Autophagy: assays and artifacts
Autophagy is a fundamental and phylogenetically conserved self-degradation process that is characterized by the formation of double-layered vesicles (autophagosomes) around intracellular cargo for delivery to lysosomes and proteolytic degradation. The increasing significance attached to autophagy in...
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| Published in | The Journal of pathology Vol. 221; no. 2; pp. 117 - 124 |
|---|---|
| Main Authors | , , |
| Format | Journal Article |
| Language | English |
| Published |
Chichester, UK
John Wiley & Sons, Ltd
01.06.2010
Wiley |
| Subjects | |
| Online Access | Get full text |
| ISSN | 0022-3417 1096-9896 1096-9896 |
| DOI | 10.1002/path.2694 |
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| Abstract | Autophagy is a fundamental and phylogenetically conserved self-degradation process that is characterized by the formation of double-layered vesicles (autophagosomes) around intracellular cargo for delivery to lysosomes and proteolytic degradation. The increasing significance attached to autophagy in development and disease in higher eukaryotes has placed greater importance on the validation of reliable, meaningful and quantitative assays to monitor autophagy in live cells and in vivo in the animal. To date, the detection of processed LC3B-II by western blot or fluorescence studies, together with electron microscopy for autophagosome formation, have been the mainstays for autophagy detection. However, LC3 expression levels can vary markedly between different cell types and in response to different stresses, and there is also concern that over-expression of tagged versions of LC3 to facilitate imaging and detection of autophagy interferes with the process itself. In addition, the realization that it is not sufficient to monitor static levels of autophagy but to measure 'autophagic flux' has driven the development of new or modified approaches to detecting autophagy. Here, we present a critical overview of current methodologies to measure autophagy in cells and in animals. Copyright © 2010 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd. |
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| AbstractList | Autophagy is a fundamental and phylogenetically conserved self-degradation process that is characterized by the formation of double-layered vesicles (autophagosomes) around intracellular cargo for delivery to lysosomes and proteolytic degradation. The increasing significance attached to autophagy in development and disease in higher eukaryotes has placed greater importance on the validation of reliable, meaningful and quantitative assays to monitor autophagy in live cells and in vivo in the animal. To date, the detection of processed LC3B-II by western blot or fluorescence studies, together with electron microscopy for autophagosome formation, have been the mainstays for autophagy detection. However, LC3 expression levels can vary markedly between different cell types and in response to different stresses, and there is also concern that over-expression of tagged versions of LC3 to facilitate imaging and detection of autophagy interferes with the process itself. In addition, the realization that it is not sufficient to monitor static levels of autophagy but to measure 'autophagic flux' has driven the development of new or modified approaches to detecting autophagy. Here, we present a critical overview of current methodologies to measure autophagy in cells and in animals. Copyright © 2010 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd. Autophagy is a fundamental and phylogenetically conserved self‐degradation process that is characterized by the formation of double‐layered vesicles (autophagosomes) around intracellular cargo for delivery to lysosomes and proteolytic degradation. The increasing significance attached to autophagy in development and disease in higher eukaryotes has placed greater importance on the validation of reliable, meaningful and quantitative assays to monitor autophagy in live cells and in vivo in the animal. To date, the detection of processed LC3B‐II by western blot or fluorescence studies, together with electron microscopy for autophagosome formation, have been the mainstays for autophagy detection. However, LC3 expression levels can vary markedly between different cell types and in response to different stresses, and there is also concern that over‐expression of tagged versions of LC3 to facilitate imaging and detection of autophagy interferes with the process itself. In addition, the realization that it is not sufficient to monitor static levels of autophagy but to measure ‘autophagic flux’ has driven the development of new or modified approaches to detecting autophagy. Here, we present a critical overview of current methodologies to measure autophagy in cells and in animals. Copyright © 2010 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd. Autophagy is a fundamental and phylogenetically conserved self-degradation process that is characterized by the formation of double-layered vesicles (autophagosomes) around intracellular cargo for delivery to lysosomes and proteolytic degradation. The increasing significance attached to autophagy in development and disease in higher eukaryotes has placed greater importance on the validation of reliable, meaningful and quantitative assays to monitor autophagy in live cells and in vivo in the animal. To date, the detection of processed LC3B-II by western blot or fluorescence studies, together with electron microscopy for autophagosome formation, have been the mainstays for autophagy detection. However, LC3 expression levels can vary markedly between different cell types and in response to different stresses, and there is also concern that over-expression of tagged versions of LC3 to facilitate imaging and detection of autophagy interferes with the process itself. In addition, the realization that it is not sufficient to monitor static levels of autophagy but to measure 'autophagic flux' has driven the development of new or modified approaches to detecting autophagy. Here, we present a critical overview of current methodologies to measure autophagy in cells and in animals.Autophagy is a fundamental and phylogenetically conserved self-degradation process that is characterized by the formation of double-layered vesicles (autophagosomes) around intracellular cargo for delivery to lysosomes and proteolytic degradation. The increasing significance attached to autophagy in development and disease in higher eukaryotes has placed greater importance on the validation of reliable, meaningful and quantitative assays to monitor autophagy in live cells and in vivo in the animal. To date, the detection of processed LC3B-II by western blot or fluorescence studies, together with electron microscopy for autophagosome formation, have been the mainstays for autophagy detection. However, LC3 expression levels can vary markedly between different cell types and in response to different stresses, and there is also concern that over-expression of tagged versions of LC3 to facilitate imaging and detection of autophagy interferes with the process itself. In addition, the realization that it is not sufficient to monitor static levels of autophagy but to measure 'autophagic flux' has driven the development of new or modified approaches to detecting autophagy. Here, we present a critical overview of current methodologies to measure autophagy in cells and in animals. Autophagy is a fundamental and phylogenetically conserved self-degradation process that is characterized by the formation of double-layered vesicles (autophagosomes) around intracellular cargo for delivery to lysosomes and proteolytic degradation. The increasing significance attached to autophagy in development and disease in higher eukaryotes has placed greater importance on the validation of reliable, meaningful and quantitative assays to monitor autophagy in live cells and in vivo in the animal. To date, the detection of processed LC3B-II by western blot or fluorescence studies, together with electron microscopy for autophagosome formation, have been the mainstays for autophagy detection. However, LC3 expression levels can vary markedly between different cell types and in response to different stresses, and there is also concern that over-expression of tagged versions of LC3 to facilitate imaging and detection of autophagy interferes with the process itself. In addition, the realization that it is not sufficient to monitor static levels of autophagy but to measure 'autophagic flux' has driven the development of new or modified approaches to detecting autophagy. Here, we present a critical overview of current methodologies to measure autophagy in cells and in animals. Autophagy is a fundamental and phylogenetically conserved self-degradation process that is characterized by the formation of double-layered vesicles (autophagosomes) around intracellular cargo for delivery to lysosomes and proteolytic degradation. The increasing significance attached to autophagy in development and disease in higher eukaryotes has placed greater importance on the validation of reliable, meaningful and quantitative assays to monitor autophagy in live cells and in vivo in the animal. To date, the detection of processed LC3B-II by western blot or fluorescence studies, together with electron microscopy for autophagosome formation, have been the mainstays for autophagy detection. However, LC3 expression levels can vary markedly between different cell types and in response to different stresses, and there is also concern that over-expression of tagged versions of LC3 to facilitate imaging and detection of autophagy interferes with the process itself. In addition, the realization that it is not sufficient to monitor static levels of autophagy but to measure ‘autophagic flux’ has driven the development of new or modified approaches to detecting autophagy. Here, we present a critical overview of current methodologies to measure autophagy in cells and in animals. |
| Author | Glick, Danielle Macleod, Kay F Barth, Sandra |
| AuthorAffiliation | 1 Ben May Department for Cancer Research, Gordon Center for Integrative Sciences, University of Chicago, IL, USA 2 Committee on Cancer Biology, Gordon Center for Integrative Sciences, University of Chicago, IL, USA |
| AuthorAffiliation_xml | – name: 1 Ben May Department for Cancer Research, Gordon Center for Integrative Sciences, University of Chicago, IL, USA – name: 2 Committee on Cancer Biology, Gordon Center for Integrative Sciences, University of Chicago, IL, USA |
| Author_xml | – sequence: 1 fullname: Barth, Sandra – sequence: 2 fullname: Glick, Danielle – sequence: 3 fullname: Macleod, Kay F |
| BackLink | http://pascal-francis.inist.fr/vibad/index.php?action=getRecordDetail&idt=22689810$$DView record in Pascal Francis https://www.ncbi.nlm.nih.gov/pubmed/20225337$$D View this record in MEDLINE/PubMed |
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| Copyright | Copyright © 2010 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd. 2015 INIST-CNRS Copyright (c) 2010 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd. Copyright © 2010 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd. 2010 |
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| ISSN | 0022-3417 1096-9896 |
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| Issue | 2 |
| Keywords | Assay autophagic flux Anatomic pathology process Flux Artefact Method Technique analysis Autophagy LC3 Mechanism |
| Language | English |
| License | CC BY 4.0 Copyright (c) 2010 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd. |
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| Notes | http://dx.doi.org/10.1002/path.2694 ark:/67375/WNG-98PQ5229-9 istex:F2F6068829E51881609754E92D2B759B976E281D Swiss National Foundation - No. PBZHP3-123296 ArticleID:PATH2694 Supporting information: Teaching materials; Figures 1 - 2 as PowerPoint slides No conflicts of interest were declared. National Cancer Institute - No. RO1 CA131188 ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 ObjectType-Review-3 content type line 23 |
| OpenAccessLink | http://doi.org/10.1002/path.2694 |
| PMID | 20225337 |
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| PublicationDate | June 2010 |
| PublicationDateYYYYMMDD | 2010-06-01 |
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| PublicationDecade | 2010 |
| PublicationPlace | Chichester, UK |
| PublicationPlace_xml | – name: Chichester, UK – name: Chichester – name: England |
| PublicationTitle | The Journal of pathology |
| PublicationTitleAlternate | J. Pathol |
| PublicationYear | 2010 |
| Publisher | John Wiley & Sons, Ltd Wiley |
| Publisher_xml | – name: John Wiley & Sons, Ltd – name: Wiley |
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Ding ZB, Shi YH, Zhou J, Qiu SJ, Xu Y, Dai Z, e 2007; 104 2005; 170 2007; 128 2007; 282 2010 2007; 581 2009 2009; 452 2008 2008; 15 2009; 453 1962; 12 2008; 445 2008; 4 1993; 268 2003; 278 2009; 114 2009; 137 2008; 283 2003; 33 2009; 29 2009; 11 2000; 19 2009; 10 2004; 432 2005; 120 1967; 33 2007; 130 2008; 27 2007; 131 1999; 274 2008; 68 2009; 5 2007; 3 2008; 454 2009; 461 2008; 112 2007; 21 2006; 126 1990; 111 2009; 1793 2006; 441 2001; 114 2007; 26 e_1_2_9_52_2 e_1_2_9_50_2 e_1_2_9_10_2 e_1_2_9_33_2 e_1_2_9_56_2 Miracco C (e_1_2_9_60_2) 2009 e_1_2_9_12_2 e_1_2_9_31_2 e_1_2_9_54_2 e_1_2_9_14_2 e_1_2_9_37_2 e_1_2_9_16_2 e_1_2_9_35_2 e_1_2_9_58_2 e_1_2_9_18_2 e_1_2_9_39_2 e_1_2_9_41_2 e_1_2_9_62_2 e_1_2_9_20_2 e_1_2_9_45_2 e_1_2_9_22_2 e_1_2_9_43_2 e_1_2_9_64_2 e_1_2_9_6_2 e_1_2_9_4_2 e_1_2_9_2_2 e_1_2_9_8_2 e_1_2_9_24_2 e_1_2_9_49_2 e_1_2_9_26_2 e_1_2_9_47_2 e_1_2_9_28_2 e_1_2_9_51_2 e_1_2_9_30_2 e_1_2_9_34_2 e_1_2_9_55_2 e_1_2_9_11_2 e_1_2_9_32_2 e_1_2_9_53_2 e_1_2_9_13_2 e_1_2_9_38_2 e_1_2_9_59_2 e_1_2_9_15_2 e_1_2_9_36_2 e_1_2_9_57_2 e_1_2_9_17_2 e_1_2_9_19_2 e_1_2_9_40_2 e_1_2_9_63_2 e_1_2_9_61_2 e_1_2_9_21_2 e_1_2_9_44_2 e_1_2_9_23_2 e_1_2_9_42_2 e_1_2_9_65_2 e_1_2_9_7_2 e_1_2_9_5_2 e_1_2_9_3_2 e_1_2_9_9_2 e_1_2_9_25_2 e_1_2_9_48_2 e_1_2_9_27_2 e_1_2_9_46_2 e_1_2_9_29_2 |
| References_xml | – reference: Mizushima N, Yoshimori T. How to interpret LC3 immunoblotting. Autophagy 2007; 3: 542-545. – reference: Klionsky DJ, Agostinis P, Agrawal DK, Bamber BA, Bassham DC, Bergamini E, et al. Guidelines for monitoring autophagy in higher eukaryotes. Autophagy 2008; 4: 151-175. – reference: Ueno T, Ishidoh K, Mineki R, Tanida I, Murayama K, Kadowaki M, et al. Autolysosomal membrane-associated betaine homocysteine methyltransferase. Limited degradation fragment of a sequestered cytosolic enzyme monitoring autophagy. J Biol Chem 1999; 274: 15222-15229. – reference: Ashford TP, Porter KR. Cytoplasmic components in hepatic cell lysosomes. J Cell Biol 1962; 12: 198-202. – reference: Egner R, Thumm M, Straub M, Simeon A, Schuller HJ, Wolf DH. Tracing intracellular proteolytic pathways. Proteolysis of fatty acid synthase and other cytoplasmic proteins in the yeast Saccharomyces cerevisiae. J Biol Chem 1993; 268: 27269-27276. – reference: Perry CN, Kyoi S, Hariharan N, Takagi H, Sadoshima J, Gottlieb RA. Novel methods for measuring cardiac autophagy in vivo. Methods Enzymol 2009; 453: 325-342. – reference: Kimura S, Noda T, Yoshimori T. Dissection of the autophagosome maturation process by a novel reporter protein, tandem fluorescent-tagged LC3. Autophagy 2007; 3: 452-460. – reference: Tolkovsky AM. Mitophagy. Biochim Biophys Acta 2009; 1793: 1508-1515. – reference: Zhang H, Bosch-Marce M, Shimoda LA, Tan YS, Baek JH, Wesley JB, et al. Mitochondrial autophagy is a HIF-1 dependent adaptive metabolic response to hypoxia. J Biol Chem 2008; 283: 10892-10903. – reference: Deter RL, De Duve C. Influence of glucagon, an inducer of cellular autophagy, on some physical properties of rat liver lysosomes. J Cell Biol 1967; 33: 437-449. – reference: Mizushima N. Autophagy: process and function. Genes Dev 2007; 21: 2861-2873. – reference: Cecconi F, Levine B. The role of autophagy in mammalian development: cell makeover rather than cell death. Dev Cell 2008; 15: 344-357. – reference: Tracy K, Macleod KF. Regulation of mitochondrial integrity, autophagy and cell survival by BNIP3. Autophagy 2007; 3: 616-619. – reference: Mercer CA, Kaliappan A, Dennis PB. Macroautophagy-dependent, intralysosomal cleavage of a betaine homocysteine methyltransferase fusion protein requires stable multimerization. Autophagy 2008; 4: 185-194. – reference: Li B, Li CY, Peng RQ, Wu XJ, Wang HY, Wan DS, et al. The expression of beclin1 is associated with favorable prognosis in stage IIIB colon cancers. Autophagy 2009; 5: 303-306. – reference: Rubinsztein DC, Cuervo AM, Ravikumar B, Sarkar S, Korolchuk V, Kaushik S, et al. In search of an 'autophagometer'. Autophagy 2009; 5: 1-5. – reference: Bauvy C, Meijer AJ, Codogno P. Assaying of autophagic protein degradation. Methods Enzymol 2009; 452: 47-61. – reference: Munafo DB, Colombo MI. A novel assay to study autophagy: regulation of autophagosome vacuole size by amino acid deprivation. J Cell Sci 2001; 114: 3619-3629. – reference: Pankiv S, Clausen TH, Lamark T, Brech A, Bruun JA, Outzen H, et al. p62/SQSTM1 binds directly to Atg8/LC3 to facilitate degradation of ubiquitinated protein aggregates by autophagy. J Biol Chem 2007; 282: 24121-24145. – reference: Kundu M, Lindsten T, Yang CY, Wu J, Zhao F, Zhang J, et al. Ulk1 plays a critical role in the autophagic clearance of mitochondria and ribosomes during reticulocyte maturation. Blood 2008; 112: 1493-1502. – reference: Nishida Y, Arakawa S, Fujitani K, Yamaguchi H, Mizuta T, Kanaseki T, et al. Discovery of Atg5/Atg7-independent alternative macroautophagy. Nature 2009; 461: 654-659. – reference: Komatsu M, Waguri S, Koike M, Sou YS, Ueno T, Hara T, et al. Homeostatic levels of p62 control cytoplasmic inclusion body formation in autophagy-deficient mice. Cell 2007; 131: 1149-1163. – reference: Kuma A, Hatano M, Matsui M, Yamamoto A, Nakaya H, Yoshimori T, et al. The role of autophagy during the early neonatal starvation period. Nature 2004; 432: 1032-1036. – reference: Yla-Anttila P, Vihinen H, Jokitalo E, Eskelinen EL. 3D tomography reveals connections between the phagophore and endoplasmic reticulum. Autophagy 2009; 5: 1180-1185. – reference: Kuma A, Mizushima N. Chromosomal mapping of the GFP-LC3 transgene in GFP-LC3 mice. Autophagy 2008; 4: 61-62. – reference: Nakatogawa H, Suzuki K, Kamada Y, Ohsumi Y. Dynamics and diversity in autophagy mechanisms: lessons from yeast. Nat Rev Mol Cell Biol 2009; 10: 458-467. – reference: Glick D, Barth S, Macleod KF. Autophagy: cellular and molecular mechanisms. J Pathol 2010; DOI: 10.1002/path.2697. – reference: Lum JJ, Bauer DE, Kong M, Harris MH, Li CY, Lindsten T, et al. Growth factor regulation of autophagy and cell survival in the absence of apoptosis. Cell 2005; 120: 237-249. – reference: Copetti T, Bertoli C, Dalla E, Demarchi F, Schneider C. p65/RelA modulates BECN1 transcription and autophagy. Mol Cell Biol 2009; 29: 2594-2608. – reference: Qu X, Zou Z, Sun Q, Luby-Phelps K, Cheng P, Hogan RN, et al. Autophagy gene-dependent clearance of apoptotic cells during embryonic development. Cell 2007; 128: 931-946. – reference: He H, Dang Y, Dai F, Guo Z, Wu J, She X, et al. Post-translational modifications of three members of the human MAP1LC3 family and detection of a novel type of modification for MAP1LC3B. J Biol Chem 2003; 278: 29278-29287. – reference: Hara T, Nakamura K, Matsui M, Yamamoto A, Nakahara Y, Suzuki-Migishima R, et al. Suppression of basal autophagy in neural cells causes neurodegenerative disease in mice. Nature 2006; 441: 885-889. – reference: Zhang J, Randall MS, Loyd MR, Dorsey FC, Kundu M, Cleveland JL, et al. 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| Snippet | Autophagy is a fundamental and phylogenetically conserved self-degradation process that is characterized by the formation of double-layered vesicles... Autophagy is a fundamental and phylogenetically conserved self‐degradation process that is characterized by the formation of double‐layered vesicles... |
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| SubjectTerms | analysis Animals autophagic flux autophagy Autophagy - physiology Biological and medical sciences Biomarkers Flow Cytometry - methods Humans Investigative techniques, diagnostic techniques (general aspects) LC3 Lysosomes - metabolism mechanism Medical sciences method Microscopy, Electron Microscopy, Fluorescence Microtubule-Associated Proteins - metabolism Pathology. Cytology. Biochemistry. Spectrometry. Miscellaneous investigative techniques Phagosomes - physiology Phagosomes - ultrastructure process technique |
| Title | Autophagy: assays and artifacts |
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