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

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 Cotomontes; 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; Pyo Kim Hong; 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; Paula I. Moreira; 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 Proikascezanne; Nina Raben; Abdelhaq Rami; Fulvio Reggiori; Bärbel Rohrer; David C. Rubinsztein; Kevin M. Ryan; Junichi Sadoshima; Hiroshi Sakagami; Yasuyoshi Sakai; Marco Sandri; Chihiro Sasakawa; Miklos 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; Crisfiano 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

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

Journal article

Peer reviewed

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

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, …

Autophagy, Vol.4(2), pp.151-175

02/16/2008

PMCID: PMC2654259

PMID: 18188003

Abstract

Cell Biology

Molecular Biology

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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Title: Guidelines for the use and interpretation of assays for monitoring autophagy in higher eukaryotes
Creators: Daniel J. Klionsky (Author) - University of Michigan, Ann Arbor
Hagai Abeliovich (Author) - Hebrew University of Jerusalem
Patrizia Agostinis (Author) - KU Leuven
Devendra K. Agrawal (Author) - Department of Clinical Research and Public Health
Gjumrakch Aliev (Author) - University of Texas at San Antonio
David S. Askew (Author) - University of Cincinnati
Misuzu Baba (Author) - Japan Women's University
Eric H. Baehrecke (Author) - University of Massachusetts Medical School
Ben A. Bahr (Author) - University of Connecticut
Andrea Ballabio (Author) - Fondazione Telethon
Bruce A. Bamber (Author) - University of Toledo
Diane C. Bassham (Author) - Iowa State University
Ettore Bergamini (Author) - University of Pisa
Xiaoning Bi (Author) - Western University of Health Sciences
Martine Biard-Piechaczyk (Author) - Université de Montpellier
Janice S. Blum (Author) - Indiana University-Purdue University Indianapolis
Dale E. Bredesen (Author) - Buck Institute for Age Research
Jeffrey L. Brodsky (Author) - University of Pittsburgh
John H. Brumell (Author) - University of Toronto
Ulf T. Brunk (Author) - Linköping University
Wilfried Bursch (Author) - Medical University of Vienna
Nadine Camougrand (Author) - Université de Bordeaux
Eduardo Cebollero (Author) - CSIC
Francesco Cecconi (Author) - University of Rome Tor Vergata
Yingyu Chen (Author) - Peking University
Lih Shen Chin (Author) - Emory University
Augustine Choi (Author) - Harvard University
Charleen T. Chu (Author) - University of Pittsburgh
Jongkyeong Chung (Author) - Korea Advanced Institute of Science and Technology
Peter G H Clarke (Author) - University of Lausanne
Robert S B Clark (Author) - University of Pittsburgh
Steven G. Clarke (Author) - University of California at Los Angeles
Corinne Clavé (Author) - Université de Bordeaux
John L. Cleveland (Author) - Scripps Research Institute
Patrice Codogno (Author) - Université Paris-Sud
María I. Colombo (Author) - Universidad Nacional de Cuyo
Ana Cotomontes (Author) - University of Oviedo
James M. Cregg (Author) - Keck Graduate Institute
Ana Maria Cuervo (Author) - Yeshiva University
Jayanta Debnath (Author) - University of California at San Francisco
Francesca Demarchi (Author) - Laboratorio Nazionale Consorzio Interuniversitario Biotecnologie
Patrick B. Dennis (Author) - University of Cincinnati
Phillip A. Dennis (Author) - National Institutes of Health
Vojo Deretic (Author) - University of New Mexico
Rodney J. Devenish (Author) - Monash University
Federica Di Sano (Author) - University of Rome Tor Vergata
J. Fred Dice (Author) - Tufts University
Marian DiFiglia (Author) - Harvard University
Savithramma Dinesh-Kumar (Author) - Yale University
Clark W. Distelhorst (Author) - Case Western Reserve University
Mojgan Djavaheri-Mergny (Author) - Université Paris-Sud
Frank C. Dorsey (Author) - Scripps Research Institute
Wulf Dröge (Author) - Immunotec Research Ltd.
Michel Dron (Author) - Université Paris-Saclay
William A. Dunn (Author) - University of Florida
Michael Duszenko (Author) - University of Tübingen
N. Tony Eissa (Author) - Baylor College of Medicine
Zvulun Elazar (Author) - Weizmann Institute of Science
Audrey Esclatine (Author) - Université Paris-Sud
Eeva Liisa Eskelinen (Author) - University of Helsinki
László Fésüs (Author) - University of Debrecen
Kim D. Finley (Author) - Salk Institute for Biological Studies
José M. Fuentes (Author) - University of Extremadura
Juan Fueyo (Author) - University of Texas MD Anderson Cancer Center
Kozo Fujisaki (Author) - Kagoshima University
Brigitte Galliot (Author) - University of Geneva
Fen Biao Gao (Author) - University of California at San Francisco
David A. Gewirtz (Author) - Virginia Commonwealth University
Spencer B. Gibson (Author) - University of Manitoba
Antje Gohla (Author) - Heinrich Heine University Düsseldorf
Alfred L. Goldberg (Author) - Harvard University
Ramon Gonzalez (Author) - CSIC
Cristina González-Estévez (Author) - University of Nottingham
Sharon Gorski (Author) - University of British Columbia
Roberta A. Gottlieb (Author) - San Diego State University
Dieter Häussinger (Author) - Heinrich Heine University Düsseldorf
You Wen He (Author) - Duke University
Kim Heidenreich (Author) - University of Colorado Denver
Joseph A. Hill (Author) - University of Texas Southwestern Medical Center
Maria Høyer-Hansen (Author) - Institute of Cancer Biology
Xun Hu (Author) - Zhejiang University
Wei Pang Huang (Author) - National Taiwan University
Akiko Iwasaki (Author) - Yale University
Marja Jäättelä (Author) - Institute of Cancer Biology
William T. Jackson (Author) - Medical College of Wisconsin
Xuejun Jiang (Author) - Memorial Sloan-Kettering Cancer Center
Shengkan Jin (Author) - Rutgers - The State University of New Jersey, New Brunswick
Terje Johansen (Author) - UiT The Arctic University of Norway
Jae U. Jung (Author) - University of Southern California
Motoni Kadowaki (Author) - Niigata University
Chanhee Kang (Author) - University of Texas Southwestern Medical Center
Ameeta Kelekar (Author) - University of Minnesota Twin Cities
David H. Kessel (Author) - Wayne State University
Jan A K W Kiel (Author) - University of Groningen
Pyo Kim Hong (Author) - University of Pittsburgh
Adi Kimchi (Author) - Weizmann Institute of Science
Timothy J. Kinsella (Author) - Case Western Reserve University
Kirill Kiselyov (Author) - University of Pittsburgh
Katsuhiko Kitamoto (Author) - The University of Tokyo
Erwin Knecht (Author) - Centro de Investigacion Principe Felipe
Masaaki Komatsu (Author) - Tokyo Metropolitan Institute of Medical Science
Eiki Kominami (Author) - Juntendo University
Seiji Kondo (Author) - University of Texas MD Anderson Cancer Center
Attila L. Kovács (Author) - Eotvos Lorand University
Guido Kroemer (Author) - Université Paris-Sud
Chia Yi Kuan (Author) - Cincinnati Children's Hospital Medical Center
Rakesh Kumar (Author) - University of Texas MD Anderson Cancer Center
Mondira Kundu (Author) - University of Pennsylvania
Jacques Landry (Author) - Université Laval
Marianne Laporte (Author) - Eastern Michigan University
Weidong Le (Author) - Shanghai Jiao Tong University
Huan Yao Lei (Author) - National Cheng Kung University
Michael J. Lenardo (Author) - National Institutes of Health
Beth Levine (Author) - University of Texas Southwestern Medical Center
Andrew Lieberman (Author) - University of Michigan, Ann Arbor
Kah Leong Lim (Author) - National Neuroscience Institute of Singapore
Fu Cheng Lin (Author) - Zhejiang University
Willisa Liou (Author) - Chang Gung University
Leroy F. Liu (Author) - Rutgers - The State University of New Jersey, New Brunswick
Gabriel Lopez-Berestein (Author) - University of Texas MD Anderson Cancer Center
Carlos López-Otín (Author) - University of Oviedo
Bo Lu (Author) - Vanderbilt University
Kay F. Macleod (Author) - The University of Chicago
Walter Malorni (Author) - Istituto Superiore di Sanita
Wim Martinet (Author) - University of Antwerp
Ken Matsuoka (Author) - Kyushu University
Josef Mautner (Author) - Helmholtz Zentrum München - German Research Center for Environmental Health
Alfred J. Meijer (Author) - University of Amsterdam
Alicia Meléndez (Author) - City University of New York
Paul Michels (Author) - Université catholique de Louvain
Giovanni Miotto (Author) - University of Padua
Wilhelm P. Mistiaen (Author) - University College of Antwerp
Noboru Mizushima (Author) - Tokyo Medical and Dental University
Baharia Mograbi (Author) - Institut national de la santé et de la recherche médicale
Iryna Monastyrska (Author) - Utrecht University
Michael N. Moore (Author) - Plymouth Marine Laboratory
Paula I. Moreira (Author) - University of Coimbra
Yuji Moriyasu (Author) - Saitama University
Tomasz Motyl (Author) - Warsaw University of Life Sciences
Christian Münz (Author) - Rockefeller University
Leon O. Murphy (Author) - Novartis USA
Naweed I. Naqvi (Author) - National University of Singapore
Thomas P. Neufeld (Author) - University of Minnesota Twin Cities
Ichizo Nishino (Author) - National Center of Neurology and Psychiatry Kodaira
Ralph A. Nixon (Author) - New York University
Takeshi Noda (Author) - Osaka University
Bernd Nürnberg (Author) - Heinrich Heine University Düsseldorf
Michinaga Ogawa (Author) - The University of Tokyo
Nancy L. Oleinick (Author) - Case Western Reserve University
Laura J. Olsen (Author) - University of Michigan, Ann Arbor
Bulent Ozpolat (Author) - University of Texas MD Anderson Cancer Center
Shoshana Paglin (Author) - Sheba Medical Center at Tel Hashomer
Glen E. Palmer (Author) - Louisiana State University Health Sciences Center
Issidora Papassideri (Author) - Department of Cell Biology and Biophysics
Miles Parkes (Author) - University of Cambridge
David H. Perlmutter (Author) - University of Pittsburgh
George Perry (Author) - University of Texas at San Antonio
Mauro Piacentini (Author) - University of Rome Tor Vergata
Ronit Pinkas-Kramarski (Author) - Tel Aviv University
Mark Prescott (Author) - Monash University
Tassula Proikascezanne (Author) - University of Tübingen
Nina Raben (Author) - National Institutes of Health
Abdelhaq Rami (Author) - Goethe University Frankfurt
Fulvio Reggiori (Author) - Utrecht University
Bärbel Rohrer (Author) - Medical University of South Carolina
David C. Rubinsztein (Author) - University of Cambridge
Kevin M. Ryan (Author) - Cancer Research UK
Junichi Sadoshima (Author) - Rutgers - The State University of New Jersey, Newark
Hiroshi Sakagami (Author) - Meikai University
Yasuyoshi Sakai (Author) - Kyoto University;Japan Science and Technology Agency
Marco Sandri (Author) - University of Padua;Venetian Institute of Molecular Medicine
Chihiro Sasakawa (Author) - The University of Tokyo
Miklos Sass (Author) - Eotvos Lorand University
Claudio Schneider (Author) - Laboratorio Nazionale Consorzio Interuniversitario Biotecnologie
Per O. Seglen (Author) - University of Oslo
Oleksandr Seleverstov (Author) - University of Wyoming
Jeffrey Settleman (Author) - Harvard University
John J. Shacka (Author) - University of Alabama at Birmingham
Irving M. Shapiro (Author) - Thomas Jefferson University
Andrei Sibirny (Author) - NASU - Institute of Cell Biology
Elaine C M Silva-Zacarin (Author) - Universidade Federal de São Carlos
Hans Uwe Simon (Author) - University of Bern
Crisfiano Simone (Author) - Consorzio Mario Negri Sud
Anne Simonsen (Author) - University of Oslo
Mark A. Smith (Author) - Case Western Reserve University
Katharina Spanel-Borowski (Author) - Leipzig University
Vickram Srinivas (Author) - Thomas Jefferson University
Meredith Steeves (Author) - Scripps Research Institute
Harald Stenmark (Author) - University of Oslo
Per E. Stromhaug (Author) - University of Missouri
Carlos S. Subauste (Author) - Case Western Reserve University
Seiichiro Sugimoto (Author) - National Hospital Organization, Japan
David Sulzer (Author) - Columbia University
Toshihiko Suzuki (Author) - University of the Ryukyus
Michele S. Swanson (Author) - University of Michigan, Ann Arbor
Ira Tabas (Author) - Columbia University
Fumihiko Takeshita (Author) - Yokohama City University
Nicholas J. Talbot (Author) - University of Exeter
Zsolt Tallóczy (Author) - Columbia University
Keiji Tanaka (Author) - Tokyo Metropolitan Institute of Medical Science
Kozo Tanaka (Author) - Tohoku University
Isei Tanida (Author) - National Institute of Infectious Diseases
Graham S. Taylor (Author) - University of Birmingham
J. Paul Taylor (Author) - University of Pennsylvania
Alexei Terman (Author) - Linköping University
Gianluca Tettamanti (Author) - University of Insubria
Craig B. Thompson (Author) - University of Pennsylvania
Michael Thumm (Author) - University of Göttingen
Aviva M. Tolkovsky (Author) - University of Cambridge
Sharon A. Tooze (Author) - Cancer Research UK
Ray Truant (Author) - McMaster University
Lesya V. Tumanovska (Author) - Bogomoletz Institute of Physiology
Yasuo Uchiyama (Author) - Osaka University
Takashi Ueno (Author) - Juntendo University
Néstor L. Uzcátegui (Author) - Universidad Central de Venezuela
Ida Van Der Klei (Author) - University of Groningen
Eva C. Vaquero (Author) - University of Barcelona
Tibor Vellai (Author) - Eotvos Lorand University
Michael W. Vogel (Author) - University of Maryland, Baltimore
Hong Gang Wang (Author) - University of South Florida
Paul Webster (Author) - House Ear Institute
John W. Wiley (Author) - University of Michigan, Ann Arbor
Zhijun Xi (Author) - Peking University
Gutian Xiao (Author) - University of Pittsburgh
Joachim Yahalom (Author) - Memorial Sloan-Kettering Cancer Center
Jin Ming Yang (Author) - Rutgers - The State University of New Jersey, New Brunswick
George Yap (Author) - Rutgers - The State University of New Jersey, Newark
Xiao Ming Yin (Author) - University of Pittsburgh
Tamotsu Yoshimori (Author) - Osaka University
Li Yu (Author) - National Institutes of Health
Zhenyu Yue (Author) - Icahn School of Medicine at Mount Sinai
Michisuke Yuzaki (Author) - Keio University
Olga Zabirnyk (Author) - National Institutes of Health, Bethesda
Xiaoxiang Zheng (Author) - Zhejiang University
Xiongwei Zhu (Author) - Case Western Reserve University
Russell L. Deter (Author) - Baylor College of Medicine
Publication Details: Autophagy, Vol.4(2), pp.151-175
Series: 4
Number of pages: 25
Identifiers: 991005930458202656
Academic Unit: Clinical Research and Public Health
Language: English
Resource Type: Journal article

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

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