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Guidelines for the use and interpretation of assays for monitoring autophagy (3rd edition)

Daniel Klionsky 1 Kotb Ko Akihisa Abe 2 Md Joynal Jo Hagai Abeliovich 3 Abraham Acevedo Arozena 4 Hiroaki Adachi 5 Chris Adams Peter Adams Khosrow Adeli 6 Peter Adhihetty Sharon Adler Galila Agam 7 Rajesh Agarwal 8 Manish Man Patrizia Agostinis 9 Patricia Aguilar Julio Ju Ai Airoldi Ai Ait-Si-Ali Takahiko Akematsu 10 Emmanuel Akporiaye Mohamed Al-Rubeai 11 Guillermo Albaiceta Chris Albanese 12 Diego Albani 13 Jesus Aldudo 14 Hana Han Alireza Alirezaei Iraide Alloza 15 Alexandru Almasan 16 Maylin Ma Emad Alnemri 17 Alon Alonso Bo Altan-Bonnet Dario Altieri Silvia Alvarez 18 Lydia Alvarez-Erviti 19 Sandro Alves 20 Giuseppina Amadoro 21 Atsuo Amano 22 Consuelo Amantini 23 Santiago Ambrosio 24 Ivan Amelio Amal Amer Mohamed Amessou 25, 26, 27, 28 Angel An Zhen An Frank Anania Anders Andersen 29 Usha Andley Andrea Andreadi Na Andrieu-Abadie Alberto Anel 30 David Ann Shailendra Du Antonio Man Hiroshi Aoki Na Apostolova Saveria Aquila 31 Katia Aquilano Koichi Ko Eli Arama Agustin Aranda Jun Ju Alexandre Arcaro Esperanza Arias Hirokazu Arimoto Ai Ariosa Jane Armstrong Thierry Arnould 32 Ivica Arsov Katsuhiko Asanuma Valerie Askanas 33 Ryuichiro Atarashi Sally Atherton Julie Ju Laura Attardi Patrick Auberger 34 Georg Ge Aurelia Aurelian Riccardo Autelli Laura Avagliano Li Lim Suresh Su Neelam Azad Tiziana Bachetti 35 Jon Jo Dong Hu Jae Bae Na Bae Soo Han Soo Seung-Hoon Baek Stephen Baghdiguian 36 Agnieszka Bagniewska-Zadworna Jie Bai 37 Na Balaji Walter Walter Andrea Ballabio 38 Bal Ren Rajkumar Banerjee Gábor Bánhegyi Hai Bao Benoit Barbeau 39 Esther Barreiro Bo Bartel Bart Bartolomé Diane Bassham Robert Bast Alakananda Basu Henri He Maurizio Ma Kyle Bauckman Bradley Baumgarner Ulrich Bayer Rupert Beale Jean Jean George Ge Chris Becker David Beckham Pierre Pierre Patrick Bednarski Thomas Thomas Chris Behl Chris Behrends Georg Mn Ge Kevin Ke Eloy Bejarano Amine Belaïd 40 Francesca Belleudi 41 Giovanni Benard 42 Gu Berchem Daniel Bergamaschi Matteo Ma Ben Berkhout 43 Laura Berliocchi Amélie Bernard Monique Bernard 44 Francesca Bernassola Anne Bertolotti Amanda Bess Sébastien Besteiro 45 Saverio Bettuzzi Savita Bhalla Shalmoli Bhattacharyya Sujit Su Caroline Biagosch Mar Martin 46 Viktor Billes Claudia Bincoletto Bing Bingol Sara Bird Ivan Bjedov Craig Blackstone Guillermo Blanco Heidi Kiil He Bo Boada-Romero Stefan Böckler Bo Boesze-Battaglia Bo Law Bo Bolino Bo Boman Bo Bonaldo Bo Ma Bo Bosch Bo Lü Bo Jo Bo Ge Bo Marin Bo Mari Bo Bouret Patricia Boya 47 Bo Mi Bo Bozhkov Na Brady Vania Braga Claudio Brancolini Gerhard Ge José Jo Emery Bresnick Patrick Brest 48 Dave Bridges Mari Mari Glauber Brito Bertha Brodin Paul Brookes Karen Brown 49 Hal Broxmeyer Alain Bruhat 50 Patricia Brum Nicola Brunetti-Pierri Richard Richardson Shi Shi Alastair Buchan Hikmet Budak 51 Dmitry Bulavin Scott Bultman Geert Ge Vladimir Bumbasirevic Yan Yan 52 Robert Burke Peter Bütikofer Laura Caberlotto 53 Ken Ke Monika Cahova Jing Jin 54 Qi Qian Sara Calatayud Cam Camougrand Cam Grant Camille Martinand-Mari 36 Cam Campello Robin Candau 55 Isabel Caniggia Lavinia Cantoni Li Li 56 Allan Caplan Michel Mi Claudio Cardinali Sandra Cardoso Jennifer Carew Carl Carleton Carl Carlin Carl Carloni Carl Carlsson Gu Gutierrez Leticia Carneiro Oliana Carnevali 57 Serena Carra Alice Carrier 58 Bernadette Carroll Caty Casas 59 Giuliana Cassinelli 60 Per Castets Gabriella Cavallini 61 Isabel Ceccherini Francesco Cecconi 62 Arthur Cederbaum Valentín Ceña Simon Simone Claudia Cerella 63 David Cervia Silvia Cetrullo Hassan Chaachouay Andrei Chagin Gopal Chakrabarti Georgios Ge Chan Chan Matthew Ma Chan Chandra Peng Peng 64 Chan Ray Yu Yuan John Jo Saurabh Chatterjee Santosh Chauhan Yong Che Rajkumar Cheluvappa Jun Jung Gang Chen 65 Gu Guan Guo Guo Hong Hong Jeff Chen 66 Jian Kang 67 Min Mi Min Ming Peiwen Chen Qi Qi Quan Qu Shang-Der Der Si Chen 68 Steve Chen Wei Wei 69 Jun Wei 70 Qi Wen Wenli Wen Xian Xia Ya Hu Yi Yin Ying Yin 71 Yong Chen 72 Qi Yue Yu Yu 73 Zhen Chen Zhong Zhong Cheng Cheng 74 Chris Cheng Hua Hua Heesun He Sara Cherry 75 Jason Chesney Antonio He Eric Eri Chi Chi Chi Sung 76 Fulvio Fu Lin Lin 77 Roberto Chiarelli Marc Ma Li Shen 78 Chi Chiu Dong Dong Ssang-Goo Cho William Cho Ye Ye Young Young Augustine Mk Choi Eui-Ju Ju Eun-Kyoung Choi Jayoung Choi Seung-Il Choi Fen Chou Salem Chouaib Divaker Choubey Vinay Choubey Chi Chow Kamal Chowdhury Charleen Chu Tsung-Hsien Tsung Taehoon Chun Hyewon Chung Taijoon Chung 79 Li Yue Yong Jo Valentina Cianfanelli Roberto Ciarcia Iwona Ciechomska 80 Maria Rosa Mar Ma Sofie Claerhout Michael Mi Joan Jo Peter Clarke Robert Clarke Emil Clementi Cédric Cleyrat 81 Miriam Mi Eliana Coccia Tiziana Cocco Patric Codogno Jörn Coers Ezra Ew Cohen David Colecchia Luisa Lu Núria Coll Gu Colucci-Guyon Sergio Comincini Katherine Cook Graham Coombs Cynthia Cooper Isabel Coppens Marco Ma Ramon Corbalan Elisa Corcelle-Termeau Mario Mari Cristina Corral-Ramos Olga Corti 82 Andrea Cossarizza 83 Paola Costelli 84 Safia Costes 85 Susan Su Ana Coto-Montes Sandra Cottet Eduardo Couve 86 Lori Covey L Ashley Cowart Jeff Cox Fraser Fraser Carolyn Coyne Rolf Craven Tiziana Crepaldi Alfred Criollo Valeria Crippa Teresa Mari Jose Jo Taixing Cui Pedro Cutillas Mark Ma Maria Mari 87 Ruben Dagda Uta Dahmen 88 Chunsun Dai Wenjie Wen Bart Staels 89 Frank Lafont 90 Emma Colucci-Guyon 91 Matthew L Albert 92 Marc Lecuit 93, 94 Helene Duez 89 Isabelle Dugail Verónica Dumit Mara Duncan Elaine Dunlop William Dunn Nicolas Dupont Luc Dupuis Raúl Durán Thomas Durcan Stéphane Duvezin-Caubet Umamaheswar Duvvuri Vinay Eapen Darius Ebrahimi- Fakhari Arnaud Echard 95 Leopold Eckhart Charles Edelstein Aimee Edinger Ludwig Eichinger Tobias Eisenberg Avital Eisenberg-Lerner Tony Eissa Wafik El-Deiry Victoria El-Khoury Zvulun Elazar Hagit Eldar- Finkelman Chris Elliott Enzo Emanuele Urban Emmenegger Nikolai Engedal Anna-Mart Engelbrecht Simone Engelender Jorrit Enserink Ralf Erdmann Jekaterina Erenpreisa Rajaraman Eri Jason Eriksen Andreja Erman Ricardo Escalante Eeva-Liisa Eskelinen Lucile Espert Lorena Esteban-Martínez Thomas Evans Mario Fabri Gemma Fabrias Cinzia Fabrizi Antonio Facchiano Nils Færgeman Alberto Faggioni Douglas Fairlie Chunhai Fan Daping Fan Jie Fan Shengyun Fang Manolis Fanto Alessandro Fanzani Thomas Farkas Mathias Faure Francois Favier Howard Fearnhead Massimo Federici Erkang Fei Tania Felizardo Hua Feng Yibin Feng Yuchen Feng Thomas A Ferguson Álvaro Fernández Maite Fernandez-Barrena Jose Fernandez-Checa Arsenio Fernández- López Martin Fernandez-Zapico Olivier Feron Elisabetta Ferraro Carmen Veríssima Ferreira-Halder Laszlo Fesus Ralph Feuer Fabienne Fiesel Eduardo Filippi-Chiela Giuseppe Filomeni Gian Maria Fimia John Fingert Steven Finkbeiner Toren Finkel Filomena Fiorito Paul Fisher Marc Flajolet Flavio Flamigni Oliver Florey Salvatore Florio Andres Floto Marco Folini Carlo Follo Edward Fon Francesco Fornai Franco Fortunato Alessandro Fraldi Rodrigo Franco Arnaud Francois Aurélie François Lisa Frankel Iain Fraser Norbert Frey Damien Freyssenet Christian Frezza Scott Friedman Daniel Frigo Dongxu Fu José Fuentes Juan Fueyo Yoshio Fujitani Yuuki Fujiwara Mikihiro Fujiya Mitsunori Fukuda Bertrand H. Rihn 96
1 Life Sciences Institute and Department of Molecular, Cellular, and Developmental Biology and Biological Chemistry
2 Tokyo Medical University
3 HUJ - The Hebrew University of Jerusalem
4 Mammalian Genetics Unit
5 University of Occupational and Environmental Health School of Medicine
6 University of Toronto
7 BGU - Ben-Gurion University of the Negev
8 University of Colorado [Boulder]
9 Cell Death Research & Therapy (CDRT) Lab
10 University of Vienna [Vienna]
11 Conway Institute of Biomolecular and Biomedical Research and School of Chemical and Bioprocess Engineering
12 Georgetown University
13 IRCCS - Candiolo Cancer Institute
14 CIBERNED - Centro de Investigacion Biomédica en Red sobre Enfermedades Neurodegenerativas
15 Ikerbasque - Basque Foundation for Science
16 Cleveland Clinic
17 Sidney Kimmel Cancer Center
18 UBA - Universidad de Buenos Aires
19 Department of Clinical Neurosciences
20 U 1169 - Thérapie génique, Génomique et Epigénomique
21 CNR - Consiglio Nazionale delle Ricerche
22 Osaka University
23 Department of Experimental Medicine and Public Health
24 University of Barcelona
25 IUH - Institut Universitaire d'Hématologie
26 U1162 - Génomique Fonctionnelle des Tumeurs Solides
27 UPD5 - Université Paris Descartes - Paris 5
28 INSERM - Institut National de la Santé et de la Recherche Médicale
29 Department of Physics
30 University of Zaragoza - Universidad de Zaragoza [Zaragoza]
31 Department of Pharmaco-Biology
32 FUNDP - Fondation Universitaire Notre Dame de la Paix
33 USC Neuromuscular Center, Department of Neurology
34 Physiopathologie de la survie et de la mort cellulaire et infection virale
35 Giannina Gaslini Institute
36 UMR ISEM - Institut des Sciences de l'Evolution de Montpellier
37 IMAU - Inner Mongolia Agricultural University
38 POLIMI - Politecnico di Milano [Milan]
39 Department of Civil, Geological, and Mining Engineering
40 IRCAN - Institut de Recherche sur le Cancer et le Vieillissement
41 Department of Molecular Medicine
42 Physiopathologie du système nerveux central - Institut François Magendie
43 Laboratory of Experimental Virology - Department of Medical Microbiology [Amsterdam, The Netherlands]
44 CRMBM - Centre de résonance magnétique biologique et médicale
45 DIMNP - Dynamique des interactions membranaires normales et pathologiques
46 Department of Internal Medicine
47 Celullar and Molecular Medicine
48 Infection bactérienne, inflammation, et carcinogenèse digestive
49 University of Edinburgh
50 UNH - Unité de Nutrition Humaine - Clermont Auvergne
51 Faculty of Engineering and Natural Sciences
52 USTB - University of Science and Technology Beijing [Beijing]
53 Centre for Computational and Systems Biology (COSBI)
54 SYSU - Sun Yat-Sen University [Guangzhou]
55 DMEM - Dynamique Musculaire et Métabolisme
56 IOCAS - CAS Institute of Oceanology
57 Polytechnic University of Marche
58 CRCM - Centre de Recherche en Cancérologie de Marseille
59 Cell Biology, Physiology and Immunology
60 Department of Experimental Oncology and Molecular Medicine
61 University of Pisa - Università di Pisa
62 Dulbecco Telethon Institute/Department of Biology
63 Fondation de Recherche Cancer et Sang - Hôpital Kirchberg
64 China University of Petroleum
65 Unilever R&D
66 University of Queensland [Brisbane]
67 University of Minnesota [Twin Cities]
68 LGPM - Laboratoire de Génie des Procédés et Matériaux - EA 4038
69 Institute for Advanced Study [Tsinghua]
70 NTU - Nanayang Technological University
71 IMETU - Institute of Microelectronics [Beijing]
72 LPN - Laboratoire de photonique et de nanostructures
73 IBMP - Institut de biologie moléculaire des plantes
74 NPU - Northwestern Polytechnical University [Xi'an]
75 University of Pennsylvania [Philadelphia]
76 CityU - City University of Hong Kong
77 Department of Mathematics [Berkeley]
78 ZJU-ENS Joint Laboratory of Medicinal Chemistry,
79 UC - University of Cincinnati
80 Réponses immunes : régulation et développement
81 The University of New Mexico [Albuquerque]
82 CRICM - Centre de Recherche de l'Institut du Cerveau et de la Moelle épinière
83 Dipartimento di Scienze Biomediche
84 Department of Experimental Medicine and Oncology
85 IGF - Institut de Génomique Fonctionnelle
86 CNV
87 UP1 UFR04 - Université Paris 1 Panthéon-Sorbonne - UFR d'Arts plastiques et sciences de l'art
88 Department of General, Visceral and Vascular Surgery [Jena]
89 RNMCD - Récepteurs nucléaires, maladies cardiovasculaires et diabète - U 1011
90 Institut Pasteur de Lille
91 Macrophages et Développement de l’Immunité
92 Immunobiologie des Cellules Dendritiques
93 Centre d'infectiologie Necker-Pasteur [CHU Necker]
94 Institut Pasteur [Paris]
95 Trafic membranaire et Division cellulaire - Membrane Traffic and Cell Division
96 CITHEFOR - Cibles thérapeutiques, formulation et expertise pré-clinique du médicament
Abstract : In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes. For example, a key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process versus those that measure flux through the autophagy pathway (i.e., the complete process including the amount and rate of cargo sequestered and degraded). In particular, a block in macroautophagy that results in autophagosome accumulation must be differentiated from stimuli that increase autophagic activity, defined as increased autophagy induction coupled with increased delivery to, and degradation within, lysosomes (in most higher eukaryotes and some protists such as Dictyostelium) or the vacuole (in plants and fungi). In other words, it is especially important that investigators new to the field understand that the appearance of more autophagosomes does not necessarily equate with more autophagy. In fact, in many cases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity. It is worth emphasizing here that lysosomal digestion is a stage of autophagy and evaluating its competence is a crucial part of the evaluation of autophagic flux, or complete autophagy. Here, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes. These guidelines are not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to monitor autophagy. Along these lines, because of the potential for pleiotropic effects due to blocking autophagy through genetic manipulation, it is imperative to target by gene knockout or RNA interference more than one autophagy-related protein. In addition, some individual Atg proteins, or groups of proteins, are involved in other cellular pathways implying that not all Atg proteins can be used as a specific marker for an autophagic process. In these guidelines, we consider these various methods of assessing autophagy and what information can, or cannot, be obtained from them. Finally, by discussing the merits and limits of particular assays, we hope to encourage technical innovation in the field.
Keywords : autophagosome stress lysosome flux chaperone-mediated autophagy autolysosome macroautophagy LC3 phagophore
Document type :
Journal articles
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https://hal.umontpellier.fr/hal-01921322
Contributor : Camille Martinand-Mari <>
Submitted on : Tuesday, November 13, 2018 - 5:32:43 PM
Last modification on : Tuesday, January 19, 2021 - 11:14:14 AM

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UNIV-MONTPELLIER | CNRS | INRA | RIIP | AGROPOLIS | UNIV-PARIS1 | USPC | UNIV-PARIS5 | CENTRALESUPELEC | ICM | UPMC | BS | UNICE | PRES_CLERMONT | UNH | UNIV-COTEDAZUR | LGPM | SITE-ALSACE | B3ESTE | CRMBM | ISEM | DMEM | UNIV-AMU | UNIV-PARIS13 | SORBONNE-UNIVERSITE | CRCM | PASTEUR | RIIP_LILLE | ATP-IMMUN | SU-MEDECINE | UNIV-PARIS7 | EPHE | CIRAD | IBPS | SU-SCIENCES | LBD-E03 | CITHEFOR-UL | UNIV-LORRAINE | INRAE | UNIV-PARIS | PSL | CEA | CEA-UPSAY | BMS-UL | UNIV-LILLE | RNMCD | POLITIQUES-PUBLIQUES | SU-TI

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Daniel Klionsky, Kotb Ko, Akihisa Abe, Md Joynal Jo, Hagai Abeliovich, et al.. Guidelines for the use and interpretation of assays for monitoring autophagy (3rd edition). Autophagy, Taylor & Francis, 2016, 12 (1), pp.1-222. ⟨10.1080/15548627.2015.1100356⟩. ⟨hal-01921322⟩

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