Guidelines for the use and interpretation of assays for monitoring autophagy in higher eukaryotes.

Authors:
Prof. Paula I Moreira, PhD
Prof. Paula I Moreira, PhD
University of Coimbra
Neuroscience; Cell and Molecular Biology; Biochemistry
Coimbra | Portugal
Daniel J Klionsky Hagai Abeliovich Patrizia Agostinis Devendra K Agrawal Gjumrakch Aliev David S Askew Misuzu Baba Eric H Baehrecke Ben A Bahr Andrea Ballabio Bruce A Bamber Diane C Bassham Ettore Bergamini Xiaoning Bi Martine Biard-Piechaczyk Janice S Blum Dale E Bredesen Jeffrey L Brodsky John H Brumell Ulf T Brunk Wilfried Bursch Nadine Camougrand Eduardo Cebollero Francesco Cecconi Yingyu Chen Lih-Shen Chin Augustine Choi Charleen T Chu Jongkyeong Chung Peter G H Clarke Robert S B Clark Steven G Clarke Corinne Clavé John L Cleveland Patrice Codogno María I Colombo Ana Coto-Montes James M Cregg Ana Maria Cuervo Jayanta Debnath Francesca Demarchi Patrick B Dennis Phillip A Dennis Vojo Deretic Rodney J Devenish Federica Di Sano J Fred Dice Marian Difiglia Savithramma Dinesh-Kumar Clark W Distelhorst Mojgan Djavaheri-Mergny Frank C Dorsey Wulf Dröge Michel Dron William A Dunn Michael Duszenko N Tony Eissa Zvulun Elazar Audrey Esclatine Eeva-Liisa Eskelinen László Fésüs Kim D Finley José M Fuentes Juan Fueyo Kozo Fujisaki Brigitte Galliot Fen-Biao Gao David A Gewirtz Spencer B Gibson Antje Gohla Alfred L Goldberg Ramon Gonzalez Cristina González-Estévez Sharon Gorski Roberta A Gottlieb Dieter Häussinger You-Wen He Kim Heidenreich Joseph A Hill Maria Høyer-Hansen Xun Hu Wei-Pang Huang Akiko Iwasaki Marja Jäättelä William T Jackson Xuejun Jiang Shengkan Jin Terje Johansen Jae U Jung Motoni Kadowaki Chanhee Kang Ameeta Kelekar David H Kessel Jan A K W Kiel Hong Pyo Kim Adi Kimchi Timothy J Kinsella Kirill Kiselyov Katsuhiko Kitamoto Erwin Knecht Masaaki Komatsu Eiki Kominami Seiji Kondo Attila L Kovács Guido Kroemer Chia-Yi Kuan Rakesh Kumar Mondira Kundu Jacques Landry Marianne Laporte Weidong Le Huan-Yao Lei Michael J Lenardo Beth Levine Andrew Lieberman Kah-Leong Lim Fu-Cheng Lin Willisa Liou Leroy F Liu Gabriel Lopez-Berestein Carlos López-Otín Bo Lu Kay F Macleod Walter Malorni Wim Martinet Ken Matsuoka Josef Mautner Alfred J Meijer Alicia Meléndez Paul Michels Giovanni Miotto Wilhelm P Mistiaen Noboru Mizushima Baharia Mograbi Iryna Monastyrska Michael N Moore Yuji Moriyasu Tomasz Motyl Christian Münz Leon O Murphy Naweed I Naqvi Thomas P Neufeld Ichizo Nishino Ralph A Nixon Takeshi Noda Bernd Nürnberg Michinaga Ogawa Nancy L Oleinick Laura J Olsen Bulent Ozpolat Shoshana Paglin Glen E Palmer Issidora Papassideri Miles Parkes David H Perlmutter George Perry Mauro Piacentini Ronit Pinkas-Kramarski Mark Prescott Tassula Proikas-Cezanne Nina Raben Abdelhaq Rami Fulvio Reggiori Bärbel Rohrer David C Rubinsztein Kevin M Ryan Junichi Sadoshima Hiroshi Sakagami Yasuyoshi Sakai Marco Sandri Chihiro Sasakawa Miklós Sass Claudio Schneider Per O Seglen Oleksandr Seleverstov Jeffrey Settleman John J Shacka Irving M Shapiro Andrei Sibirny Elaine C M Silva-Zacarin Hans-Uwe Simon Cristiano Simone Anne Simonsen Mark A Smith Katharina Spanel-Borowski Vickram Srinivas Meredith Steeves Harald Stenmark Per E Stromhaug Carlos S Subauste Seiichiro Sugimoto David Sulzer Toshihiko Suzuki Michele S Swanson Ira Tabas Fumihiko Takeshita Nicholas J Talbot Zsolt Tallóczy Keiji Tanaka Kozo Tanaka Isei Tanida Graham S Taylor J Paul Taylor Alexei Terman Gianluca Tettamanti Craig B Thompson Michael Thumm Aviva M Tolkovsky Sharon A Tooze Ray Truant Lesya V Tumanovska Yasuo Uchiyama Takashi Ueno Néstor L Uzcátegui Ida van der Klei Eva C Vaquero Tibor Vellai Michael W Vogel Hong-Gang Wang Paul Webster John W Wiley Zhijun Xi Gutian Xiao Joachim Yahalom Jin-Ming Yang George Yap Xiao-Ming Yin Tamotsu Yoshimori Li Yu Zhenyu Yue Michisuke Yuzaki Olga Zabirnyk Xiaoxiang Zheng Xiongwei Zhu Russell L Deter

Autophagy 2008 Feb 21;4(2):151-75. Epub 2007 Nov 21.

Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109-2216, USA.

Research in autophagy continues to accelerate,(1) and as a result many new scientists are entering the field. Accordingly, it is important to establish a standard set of criteria for monitoring macroautophagy in different organisms. Recent reviews have described the range of assays that have been used for this purpose.(2,3) There are many useful and convenient methods that can be used to monitor macroautophagy in yeast, but relatively few in other model systems, and there is much confusion regarding acceptable methods to measure macroautophagy in higher eukaryotes. A key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers of autophagosomes versus those that measure flux through the autophagy pathway; thus, a block in macroautophagy that results in autophagosome accumulation needs to be differentiated from fully functional autophagy that includes delivery to, and degradation within, lysosomes (in most higher eukaryotes) or the vacuole (in plants and fungi). Here, we present a set of guidelines for the selection and interpretation of the methods that can be used by investigators who are attempting to examine macroautophagy and related processes, as well as by reviewers who need to provide realistic and reasonable critiques of papers that investigate these processes. This set of guidelines is 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 verify an autophagic response.

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February 2008
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