Tools for cell death series 2

Autophagy

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Introduction to cell death
Autophagy• Types of autophagy
		> Macroautophagy
		> Microautophagy
		> Chaperone-mediated autophagy

Autophagy: cellular and molecular mechanisms••••

Induction and phagophore formation
Phagophore elongation and autophagosome formation
Fusion, degradation and recycling
Autophagy regulation

Autophagy and disease••••

CancerNeurodegenerative diseases
Cardiovascular diseases
Infectious disease

Autophagy detection• Markers of autophagy• Visual identification• ATG8/LC3 detection
		> Western Blotting
		> Turnover of LC3-II/ATG8–PE
		> Luminescence based assays
		> GFP-ATG8/LC3 detection
		> Fluorescence microscopy
		> Tandem mRFP/mcherry-GFP fluorescence microscopy
		> Flow and multispectral imaging cytometry
		> Immunohistochemistry• SQSTM1/p62 and related LC3 binding protein detection• TOR, AMPK and ATG1/ULK1 detection• Additional autophagy related markers
		> ATG9
		> ATG14
		> ATG18
		> BECLIN1
		> DRAM1

General considerations for autophagy detection
References

Discover more at abcam.com/celldeath2Introduction to cell death
Cell death happens when a biological cell fails to maintain essential life functions. This may be theresult of the natural process of development or protection against cellular defects, of normal cells
replacement, or factors such as disease or localized injury.
Cell death can be classified according to its morphological appearance (such as apoptotic or
necrotic), enzymological criteria (with or without involvement of distinct proteases), functional aspects(programmed or accidental) or immunological characteristics (immunogenic or non-immunogenic).
In this guide, we want to examine the role of autophagy, a self-degradation process that has been
historically linked to non-apoptotic cell death.

Autophagy
Autophagy (from the Greek “auto”-self and “phagein”-to eat) is a general term for processes by which
dysfunctional cellular components are degraded inside the cell through the action of lysosomes.
Components of the cytoplasm, including organelles, are sequestered and moved into the lumen oflysosomes/vacuoles where they are broken down into basic components and returned to the cytosol
for reuse.
Under physiological conditions, autophagy has a number of vital roles such as maintenance of theamino acid pool during starvation, preimplantation development, clearance of intracellular microbes,
and regulation of innate and adaptive immunity (Mizushima et al., 2010).
Autophagy has been widely implicated in many pathophysiological processes such as cancer,
metabolic and neurodegenerative disorders as well as cardiovascular and pulmonary diseases. It also
has an important role in aging and exercise (Choi et al., 2013).
One of the characteristic features of autophagy is its dynamic regulation; cellular autophagic activity is
usually low under basal conditions, but there are a number of stimuli that can lead to its upregulation.
Nutrient starvation is the most well-known inducer of autophagy, but other biological stress stimuli
such as hypoxia or energy depletion, hormonal stimulation or pharmaceutical agents can increase
autophagy in the cells as well.
Autophagy is a common morphological feature in dying cells, and therefore it was presumed for a longtime to be a cell death pathway. Recent investigations show that one of its major functions is to workon keeping cells alive under stressful conditions that could otherwise lead to cell death.

Discover more at abcam.com/celldeath3Types of autophagy

There are currently three types of autophagy in mammalian cells: macroautophagy, microautophagy
and chaperone-mediated autophagy, macroautophagy being the most extensively studied type (Glicket al., 2010).
Macroautophagy
Macroautophagy is the main autophagic pathway, generally referred to as autophagy. It ischaracterized by the delivery of cytoplasmic cargo to the lysosome through an intermediary double
membrane-bound vesicle, known as autophagosome, which fuses with the lysosome to form an
autolysosome.
Throughout this guide we will review the cellular and molecular mechanism involved inmacroautophagy (referred to as autophagy from now on), as well as methods and assays which canbe used to monitor autophagy.
Microautophagy
Microautophagy, on the other hand, involves the direct engulfment of cytoplasmic cargo into thelysosome through invagination of the lysosomal membrane. Microautophagy is important in themaintenance of organellar size, membrane homeostasis and cell survival under nitrogen restriction (Liet al., 2012).
Chaperone-mediated autophagy
Chaperone-mediated autophagy (CMA) involves the direct translocation of cytoplasmic proteins
across the lysosomal membrane in a complex with chaperone proteins that are recognized by thelysosomal membrane receptor LAMP-2A (lysosomal-associated membrane protein 2A), resulting intheir unfolding and degradation.

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Figure 1. Types of Autophagy

Isolation
membrane

Protein

KFERQ
motif

Cytosol

Phagophore

Hsc70
chaperone

Lamp2A

Autophagosome

Lysosome

Chaperone
Mediated
Autophagy

Macroautophagy

Microautophagy

Discover more at abcam.com/celldeath5Autophagy: Cellular and molecular mechanisms
Autophagy is a tightly regulated pathway which at basal level has an important housekeeping role
allowing cells to eliminate damaged or harmful components through catabolism and recycling tomaintain nutrient and energy homeostasis. Autophagy is also a major protective mechanism whichallows cells to survive in response to multiple stress conditions such as: nutrient or growth factor
deprivation, hypoxia, reactive oxygen species, DNA damage or intracellular pathogens (Levine &Kroemer, 2008).
The process of autophagy begins with an expanding membrane structure termed the phagophore
which enwraps portions of the cytoplasm. This leads to the formation of a double-membranesequestering vesicle, termed the autophagosome. Autophagosomes subsequently fuse withlysosomes, releasing their inner compartment to the lysosomal lumen. The inner membrane part of the
autophagosome, together with the enclosed cargo, is degraded, and the resulting macromolecules are
released into the cytosol through lysosomal membrane permeases for recycling (Mizushima, 2007).

Discover more at abcam.com/celldeath6Figure 2. Autophagy process - overview> Starvation> Hypoxia> ROS> Infection> Chemotherapy> Others

Recycling

Isolation
membrane

Degradation

Degradation
and recycling
Lysosome
fusionInduction andphagophore
formation
Elongation andautophagosome
formation
Phagophore

Lysosome
Autolysosome
Autophagosome

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Induction and phagophore formation

The molecular mechanism of autophagy involves several conserved Atg (autophagy –related)
proteins. In response to various stimuli (nutrient starvation, hypoxia, ROS, infection, DNA damage andothers) a unique flat membrane (phagophore) is formed. Two protein complexes are involved in thisinitiation step: one complex contains the class III PI3 K/Vps34, Atg6/Beclin1, Atg14, and Vps15/p150,
and the other complex includes a serine/threonine kinase Atg1/ULK1 which is an essential positive
regulator of autophagosome formation. When nutrients are abundant, binding of the ULK1 complex by
the mammalian target of rapamycin (mTOR) complex 1 (mTORC1) inhibits autophagy. The mTORC1
is an important regulator of cell growth and metabolism. It is composed of five subunits that include
Raptor, which binds ULK1, and mTOR, a serine-threonine kinase. By phosphorylating ULK1, mTOR
inhibits autophagy initiation. In starvation, mTORC1 dissociates from the ULK1 complex, freeing it totrigger autophagosome nucleation and elongation. The kinase activity of Atg1 requires the function of
two other autophagy proteins, Atg13 or Atg8 and Atg17 (Badadani, 2012).

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Induction

Phagophore
formation

Elongation andautophagosome formation> Starvation> Hypoxia> ROS> Infection> Chemotherapy> Others

Atg14L
Beclin 1
hVps34
Ambra1
hVps15

Atg2

Atg9

WIPI1/2

VMP1

Class III PI 3-K complex
LC3 conjugation system

Ulk1/2
Atg13
FIP200
Atg101
Atg/ULK1 complex

Atg12 conjugation sy

Atg12

LC3

At

Atg4
LC3-I
Atg7
PE
LC3-II

Atg12

At

PE

Atg

Atg12
At
Atg16

Figure 3. Induction andphagophore formation
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Autophagosome

9Phagophore elongation and autophagosome formation

The elongation of the phagophore results in the formation of autophagosome, which is typicallya double-membraned organelle. This step is a simple sequestration, and no degradation occurs.
Phagophore elongation and autophagosome completion requires two ubiquitin-like conjugation
pathways, both catalyzed by Atg7.
The first leads to the conjugation of Atg5-Atg12 which then form a multimeric complex with Atg16L.
The Atg5-Atg12-Atg16L complex associates with the outer membrane of the extending phagophore(Glick et al., 2010, Kaur & Debnath, 2015).The association of Atg5–Atg12–Atg16L complexes
is thought to induce curvature into the growing phagophore through asymmetric recruitment ofprocessed LC3B-II. Atg5–Atg12 conjugation is not dependent on activation of autophagy and once theautophagosome is formed, Atg5–Atg12–Atg16L dissociates from the membrane, making conjugatedAtg5–Atg12 a relatively insufficient marker of autophagy (Barth et al., 2010).
The second ubiquitin-like system involved in autophagosome formation, results in the processing of
microtubule-associated protein light chain 3 (LC3B), which is encoded by the principal mammalian
homologue of the yeast Atg8. Upon autophagy induction LC3B, expressed in most cell types as afull-length cytosolic protein, is proteolytically cleaved by Atg4 to generate LC3B-I. LC3B-I is activatedby Atg7 and then transferred to Atg3 followed by conjugation to phosphatidylethanolamine (PE) togenerate processed LC3B-II.
Processed LC3B-II is recruited onto the growing phagophore and its integration is dependent on Atg5–
Atg12. Unlike Atg5-Atg12-Atg16L, LC3B-II is found on both the inner and the outer surfaces of the
autophagosome, where it is required for the expansion and completion of the autophagic membraneand plays a role in selecting cargo for degradation as well as in the fusion of the autophagosome
with the lysosome. LC3B-II has been proposed to act as a receptor for selective substrate, p62/
SQSTM1 (Bjørkøy et al., 2005). During autophagy the synthesis and processing of LC3 is increased.
Recent research indicates that the deacetylation and cytosolic translocation of a nuclear pool of LC3
is required for its lipidation with PE during starvation-induced autophagy (Huang et al., 2015). Afterthe closure of the autophagosome Atg16-Atg5-Atg12 complex dissociates from the autophagosome
whereas a proportion of LC3B-II remains covalently bound to the membrane and therefore LC3B-II
could be used as a marker to monitor levels of autophagy in cells. Now the completed autophagosome
is ready for fusion with the lysosome (Badadani, 2012). Various sources, including mitochondria, theGolgi complex, and the ER, are proposed to be the origins of the autophagosomal membrane (He &Klionsky, 2010). However, it is not completely clear by what mechanism the additional membranes
are delivered to and fused with the growing phagophore. Recent studies demonstrate that selfmultimerization of Atg9 may facilitate membrane tethering and/or fusion (He et al., 2008). Atg9 is the
only identified integral membrane protein required for autophagosome formation.

Discover more at abcam.com/celldeath10Figure 4. Autophagosome formation

Phagophore
formation

Elongation andautophagosome formation

Atg14L
eclin 1
hVps34a1
hVps15

Lysosomfusion

Atg2

Atg9

LAMP2

WIPI1/2

VMP1

Rab7
UVRAG

lass III PI 3-K complex

Ulk1/2
tg13
FIP200
Atg101
Atg/ULK1 complex

RubiconLC3 conjugation system

Atg12 conjugation system

LC3

Atg12
Atg5

Atg4

SNARES
HOPS

LC3-I
Atg7
PE
LC3-II

Atg12
PE

Atg5
Atg16
Atg12
Atg5
Atg16

Autophagosome

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Fusion, degradation and recycling

When autophagosome formation is completed, LC3B-II attached to the outer membrane is cleaved
from PE by Atg4 and released back to the cytosol. However, the retrieval and uncoating mechanismsof other Atg proteins remain to be studied. Autophagosome-lysosome fusion is mediated by the samemachinery that is involved in homotypic vacuole membrane fusion. In mammalian cells, the fusion
event is thought to require the lysosomal membrane protein LAMP-2 and the small GTPase Rab7.
In yeast, the machinery consists of the Rab family GTPase Ypt7 (the homolog of Rab7), the NSF
homolog Sec18, the SNARE (N-ethylmaleimide-sensitive factor attachment protein receptors) proteins
Vam3, Vam7, Vti1, and Ykt6, the class C Vps/HOPS complex proteins, and two other proteins, Ccz1
and Mon1.
After fusion, degradation of the inner vesicle is dependent on a series of lysosomal/vacuolar acidhydrolases, including proteinases A and B (encoded by PEP4 and PRB1, respectively) and thelipase Atg15 in yeast and cathepsin B, D (a homolog of proteinase A), and Lin mammalian cells. The
resulting small molecules from the degradation, particularly amino acids, are transported back to thecytosol for protein synthesis and maintenance of cellular functions under starvation conditions. The
identification of Atg22, together with other vacuolar permeases (such as Avt3 and Avt4) as vacuolaramino acid effluxers during yeast autophagy, has helped in the understanding of the mechanisms ofnutrient recycling; these permeases represent the last step in the degradation and recycling process(He & Klionsky, 2010).

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LysosomefusionDegradation
and recycling

LAMP2

Atg22

Rab7
UVRAG
Rubicon
SNARES
HOPS

Figure 5. Fusion, degradation and recycling
Discover more at abcam.com/celldeath13Autophagy regulation

Amino acid and insulin/growth factor signals are thought to converge on mTOR, which is a master
regulator of nutrient signaling. Indeed, treatment with inhibitors of TOR such as rapamycin and
CCI-779 induces autophagy in yeast and even in animals. However, not all autophagy signals
are transduced through mTOR; some amino acid signaling can suppress autophagy in an
mTOR-independent manner. More recently, small-molecule enhancers of the cytostatic effects of
rapamycin (called SMERs) were identified to induce autophagy, which acts independently of mTOR
(Mizushima, 2007).
In addition to insulin and amino acid signaling, the involvement of many other factors in autophagy
regulation has been reported. These include Bcl2, reactive oxygen species (ROS), calcium(Høyer-Hansen et al., 2007), AMP-activated protein kinase (AMPK), BNIP3, p19 ARF, DRAM,
calpain, TRAIL, FADD, and myo-inositol-1,4,5-triphosphate (IP3) (Mizushima, 2007). Other regulatorsof autophagy include UVRAG (UV irradiation resistance-associated gene) which interacts via thecoiled-coil region of Beclin 1. UVRAG was shown to be a member of the class III PI3-kinase complex
and a positive regulator of autophagy. Also, Ambra1, which is primarily expressed in neural tissues
and is indispensable for normal neural tube development, has been found to be a Beclin 1-interacting
protein and was shown to positively regulate Beclin 1-dependent autophagy.

Autophagy and disease
The autophagic response has been described in various pathophysiological situations, including
neurobiology, cancer, cardiovascular disease, and infectious diseases. However, its role in diseases is
not fully understood as it can act in different conditions to work towards cell survival or induce cell death.

Cancer

The role of autophagy in cancer is complex and may differ depending on the tumor type andconditions. Autophagy was first linked to cancer through the role of Beclin 1 (Liang et al., 1999),
which is essential for autophagy pathway and has been mapped to tumor susceptibility. Since then,a number of tumor-suppressor proteins that are involved in control of autophagy have been identified(e.g. p53, Bcl2, PTEN etc.). Autophagy is also required for normal embryonic, neonatal and adultdevelopment (Qu et al., 2007; Kuma et al., 2004). Therefore, it would seem reasonable to assume
that a decrease in autophagy would lead to tumor progression (Meijer & Codogno, 2004; Gozuacik& Kimchi, 2004; Shintani & Klionsky, 2004). There are many studies that suggest up-regulation of
autophagy can either be a cell-protective mechanism or in fact an alternative cell-death mechanism
given that in cancer cells the apoptosis pathway is commonly altered (Meijer & Codogno, 2004).
The current consensus is that autophagy has a dual role in cancer. In normal cells, autophagy
protects cells from transforming into tumor cells by clearing reactive oxygen species (ROS), organelle
abnormalities and reducing DNA damage. However, once established, the tumor cells exploit the
autophagic mechanism to provide a way for them to overcome nutrient-limiting conditions and facilitate
tumor growth. Studies show that autophagy can modulate the tumor microenvironment by promoting
angiogenesis, supply nutrients, and modulate inflammatory response (Yang et al., 2015)
Many types of cancer cells including pancreatic and lung cancers are highly reliant on autophagy
activation to meet growth demands. Tumor cells can meet the high metabolic demand of growth by

Discover more at abcam.com/celldeath14autophagic activation using metabolite turnover and absorption, inhibition of apoptosis caused by
mitochondrial malfunction and ROS production (Yang et al., 2011).
Tumor resistance to radiotherapy and chemotherapy is also associated with autophagy. Various tumor
associated animal models have confirmed that autophagy inhibition has the effects of enhancing
chemosensitivity and promoting tumor regression. These findings make autophagy inhibition a viablestrategy for therapeutic intervention.
Chloroquine and its derivatives are the most widely tested in clinical trials either alone or in
combination with chemotherapy or targeted agents. These trials have been showing some promising
results providing for some much needed strategies for treatment (Yang et al., 2011).

Neurodegenerative diseases

Neurodegenerative diseases are characterized by accumulation of mutant or toxic proteins(Ravikumar et al., 2002; Ravikumar et al., 2004). It has been shown that autophagic pathway helps incell survival by removing unwanted cellular organelle and protein aggregates.
In neurons, although autophagy-related proteins (ATGs) are highly expressed, markers for autophagic
activity are low compared with other cell types. There is growing evidence to suggest its importancein neural homeostasis (Shehata et al., 2012). It has been demonstrated that disruption of autophagy
specific genes in neural cells lead to neurodegeneration (Komatsu et al., 2006; Hara et al., 2006).
PARP1 has been shown to act as a sensor in neurons under acute stress, which can either promote
cell survival through autophagy or induce necrotic cell death (Nikoletopoulou et al., 2014).
Autophagy also plays a very important role in the regulation of adult neurogenesis and synaptic
plasticity in the brain. Autophagy interacts with many pathways that are known to underlie synaptic
plasticity and memory and can responds to environmental clues to help regulate synaptic growth andplasticity (Hernandez et al., 2012). There is recent evidence to suggest that change in constitutive
autophagy in neurons can impact the number and quality of synaptic plasticity and regulation ofpresynaptic signaling. Many neurodevelopmental disorders are associated with dysfunction in
autophagy related pathways (e.g. mTOR). Autophagy is also required for maintenance and functionof adult neural stem cells. Ablation of genes essential for autophagy lead to progressive loss of neuralstem cells and impairment of neural differentiation (Wang et al., 2013).

Cardiovascular diseases

Cardiovascular disease is the leading cause of mortality through the developed world. Autophagy
has been reported in almost all differentiated cells including the cardiovascular system. Autophagic
pathway is essential for normal maintenance, repair, and adaptation of the heart tissue. Therefore,
autophagic deficiencies have been associated with a variety of cardiac pathologies.
Changes in autophagic flux are seen in essentially all forms of heart disease and in all cell types. It
can either be beneficial or aid in disease progression. Ischemic heart disease is characterized bylack of nutrients and oxygen to the myocardium. Studies looking at models of ischemia have shownthat autophagy functions as a pro-survival mechanism by adapting to changing metabolic needs andeliminate damaged mitochondria, which can release ROS and initiate apoptosis to prevent any tissue
damage. Inhibition of autophagy can exacerbate cardiac dysfunction and remodeling (Kanamori et al.,Discover more at abcam.com/celldeath15

2011). Once oxygen and nutrients are restored, autophagy can either be adaptive or detrimental to thetissue. Some studies have shown that reperfusion following an ischemic attack leads to an increase in
autophagy but an impairment of autophagosome clearance leading to cell death (Ma et al., 2012).
Deficiency of the autophagy gene LAMP-2 was shown to cause Danon disease. Patients have an
increase of autophagic vacuoles leading to cardiomyopathy (Nishino et al., 2000), a phenotype seen inmice with inactivation of the LAMP-2 protein (Tanaka et al., 2000).
Autophagic vacuoles have been described in the heart tissue of patients with idiopathic dilated
cardiomyopathy (Kostin et al., 2003). Cardiac hypertrophy is characterized by an increase in
cardiomyocyte size, disarrangement of sarcomeric structure, enhanced protein synthesis andre-expression of fetal genes (Harvey & Leinwand, 2011). Cardiac hypertrophy is accomplished by
dysfunction of numerous signaling pathways that are involved in autophagy. PI3K/AKT, GSK3, MAPKs
and mTOR pathways have all been associated in regulation of cardiomyocyte autophagy (Li et al.,2015).
Autophagy acts as a defense mechanism against aging of cardiomyocytes. The heart develops cardiac
hypertrophy and diastolic dysfunction with aging when autophagy is inhibited (Linton et al., 2015).
Recent studies have showed that miRNAs play an important role in regulating cardiac autophagy (Liet al., 2014) and there are growing number of studies targeting autophagy regulating miRNAs as apotential strategy in the treatment of cardiac disorders.
Further study of the autophagic pathway will lead to increased understanding of the regulation of thiscritical homeostatic pathway and identify new therapeutic potentials for cardiac disease.

Infectious disease

Autophagy plays a key role in immune defense against invading bacteria and pathogens. Upon
infection, autophagy regulates inflammation, antigen presentation and micro-organism capture anddegradation (Levine et al., 2011).
Autophagy is induced by pattern recognition receptors and, through autophagic adaptors, it provides
a mechanism for the elimination of intracellular microorganisms. Autophagy controls inflammation
through regulatory interactions with innate immune signaling pathways, by removing endogenous
inflammasome agonists and through effects on the secretion of immune mediators.
Moreover, autophagy contributes to antigen presentation and to T cell homeostasis, and it affects T
cell repertoires and polarization (Deretic et al., 2013).

Discover more at abcam.com/celldeath16Autophagy detection
The cells respond to changes in the extracellular environment by regulating autophagic flux to meetintracellular metabolic demands. The impact of autophagic flux on cell death and human pathologies
therefore demands accurate tools. It is important to measure the autophagic flux through the entire
autophagy pathway to correctly interpret the results of autophagic activity. The autophagic substrates need
to be monitored dynamically over time to verify that they have reached the correct endpoint of degradation.
In 2008 and 2012, DJ Klinosky and collaborators (Klinosky et al., 2008; Klinosky et al., 2012)published a comprehensive guide to help standardize how autophagy should be monitored. These
guidelines were created to help establish criteria that are essential for reliable detection of autophagy
in various experimental systems. The methods below are created using their guidelines for each ofthese techniques.
An important step towards understanding the role autophagy plays in these diseases is to establish
assays and screening systems to measure autophagic flux rapidly and precisely. This becomes more
important as we explore new methods to manipulate autophagy for therapeutic purposes.

Markers of autophagy

There are no absolute criteria for determining autophagic status that are applicable in every biologicalor experimental context. The key issue is to differentiate between the often transient changes in theamount of autophagosomes due to increased induction and from accumulation due to inefficientcompletion of autophagy.
Autophagy is always present at a baseline level in a given system and the key to accurately analyze
autophagic flux is to measure change from baseline activity under various conditions.
Table 1. Key markers of autophagy
Key Markers

FunctionRole in Autophagy

Atg1/ULKs

Protein kinase, phosphorylated by mTORC1

Involved in autophagy
induction and possibly inphagophore formation

Atg2

Interacts with Atg18/WIPI4

Possibly involved inphagophore formation

Atg3

E2-like enzyme involved in Atg8/LC3
lipidation

Involved in phagophore
expansion

Atg4

Cysteine protease involved in processing
and delipidation of Atg8/LC3

Involved in phagophore
expansion

Atg5

Ubiquitin-like modifier that covalently
binds to Atg12, generating the Atg12–Atg5
conjugate to lipidate Atg8

Involved in phagophore
expansion

Atg6/beclin 1

Inhibited by binding to Bcl2. Componentof various PI(3)K complexes. Interacts
with PIK3C3/VPS34 to signal the onset of
autophagy

Involved in autophagy
induction and phagophore
formation

Discover more at abcam.com/celldeath17Key Markers

FunctionRole in Autophagy

Atg7

E1-like enzyme involved in LC3 ubiquitin
chain

Involved in phagophore
expansion

Atg8/LC3s

Ubiquitin-like protein

Involved in phagophore
expansion andautophagosome formation

GABARAP

Ubiquitin-like modifier that conjugates to
LC3 to PE

Involved in a later stage of
autophagosome maturation

GABARAPL1/Atg8L/
GEC1

Ubiquitin-like modifier

Involved in a later stage of
autophagosome maturation

GABARAPL2/
GATE-16/GEF2

Ubiquitin-like modifier involved in intra-Golgi
traffic

Involved in a later stage of
autophagosome maturation

Atg9

Transmembrane protein involved indirecting membrane to the phagophore

Involved in the induction of
autophagy and phagophore
formation

Atg10

E2-like enzyme for the ubiquitin-likeconjugation system that mediates theformation of Atg12–Atg5 conjugate

Involved in phagophore
expansion

Atg12

Ubiquitin-like protein that conjugates to Atg5
to lipidate Atg8

Involved in phagophore
expansion

Atg13

Binding partner and regulator of Atg1/ULKs,
phosphorylated by mTORC1

Involved in autophagy
induction and possibly
phagophore formation

Atg14

Component of the PI(3)K complex
I. Required for both basal andinducible autophagy. Essential for the
autophagy-dependent phosphorylation of
Beclin1/Atg6

Involved in autophagy
induction and possibly
phagophore formation.
Associated with phagophoreand mature autophagosome

Atg16/Atg16L1

Interacts with Atg12-Atg5 conjugate toform a large complex, which mediates LC3
lipidation on autophagosomal membranes

Involved in phagophore
expansion

Atg17/FIP200

Binding partner and regulator of Atg1/ULKs,
scaffold for ULK1 and Atg13

Involved in autophagy
induction and possibly
phagophore formation

Atg18/WIPIs

PIP3P-binding protein that functions
downstream the Class III PI3-kinase
complex and upstream the Atg12 and LC3
ubiquitin-like complexes

Involved in phagophore andautophagosome formation

Ambra1

Regulator of the PI(3)K and Atg1/ULK
complexes. Interacts with Beclin1

Involved in autophagy
inductionZFYVE1/DFCP1

PtdIns3P-binding protein localized in Golgi
and ER, the later population being involvedin omegasome formation

Involved in autophagy
induction and possibly
phagophore formation

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Key Markers

FunctionRole in Autophagy

VMP1

Transmembrane protein

Involved in regulation of
autophagy induction

DRAM1

Lysosomal modulator induced by activated
p53/TP53

Involved in autolysosome
formation

Vps34/PtdIns3PKC3Component of various PI(3)K complexes

Involved in autophagy
induction and phagophore
formation

SQSTM1/p62

Ubiquitin-binding scaffold protein which
colocalizes with ubiquitinated protein
aggregates. P62/SQSTM1 binds directly to
LC3 and GABARAP family proteins

Involved in autophagy
regulation and possibly
autophagosome formation

mTORC1

Central cell-growth regulator which uponactivation, phosphorylates Atg13, preventing
it from entering the ULK1 kinase complex

Negative regulator of
autophagy

AMPK

Key energy sensor which regulates cellular
metabolism to maintain energy homeostasis

Positive regulator of
autophagy

Visual identification
Visually analysis using techniques such as Transmission Electron Microscopy (TEM) is one of themost widely used and important method to monitor autophagy. It is also one of the most problematicdue to misinterpretations mostly due to challenges in classification of compartments into discretemorphological subset.
It is very important to take care in the selection of sample to be analyzed and its fixation method.
Perfusion fixation of the tissue is recommended when studying autophagy.
The accurate identification of the autophagosome is essential for a useful analysis. It is also recommended
to consider monitoring autophagy using at least two time points. The advantage of this approach is that it
can provide accurate information on flux even when the autophagosomes are abnormal.
• The phagophore and autophagosomes contain few, or no detectable intramembrane particles(IMPs) when compared with lysosomes.
• Autophagosomes that become fused with an endosome and a lysosome contain an increased
density of IMPs in the membrane.
• Autolysosomes generally have only a single membrane because the inner membrane is degradedby the lytic enzymes in addition to the engulfed material.
The best approach is to estimate the volume occupied by autophagic structures (as percentage ofcytoplasmic or cellular volume, using volumetric morphometry/stereology) in at least 20 cell profiles
per sample (the number needed should be dictated by some form of power analysis, which indicatesthat the data are significant).

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Product highlight:
CytoPainter LysoOrange Indicator Reagent(ab176827)

CytoPainter Lysosome/ER/NuclearStaining
Reagent (ab139488)

Image of HeLa cells stained with Abcam’s
CytoPainter LysoOrange Indicator Reagent(ab176827). Also available in other colours.

Live cells treated with Chloroquine and stainedwith Organelle Reagent II showing composite of(A) lysosomes in red, (B) endoplasmic reticulain green, and (C) nuclei in blue.

ATG8/LC3 detection
Western Blotting
Atg8/LC3 is an excellent marker for autophagy. It belongs to ubiquitin-like protein family and exist in
non-lipidated and lipidated forms called LC3-I and LC3-II respectively. LC3 (Atg8) is converted fromproLC3 into a cleaved form, LC3-I. This processed LC3-I is finally modified into the PE-conjugatedform, LC3-II. LC3-II/Atg8–PE is the only protein marker that is reliably associated with completed
autophagosomes. In western blot experiments, mammalian marker LC3-I migrates at approximately
18 kDa and LC3-II at approximately 16 kDa when both are detectable.
Because of the dynamic nature of the autophagic process there are several important factors toconsider when performing western blotting.
Atg8/LC3-II detection
1. Samples Types
a. LC3-II levels are dependent on tissue and cell type.
b. Variation in the amounts of LC3-I vs. LC3-II expression in the different tissues can present
technical problems. LC3-I is very abundant in brain tissue.
c. Asynchronous and heterogeneous cell populations can present with variable results whenanalyzing LC3 by western blotting.
d. Cells can exhibit low levels of LC3-II due to an intense autophagic flux and tumor-derived cells
can have high basal levels of LC3-II (e.g. MDA-MB-231).
e. Autophagy can be induced by transfection or nucleofection. The amount of autophagy induced bytransfection of a control empty vector can be too high to make any meaningful reading.

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f. siRNA transfection does not show any induction of autophagy; but transfection of plasmid shRNAor plasmid expression constructs causes increase in autophagy. It is recommended to use
endotoxin-free DNA to help address this problem.
g. If transfection efficiency is too low, it may be necessary to use methods, such as fluorescencemicroscopy, that allow autophagy to be monitored in single cells.
h. Certain media components have shown effects on basal autophagy levels.
2. Visual detection of LC3-II
a. Autophagosome accumulation and amount of LC3-II are not well correlated using high resolution
microscopy.
b. Formation of LC3-II is not sufficient evidence for autophagy. Deletion of genes involved information of LC3-II (e.g. Beclin) does not alter levels of LC3-II even though autophagy issubstantially reduced.
c. LC3-II is also associates with the membranes of certain non-autophagic structures.
d. LC3 can be recruited directly to bacteria or virus containing phagosome membranes under certain
immune activating conditions.
3. Antibodies
a. LC3-I may be less sensitive to detection by certain anti-LC3 antibodies.
b. LC3 is expressed as four isoforms in mammalian cells, LC3A, LC3B, LC3B2 and LC3C, which
exhibit different tissue distributions.
c. Certain commercial anti-LC3B antibodies also recognize LC3A, but do not recognize LC3C,
which share less sequence homology. It is important to note that LC3C possesses in its primaryamino acid sequence the DYKD motif that is recognized with a high affinity by anti-DDDDK tag
antibodies, such as anti-DDDDK tag antibody (ab1162).
4. SDS-PAGE
a. Not all of the autophagy-related proteins are required for Atg8/LC3 processing, including lipidation.
b. PVDF membranes are better suited for stronger LC3-II retention than nitrocellulose membranes.
c. Triton X-100 does not efficiently solubilize LC3-II in some systems. Heating in the presence of 1%
SDS, or analysis of membrane fractions is recommended.
d. LC3-II levels should be compared with actin or other appropriate “housekeeping” proteins and not
to LC3-I.
e. No special treatments are needed for the separation of mammalian LC3-I from LC3-II.

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Product highlight:
Anti-LC3B antibody (ab48394)

Anti- MAP1LC3A RabMAb antibody (ab52768)

Western Blot image of Mouse hepatocytes
treated with 20 µg/ml of poly(I:C) for 12hr using
anti-LC3B antibody (ab48394).

Immunocytochemistry/Immunofluorescenceanalysis of human keratinocytes (panel A) and
VZV-infected melanoma cells (panel E) labeling
MAP1LC3A with ab52768.

Image courtesy of an anonymous Abreview.
Image from Buckingham EM et al.,Biotechniques. 2014;57(5):241-4. Fig 1.; doi:
10.2144/000114226.

GABARAP-PE detection
1. GABARAPL1 should be analyzed by western blot using high concentration (15%) gels.
2. GABARAP migrates faster than GABARAPL1.
3. It is very difficult to differentiate between GABARAPL1 and GABARAPL3 proteins, which have
94% identity and their expression patterns are apparently identical. GABARAPL3 lacks an
ortholog in mice.
Atg8 (yeast) detection
1. Atg8 and Atg8–PE can be resolved by including 6M urea in the SDS-PAGE separating gel, or byusing a 15% resolving gel without urea.
2. Atg8 in plants can be resolved by using urea combined with prior treatment of the samples with(or without) Phospholipase D. Phospholipase D removes the PE moiety from Atg8.
3. Atg8–PE migrates faster than unconjugated Atg8 during SDS-PAGE, even though the former hasa larger molecular mass.
4. It is also possible to label cells with radioactive ethanolamine, followed by autoradiography toidentify Atg8–PE, and a C-terminal peptide can be analyzed by mass spectrometry to identify thelipid modification at the terminal glycine residue.
Turnover of LC3-II/ATG8–PE
There are very important differences between monitoring the steady-state level of Atg8/LC3 andautophagic flux. The autophagic flux is monitored by following Atg8/LC3 in the absence and presenceof autophagy inhibitors, and/or by examining the autophagy-dependent degradation of appropriate
substrates.

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Lysosomal degradation can be prevented through the use of the following –• Protease inhibitors - Pepstatin A and E-64d.
• Compounds such as bafilomycin A1, chloroquine or NH4Cl that neutralize the lysosomal pH.
• Agents that can block autophagosomes and lysosome fusion (note that bafilomycin A1 will
ultimately cause a fusion block as well as neutralize the pH).
• Knock down or knock out of LAMP2 to block the fusion of autophagosomes and lysosomes.
Table 2. Autophagy inhibitors
AbID

Inhibitors

Description

Target point

ab120497

Bafilomycin A1

Highly potent, selective(V)-ATPase inhibitor

Autophagosome
formation

ab120366(±)-BAYK8644

Potent L-type Ca2+ channel
activator

mTOR-independent
signaling pathway

ab142116

Chloroquinediphosphate

Antimalarial; apoptosis andautophagy inhibitor

Autophagolysosome

ab144227

Concanamycin A(Folimycin)

Potent, selective vacuolar-type
H+-ATPase inhibitor. Macrolide
antibiotic agent.

Autophagosome
formationab141254

DBeQ

Selective, potent, reversible andATP competitive p97 ATPase
inhibitor

Autophagosome
formation

ab144048

E-64d (Aloxistatin)

Irreversible cell-permeable
cathepsin B and L inhibitor

Autophagolysosome

ab120243

LY 294002

PI3K inhibitor

Autophagosome
formation

ab120841

3-Methyladenine

Selective PI3K inhibitor

Autophagosome
formation

ab120630

Nocodazole

Microtubule inhibitor

Autophagosome
formationab141416

Pepstatin A

Potent selective aspartic
protease inhibitor

Autophagolysosome

ab142205

Spautin-1

Cell-permeable USP10 and
USP13 inhibitor

Autophagosome
formation

ab120143

Paclitaxel

Anticancer agent

Autophagosome
formationab141475

Vinblastine sulfate

Potent microtubule dynamics
inhibitor

Autophagosome
formation

ab120148

Wortmannin

PI3K inhibitor

Autophagosome
formation

ab144590

Xanthohumol

Valosin-containing
protein inhibitor. Potent
chemopreventive agent.

Autophagosome
formation

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23

AbID

Inhibitors

Description

Target pointab143032

Acetylcysteine (NAcetyl-L-cysteine)

ROS inhibitor.

Autophagosome
formationab141404

Leupeptin
hemisulfate

Reversible competitive serine/
cysteine protease inhibitor

Autophagolysosome

ab120093

Cycloheximide

Protein synthesis inhibitor

Autophagosome
formation

ab120827

Hydroxychloroquine
sulfateAnti-inflammatory agent

Autophagolysosome

For the full list of autophagy inhibitors please visit our website: www.abcam.com/autophagy-inhibitors
Factors to consider while using inhibitors of autophagy –1. Increase in the levels of LC3-II in the presence of bafilomycin A1 indicates presence of autophagic
flux. However, a lack of increased LC3-II levels in the presence of bafilomycin A1 suggests a blockin autophagy at the terminal stages.
2. It is essential to avoid assay saturation when using inhibitors of autophagy.
3. The duration of the bafilomycin A1 treatment needs to be relatively short (1–2h) to allow
comparisons of the amount of LC3 that is lysosomally degraded over a given time frame.
4. Control experiments are important to demonstrate the efficacy of this approach in each experimental
context.
Autophagic flux can also be measured by the amount of cytosolic LC3-IIs. The ratio between LC3-I
and LC3-IIs can provide a more accurate measure of autophagic flux than ratios based on the total
level of LC3-II.
One key advantage of this approach is that it does not require the presence of autophagic orlysosomal inhibitors to block the degradation of LC3-II.

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Product highlight:
Autophagy Detection Kit (ab139484)

Fluorescent microscopy analysis showing nucleus (blue nuclear stain; DAPI filter) and autophagic
vesicules (green, FITC filter) in control HepG2 cells or cells starved in serum free medium for 5
hours, treated with 0.1 mM chloriquine for 24 hours or starved and chloriquine treated for 5 hours.

Luminescence based assays
Autophagic flux can be monitored based on the turnover of LC3-II, by utilizing a luminescence-based
assay. A reporter assay based on the degradation of Luciferase-LC3 fusion proteins. LC3- turnover
can thus be estimated by monitoring the change in the ratio of luciferase between the two cell
populations. Luc-LC3-assay can be used to estimate autophagic flux at a single time point by defining
the luciferase activities in cell extracts. The live cell luciferase substrate makes it possible to monitorchanges in autophagic activity in living cells in real time.
• Soluble form of LC3-II (i.e., LC3-IIs) is not observed in many standard cell types including HeLa,
HEK 293 and PC12.
• LC3-IIs/ LC3-I ratio must be analyzed using the cytosolic fractions rather than the total
homogenates.
• LC3-II turnover can be a result of partial autophagy block and care should be taken in interpreting
the results as disruption in autophagy will still result in an increase in LC3-II.
• It is necessary to follow LC3-II turnover if other substrates are being monitored simultaneously.
• Inhibitor concentration and incubation times are very important when using lysosomal proteaseinhibitor. In contrast to the protease inhibitors, chloroquine (10mM) or bafilomycin A1 (1–100nM) canbe added to cells immediately prior to autophagy induction.
GFP-ATG8/LC3 detection
The GFP-Atg8/LC3 processing assay is another convenient way to monitor autophagy. When
GFP-LC3 is delivered to a lysosome/vacuole, Atg8/LC3 is sensitive to degradation but GFP protein isrelatively resistant. Therefore, the appearance of free GFP on western blots can be used to monitor
autophagic flux. But there are considerations and limitations of using this method and it is not as easy
to quantify as enzyme-based assays. Some of the factors are listed below Lysosomal pH is a critical factor in the detection of free GFP to monitor flux.

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Free GFP fragments are only detectable in the presence of non-saturating levels of lysosomotropic
compounds or when autophagic/degradative machinery allows the accumulation of the proteolytic fragment.
There are some limitations of using free GFP to detect autophagy ••••The assay depends on cell type and culture conditions.
GFP is more sensitive to mammalian lysosomal hydrolases than of the yeast vacuole.
When the lysosomal pH becomes particularly low, free GFP is undetectable.
Immunoblotting should be included as a control to address the stability of non-lysosomal GFP suchas GFP-LC3-I.
• It should also be noted that free GFP can be detected when cells are treated with non-saturating
doses of lysosomal inhibitors such as chloroquine, E-64d and bafilomycin A1.
• The saturating concentrations of these lysosomal inhibitors vary in different cell lines, and it would
be better to use a saturating concentration of lysosomal inhibitors when performing an autophagic
flux assay. Therefore, caution must be exercised in interpreting the data using this assay; it would
be helpful to combine an analysis of GFP-LC3 processing with other assays such as the monitoringof endogenous LC3-II by western blot.
• Lysosomal inhibition needs to be carefully controlled. Prolonged inhibition of lysosomal hydrolases(6h) is likely to induce a secondary autophagic response triggered by the accumulated undigested
autophagy cargo.
Fluorescence microscopy
The use of cell imaging allows rapid and quantitative measures of the number of LC3 puncta and theirrelative number in individual or mixed cell types. Immunofluorescence microscopy method utilizes afluorescent protein tag at its N terminus. Autophagy is measured by observing increase in punctate
LC3 or GFP-LC3.
The tagged fusion proteins are useful for in vivo studies and live cell imaging experiments usingtransgenic models. Different tags have limitations and are recommended for different applications.
Table 3. Key tags that can be used in fluorescence microscopy
Tag

Requirements

Recommendation

GFP/EGFP

Requires Neutral pH

Not recommended in live cell
imaging.
Can be used inparaformaldehyde fixed cells

PA-GFP

Photon activation

Can induce DNA damage andproduce additional autophagy

mRFP/mCherry

Photostable at acidic pH.
Overexpression can be toxic

mCherry signal can persist inacidic environment

Dendra2

Photoswitchable – Low
phototoxic activation, efficientchromophore maturation

Recommended for live cell
imaging

Venus (YFP variant)

Brighter than mRFP, lesssensitive to pH

Recommended for live cell
imaging

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Viral vectors can also be used to transfect fusion protein GFP-LC3. Care must be taken as viral
vectors can also activate stress pathways in some cells and possibly induce autophagy.
There are some limitations when using GFP as a tag for monitoring autophagy • GFP tag is large relative to the size of LC3 and the fusion protein LC3-GFP can behave differently
from the native protein.
• GFP is not native in cells and can be targeted for degradation, which has obvious implications whenstudying autophagy.
• Some forms of GFP tend to oligomerize, which may interfere with protein function and/or localization.
• EGFP inhibits polyubiquitination and may cause defects in other cellular processes.
Leupeptin is an inhibitor of lysosomal cysteine and serine proteases that can help stabilize the GFP-LC3
signal during fluorescence microscopy, especially under conditions of induced autophagic flux.

Product highlight:
Autophagy/Cytotoxicity Dual Staining Kit (ab133075)

Ab133075 uses monodansylcadaverine (MDC), a fluorescent compound used as a probe fordetection of autophagic structures in cultured cells.
A: MDC staining of untreated HepG2 cells that show basal level of autophagy
B: PI staining of untreated HepG2 cells
C: MDC staining of HepG2 cells treated with 10 μM Tamoxifen that show increase in autophagy
D: PI staining of HepG2 cells treated with 10 μM Tamoxifen.
Immunocytochemistry or immunohistochemistry procedures can utilize anti-LC3/Atg8 antibodies forthe detection of endogenous proteins without the need for transfection and or the generation of atransgenic organism. This method helps avoid potential overexpression artefacts. If the endogenous
amount is below the level of detection, exogenous construct is recommended provided the system isamenable to introduction of exogenous genes.
It is important to consider the use of stable transfectants vs. transient transfections.

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Table 4. Key advantages of stable and transient transfection
Stable Transfectants

Transient transfections

Reduced background

Higher gene expression

Eliminates artefacts

Immediate effects of the transfection

All cells express the construct

Double transfections

Screen for clones with best signal/noise ratio

Optimize DNA concentration

The following must be considered when using this method • It is recommended to include additional assays to measure autophagy and not rely solely on
monitoring GFP-LC3.
• It is better to determine the number of puncta corresponding to GFP-LC3 on a per cell basis rather
than simply the total number of cells displaying puncta.
• Software programs can help count the puncta including ImageJ, Imaris or CellProfiler.
• Although it is possible to detect changes in the size of GFP-Atg8/LC3 puncta by fluorescencemicroscopy, it is not possible to correlate size with autophagy activity without additional assay
methods. Therefore, size determinations are not recommended as a method for monitoring autophagy.
• Quantification of the fluorescence intensity of GFP-Atg8/LC3 at specific puncta provides a valid
measure of protein recruitment. But the number of puncta visible will be influenced by both the levelof expression of GFP-LC3 in a given cell and by the exposure time of the microscope.
• In many cell types it is essential to establish a cut-off value for the number of puncta per cell in
conditions of “low” and “high” autophagy.
• When using automated analysis methods, care must be taken to manually evaluate parameters
used to establish background cut off values for different treatment conditions and cell types and itis critical that the researchers also specify the baseline number of puncta that are used to define“normal” or “low” autophagy.
• GFP-LC3 can associate with aggregates, especially when expressed at high levels. Inhibition of
autophagy in vitro and in vivo leads to the accumulation of these aggregates, suggesting a role for
autophagy in mediating their clearance.
• One way to control for background levels of puncta is to determine fluorescence from untagged GFP.
• Controls are needed to verify that the transfection protocol does not artificially induce GFP-LC3
puncta or cause LC3 aggregation.
Tandem mRFP/mcherry-GFP fluorescence microscopy
As explained in the previous method, the GFP signal is sensitive to the acidic and/or proteolytic
conditions of the lysosome lumen, whereas the mRFP is more stable. This method enables
simultaneous estimation of both the induction of autophagy and flux through autophagic compartments
using a tandem monomeric RFP-GFP-tagged LC3. Based on the fluorescence the status of the LC3protein is determined –• Yellow color – presence of GFP and mRFP fluorescence indicates a compartment that has not
fused with a lysosome, such as the phagophore or an autophagosome.
• Red color - mRFP signal without GFP corresponds to an autolysosome.
This method can also be used to monitor autophagy in high-throughput drug screening studies andcan be automated.

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An alternative dual fluorescence assay involves the Rosella biosensor. This assay monitors the uptakeof material to the lysosome/vacuole and complements the use of the tandem mRFP/ mCherry-GFP
reporter. The assay is based upon the genetically encoded dual color-emission biosensor Rosella, afusion between a relatively pH-stable fast-maturing RFP variant, and a pH sensitive GFP variant.
When targeted to specific cellular compartments or fused to an individual protein, the Rosellabiosensor provides information about the identity of the cellular component being delivered to thevacuole/lysosome for degradation. Importantly, the pH-sensitive dual color fluorescence emission
provides information about the environment of the biosensor during autophagy of various cellularcomponents.
The Rosella assay has not been tested in a wide range of mammalian cell types and sensitivity andthe specificity of the assay must be verified independently.
Care must be taken when using the tandem fusion protein method to detect autophagy –• The motion of LC3/Atg8 puncta are difficult to measure in live imaging experiments.
• Conventional confocal microscopy may not allow visualization of colocalized mRFP/mCherry-GFP
puncta.
• The use of mTagRFP-mWasabi-LC3 chimera is recommended, as mTagRFP is brighter
than mRFP1 and mCherry, and mWasabi is brighter than EGFP. Overexpression ofmTagRFP-mWasabi-LC3 does not appear to be toxic to HeLa cells.
• If used fixed cells, the tissue or cell samples must be properly processed to avoid losing the acidic
environment of the autolysosomes.
• Monomeric green fluorescent protein is more acid sensitive than EGFP and is well suited forassaying autophagic flux using this method.
• Another caution in the interpretation of the tandem fluorescent marker is that colocalization of
GFP and mRFP/mCherry might also be seen in the case of impaired proteolytic degradation within
autolysosomes, or altered lysosomal pH.
• Expression of tandem mRFP-GFP-LC3 is toxic to some cancer cell lines relative to GFP-LC3 or
RFP-LC3.
• The cytotoxicity of DsRed and its variants such as mRFP1 is associated with downregulation of
BCL2L1/Bcl-X(L).
Flow and multispectral imaging cytometry
Flow cytometry and multispectral cytometry is a method to analyze autophagy at medium- tohigh-throughput. The advantage of this approach is that larger numbers of cells can be analyzed withregards to GFP-LC3 puncta, cell morphology and/or autophagic flux, and concomitant detection of
surface markers can be included, potentially providing more robust data than is achieved with othermethods.
Since EGFP-LC3 is a substrate for autophagic degradation, total fluorescence intensity of EGFP-LC3
can be used to indicate levels of autophagy in living mammalian cells. When autophagy is induced, thedecrease in total cellular fluorescence can be precisely quantified in large numbers of cells to obtainrobust data.
Multispectral imaging flow cytometry allows characterization of single cells within a population
by assessing a combination of morphology and immunofluorescence patterns, thereby providing

Discover more at abcam.com/celldeath29statistically meaningful data. These approaches make it possible to capture high-content images ofcells in flow (up to 1,000 cells/sec), and are particularly useful for cells that grow in suspension.
The preparation of single cell suspensions causes significant levels of plasma membrane disruption
and injury that can induce further autophagy.
Therefore, staining for plasma membrane permeabilization (e.g., cell death) before vs. after isolation is
an important control.
Optimization of image analysis permits the study of cells with heterogeneous LC3 puncta, thus making
it possible to quantify autophagic flux accurately in situations that might disturb normal processes(e.g., microbial infection).
Soluble EGFP-LC3-I can be depleted from the cell by a brief saponin extraction so that the total
fluorescence of EGFP-LC3 then represents that of EGFP-LC3-II alone. Since EGFP-LC3 transfection
typically results in high relative levels of EGFP-LC3-I, this treatment significantly reduces the
background fluorescence due to non-autophagosome associated reporter protein. By comparing
treatments in the presence or absence of lysosomal degradation inhibitors, subtle changes in the flux
rate of the GFP-LC3 reporter construct can be detected.
Saponin extraction method should include carefully titrated saponin concentrations and times oftreatment in order to ensure specific extraction of LC3-I in their systems.
Cell membrane permeabilization with digitonin and extraction of the non-membrane bound form of LC3
allows combined staining of membrane-associated LC3-II protein and any markers for detection of
autophagy in relation to other cellular events/ processes.

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Product highlight:
Propidium Iodide Flow Cytometry Kit (ab139418)

ab139418 on HeLa cells treated with Thymidine and Nocodazole.
A Untreated HeLa cells with the expected distribution of cells with 2N, 2N-4N and 4N DNA content.
B HeLa cells treated with Thymidine have predominantly 2N DNA content. Thymidine inhibits DNA
synthesis.
C HeLa cells treated with Nocodazole are predominantly have predominantly 4N DNA content.

A number of methods have been developed that allow the determination of autophagic flux using thefluorescence-activated cell sorter.
Immunohistochemistry
Immunodetection of autophagic proteins (particularly LC3 and BECN1) is also used as prognostic
factor in various human carcinomas, including lymphoma, breast carcinoma, endometrial
adenocarcinoma, head and neck squamous cell carcinoma, hepatocellular carcinoma, gliomas,
non-small cell lung carcinomas, pancreatic and colon adenocarcinomas, as well as in cutaneous anduveal melanomas. One of the main challenges of using immunohistochemistry for LC3 detection isthat in some tissues this protein can be localized in structures other than autophagosomes including
lipid droplets. Thus, immunodetection of LC3 in cytoplasmic granules is not sufficient to monitor
autophagy in vivo.
Importantly, this kind of assay should be performed as recommended by the Reporting
Recommendations for Tumor Marker Prognostic Studies (Altman et al., 2012).

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Product highlight:
Anti-LC3B N-terminal antibody (ab168831)

Anti-LC3C C-terminal antibody (ab191574)

Immunohistochemical analysis of wild-type(Cln3+/+) or homozygous Cln3Äex7/8 (Cln3Äex7/8/
Äex7/8) paraffin-embedded murine brain sections
labeling LC3B using ab168831 at a 1/50 dilution.

Immunohistochemical analysis ofparaffin-embedded human brain tissue labeling
LC3C with ab191574 at 20 µg/mL.

SQSTM1/p62 and related LC3 binding protein detection
SQSTM1/p62 serves as a link between LC3 and ubiquitinated substrates and is efficiently degradedby autophagy. Thus, the level of SQSTM1/p62 proteins can be used to monitor autophagic flux.
SQSTM1/p62 amount is generally considered to inversely correlate with autophagic activity.
Accumulation of SQSTM1/p62-positive inclusions during immunocytochemistry or elevated p62 levels
on western blots are frequently used as signs of autophagy impairment.
Although the measurement of the cellular SQSTM1/p62 level appears to correlate well with othermarkers of autophagic flux, it is important to note the following • SQSTM1/p62 is degraded by both the autophagy and ubiquitin-proteasome system, and its levelmay be increased when the proteasome is inhibited.
• Besides LC3, SQSTM1/p62 contains domains that interact with several signaling molecules,
indicating that SQSTM1/p62 may have other functions with regards to its role in autophagy.
• It is necessary to examine endogenous SQSTM1/p62 because overexpression of this protein tends
to self-aggregate and may no longer indicate autophagy activity.
• SQSTM1/p62 can be transcriptionally upregulated under certain conditions.
Measurement of the SQSTM1/p62 levels must be performed in combination with other methods suchas LC3-II turnover.
SQSTM1/p62 aggregates are insoluble in NP40 or Triton X-100 lysis conditions. Therefore, in order
to conclusively establish SQSTM1/p62 degradation by autophagy, SQSTM1/p62 levels in both Triton
X-100 soluble and insoluble fractions need to be determined upon treatment with autophagy inducers
or autophagy inhibitors.

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Product highlight:
Anti-SQSTM1/p62 [EPR4844] RabMAb
antibody (ab109012)

SQSTM1/p62 full length Protein (ab132366)

Overlay histogram showing HeLa cells stainedwith ab109012 (red line). Isotype control
antibody (black line) was rabbit IgG (monoclonal)
used under the same conditions. Unlabeled
sample (blue line) was also used as a control.

12.5% SDS-PAGE analysis of ab132366
stained with Coomassie Blue.

TOR, AMPK and ATG1/ULK1 detection
Both mTORC1 and AMPK are able to oppositely regulate ULK1 (and ULK2) kinase activity bydirect phosphorylation. Under glucose starvation AMPK promotes autophagy by directly activating
ULK1 through phosphorylation. Under nutrient sufficiency, high TORC1 activity inhibits ULK1 byphosphorylating alternate ULK1 residues and preventing the interaction between ULK1 and AMPK.
TORC1 is an autophagy suppressive regulator which integrates growth factors, nutrient and energy
signals. TORC1 activity can be monitored by analyzing the phosphorylation of its substrates such
as EIF4EBP1 (at Thr37 and Thr46) and RPS6KB1 (at Thr389) using phospho-specific antibodies.
Generally a decrease in TORC1 activity is a good measure for autophagy induction, however:• TORC1 selectivity and sensitivity to its substrates depend on its integrity and configuration. Various
stimuli may affect TORC1 integrity and therefore a decrease or increase in the phosphorylation
status of one TORC1 substrate does not necessarily reflect changes in others, including ULK1.
Therefore reliable antibodies should be used to directly assess the phosphorylation state of ULK1.
• Furthermore, TORC1 activity does not necessarily prevent autophagy induction, because there are
TORC1- independent mechanisms that induce autophagy.
• Also, under conditions of ongoing starvation, persistent autophagy induction can cause negative
feedback which reactivates TORC1.
TORC1 must be used in combination with other assays which directly measure autophagy.
AMPK is a multimeric serine/threonine protein kinase. The enzymatic activity of AMPK depends
on phosphorylation at Thr172 of the alpha subunit and its activity can be monitored using a

Discover more at abcam.com/celldeath33phospho-specific antibody in western blotting. However, the role of AMPK in autophagy is complex
and depending on cell type and metabolic conditions AMPK can suppress autophagy (in liver cells) or
stimulate autophagy (e.g., fibroblasts, colon carcinoma cells and skeletal muscles).
ULK1 has been identified as a direct target for TORC1 and AMPK; however, there is not a consensus
on the specific residues of ULK1 which are targeted by AMPK and TORC1.
Activation of the ULK1 complex is one of the initial steps of autophagy induction. The phosphorylation
status of ULK1 at the activating sites (Ser317, Ser467, Ser555, Ser637, Ser777 or Thr574) ordephosphorylation at the inhibiting sites (Ser638, Ser757) can be used to monitor autophagy induction
by using phospho - specific antibodies in western blotting and immunoprecipitation. When using ULK1complex assembly to monitor autophagy induction it is important to note:• Endogenous levels of ULK1 are low in many systems.
• ULK1 is phosphorylated by multiple kinases and the amount of phosphorylation can vary during
autophagy induction.
Therefore, it can be difficult to detect phospho-ULK1 in western blotting without prior assay optimization.
Using ULK1 kinase activity as a tool to monitor autophagy is yet limited because further studies
identifying physiological substrates of ULK1 are needed to understand how ULK1 dependant
phosphorylation affects the initiation of the autophagy and therefore, is not a direct assay for autophagy.

Additional autophagy related markers
ATG9
Atg9 is the only known transmembrane protein required for autophagy and is proposed to deliver
membrane to the phagophore structures and autophagosomes. Atg9 shuttles to and from thephagophore assembly site. Atg9 localizes distinctively to multiple discrete vesicles throughout thecytoplasm, compared to the other Atg proteins which are mainly detected in a single punctum or
diffusely within the cytosol. Atg9 vesicles are 30–60 nm in diameter and contain approximately 30
molecules of Atg9 (Yamamoto et al., 2012). These vesicles fuse to form the preautophagosomal
structure, and subsequently Atg9 becomes integrated into the outer autophagosomal membrane. After
fusion of autophagosomes with the lysosome or vacuole, Atg9 is recycled.
Atg12-Atg5/Atg16L1 complex associates with the phagophore and can be detected byimmunofluorescence. During starvation there is an increased proportion of cells with punctate
Atg5, Atg12 and Atg16L1, whereas under physiological conditions, the endogenous proteins are
predominantly diffusely distributed throughout the cytoplasm. Autophagosome formation inhibitors,
used in mammalian cells assays, result in blocking of the starvation induced puncta. Monitoring
conjugation of Atg12-Atg5 may not be useful way to measure autophagy induction because it appears
that in some mammalian cells all Atg12 and Atg5 proteins exist in the conjugated form and at leastin short term starvation the expression levels don’t seem to change. Atg16L1 is located on thephagophore, but not on the completed autophagosome, therefore can be used to monitor early stepsof the process by immunostaining, Immune-TEM or by the use of tagged Atg16L1.
ATG14
Atg14 localizes primarily on the phagophore and can be detected by immunostaining and used as a

Discover more at abcam.com/celldeath34phagophore marker. However, since Atg14 is not exclusively localized on the phagophore, but can bedetected on the autophagosome and on the ER, its detection should be performed together with otherphagophore and autophagosome markers.
ATG18
Atg18/WIPI family proteins bind to phosphatidylinositol 3- phosphate (PtdIns3P) that is present at
both the phagophore and the autophagosome. When autophagy is initiated WIPI1 and WIPI2 bindPtdIns3P and accumulate at membranes such as ER where they participate in the autophagosome
formation. Upon starvation or rapamycin administration, autophagy activity is increased and thenumber of cells which display WIPI puncta at the autophagosomal membrane is also increased.
Respectively, under autophagy inhibited conditions, reduced number cells display WIPI puncta whenstudied by fluorescence microscopy or immunostaining.  It may be possible to use the formation anddisappearance of WIPI puncta to monitor autophagy but it is important to note that overexpression of
WIPI1 and WIPI2 can cause formation of aggregates which are stable in the presence of PtdIns3K
inhibitors.
BECLIN1
BECN1 and PIK3C3 are involved in the complex which signals the onset of autophagy and could be
used to monitor autophagy. BECN1 is inhibited by it binding to anti-apoptotic protein Bcl2. Autophagy
is induced when BECN1 is released from Bcl2, however, it is important to note that autophagy canalso be induced in a BECN1-independent manner. BECN1 and PIK3C3 can be part of multiple
complexes and monitoring their localization should be used cautiously. Upon autophagy stimulation
BECN1 and PIK3C3 form aggregates at the region of the Golgi complex and therefore BECN1-GFP
puncta can be used as marker for autophagy induction by immunofluorescence. However:• GFP moiety can interfere with the correct localization of BECN1 so appropriate controls andinhibitors should be used in the experiments.
• In BECN1-independent autophagy such aggregates are not formed despite the cells ability to
express BECN1 (assessed by western blotting).
DRAM1
DRAM1 (DNA-Damage Regulated Autophagy Modulator 1) is a small hydrophobic protein with six
transmembrane domains. Elimination of DRAM1 by siRNA blocks autophagy which indicates its
importance in this process. Detection of DRAM1 RNA during autophagy is easy by qRT-PCR, however
DRAM1 protein measurement and detection is very difficult because of its hydrophobicity and small size.

Discover more at abcam.com/celldeath35General considerations for autophagy detection
Detection of autophagy is a complex process and there is no one perfect method to measureautophagosome numbers or autophagic flux. We recommend the use of multiple assays wheneverpossible rather than relying on the results from a single method.
The table below (Table 5) highlights some of the recommended methods for monitoring autophagy in awide range of systems.
Table 5. Recommended methods for monitoring autophagy
MethodDescription

Electron Microscopy

Quantitative electron microscopy, immune-TEM;
monitor autophagosome number and/or volume

Atg8/LC3 western blotting

Western blot. The analysis is performed in the absence
and presence of lysosomal protease or fusion inhibitors
to monitor flux; an increase in the LC3-II amount in thepresence of the inhibitor is usually indicative of flux

GFP-Atg8/LC-3 lysosomal delivery andproteolysis

Western blot ± lysosomal function or degradation
inhibitors; the generation of free GFP indicateslysosomal/vacuolar delivery

GFP-Atg8/LC3 fluorescence microscopy

Fluorescence microscopy, flow cytometry to monitor
vacuolar/lysosomal localization. Also, increase of inpunctuate GFP-Atg8/LC3 or Atg18/WIPI

Tandem mRFP/mCherry-GFP
fluorescence microscopy

Flux can be monitored as a decrease in green/red(yellow) fluorescence (phagophores, autophagosomes)
and an increase in red fluorescence (autolysosomes)

SQSTM1/p62 and related LC3 binding
protein turnover

The amount of SQSTM1 increases when autophagy isinhibited and decreases when autophagy is induced

mTOR, AMPK and Atg1/ULK1 kinase activity

Western blot, immunoprecipitation or kinase assays

Autophagic sequestration assays

Lysosomal accumulation by biochemical or multilabel
fluorescence techniques and TEM with a maturation inhibitor

Turnover of autophagic compartments

Electron microscopy with morphometry/stereology

Autophagosome-lysosome colocalization

Fluorescence microscopy

Sequestration and processing assays inplantsChimeric RFP fluorescence and processing, and lightand electron microscopy

Tissue fractionation

Centrifugation, western blot and electron microscopy

Degradation of endogenous lipofuscin

Fluorescence microscopy

When deciding which methods to use for their experiment, researchers need to keep in mind that theappropriate assay will depend on the question being asked and the system being used.
We hope that this summary, based on the recommendations by DJ Klinosky and others (Klinosky etal., 2012) is useful in helping you decide the best assay(s) for your experiment.

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