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

Daniel Klionsky 1 Kotb Ko Akihisa Abe Md Joynal Jo Hagai Abeliovich Abraham Acevedo Arozena Hiroaki Adachi Chris Adams Peter Adams Khosrow Adeli Peter Adhihetty Sharon Adler Galila Agam Rajesh Agarwal Manish Man Patrizia Agostinis 2 Patricia Aguilar Julio Ju Ai Airoldi Ai Ait-Si-Ali Takahiko Akematsu Emmanuel Akporiaye Mohamed Al-Rubeai 3 Guillermo Albaiceta Chris Albanese Diego Albani Jesus Aldudo Hana Han Alireza Alirezaei Iraide Alloza Alexandru Almasan Maylin Ma Emad Alnemri 4 Alon Alonso Bo Altan-Bonnet Dario Altieri Silvia Alvarez Lydia Alvarez-Erviti Sandro Alves Giuseppina Amadoro Atsuo Amano Consuelo Amantini 5 Santiago Ambrosio Ivan Amelio Amal Amer Mohamed Amessou 6, 7, 8, 9 Angel An Zhen An Frank Anania Anders Andersen 10 Usha Andley Andrea Andreadi Na Andrieu-Abadie Alberto Anel 11 David Ann Shailendra Du Antonio Man Hiroshi Aoki Na Apostolova Saveria Aquila 12 Katia Aquilano Koichi Ko Eli Arama Agustin Aranda Jun Ju Alexandre Arcaro Esperanza Arias Hirokazu Arimoto Ai Ariosa Jane Armstrong Thierry Arnould 13 Ivica Arsov Katsuhiko Asanuma Valerie Askanas 14 Ryuichiro Atarashi Sally Atherton Julie Ju Laura Attardi Patrick Auberger 15 Georg Ge Aurelia Aurelian Riccardo Autelli Laura Avagliano Li Lim Suresh Su Neelam Azad Tiziana Bachetti 16 Jon Jo Dong Hu Jae Bae Na Bae Soo Han Soo Seung-Hoon Baek Stephen Baghdiguian 17 Agnieszka Bagniewska-Zadworna Jie Bai 18 Na Balaji Walter Walter Andrea Ballabio 19 Bal Ren Rajkumar Banerjee Gábor Bánhegyi Hai Bao Benoit Barbeau 20 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 21 Francesca Belleudi 22 Giovanni Benard 23 Gu Berchem Daniel Bergamaschi Matteo Ma Ben Berkhout 24 Laura Berliocchi Amélie Bernard Monique Bernard 25 Francesca Bernassola Anne Bertolotti Amanda Bess Sébastien Besteiro 26 Saverio Bettuzzi Savita Bhalla Shalmoli Bhattacharyya Sujit Su Caroline Biagosch Mar Martin 27 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 28 Bo Mi Bo Bozhkov Na Brady Vania Braga Claudio Brancolini Gerhard Ge José Jo Emery Bresnick Patrick Brest 29 Dave Bridges Mari Mari Glauber Brito Bertha Brodin Paul Brookes Karen Brown 30 Hal Broxmeyer Alain Bruhat 31 Patricia Brum Nicola Brunetti-Pierri Richard Richardson Shi Shi Alastair Buchan Hikmet Budak 32 Dmitry Bulavin Scott Bultman Geert Ge Vladimir Bumbasirevic Yan Yan 33 Robert Burke Peter Bütikofer Laura Caberlotto 34 Ken Ke Monika Cahova Jing Jin 35 Qi Qian Sara Calatayud Cam Camougrand Cam Grant Camille Martinand-Mari 17 Cam Campello Robin Candau 36 Isabel Caniggia Lavinia Cantoni Li Li 37 Allan Caplan Michel Mi Claudio Cardinali Sandra Cardoso Jennifer Carew Carl Carleton Carl Carlin Carl Carloni Carl Carlsson Gu Gutierrez Leticia Carneiro Oliana Carnevali 38 Serena Carra Alice Carrier 39 Bernadette Carroll Caty Casas 40 Giuliana Cassinelli 41 Per Castets Gabriella Cavallini 42 Isabel Ceccherini Francesco Cecconi 43 Arthur Cederbaum Valentín Ceña Simon Simone Claudia Cerella 44 David Cervia Silvia Cetrullo Hassan Chaachouay Andrei Chagin Gopal Chakrabarti Georgios Ge Chan Chan Matthew Ma Chan Chandra Peng Peng 45 Chan Ray Yu Yuan John Jo Saurabh Chatterjee Santosh Chauhan Yong Che Rajkumar Cheluvappa Jun Jung Gang Chen 46 Gu Guan Guo Guo Hong Hong Jeff Chen 47 Jian Kang 48 Min Mi Min Ming Peiwen Chen Qi Qi Quan Qu Shang-Der Der Si Chen 49 Steve Chen Wei Wei 50 Jun Wei 51 Qi Wen Wenli Wen Xian Xia Ya Hu Yi Yin Ying Yin 52 Yong Chen 53 Qi Yue Yu Yu 54 Zhen Chen Zhong Zhong Cheng Cheng 55 Chris Cheng Hua Hua Heesun He Sara Cherry 56 Jason Chesney Antonio He Eric Eri Chi Chi Chi Sung 57 Fulvio Fu Lin Lin 58 Roberto Chiarelli Marc Ma Li Shen 59 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 60 Li Yue Yong Jo Valentina Cianfanelli Roberto Ciarcia Iwona Ciechomska 61 Maria Rosa Mar Ma Sofie Claerhout Michael Mi Joan Jo Peter Clarke Robert Clarke Emil Clementi Cédric Cleyrat 62 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 63 Andrea Cossarizza 64 Paola Costelli 65 Safia Costes 66 Susan Su Ana Coto-Montes Sandra Cottet Eduardo Couve 67 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 68 Ruben Dagda Uta Dahmen 69 Chunsun Dai Wenjie Wen Bart Staels 70 Arnaud Echard 71 Frank Lafont 72 Emma Colucci-Guyon 73 Matthew L Albert 74 Marc Lecuit 75, 76 Helene Duez 70
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.
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Contributeur : Camille Martinand-Mari <>
Soumis le : mardi 13 novembre 2018 - 17:32:43
Dernière modification le : mardi 13 août 2019 - 11:10:04

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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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