Cited by 258Autophagy in Disease and TherapyAdvanced Electron Microscopy Techniques and ApplicationsCellular transport and secretion

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Chapter 10 Monitoring Autophagy by Electron Microscopy in Mammalian Cells

Ylä‐Anttila, Päivi, Vihinen, Helena, Jokitalo, Eija, Eskelinen, Eeva‐Liisa·2009·Methods in Enzymology

DOI 10.1016/s0076-6879(08)03610-0

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Abstract

Electron microscopy remains one of the most accurate methods for the detection of autophagy and quantification of autophagic accumulation. Compared to fluorescence microscopy, the resolution of transmission electron microscopy is superior. In this chapter we describe the fine structure of early and late autophagic compartments in mammalian cells. Instructions are given for the preparation of samples for conventional electron microscopy using three different protocols suitable for cultured cells and animal tissues. We also introduce tomography as a tool to study the three-dimensional morphology of autophagic organelles and show the morphology of a phagophore as an example. Finally, we describe a protocol for the quantification of autophagic compartments by electron microscopy and point counting.

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LC3, a mammalian homologue of yeast Apg8p, is localized in autophagosome membranes after processing.
Kabeya, Y., Mizushima, N., Ueno, T., Yamamoto, A., Kirisako, T., Noda, T., Kominami, E., Ohsumi, Y., & Yoshimori, T. (2000) · The EMBO Journal · doi:10.1093/emboj/19.21.5720 · Cited by 6,605
Autophagosome formation: core machinery and adaptations
Xie, Z., & Klionsky, D. J. (2007) · Nature Cell Biology · doi:10.1038/ncb1007-1102 · Cited by 2,237
Guidelines for the use and interpretation of assays for monitoring autophagy in higher eukaryotes
Klionsky, D. J., Abeliovich, H., Agostinis, P., Agrawal, D. K., Aliev, G., Askew, D. S., Baba, M., Baehrecke, E. H., Bahr, B. A., Ballabio, A., et al. (2008) · Autophagy · doi:10.4161/auto.5338 · Cited by 2,230
Principles and Techniques of Electron Microscopy: Biological Applications
Maugel, T. K., & Hayat, M. A. (1979) · Transactions of the American Microscopical Society · doi:10.2307/3226038 · Cited by 1,327
A Unified Nomenclature for Yeast Autophagy-Related Genes
Klionsky, D. J., Cregg, J. M., Dunn, W. A., Emr, S. D., Sakai, Y., Sandoval, I. V., Sibirny, A. А., Subramani, S. E., Thumm, M., Marten Veenhuis, A., et al. (2003) · Developmental Cell · doi:10.1016/s1534-5807(03)00296-x · Cited by 1,305
Unbiased Stereology: Three-Dimensional Measurement in Microscopy
Howard, C. V., & Reed, M. (1998) · Cited by 1,149
Role for Rab7 in maturation of late autophagic vacuoles
Jäger, S., Bucci, C., Tanida, I., Ueno, T., Kominami, E., Säftig, P., & Eskelinen, E. (2004) · Journal of Cell Science · doi:10.1242/jcs.01370 · Cited by 970
Unbiased Stereology. Three‐Dimensional Measurement in Microscopy.
Sandau, K. (1999) · Journal of Microscopy · doi:10.1046/j.1365-2818.1999.0429a.x · Cited by 890
Studies on the mechanisms of autophagy: formation of the autophagic vacuole.
Dunn, W. A. (1990) · The Journal of Cell Biology · doi:10.1083/jcb.110.6.1923 · Cited by 787
Maturation of Autophagic Vacuoles in Mammalian Cells
Eskelinen, E.-L. (2005) · Autophagy · doi:10.4161/auto.1.1.1270 · Cited by 626

Show all 26 references

Research works printed but not linked: 1

Eskelinen, 2008, Fine structure of the autophagosome, Methods Mol. Biol., 445, 11, 10.1007/978-1-59745-157-4_2 · DOI

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Method
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Method
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Background
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BackgroundMethod
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Background
GDF-15 Deficiency Reduces Autophagic Activity in Human Macrophages In Vitro and Decreases p62-Accumulation in Atherosclerotic Lesions in Mice
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Background
Abnormal cell-clearance and accumulation of autophagic vesicles in lymphocytes from patients affected with Ataxia-Teleangiectasia
D’Assante, R., Fusco, A., Palamaro, L., Polishchuk, E., Polishchuk, R., Bianchino, G., Grieco, V., Prencipe, M. R., Ballabio, A., & Pignata, C. (2016) · Clinical Immunology · doi:10.1016/j.clim.2016.11.015 · Cited by 20
ACTP: A webserver for predicting potential targets and relevant pathways of autophagy-modulating compounds
Xie, T., Zhang, L., Zhang, S., Ouyang, L., Cai, H., & Liu, B. (2016) · Oncotarget · doi:10.18632/oncotarget.7015 · Cited by 19
“If cellular stress leads to continuous or excessively induced autophagy, cell death will ensue [6, 7].”
Reduced Dendritic Spines in the Visual Cortex Contralateral to the Optic Nerve Crush Eye in Adult Mice
Zhan, Z., Wu, Y., Liu, Z., Quan, Y., Li, D., Huang, Y., Yang, S., Wu, K., Huang, L., & Yu, M. (2020) · Investigative Ophthalmology & Visual Science · doi:10.1167/iovs.61.10.55 · Cited by 18
Improved Electron Microscopy Fixation Methods for Tracking Autophagy-Associated Membranes in Cultured Mammalian Cells
Arai, R., & Waguri, S. (2019) · Methods in molecular biology · doi:10.1007/978-1-4939-8873-0_13 · Cited by 18
Downregulation of BAG3 attenuates cisplatin resistance by inhibiting autophagy in human epithelial ovarian cancer cells
Qiu, S., Sun, L., Zhang, Y., & Han, S. (2019) · Oncology Letters · doi:10.3892/ol.2019.10494 · Cited by 18
Hydatid fluid from Echinococcus granulosus induces autophagy in dendritic cells and promotes polyfunctional T-cell responses
Chop, M., Ledo, C., Nicolao, M. C., Loos, J. A., Cumino, A. C., & Rodrígues, C. R. (2024) · Frontiers in Cellular and Infection Microbiology · doi:10.3389/fcimb.2024.1334211 · Cited by 16
Compound C inhibits nonsense-mediated RNA decay independently of AMPK
Cheruiyot, A., Li, S., Nickless, A., Roth, R. A., Fitzpatrick, J. A. J., & You, Z. (2018) · PLoS ONE · doi:10.1371/journal.pone.0204978 · Cited by 15
“Autophagosomes were identified as vacuoles containing cytoplasmic organelles, such as ribosomes or mitochondria, with a limited membrane as described in standard guidelines[63, 64].”
Correlative Light and Electron Microscopy of Autophagosomes
Gudmundsson, S. R., Kahlhofer, J., Baylac, N., Kallio, K., & Eskelinen, E. (2019) · Methods in molecular biology · doi:10.1007/978-1-4939-8873-0_12 · Cited by 15
Heterogeneous Vancomycin-Intermediate Staphylococcus aureus Uses the VraSR Regulatory System to Modulate Autophagy for Increased Intracellular Survival in Macrophage-Like Cell Line RAW264.7
Dai, Y., Gao, C., Chen, L., Chang, W., Yu, W., Ma, X., & Li, J. (2019) · Frontiers in Microbiology · doi:10.3389/fmicb.2019.01222 · Cited by 15
Parkin-dependent mitophagy occurs via proteasome-dependent steps sequentially targeting separate mitochondrial sub-compartments for autophagy
Lechado‐Terradas, A., Schepers, S., Zittlau, K. I., Sharma, K., Ok, O., Fitzgerald, J. C., Geimer, S., Westermann, B., Maček, B., & Kahle, P. J. (2022) · Autophagy Reports · doi:10.1080/27694127.2022.2143214 · Cited by 17
“…on tissue-speci ﬁ c cells where mitochondrial survival is crucial for their metabolic or physiological demands (i.e: neurons and hepatocytes) [8,37,38], it is possible that when cell survival is not strictly dependent on mitochondrial functions, wholesale mitophagy partially switches to…”
Experimental determination and mathematical modeling of standard shapes of forming autophagosomes
Sakai, Y., Takahashi, S., Koyama‐Honda, I., Saito, C., & Mizushima, N. (2024) · Nature Communications · doi:10.1038/s41467-023-44442-1 · Cited by 14
“We collected 117 entire 3D structures of phagophores from 23 chemically ﬁ xed cells based on their characteristic 3D morphology and strong contrast after osmium staining 9 (Fig.”
Method
Design and Evaluation of Autophagy-Inducing Particles for the Treatment of Abnormal Lipid Accumulation
Zagkou, S., Marais, V., Zeghoudi, N., Guillou, É. L., Eskelinen, E., Panasyuk, G., Verrier, B., & Primard, C. (2022) · Pharmaceutics · doi:10.3390/pharmaceutics14071379 · Cited by 15
Different routes lead to apoptosis in unfertilized sea urchin eggs
Philippe, L., Tosca, L., Zhang, W. L., Piquemal, M., & Ciapa, B. (2013) · APOPTOSIS · doi:10.1007/s10495-013-0950-3 · Cited by 14
Autophagy-mediated Nutrient Recycling and Regulation in Plants: A Molecular View
Islam, M. S., Proshad, R., Kormoker, T., & Tusher, T. R. (2019) · Journal of Plant Biology · doi:10.1007/s12374-019-0213-0 · Cited by 13
Upregulation of the ESCRT pathway and multivesicular bodies accelerates degradation of proteins associated with neurodegeneration
Benyair, R., Giridharan, S. S. P., Rivero-Ríos, P., Hasegawa, J., Bristow, E., Eskelinen, E., Shmueli, M. D., Fishbain-Yoskovitz, V., Merbl, Y., Sharkey, L. M., et al. (2023) · Autophagy Reports · doi:10.1080/27694127.2023.2166722 · Cited by 13
“Quantification of cytoplasmic area was performed by point counting using images taken at 3000X primary magnification, as described [93].”
FTY720 in resistant human epidermal growth factor receptor 2-positive breast cancer
Chung, W., Huang, W.-L., Liao, W., Hung, C.-H., Chiang, C., Cheung, C. H. A., & Su, W. (2022) · Scientific Reports · doi:10.1038/s41598-021-04328-y · Cited by 13
Automated Bright Field Segmentation of Cells and Vacuoles Using Image Processing Technique
Chiang, P., Wu, S., Tseng, M., & Huang, P.-J. (2018) · Cytometry Part A · doi:10.1002/cyto.a.23595 · Cited by 13
“Some of the most common methods for detecting autophagy include electron microscopy, flow cytometry (12,16–18), Western blotting (9–13,19–22), and fluorescence microscopy (9,23,24).”
Method
Autophagy contributes to resistance to the oxidative stress induced by pine reactive oxygen species metabolism, promoting infection by Bursaphelenchus xylophilus
Liu, H., Rui, L., Feng, Y., & Wu, X. P. P. (2020) · Pest Management Science · doi:10.1002/ps.5823 · Cited by 13
HEXA-018, a Novel Inducer of Autophagy, Rescues TDP-43 Toxicity in Neuronal Cells
Lee, S., Jo, M., Lee, H., Jeon, Y., Kim, S., Kwon, Y., Woo, J., Han, S., Mun, J. Y., & Kim, H. (2021) · Frontiers in Pharmacology · doi:10.3389/fphar.2021.747975 · Cited by 12
“Moreover, rotenone-induced α-synuclein aggregates are significantly decreased by rapamycin treatment (Yu et al., 2009).”
Background
Autophagy, a new target for disease treatment
Xie, F., Li, L., & Chen, L. (2013) · Science China Life Sciences · doi:10.1007/s11427-013-4530-0 · Cited by 12
Ultrastructural Patterns of the Activated Cell Death Programs in the Human Brain
Pais, V., Danaila, L., & Pais, E. (2013) · Ultrastructural Pathology · doi:10.3109/01913123.2012.751949 · Cited by 11
“Electron microscopy remains one of the most accurate methods for the detection of cell death forms and even for the quantification of some processes; for example, autophagic accumulation was first discovered by transmission electron microscopy [16].”
Sequential steps of macroautophagy and chaperone-mediated autophagy are involved in the irreversible process of posterior silk gland histolysis during metamorphosis ofBombyx mori
Shiba, H., Yabu, T., Sudayama, M., Mano, N., Arai, N., Nakanishi, T., & Hosono, K. (2016) · Journal of Experimental Biology · doi:10.1242/jeb.130815 · Cited by 11
“3, autophagosomes, which are characterized by a double membrane, and autolysosomes, which contain degraded organelles (Ylä-Anttila et al., 2009), were found in BA DC Fig.”
Background
Effects of different autophagy inhibitors on sensitizing KG ‐1 and HL ‐60 leukemia cells to chemotherapy
Haghi, A., Salemi, M., Fakhimahmadi, A., Kian, M. M., Yousefi, H., Rahmati, M., Mohammadi, S., Ghavamzadeh, A., Moosavi, M. A., & Nikbakht, M. (2020) · IUBMB Life · doi:10.1002/iub.2411 · Cited by 11
“The specimens were stained with 2% aqueous uranyl acetate, and lead citrate to contrast staining.(33) Finally, all of the thin samples were observed by TEM (Philips EM208S) at an acceleration voltage of 100 kV.”
Method
Autophagy in oral cancer: Promises and challenges (Review)
Li, Z., Zhang, Y., Lei, J., & Wu, Y. (2024) · International Journal of Molecular Medicine · doi:10.3892/ijmm.2024.5440 · Cited by 11
“Transmission electron microscopy is considered to be the gold standard in numerous autophagy research applications (46); its advantage is that it can directly evaluate the size of autophagosomes in cells and the continuous morphological changes during autophagy.”
Background
Deciphering the Rules of in Silico Autophagy Methods for Expediting Medicinal Research
Chen, Y., Wang, G., Cai, H., Sun, Y., Ouyang, L., & Liu, B. (2019) · Journal of Medicinal Chemistry · doi:10.1021/acs.jmedchem.8b01673 · Cited by 10
An Experimental Study Reveals the Protective Effect of Autophagy against Realgar-Induced Liver Injury via Suppressing ROS-Mediated NLRP3 Inflammasome Pathway
Yang, J., Li, J., Guo, H., Zhang, Y., Guo, Z., Liu, Y., & Huo, T. (2022) · International Journal of Molecular Sciences · doi:10.3390/ijms23105697 · Cited by 10
“Autolysosomes typically have only one limiting membrane, which usually contains electron-dense cytoplasmic material and/or organelles at various stages of degradation [25].”
Background
Enhanced autophagic flux by endoplasmic reticulum stress in human hepatocellular carcinoma cells contributes to the maintenance of cell viability
Ma, T., Li, Y., Zhu, J., Fan, L., Du, W., Wu, C., Sun, G., & Li, J. (2013) · Oncology Reports · doi:10.3892/or.2013.2474 · Cited by 11
Invaginating Presynaptic Terminals in Neuromuscular Junctions, Photoreceptor Terminals, and Other Synapses of Animals
Petralia, R. S., Wang, Y., Mattson, M. P., & Yao, P. J. (2017) · NeuroMolecular Medicine · doi:10.1007/s12017-017-8445-y · Cited by 10
“Phagocytosis seems to be a likely explanation for these structures, as the invagination with its surrounding cistern generally resembles phagophore formation in early autophagy (Ylä-Anttila et al. 2009; Biazik et al. 2015).”
Platelet vacuoles in a dog with severe nonregenerative anemia: evidence of platelet autophagy
Pieczarka, E. M., Yamaguchi, M., Wellman, M. L., & Radin, M. J. (2014) · Veterinary Clinical Pathology · doi:10.1111/vcp.12170 · Cited by 9
Assessing methods to quantitatively validate TGFβ-dependent autophagy
Trelford, C. B., & Guglielmo, G. M. D. (2020) · Biology Open · doi:10.1242/bio.055103 · Cited by 9
“The explanation for this is that many techniques rely on autophagosome structures to make interpretations of autophagy (Klionsky et al., 2016; Ylä-Anttila et al., 2009).”
Background
Molecular targets and approaches to restore autophagy and lysosomal capacity in neurodegenerative disorders
Bastien, J., Menon, S., Messa, M., & Nyfeler, B. (2021) · Molecular Aspects of Medicine · doi:10.1016/j.mam.2021.101018 · Cited by 9
Secondary Biliary Cholestasis Promotes Testicular Macrophage Infiltration and Autophagy in Rats
Shi, S., Jiang, L., Xie, H., Zhu, Y., Zhang, W., & Zheng, S. (2014) · American Journal of Reproductive Immunology · doi:10.1111/aji.12292 · Cited by 9
Autophagic defects observed in fibroblasts from a patient with β‐propeller protein‐associated neurodegeneration
Lee, J., Nam, S. O., Kim, E. K., Shin, J., Oh, S. H., Ryu, D., Lee, H. E., & Mun, J. Y. (2021) · American Journal of Medical Genetics Part A · doi:10.1002/ajmg.a.62442 · Cited by 9
“The amount of LC3-II is known to reflect the number of autophagosomes and autophagy-related structures (Yoshii & Mizushima, 2017).”
Background
Morphometric analysis of the thymic epithelial cell network using integrated and orthogonal digital pathology approaches
Lagou, M. K., Markaki, M. P., Vodopyanov, S., Argyris, D. G., Karagiorgis, G. K., Gunther-Cummins, L., Hardas, A., Panorias, C., DesMarais, S., Entenberg, C., et al. (2026) · Communications Biology · doi:10.1038/s42003-026-10038-w · Cited by 9
“4P, Q), based on their ultra-structural morphology, as described in previous studies 74 – 80 : Autophago-somes (APGs); Early and Late Autolysosomes (early AUTs and late AUTs, respectively); Multilamellar Bodies (MLBs); Multivesicular Bodies (MVBs) (see Materials and Methods).”
Apoptotic and autophagic cell death induced by glucolaxogenin in cervical cancer cells
Sánchez‐Sánchez, L., Escobar, M. L., Sandoval-Ramı́rez, J., López‐Muñoz, H., Fernández‐Herrera, M. A., Hernández-Vázquez, J. M. V., Hilario-Martínez, J. C., & Zenteno, E. (2015) · APOPTOSIS · doi:10.1007/s10495-015-1181-6 · Cited by 8
Galectin-3 Expression in Pancreatic Cell Lines Under Distinct Autophagy-Inducing Stimulus
Filho, A. F. D. S., de Sousa, L. M., Consonni, S. R., Pitta, M. G. D. R., Carvalho, H. F., & Rêgo, M. J. B. D. M. (2020) · Microscopy and Microanalysis · doi:10.1017/s1431927620024526 · Cited by 8
“…vacuoles can be further classified into early or initial autophagic vacuoles (AVi) containing morphologically intact cytosol or organelles, and too late or degradative autophagic vacuoles (AVd) containing partially degraded cytoplasmic material (Eskelinen, 2008; Yla-Anttila et al., 2009).”
Background
Biosensors; a novel concept in real-time detection of autophagy
Nasrollahpour, H., Mirzaie, A., Sharifi, M., Rezabakhsh, A., Khalilzadeh, B., Rahbarghazi‬, R., Yousefi, H., & Klionsky, D. J. (2024) · Biosensors and Bioelectronics · doi:10.1016/j.bios.2024.116204 · Cited by 8
NAC1 confines virus‐specific memory formation of CD4+ T cells through the ROCK1‐mediated pathway
Wang, L., Peng, H., Das, J. K., Kumar, A., Ren, Y., Ballard, D. J., Xiong, X., Yang, W., Ren, X., de Figueiredo, P., et al. (2023) · Journal of Medical Virology · doi:10.1002/jmv.28957 · Cited by 7
“The cells were fixed, dehydrated, and infiltrated into resin according to the cited protocol with minor modifications.(17)”
Method
Immunogold Electron Microscopy of the Autophagosome Marker LC3
Mattoscio, D., Raimondi, A., Tacchetti, C., & Chiocca, S. (2017) · BIO-PROTOCOL · doi:10.21769/bioprotoc.2648 · Cited by 7
“Indeed, in addition to their peculiar morphology (Yla-Anttila et al., 2009), autophagosomes Copyright © 2017 The Authors; exclusive licensee Bio-protocol LLC. 2 is generally recruited on autophagic membranes after lipidation with phosphatidylethanolamine (LC3-II) during autophagic activation…”
Background
An Overview of Golgi Membrane-Associated Degradation (GOMED) and Its Detection Methods
Sakurai, H. T., Arakawa, S., Yamaguchi, H., Torii, S., Honda, S., & Shimizu, S. (2023) · Cells · doi:10.3390/cells12242817 · Cited by 6
“The method we use to differentiate between the two is to analyze the difference in electron density between the interior and exterior of these structures, because the density is different in closed structures but the same in open structures [28,29].”
Method

Authors: Ylä‐Anttila, P., Vihinen, H., Jokitalo, E., & Eskelinen, E.
Affiliations: University of Helsinki (FI)
ORCID: Ylä‐Anttila, Päivi
Vihinen, Helena
Jokitalo, Eija
Eskelinen, Eeva‐Liisa
Venue: Methods in Enzymology
Publisher: Elsevier
Published: 2009
Volume: 452
Pages: 143-164
ISSN: 0076-6879 (ISSN-L)
DOI: 10.1016/s0076-6879(08)03610-0
OpenAlex: W1594293927
Cited by: 257
References: 26
Citations by year: 2026: 4 · 2025: 7 · 2024: 13 · 2023: 6 · 2022: 14 · 2021: 14 · 2020: 19 · 2019: 27 · 2018: 17 · 2017: 25 · 2016: 19 · 2015: 18 · 2014: 20 · 2013: 17 · 2012: 19
FWCI: 37.92
Type: book chapter
Language: en
Open access: closed
Locations: Methods in enzymology on CD-ROM/Methods in enzymology (publishedVersion)
PubMed (publishedVersion)
Topics: Life Sciences › Biochemistry, Genetics and Molecular Biology › Cell Biology › Autophagy in Disease and Therapy
Life Sciences › Biochemistry, Genetics and Molecular Biology › Structural Biology › Advanced Electron Microscopy Techniques and Applications
Life Sciences › Biochemistry, Genetics and Molecular Biology › Cell Biology › Cellular transport and secretion
Keywords: autophagy, phagophore, electron microscopy specimen preparation, electron tomography, three-dimensional morphology, point counts, mammalian cells
MeSH terms: Animals, Autophagy, Cells, Cultured, Microscopy, Electron, Transmission, Mice

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Chapter 10 Monitoring Autophagy by Electron Microscopy in Mammalian Cells

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