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

Klionsky, Daniel J and Abeliovich, Hagai and Agostinis, Patrizia and Agrawal, Devendra K and Aliev, Gjumrakch and Askew, David S and Baba, Misuzu and Baehrecke, Eric H and Bahr, Ben A and Ballabio, Andrea and Bamber, Bruce A and Bassham, Diane C and Bergamini, Ettore and Bi, Xiaoning and Biard-Piechaczyk, Martine and Blum, Janice S and Bredesen, Dale E and Brodsky, Jeffrey L and Brumell, John H and Brunk, Ulf T and Bursch, Wilfried and Camougrand, Nadine and Cebollero, Eduardo and Cecconi, Francesco and Chen, Yingyu and Chin, Lih-Shen and Choi, Augustine and Chu, Charleen T and Chung, Jongkyeong and Clarke, Peter G H and Clark, Robert S B and Clarke, Steven G and Clave, Corinne and Cleveland, John L and Codogno, Patrice and Colombo, Maria I and Coto-Montes, Ana and Cregg, James M and Cuervo, Ana Maria and Debnath, Jayanta and Demarchi, Francesca and Dennis, Patrick B and Dennis, Phillip A and Deretic, Vojo and Devenish, Rodney J and Di Sano, Federica and Dice, J Fred and Difiglia, Marian and Dinesh-Kumar, Savithramma and Distelhorst, Clark W and Djavaheri-Mergny, Mojgan and Dorsey, Frank C and Droge, Wulf and Dron, Michel and Dunn, William A and Duszenko, Michael and Eissa, N Tony and Elazar, Zvulun and Esclatine, Audrey and Eskelinen, Eeva-Liisa and Fesus, Laszlo and Finley, Kim D and Fuentes, Jose M and Fueyo, Juan and Fujisaki, Kozo and Galliot, Brigitte and Gao, Fen-Biao and Gewirtz, David A and Gibson, Spencer B and Gohla, Antje and Goldberg, Alfred L and Gonzalez, Ramon and González-Estévez, Cristina and Gorski, Sharon and Gottlieb, Roberta A and Haussinger, Dieter and He, You-Wen and Heidenreich, Kim and Hill, Joseph A and Hoyer-Hansen, Maria and Hu, Xun and Huang, Wei-Pang and Iwasaki, Akiko and Jaattela, Marja and Jackson, William T and Jiang, Xuejun and Jin, Shengkan and Johansen, Terje and Jung, Jae U and Kadowaki, Motoni and Kang, Chanhee and Kelekar, Ameeta and Kessel, David H and Kiel, Jan A K W and Kim, Hong Pyo and Kimchi, Adi and Kinsella, Timothy J and Kiselyov, Kirill and Kitamoto, Katsuhiko and Knecht, Erwin and Komatsu, Masaaki and Kominami, Eiki and Kondo, Seiji and Kovács, Attila L and Kroemer, Guido and Kuan, Chia-Yi and Kumar, Rakesh and Kundu, Mondira and Landry, Jacques and Laporte, Marianne and Le, Weidong and Lei, Huan-Yao and Lenardo, Michael J and Levine, Beth and Lieberman, Andrew and Lim, Kah-Leong and Lin, Fu-Cheng and Liou, Willisa and Liu, Leroy F and Lopez-Berestein, Gabriel and Lopez-Otin, Carlos and Lu, Bo and Macleod, Kay F and Malorni, Walter and Martinet, Wim and Matsuoka, Ken and Mautner, Josef and Meijer, Alfred J and Melendez, Alicia and Michels, Paul and Miotto, Giovanni and Mistiaen, Wilhelm P and Mizushima, Noboru and Mograbi, Baharia and Monastyrska, Iryna and Moore, Michael N and Moreira, Paula I and Moriyasu, Yuji and Motyl, Tomasz and Munz, Christian and Murphy, Leon and Naqvi, Naweed I and Neufeld, Thomas P and Nishino, Ichizo and Nixon, Ralph A and Noda, Takeshi and Nurnberg, Bernd and Ogawa, Michinaga and Oleinick, Nancy L and Olsen, Laura J and Ozpolat, Bulent and Paglin, Shoshana and Palmer, Glen E and Papassideri, Issidora and Parkes, Miles and Perlmutter, David H and Perry, George and Piacentini, Mauro and Pinkas-Kramarski, Ronit and Prescott, Mark and Proikas-Cezanne, Tassula and Raben, Nina and Rami, Abdelhaq and Reggiori, Fulvio and Rohrer, Bärbel and Rubinsztein, David C and Ryan, Kevin M and Sadoshima, Junichi and Sakagami, Hiroshi and Sakai, Yasuyoshi and Sandri, Marco and Sasakawa, Chihiro and Sass, Miklós and Schneider, Claudio and Seglen, Per O and Seleverstov, Oleksandr and Settleman, Jeffrey and Shacka, John J and Shapiro, Irving M and Sibirny, Andrei and Silva-Zacarin, Elaine C M and Simon, Hans-Uwe and Simone, Cristiano and Simonsen, Anne and Smith, Mark A and Spanel-Borowski, Katharina and Srinivas, Vickram and Steeves, Meredith and Stenmark, Harald and Stromhaug, Per E and Subauste, Carlos S and Sugimoto, Seiichiro and Sulzer, David and Suzuki, Toshihiko and Swanson, Michele S and Tabas, Ira and Takeshita, Fumihiko and Talbot, Nicholas J and Talloczy, Zsolt and Tanaka, Keiji and Tanaka, Kozo and Tanida, Isei and Taylor, Graham S and Taylor, J Paul and Terman, Alexei and Tettamanti, Gianluca and Thompson, Craig B and Thumm, Michael and Tolkovsky, Aviva M and Tooze, Sharon A and Truant, Ray and Tumanovska, Lesya V and Uchiyama, Yasuo and Ueno, Takashi and Uzcátegui, Néstor L and van der Klei, Ida and Vaquero, Eva C and Vellai, Tibor and Vogel, Michael W and Wang, Hong-Gang and Webster, Paul and Wiley, John W and Xi, Zhijun and Xiao, Gutian and Yahalom, Joachim and Yang, Jin-Ming and Yap, George and Yin, Xiao-Ming and Yoshimori, Tamotsu and Yu, Li and Yue, Zhenyu and Yuzaki, Michisuke and Zabirnyk, Olga and Zheng, Xiaoxiang and Zhu, Xiongwei and Deter, Russell L (2008) Guidelines for the use and interpretation of assays for monitoring autophagy in higher eukaryotes. Autophagy, 4 (2). pp. 151-175. ISSN 1554-8635

Abstract

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.

Item Type: Article
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Additional Information: archiving not formally supported by this publisher
Keywords: autolysosome; autophagosome; flux; lysosome; phagophore; stress; vacuol
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Date Deposited: 14 Dec 2009 13:51
Last Modified: 31 Jan 2013 01:03
URI: https://oak.novartis.com/id/eprint/923

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