Guidelines for the use and interpretation of assays for monitoring autophagy (4th edition)

Published on Feb 8, 2021in Autophagy9.77
· DOI :10.1080/15548627.2020.1797280
Daniel J. Klionsky139
Estimated H-index: 139
,
D.J. Klionsky + 2920 AuthorsChun Kit Tong1
Estimated H-index: 1
(Hong Kong Baptist University)
Sources
Abstract
In 2008, we published the first set of guidelines for standardizing research in autophagy. Since then, this topic has received increasing attention, and many scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Thus, it is important to formulate on a regular basis updated guidelines for monitoring autophagy in different organisms. Despite numerous reviews, there continues to be confusion regarding acceptable methods to evaluate autophagy, especially in multicellular eukaryotes. Here, we present a set of guidelines for investigators to select and interpret methods to examine autophagy and related processes, and for reviewers to provide realistic and reasonable critiques of reports that are focused on these processes. These guidelines are not meant to be a dogmatic set of rules, because the appropriateness of any assay largely depends on the question being asked and the system being used. Moreover, no individual assay is perfect for every situation, calling for the use of multiple techniques to properly monitor autophagy in each experimental setting. Finally, several core components of the autophagy machinery have been implicated in distinct autophagic processes (canonical and noncanonical autophagy), implying that genetic approaches to block autophagy should rely on targeting two or more autophagy-related genes that ideally participate in distinct steps of the pathway. Along similar lines, because multiple proteins involved in autophagy also regulate other cellular pathways including apoptosis, not all of them can be used as a specific marker for bona fide autophagic responses. Here, we critically discuss current methods of assessing autophagy and the information they can, or cannot, provide. Our ultimate goal is to encourage intellectual and technical innovation in the field.
Figures & Tables
Download
References4019
Newest
#1Dangtong ShangH-Index: 1
#2Lingling WangH-Index: 3
Last. Rongjia Zhou (WHU: Wuhan University)H-Index: 25
view all 5 authors...
Nearly all diseases in humans, to a certain extent, exhibit sex differences, including differences in the onset, progression, prevention, therapy, and prognosis of diseases. Accumulating evidence shows that macroautophagy/autophagy, as a mechanism for development, differentiation, survival, and homeostasis, is involved in numerous aspects of sex differences in diseases such as cancer, neurodegeneration, and cardiovascular diseases. Advances in our knowledge regarding sex differences in autophagy...
6 CitationsSource
#1Eugènia Almacellas (University of Barcelona)H-Index: 4
#2Joffrey PelletierH-Index: 6
Last. Caroline MauvezinH-Index: 14
view all 6 authors...
Lysosomes, as primary degradative organelles, are the endpoint of different converging pathways, including macroautophagy. To date, lysosome degradative function has been mainly studied in interpha...
6 CitationsSource
#1Wenmei Wu (SCAU: South China Agricultural University)H-Index: 4
#2Man Luo (SCAU: South China Agricultural University)H-Index: 1
Last. Ling Tian (SCAU: South China Agricultural University)H-Index: 17
view all 9 authors...
AbstractHistone deacetylases (HDACs) are important for global gene expression and contribute to numerous physiological events. Deacetylase Rpd3 in yeast and its conserved homolog HDAC1 in mammals o...
6 CitationsSource
#1Sara Puente MarínH-Index: 1
Last. M. Ortega-VillaizanH-Index: 14
view all 8 authors...
8 CitationsSource
#1Venkatesh P Thirumalaikumar (MPG: Max Planck Society)H-Index: 7
#2Mateusz Wagner (MPG: Max Planck Society)H-Index: 1
Last. Aleksandra Skirycz (MPG: Max Planck Society)H-Index: 22
view all 4 authors...
Proteogenic dipeptides are intermediates of proteolysis as well as an emerging class of small-molecule regulators with diverse and often dipeptide-specific functions. Herein, prompted by differential accumulation of dipeptides in a high-density Arabidopsis thaliana time-course stress experiment, we decided to pursue an identity of the proteolytic pathway responsible for the buildup of dipeptides under heat conditions. By querying dipeptide accumulation versus available transcript data, autophagy...
9 CitationsSource
#1Borong Zhou (Guangzhou Medical University)H-Index: 7
#2Jiao Liu (Guangzhou Medical University)H-Index: 17
Last. Daolin Tang (UTSW: University of Texas Southwestern Medical Center)H-Index: 30
view all 6 authors...
Abstract Macroautophagy (hereafter referred to as autophagy) involves an intracellular degradation and recycling system that, in a context-dependent manner, can either promote cell survival or accelerate cellular demise. Ferroptosis was originally defined in 2012 as an iron-dependent form of cancer cell death different from apoptosis, necrosis, and autophagy. However, this latter assumption came into question because, in response to ferroptosis activators (e.g., erastin and RSL3), autophagosomes...
114 CitationsSource
#1Maeve LongH-Index: 1
#2Thomas G. McWilliams (UH: University of Helsinki)H-Index: 13
Abstract Autophagy refers to an essential mechanism that evolved to sustain eukaryotic homeostasis and metabolism during instances of nutrient deprivation. During autophagy, intracellular cargo is encapsulated and delivered to the lysosome for elimination. Loss of basal autophagy in vivo negatively impacts cellular proteostasis, metabolism and tissue integrity. Accordingly, many drug development strategies are focused on modulating autophagic capacity in various pathophysiological states, from c...
15 CitationsSource
#1Avnika A. Ruparelia (Australian Regenerative Medicine Institute)H-Index: 11
#2Emily A. McKaige (Monash University)H-Index: 3
Last. Robert J. Bryson-Richardson (Monash University)H-Index: 27
view all 17 authors...
Dominant de novo mutations in the co-chaperone BAG3 cause a severe form of myofibrillar myopathy, exhibiting progressive muscle weakness, muscle structural failure, and protein aggregation. To eluc...
6 CitationsSource
#1Laury Lescat (University of Pau and Pays de l'Adour)H-Index: 2
#1Laury Lescat (University of Pau and Pays de l'Adour)H-Index: 1
Last. Iban Seiliez (University of Pau and Pays de l'Adour)H-Index: 4
view all 16 authors...
: Chaperone-Mediated-Autophagy (CMA) is a major pathway of lysosomal proteolysis recognized as a key player of the control of numerous cellular functions, and whose defects have been associated with several human pathologies. To date, this cellular function is presumed to be restricted to mammals and birds, due to the absence of an identifiable lysosome-associated membrane protein 2A (LAMP2A), a limiting and essential protein for CMA, in non-tetrapod species. However, the recent identification o...
7 CitationsSource
#1Cefan Zhou (HBUT: Hubei University of Technology)H-Index: 7
#2Qian Xuehong (HBUT: Hubei University of Technology)H-Index: 1
Last. Jingfeng Tang (HBUT: Hubei University of Technology)H-Index: 13
view all 15 authors...
ABSTRACTMacroautophagy/autophagy plays key roles in development, oncogenesis, and cardiovascular and metabolic diseases. Autophagy-specific class III phosphatidylinositol 3-kinase complex I (PtdIns...
9 CitationsSource
Cited By114
Newest
#1Nils C. Gassen (University of Bonn)H-Index: 25
#2Jan Papies (Humboldt University of Berlin)H-Index: 5
Last. Friderike Weege (Humboldt University of Berlin)H-Index: 1
view all 35 authors...
Viruses manipulate cellular metabolism and macromolecule recycling processes like autophagy. Dysregulated metabolism might lead to excessive inflammatory and autoimmune responses as observed in severe and long COVID-19 patients. Here we show that SARS-CoV-2 modulates cellular metabolism and reduces autophagy. Accordingly, compound-driven induction of autophagy limits SARS-CoV-2 propagation. In detail, SARS-CoV-2-infected cells show accumulation of key metabolites, activation of autophagy inhibit...
2 CitationsSource
#1Muhammad Asif (WIT: Wuhan Institute of Technology)
#1Muhammad Asif (WIT: Wuhan Institute of Technology)H-Index: 2
Last. Yimin Sun (WIT: Wuhan Institute of Technology)H-Index: 13
view all 4 authors...
Coronavirus diseases-2019 (COVID-19) is becoming increasing serious and major threat to public health concerns. As a matter of fact, timely testing enhances the life-saving judgments on treatment and isolation of COVID-19 infected individuals at possible earliest stage which ultimately suppresses spread of infectious diseases. Many government and private research institutes and manufacturing companies are striving to develop reliable tests for prompt quantification of SARS-CoV-2. In this review,...
3 CitationsSource
Abstract null null As a populous country, China has always attached importance to the protection of cultivated land and food security. However, in the process of promoting rural development, agricultural industrial policies introduced by local governments may affect the realization of food security. Although there are many studies paying attention to the influence of agricultural industrial policy on food security, quantitative analyses are lacking. This paper takes the “one village, one product...
Source
#1Hany H. Arab (Taif University)H-Index: 21
#2Ahmed M. Ashour (UQU: Umm al-Qura University)H-Index: 1
Last. Ahmed M. Kabel (Tanta University)H-Index: 14
view all 5 authors...
Abstract null null Aims null Saxagliptin, a selective/potent dipeptidyl peptidase-4 inhibitor, has revealed remarkable anti-inflammatory features in murine models of nephrotoxicity, hepatic injury, and neuroinflammation. However, its potential effect on ethanol-induced gastric mucosal injury has not been examined. Hence, the present work investigated the prospect of saxagliptin to attenuate ethanol-evoked gastric injury, with emphasis on the AMPK/mTOR-driven autophagy and NLRP3/ASC/caspase-1 pat...
Source
#1Consolato Sergi (WUST: Wuhan University of Science and Technology)H-Index: 32
An imbalance between protein aggregation and protein degradation may induce 'stress' in the functionality of the endoplasmic reticulum (ER). There are quality control (QC) mechanisms to minimize misfolding and to eliminate misfolded proteins before aggregation becomes lethal for the cell. Proper protein folding and maturation is one of the crucial functions of the ER. Chaperones of the ER and folding enzymes guarantee correct conformational maturation of emerging secretory proteins. Histone deac...
Source
#1John M. BarbaroH-Index: 2
#2Ana Maria CuervoH-Index: 121
Last. Joan W. BermanH-Index: 67
view all 0 authors...
HIV enters the CNS early after peripheral infection, establishing reservoirs in perivascular macrophages that contribute to development of HIV-associated neurocognitive disorders (HAND) in 15–40% of people with HIV (PWH) despite effective antiretroviral therapy (ART). Opioid use may contribute to dysregulated macrophage functions resulting in more severe neurocognitive symptoms in PWH taking opioids. Macroautophagy helps maintain quality control in long-lived cell types, such as macrophages, and...
Source
#1Belinda S. Hall (University of Surrey)H-Index: 25
#2Scott J Dos Santos (University of Surrey)H-Index: 7
Last. Rachel E. Simmonds (University of Surrey)H-Index: 22
view all 8 authors...
The Mycobacterium ulcerans exotoxin, mycolactone, is responsible for the immunosuppression and tissue necrosis that characterizes Buruli ulcer. Mycolactone inhibits SEC61-dependent co-translational translocation of proteins into the endoplasmic reticulum and the resultant cytosolic translation triggers degradation of mislocalized proteins by the ubiquitin-proteasome system. Inhibition of SEC61 by mycolactone also activates multiple EIF2S1/eIF2α kinases in the integrated stress response (ISR). He...
Source
#1Qiaoni Shi (THU: Tsinghua University)
#2Ye-Guang Chen (THU: Tsinghua University)
As a key component of Wnt signaling, Dishevelled (Dvl/Dsh) plays essential roles in development processes and adult tissue homeostasis in multicellular organisms, and its deregulation results in human development disorders and other diseases. Dvl integrates and relays complex Wnt signals by acting as a branch-point of β-catenin-dependent canonical and β-catenin-independent noncanonical pathways. It dynamically interacts with multiple proteins to modulate Wnt signaling, while its activity and sta...
Source
#2Ligen Yu (NTU: Nanyang Technological University)
Last. Daniel J. Klionsky (UM: University of Michigan)H-Index: 139
view all 3 authors...
Abstract null null The human immunity has a pivotal role in nutrition acquisition from the pathogens and damaged body tissue during the SARS-CoV-2 virus infection, which may lead to transient overnutrition in the patients, lead to lipotoxicity and further damage in non-adipose tissues, and cause hyperinflammation and cytokine storm in severe cases of COVID-19. In view of this, high-quality clinical trials on restrictive eating should be designed to investigate the possible benefits of food intak...
Source
#1Amrit Mudher (University of Southampton)H-Index: 10
#2Shreyasi Chatterjee (University of Southampton)H-Index: 5
Last. R. Robertson (University of Southampton)
view all 16 authors...
Tau becomes abnormally hyper-phosphorylated and aggregated in tauopathies like Alzheimers disease (AD). As age is the greatest risk factor for developing AD, it is important to understand how tau protein itself, and the pathways implicated in its turnover, change during aging. We investigated age-related changes in total and phosphorylated tau in brain samples from two cohorts of cognitively normal individuals spanning 19-74 years, without overt neurodegeneration. One cohort utilised resected ti...
Source