer4,5,6,7,8,9,101Center for Autophagy Research,Department of Internal Medicine,University of Texas Southwestern Medical Center,Dallas,TX 75390;2Howard Hughes Medical Institute,University of Texas Southwester
2、n Medical Center,Dallas,TX 75390;3Department of Microbiology,University of Texas Southwestern Medical Center,Dallas,TX 75390;4Equipe 11 labellise par la Ligue contre le Cancer,Centre de Recherche des Cordeliers;75006 Paris,France;5Cell Biology and Metabolomics platforms,Gustave Roussy Cancer Campus;
3、94805 Villejuif,France;6INSERM,U1138,75006 Paris,France;7Universit Paris Descartes,Sorbonne Paris Cit;75006 Paris,France;8Universit Pierre et Marie Curie,Sorbonne Universit,75006 Paris,France;9Ple de Biologie,Hpital Europen Georges Pompidou,AP-HP;75015 Paris,France;10Karolinska Institute,Department
4、of Womens and Childrens Health,Karolinska University Hospital,17176 Stockholm,SwedenAbstractThe lysosomal degradation pathway of autophagy plays a fundamental role in cellular,tissue and organismal homeostasis and is mediated by evolutionarily conserved autophagy-related(ATG)genes.Definitive etiolog
5、ical links exist between mutations in genes that control autophagy and human disease,especially neurodegenerative,inflammatory disorders and cancer.Autophagy selectively targets dysfunctional organelles,intracellular microbes and pathogenic proteins,and deficiencies in these processes may lead to di
6、sease.Moreover,ATG genes have diverse physiologically important roles in other membrane trafficking and signalling pathways.This Correspondence:Guido Kroemer Kroemerorange.fr,Beth Levine beth.levineutsouthwestern.edu.Publishers Disclaimer:This is a PDF file of an unedited manuscript that has been ac
7、cepted for publication.As a service to our customers we are providing this early version of the manuscript.The manuscript will undergo copyediting,typesetting,and review of the resulting proof before it is published in its final citable form.Please note that during the production process errors may
8、be discovered which could affect the content,and all legal disclaimers that apply to the journal pertain.CONFLICT OF INTEREST STATEMENTB.L.is a scientific co-founder of Casma Therapeutics,Inc.G.K.is a scientific co-founder of Samsara Therapeutics,Ltd.HHS Public AccessAuthor manuscriptCell.Author man
9、uscript;available in PMC 2020 January 10.Published in final edited form as:Cell.2019 January 10;176(1-2):1142.doi:10.1016/j.cell.2018.09.048.Author ManuscriptAuthor ManuscriptAuthor ManuscriptAuthor Manuscriptreview discusses the biological functions of autophagy genes from the perspective of unders
10、tanding and potentially reversing the pathophysiology of human disease and aging.IntroductionA decade has elapsed since our review in 2008 in Cell on“Autophagy in the Pathogenesis of Disease”(Levine and Kroemer,2008).During this period,more than 33,000 new articles related to autophagy were publishe
11、d;a Nobel prize was awarded for the discovery of the molecular mechanisms of autophagy(Levine and Klionsky,2017;Mizushima,2018);and considerable interest has emerged in autophagy modulation as a potential target in clinical medicine(Galluzzi et al.,2017a).The fundamental concepts discussed in our 20
12、08 review(Levine and Kroemer,2008)remain unchanged.The lysosomal degradation pathway of macroautophagy(herein referred to as autophagy)plays a crucial role in cellular physiology,including adaptation to metabolic stress,removal of dangerous cargo(e.g.protein aggregates,damaged organelles,intracellul
13、ar pathogens),renovation during differentiation and development,and prevention of genomic damage.Generally,these and other functions protect against numerous diseases,including infections,cancer,neurodegeneration,cardiovascular disorders,and aging(Mizushima and Komatsu,2011).Under certain circumstan
14、ces,autophagy may be detrimental either via its pro-survival effects(such as in cancer progression(Amaravadi et al.,2016)or via possible cell death-promoting effects(Marino et al.,2014a).Over the past ten years,significant progress has been made in understanding the molecular mechanisms of autophagy
15、,the regulation of autophagy,and the effects of autophagy on physiology and pathophysiology(Dikic and Elazar,2018;Galluzzi et al.,2014;Mizushima,2018).New major conceptual advances underscore the plurality of functions of the autophagic core machinery in various membrane trafficking and signaling ev
16、ents(Cadwell and Debnath,2018)and delineate the exquisite specificity with which autophagy targets selected cargo for degradation(Gatica et al.,2018).These advances,together with discoveries in human genetics linking ATG gene mutations to specific diseases(Jiang and Mizushima,2014;van Beek et al.,20
17、18),provide a multidimensional perspective of mechanisms by which ATG gene-dependent pathways protect against mammalian disease.Herein we review selected highlights of the past decade of research on the biological functions of autophagy genes,primarily from a perspective of understanding and treatin
18、g human disease.Autophagy and other Autophagy Gene-Dependent PathwaysThe original scientific definition of autophagy(Greek,“self-eating”)is the delivery of cytoplasmic cargo to the lysosome for degradation.There are at least three distinct forms of autophagy chaperone-mediated autophagy,microautopha
19、gy and macroautophagy which differ in terms of mode of cargo delivery to the lysosome.Macroautophagy is the major catabolic mechanism used by eukaryotic cells to maintain nutrient homeostasis and organellar quality control.It is mediated by a set of evolutionarily conserved genes,the Levine and Kroe
20、merPage 2Cell.Author manuscript;available in PMC 2020 January 10.Author ManuscriptAuthor ManuscriptAuthor ManuscriptAuthor Manuscriptautophagy-related(ATG)genes(Klionsky et al.,2003),originally discovered in yeast genetic screens(Mizushima,2018).With a few exceptions,all ATG genes are required for t
21、he efficient formation of sealed autophagosomes that proceed to fuse with lysosomes.In higher eukaryotes,many ATG genes functionally diversified to facilitate delivery of extracellular cargo to the lysosome,to promote the plasma membrane localization or extracellular release of intracellular cargo,a
22、nd to coordinate intracellular communication with various cell signaling pathways(Figure 1).These other functions are not,sensu stricto,autophagy and accordingly,will be referred to as ATG gene-dependent pathways.There are broad implications of ATG gene functions in different membrane trafficking an
23、d signaling pathways for mammalian cell biology,physiology and disease.Degradative Autophagy:The“raison dtre”of Autophagy GenesThe originally discovered function of ATG genes is to orchestrate and mediate the formation of double-membraned structures that deliver intracytoplasmic contents to the lyso
24、some for degradation.This process is conserved in all eukaryotic organisms,occurs at basal levels in nearly all cell types,and is increased by diverse intracellular and extracellular cues.It is essential for cellular homeostasis,cellular protein and organelle quality control,and organismal adaptatio
25、n to environmental stress.These principles are firmly supported by nearly two decades of studies involving genetic ablation of the autophagy machinery in diverse eukaryotic species(Levine and Kroemer,2008;Mizushima and Komatsu,2011).This lysosomal degradation pathway is usually described as involvin
26、g a set of 1620 core conserved ATG genes.The ATG proteins encoded by these genes are traditionally classified into distinct biochemical and functional groups that act at specific stages of autophagosome initiation or formation.In this scheme(see other recent reviews for details(Dikic and Elazar,2018
27、;Yu et al.,2018),the ULK1 serine threonine kinase complex(involving ULK1,FIP200,ATG13 and ATG101)plays a major role in autophagy initiation,phosphorylating multiple downstream factors.Two distinct Beclin 1/class III phosphatidylinositol 3-kinase(PI3KC3)complexes generate phosphatidylinositol 3-phosp
28、hate(PI3P)to act in autophagosome nucleation(PI3KC3C1 involving Beclin 1,VPS34,VPS15 and ATG14)or endolysosomal and autophagolysosomal maturation(PI3KC3C2 involving Beclin 1,VPS34,VPS15 and UVRAG).Vesicles containing ATG9A,the only transmembrane core ATG protein,supply membrane to autophagosomes.WIP
29、I(WD repeat domain phosphoinositide-interacting)proteins and their binding partners,ATG2A or ATG2B,function in early stages of membrane elongation at the site of PI3P generation.Autophagosome membrane expansion and completion involves two ubiquitin-like protein conjugation systems:the Ub-like ATG12
30、conjugates with ATG5 and ATL16L1 and the Ub-like LC3 subfamily(ATG8 in yeast)conjugates with membrane-resident phosphatidylethanoloamine(PE).Unlike in yeast,the ubiquitin-like protein conjugation systems are not essential for autophagosomal membrane completion in mammalian cells,although they determ
31、ine the efficiency of the process(Tsuboyama et al.,2016).This classification of the ATG proteins has provided a useful framework for studying and understanding autophagy.However,its apparent simplicity is at variance with extensive data indicating a highly complex level of interconnectivity among th
32、e ATG proteins and newly Levine and KroemerPage 3Cell.Author manuscript;available in PMC 2020 January 10.Author ManuscriptAuthor ManuscriptAuthor ManuscriptAuthor Manuscriptdescribed functions of ATG proteins at different stages of autophagy.Based on unbiased proteomic analyses,most ATG proteins int
33、eract with other ATG proteins that reside outside of their“classic”functional complex(Behrends et al.,2010).Experimentally,some of these interactions are known to be important for autophagosome formation.For example,FIP200(a member of the ULK1 kinase complex)interacts with ATG16L1 to properly target
34、 it to the isolation membrane(also known as the phagophore)of the nascent autophagosome(Nishimura et al.,2013).ATG14(a component of the autophagy-specific PI3KC3C1 complex)also functions in SNARE-driven membrane fusion(Diao et al.,2015).Similarly,Atg13(a component of the yeast Atg1/mammalian ULK1 ki
35、nase complex)interacts with Atg9 to recruit Atg9 vesicles to the pre-autophagosomal structure(Suzuki et al.,2015).The broader interconnectivity and functional multiplicity of core autophagy proteins in autophagosomal biogenesis requires further elucidation.Moreover,as indicated by a recent condition
36、al genetic interactions study using diverse yeastomics datasets(Kramer et al.2017),new systems biology approaches will likely identify additional genes required for autophagy,especially those that may function in a stimulus-dependent,cell type-dependent or species-specific manner.The core ATG protei
37、ns,conserved from yeast to humans,are necessary but not sufficient for degradative autophagy.The degradation of autophagosomal cargo cannot proceed without successful fusion to an available and functional lysosome.Research in the past decade has unmasked some of the key factors required for lysosoma
38、l biogenesis(Settembre et al.,2013b),autophagolysosomal fusion(Yu et al.,2018),lysosomal function during autophagy(Shen and Mizushima,2014)and autophagic lysosome reformation(Chen and Yu,2017).Adenoviral-mediated gene delivery of TFEB,a master transcriptional regulator of lysosomal biogenesis,improv
39、es outcomes in various rodent disease models,including Parkinsons disease,lysosomal storage disorders,tauopathies,1-antitrypsin deficiency,and hepatic hyperammonemia(Napolitano and Ballabio 2016;Soria et al.,2018).Autophagolysosomal fusion requires changes in lysosomal pH,certain cytoskeleton motor
40、proteins(dynein),tethering factors(the HOPS complex,the Rab GTPase,RAB7),SNARE proteins(the Q-SNARE,syntaxin 17 on autophagosomes which interacts with R-SNARE proteins,SNAP29 and VAMP8 on endosomes/lysosomes),phospholipids,and members of the LC3/GABARAP family(Kriegenburg et al.,2018)that are bridge
41、d to tethering factors or SNARES by adaptor proteins.Screens in C.elegans identified novel metazoan-specific genes required for fusion steps in degradative autophagy(Tian et al.,2010).One example relevant to human disease is EPG5,which encodes a RAB7 effector.Autosomal recessive mutation of EPG5 res
42、ults in Vici syndrome,a neurodevelopmental and multisystem disorder(Table 1).Mutations in genes that regulate lysosomal acidification such as ATP6AP2 and presenilin 1 are associated with X-linked Parkinsonism and Alzheimers disease(Table 1).Thus,we must consider regulators of lysosomal biogenesis,th
43、e fusion machinery,and determinants of lysosomal function in our efforts to decipher how deficient autophagy leads to disease and how autophagy can be regulated to prevent or treat disease.Beyond Self-Eating:Autophagy Genes Function in PhagocytosisSeveral core ATG genes function in a process that sh
44、ares some similarities with autophagy but involves digestion of unwanted extracellular(rather than intracellular)material.During Levine and KroemerPage 4Cell.Author manuscript;available in PMC 2020 January 10.Author ManuscriptAuthor ManuscriptAuthor ManuscriptAuthor Manuscriptthis process,termed LC3
45、-associated phagocytosis(LAP),single-membraned macroendocytic vacuoles(macropinosomes,phagosomes and entotic vacuoles)engulf extracellular cargo(such as bacteria,dead cells or live cells),become decorated by lipidated LC3,and are directed to the lysosome for degradation(Cadwell and Debnath,2018;Heck
46、mann et al.,2017).LAP is distinguished from autophagy by four main features:(1)the origin of the vacuolar contents(extracellular versus intracellular),(2)the requirement of cargo engagement of an extracellular receptor for activation,(3)the type of membrane that fuses with the lysosome(single membra
47、ne versus double membrane),and(4)the utilization of a subset versus all of the core ATG proteins.LAP requires NADPH-oxidase(NOX2)to generate reactive oxygen species(ROS),certain components of the Beclin 1/VPS34 complexes,PI3P generation,LC3-conjugation to the single membrane of the phagosome,and all
48、 components of the LC3 conjugation machinery(Martinez et al.,2011;Martinez et al.,2015;Sanjuan et al.,2007).However,it does not require other core ATG proteins,such as components of the ULK1 complex or the autophagy-specific Beclin 1/VPS34 complex component,ATG14.Somewhat enigmatically,LAP requires
49、Rubicon,an inhibitory component of the autophagy-specific Beclin 1/VPS34 complex.The precise effects of LC3 decoration of phagosomes on their fusion with lysosomes and on lysosomal function are unknown.The presence of LC3 on phagosomes may enhance efficiency of phagolysosomal maturation,perhaps thro
50、ugh a mechanism similar to that of LC3/GABARAP family members in autophagolysosomal maturation.LAP was originally described in murine macrophages during phagocytosis of particles that engage Toll-like receptors(TLRs)(Sanjuan et al.,2007)and is involved in type I interferon(IFN)secretion in response
