Autophagy Signaling Pathways and Selective Autophagy Research

Autophagy is a cellular quality control system that delivers cytoplasmic components, damaged organelles, protein aggregates, or intracellular pathogens to lysosomes for degradation. Its core significance is not simply “increased degradation,” but rather the maintenance of cellular homeostasis through autophagosome formation, lysosomal fusion, substrate degradation, and product recycling. Autophagy is also involved in stress adaptation, metabolic remodeling, immune defense, aging, and disease progression.

Keywords: autophagy; autophagic flux; ATG proteins; LC3; p62; Beclin1; mTOR; AMPK; mitophagy; selective autophagy

1 Basic Logic of Autophagy Research

1.1 Biological Significance of Autophagy

Autophagy is a dynamic degradation process. It can remove damaged components and recycle metabolites such as amino acids, lipids, and nucleotides under nutrient deprivation or stress conditions. Its function depends on cell type, stress intensity, disease stage, and whether autophagic flux is complete.

(1) Homeostasis maintenance

Basal autophagy clears abnormal proteins, damaged mitochondria, and aged organelles, thereby reducing oxidative stress, protein aggregation, and organelle functional decline.

(2) Stress adaptation

Starvation, hypoxia, energy deficiency, endoplasmic reticulum stress, infection, and drug treatment can all induce autophagy. Under these conditions, autophagy can act as a cytoprotective mechanism, but under persistent stress it may also participate in cell death or therapeutic responses.

(3) Disease association

Autophagy abnormalities are associated with cancer, neurodegenerative diseases, infection and immunity, metabolic diseases, and aging. In tumors, autophagy is stage-dependent: in early stages it may suppress damage accumulation, whereas in advanced tumors it may help tumor cells tolerate hypoxia, nutrient deficiency, and drug pressure.

1.2 Autophagy Is Not Defined by a Single Indicator

Autophagy research should not rely only on increased LC3-II or LC3 puncta. Increased LC3-II may result from enhanced autophagosome formation or from impaired lysosomal degradation. To determine whether autophagy is truly enhanced, autophagic flux should be assessed, meaning the complete process from autophagosome formation to lysosomal degradation of substrates.

Table 1 Autophagy Process and Key Interpretation Points

Stage	Core Event	Representative Molecules	Interpretation Focus
Initiation	Nutrient and energy status sensing; activation of the ULK complex	mTOR, AMPK, ULK1/2, ATG13	mTOR inhibition or AMPK activation often promotes autophagy initiation
Nucleation	Isolation membrane formation and PI3P production	Beclin1, VPS34, ATG14, AMBRA1	The Beclin1/VPS34 complex determines early autophagic membrane nucleation
Elongation and closure	LC3 lipidation and autophagosome formation	ATG5, ATG7, ATG12, ATG16L1, LC3/ATG8	LC3-II indicates autophagosome-related changes but does not equal increased flux
Fusion	Autophagosome-lysosome fusion	LAMP1/2, Rab7, SNAREs	It is necessary to determine whether autophagosomes enter the lysosomal degradation stage
Degradation and recycling	Substrates are degraded by lysosomal enzymes and recycled	p62, NBR1, lysosomal proteases	Decreased p62 often suggests enhanced substrate degradation, but it is also affected by transcriptional regulation

 

Figure 1 Schematic diagram of autophagy initiation, autophagosome maturation and mitophagy signaling

2 Core Autophagy Signaling Pathways

2.1 mTOR-ULK1 Axis

(1) Mechanistic core

mTORC1 is a major negative regulator of autophagy initiation. Under nutrient-rich conditions, mTORC1 inhibits the ULK1 complex and maintains a low autophagy level. During starvation, energy deficiency, or treatment with mTOR inhibitors, ULK1 is released from inhibition and initiates autophagosome formation.

(2) Experimental indicators

p-mTOR, p-S6K, p-4EBP1, p-ULK1, LC3-II, p62, and changes in autophagic flux are commonly detected.

(3) Result interpretation

Decreased p-mTOR and increased LC3-II may suggest enhanced autophagy initiation, but lysosomal inhibitors such as Bafilomycin A1 or chloroquine should be added to compare whether LC3-II accumulation further increases. Only then can enhanced flux be judged.

2.2 AMPK Signaling

(1) Mechanistic core

AMPK is an energy stress sensor. When ATP decreases and AMP/ADP increases, AMPK is activated. It can promote autophagy initiation by inhibiting mTORC1 and directly regulating ULK1. This pathway often links metabolic stress, mitochondrial function, and autophagy regulation.

(2) Experimental indicators

p-AMPK, p-ACC, p-ULK1, p-mTOR, mitochondrial function, ATP level, and LC3/p62 changes are commonly detected.

(3) Result interpretation

AMPK activation does not only indicate enhanced autophagy; it may also reflect a cellular energy crisis. If AMPK activation is accompanied by cell death, marked ATP depletion, or mitochondrial injury, protective autophagy should be distinguished from irreversible damage.

2.3 Beclin1-VPS34 Complex

(1) Mechanistic core

Beclin1 forms complexes with VPS34, VPS15, ATG14, UVRAG, and other molecules to promote PI3P production and isolation membrane nucleation. Bcl-2 can bind Beclin1 and inhibit autophagy, indicating crosstalk between autophagy and apoptosis.

(2) Experimental indicators

Beclin1, VPS34, ATG14, PI3P markers, LC3 puncta, and autophagosome formation are commonly detected.

(3) Result interpretation

Increased Beclin1 indicates enhanced potential for autophagic nucleation, but it does not independently prove complete autophagic flux. If Beclin1 increases while p62 accumulates and lysosomal function declines, late-stage autophagy blockade may exist.

2.4 ATG Proteins and LC3 Lipidation

(1) Mechanistic core

ATG7, ATG3, and the ATG5-ATG12-ATG16L1 system participate in LC3/ATG8 lipidation, converting LC3-I into LC3-II and localizing it to autophagic membranes. ATG4 is responsible for LC3 precursor processing and delipidation and is an important regulatory node in the LC3 cycle.

(2) Experimental indicators

LC3-I/LC3-II, ATG5, ATG7, ATG4, the ATG12-ATG5 complex, LC3 puncta, and the mRFP-GFP-LC3 reporter system are commonly detected.

(3) Result interpretation

LC3-II and puncta are not specific indicators of autophagic flux. Autophagic flux can only be determined by combining comparisons before and after lysosomal inhibitor treatment, p62 degradation, and dual-fluorescence LC3 reporter systems.

Table 2 Core Autophagy Regulatory Molecules and Functional Positioning

Molecule/Complex	Functional Positioning	Common Research Use
mTORC1	Inhibits autophagy initiation	Evaluating negative regulation of autophagy by nutrient and growth factor signaling
AMPK	Senses energy stress and promotes autophagy	Linking metabolic stress, drug treatment, and autophagy induction
ULK1 complex	Core complex for autophagy initiation	Determining whether autophagy initiation is activated
Beclin1-VPS34	Isolation membrane nucleation and PI3P production	Evaluating early autophagosome formation
ATG7/ATG5 system	LC3 lipidation and membrane elongation	Evaluating autophagosome formation capacity
ATG4	LC3 processing and delipidation	Studying LC3 cycling and autophagic membrane dynamics
LC3/ATG8	Autophagosome membrane marker	Observing autophagosome formation; flux assessment is still required
p62/SQSTM1	Selective autophagy receptor and substrate	Evaluating substrate degradation and selective autophagy activity

3 Selective Autophagy

3.1 Mitophagy

(1) Mechanistic core

Mitophagy removes damaged or depolarized mitochondria. After PINK1 accumulates on the outer membrane of damaged mitochondria, it recruits and activates Parkin, promoting ubiquitination of mitochondrial outer membrane proteins. Subsequently, receptors such as p62, NDP52, and OPTN connect these mitochondria with LC3 and drive their delivery into the autophagic degradation pathway.

(2) Experimental indicators

PINK1, mitochondrial translocation of Parkin, reduction of TOM20 or COX IV, colocalization of LC3 with mitochondria, mitochondrial membrane potential, mt-Keima, and lysosome-dependent degradation are commonly detected.

(3) Result interpretation

A decrease in mitochondrial membrane potential does not equal completion of mitophagy. If PINK1/Parkin is activated but mitochondrial markers are not degraded by lysosomes, mitochondrial recognition may have been initiated but autophagic flux may be blocked.

3.2 Aggrephagy

(1) Mechanistic core

Aggrephagy recognizes ubiquitinated protein aggregates through receptors such as p62 and NBR1 and delivers them to autophagosomes. This process is important in neurodegenerative diseases, proteostasis stress, and tumor therapeutic tolerance.

(2) Experimental indicators

p62, ubiquitinated proteins, LC3 colocalization, protein aggregates, proteasome inhibitor-induced stress, and autophagic flux are commonly detected.

(3) Result interpretation

Increased p62 may indicate increased selective autophagy substrate load, but it may also indicate blocked autophagic degradation. p62 mRNA, protein aggregate burden, and changes before and after lysosomal inhibitor treatment should be assessed together.

3.3 ER-Phagy and Lipophagy

(1) ER-phagy

ER-phagy clears excess or damaged endoplasmic reticulum and participates in protein folding stress, the unfolded protein response, and cellular homeostasis. ER-phagy receptors such as FAM134B, RTN3, and SEC62, as well as degradation of ER markers, are commonly detected.

(2) Lipophagy

Lipophagy degrades lipid droplets through lysosomes, releasing fatty acids for energy supply or participating in lipid remodeling. Common indicators include lipid droplet staining, colocalization of LC3 with lipid droplets, lysosome-dependent lipid droplet reduction, and lipid metabolism markers.

(3) Result interpretation

ER stress or lipid droplet reduction does not necessarily indicate enhanced selective autophagy. ER-phagy and lipophagy should be verified using specific receptors, LC3 colocalization, and lysosome-dependent degradation.

3.4 Xenophagy of Intracellular Pathogens

(1) Mechanistic core

Xenophagy recognizes and clears intracellular bacteria, viral components, or pathogens enclosed by damaged membranes. Molecules such as p62, NDP52, OPTN, and Galectin can participate in pathogen labeling and autophagic delivery.

(2) Experimental indicators

Colocalization of pathogens with LC3, recruitment of p62/NDP52, intracellular pathogen burden, lysosomal fusion, and inflammatory factor changes are commonly detected.

(3) Result interpretation

Reduced pathogen burden may result from autophagic clearance, immune killing, direct drug inhibition, or cell death. ATG knockdown, lysosomal inhibition, and autophagy receptor intervention should be used to validate the contribution of autophagy.

Table 3 Types of Selective Autophagy and Research Focuses

Type of Selective Autophagy	Main Substrate	Key Molecules	Research Focus
Mitophagy	Damaged mitochondria	PINK1, Parkin, p62, OPTN, NDP52	Mitochondrial quality control, Parkinson’s disease, oxidative stress
Aggrephagy	Ubiquitinated protein aggregates	p62, NBR1, LC3	Proteostasis, neurodegenerative diseases, tumor stress
ER-phagy	ER fragments	FAM134B, RTN3, SEC62	ER stress, protein folding, secretory system homeostasis
Lipophagy	Lipid droplets	LC3, lysosomes, lipid droplet-associated proteins	Lipid metabolism, energy supply, metabolic diseases
Ribophagy	Ribosomes	Selective autophagy receptors, lysosomal system	Translational control and nutrient stress
Xenophagy	Intracellular pathogens	p62, NDP52, OPTN, Galectin	Infection immunity, cellular defense, inflammatory responses

4 Autophagic Flux Detection and Result Interpretation

4.1 LC3 and p62 Detection

(1) LC3

Increased LC3-II can reflect increased autophagosome number, but it cannot determine whether autophagy is enhanced or degradation is blocked. LC3 puncta also only indicate an increase in autophagosome-related structures and cannot independently prove enhanced autophagic flux.

(2) p62

p62 is both a selective autophagy receptor and an autophagy substrate. Decreased p62 often suggests enhanced autophagic degradation. Increased p62 may represent increased substrate burden, autophagy blockade, or transcriptional upregulation.

(3) Interpretation focus

LC3-II, LC3 puncta, and p62 must be interpreted together with time-course experiments, lysosomal inhibitors, and functional phenotypes to avoid misinterpreting “autophagosome accumulation” as “enhanced autophagy.”

4.2 Comparison Before and After Lysosomal Inhibitor Treatment

(1) Mechanistic core

Bafilomycin A1, chloroquine, hydroxychloroquine, and NH4Cl can block lysosomal acidification or autophagosome degradation. If LC3-II further accumulates after treatment with lysosomal inhibitors, autophagosomes are still being generated and flux may be enhanced. If LC3-II no longer increases, autophagosome formation may be insufficient or flux may already be blocked.

(2) Experimental indicators

LC3-II, p62, LAMP1/2, lysosomal pH, cathepsin activity, and autophagic substrate degradation are commonly detected.

(3) Result interpretation

Chloroquine or Bafilomycin A1 alone artificially causes LC3-II accumulation and should not be interpreted as autophagy induction. Their main use is flux comparison, not direct evidence of “enhanced autophagy.”

4.3 Dual-Fluorescence LC3 Reporter System

(1) Mechanistic core

mRFP-GFP-LC3 can distinguish autophagosomes from autolysosomes. GFP is easily quenched in acidic lysosomes, while RFP is relatively stable. Therefore, yellow puncta represent autophagosomes, whereas red puncta more strongly indicate autophagic structures after entry into acidic lysosomes.

(2) Experimental indicators

Yellow puncta, red puncta, colocalization of LC3 with LAMP1, and lysosomal acidification status are commonly quantified.

(3) Result interpretation

Increased red puncta generally better supports entry of autophagosomes into the lysosomal stage. Accumulation of yellow puncta may indicate increased autophagosome formation or impaired fusion. Lysosomal function should be evaluated together.

Table 4 Autophagy Detection Indicators and Interpretation Points

Detection Method	Main Information	Notes
LC3-I/LC3-II Western blot	LC3 lipidation level associated with autophagosomes	Increased LC3-II does not equal increased flux
LC3 immunofluorescence	Autophagosome puncta	Puncta alone cannot prove enhanced autophagy
p62 detection	Degradation of selective autophagy substrates	p62 is affected by transcriptional regulation and should be combined with flux assessment
Bafilomycin A1/chloroquine comparison	Determines dynamics of autophagosome generation and degradation	Mainly used for flux assessment, not as evidence of autophagy induction
mRFP-GFP-LC3	Distinguishes autophagosomes from autolysosomes	Lysosomal pH and imaging conditions should be considered
Electron microscopy	Observes autophagosome ultrastructure	Strong morphological evidence, but does not directly reflect flux
mt-Keima	Indicates mitochondrial delivery into lysosomes	More suitable for mitophagy flux analysis

5 Autophagy Abnormalities and Disease Mechanisms

5.1 Tumors

(1) Mechanistic characteristics

Autophagy has dual roles in tumors. In early stages, autophagy can limit protein aggregation, ROS, and genomic instability. In advanced tumors, tumor cells can use autophagy to cope with hypoxia, nutrient deficiency, chemotherapy pressure, and metabolic remodeling.

(2) Research indicators

LC3-II, p62, Beclin1, mTOR, AMPK, mitochondrial function, drug sensitivity, colony formation, and tumor cell survival are commonly detected.

(3) Result interpretation

Enhanced autophagy does not necessarily mean promotion of cell death; it may also be a protective adaptation. If autophagy inhibition increases tumor cell sensitivity to chemotherapy, autophagy may have a protective role in that model.

5.2 Neurodegenerative Diseases

(1) Mechanistic characteristics

Neurons are highly sensitive to protein aggregation, mitochondrial injury, and lysosomal dysfunction. Insufficient autophagy and mitophagy can lead to accumulation of Aβ, Tau, α-synuclein, damaged mitochondria, and oxidative stress.

(2) Research indicators

p62, LC3, PINK1/Parkin, LAMP1/2, protein aggregates, mitochondrial membrane potential, ROS, and neuronal survival are commonly detected.

(3) Result interpretation

In neurodegenerative models, increased LC3-II may reflect compensatory autophagy enhancement or lysosomal degradation failure. p62, lysosomal function, and aggregate protein clearance must be evaluated together.

5.3 Infection and Immunity

(1) Mechanistic characteristics

Autophagy participates in intracellular pathogen clearance, antigen presentation, inflammasome regulation, and cytokine responses. Some viruses and bacteria can utilize or block autophagy to favor their own replication.

(2) Research indicators

Pathogen burden, LC3 colocalization, p62/NDP52 recruitment, inflammatory factors, MHC antigen presentation, and results of ATG gene intervention are commonly detected.

(3) Result interpretation

During infection, autophagy may restrict pathogens or may be exploited by pathogens. Its direction should be judged according to pathogen replication and the outcome after autophagy intervention, rather than LC3 changes alone.

5.4 Aging and Metabolic Diseases

(1) Mechanistic characteristics

Aging is accompanied by decline in autophagy-lysosome function, accumulation of mitochondrial damage, and weakened proteostasis. In metabolic diseases, autophagy can affect lipid droplet degradation, pancreatic β-cell function, insulin sensitivity, and hepatic lipid metabolism.

(2) Research indicators

AMPK/mTOR, LC3/p62, mitochondrial function, lipid droplets, insulin signaling, inflammation, and senescence markers are commonly detected.

(3) Result interpretation

When metabolic drugs induce autophagy, autophagy-mediated cytoprotection, energy stress responses, and drug toxicity should be distinguished. LC3-II elevation alone cannot determine whether the effect is beneficial or harmful to metabolic homeostasis.

6 Autophagy-Targeted Intervention Strategies

6.1 Autophagy-Inducing Strategies

(1) mTOR inhibition

Rapamycin and related compounds promote autophagy initiation by inhibiting mTORC1 and are commonly used to study nutrient sensing, autophagy induction, and mTOR-dependent regulation.

(2) AMPK activation

AICAR, Metformin, and related compounds can promote autophagy through energy stress or AMPK-related mechanisms and are commonly used in metabolic stress, diabetes-related mechanisms, and neuroprotection research.

(3) mTOR-independent induction

Trehalose, Spermidine, and related compounds can promote proteostasis and autophagy-associated processes through different mechanisms and are suitable for protein aggregation and neurodegenerative models.

6.2 Autophagy-Inhibiting Strategies

(1) Early-stage inhibition

3-Methyladenine and Wortmannin can inhibit PI3K/VPS34-related processes and reduce autophagosome formation. However, their effects are broad across pathways, so nonspecific effects should be considered during interpretation.

(2) Late-stage inhibition

Chloroquine, Bafilomycin A1, and NH4Cl can block lysosomal acidification or autophagosome degradation and are commonly used for autophagic flux validation and late-stage autophagy blockade research.

(3) Interpretation focus

Early-stage inhibition reduces autophagosome formation, whereas late-stage inhibition causes accumulation of autophagosomes and LC3-II. These two approaches may generate opposite LC3 results, so the action stage must be clearly defined in experimental design.

6.3 New Strategies Targeting Selective Autophagy

(1) AUTACs

AUTACs induce target proteins or organelles to be recognized by the autophagy system and promote selective degradation, representing a direction in autophagy-targeting degradation technologies.

(2) ATTECs

ATTECs promote entry of target proteins into the autophagy-lysosome degradation pathway by linking target proteins with autophagy components such as LC3.

(3) Application value

These strategies are suitable for studying protein aggregates, organelle damage, and disease-related targets that are difficult to handle with traditional enzyme inhibitors. However, target selectivity, degradation dependence, and involvement of the lysosomal pathway still require strict validation.

Table 5 Autophagy Regulation Strategies and Applicable Scenarios

Intervention Direction	Representative Mechanism	Expected Result	Applicable Research
mTOR inhibition	Inhibits mTORC1 and releases ULK1 inhibition	Promotes autophagy initiation	Nutrient sensing, tumor, metabolism, and aging research
AMPK activation	Senses energy stress and promotes ULK1 activation	Induces stress-associated autophagy	Metabolic stress, diabetes, and neuroprotection research
VPS34 inhibition	Blocks PI3P production and autophagy nucleation	Inhibits early autophagy	Validation of autophagosome formation mechanisms
Lysosomal inhibition	Blocks acidification or degradation	Causes autophagosome/LC3-II accumulation	Autophagic flux detection and late-stage blockade
Mitochondrial depolarization	Induces PINK1/Parkin recruitment	Activates mitophagy	Mitochondrial quality control and Parkinson’s disease research
Targeted autophagic degradation	AUTACs, ATTECs	Promotes autophagic degradation of specific targets	Protein aggregation, organelle quality control, and targeted degradation research

Table 6 Representative Products Related to Autophagy Research

Research Module	Representative Product	CAS No.	Mechanism or Detection Positioning	Applicable Research
mTOR-dependent autophagy induction	Rapamycin	53123-88-9	mTORC1 inhibitor that releases ULK1 inhibition	Autophagy induction, mTOR/ULK1 pathway, and nutrient sensing research
Complete mTOR inhibition research	Torin 1	1222998-36-8	ATP-competitive mTOR inhibitor	mTORC1/2 inhibition, autophagy initiation, and AKT/mTOR feedback research
AMPK-related autophagy induction	AICAR	2627-69-2	AMPK activator	Energy stress, AMPK/ULK1 signaling, and metabolic autophagy research
Metabolic drug-related autophagy	Metformin hydrochloride	1115-70-4	AMPK/mTOR-related regulator	Diabetes-related autophagy, metabolic stress, and tumor metabolism research
mTOR-independent autophagy induction	Trehalose	99-20-7	Promotes proteostasis and autophagy-associated degradation	Protein aggregation, neurodegenerative diseases, and autophagy enhancement research
Autophagy induction/anti-aging research	Spermidine	124-20-9	Polyamine compound associated with autophagy induction	Aging, proteostasis, cytoprotection, and autophagy regulation research
Early-stage autophagy inhibition	3-Methyladenine	5142-23-4	PI3K/VPS34-related inhibitor	Autophagosome formation inhibition, early autophagy validation, and pathway intervention research
PI3K-related autophagy inhibition	Wortmannin	19545-26-7	PI3K inhibitor that suppresses autophagy nucleation	VPS34/PI3P-related autophagy nucleation and signaling validation research
Lysosomal-stage blockade	Chloroquine diphosphate	50-63-5	Lysosomal acidification inhibitor and late-stage autophagy blocker	Autophagic flux detection, LC3-II accumulation, and tumor autophagy inhibition research
Lysosomal acidification blockade	Bafilomycin A1	88899-55-2	V-ATPase inhibitor that blocks lysosomal acidification	Autophagic flux, mRFP-GFP-LC3 interpretation, and late-stage autophagy blockade research
Lysosomal pH regulation	Ammonium chloride	12125-02-9	Weakly basic lysosomal neutralizing agent	Autophagic degradation blockade, lysosomal acidification, and flux validation research
Lysosomal protease inhibition	Pepstatin A	26305-03-3	Aspartyl protease inhibitor	Lysosomal degradation, cathepsin-related degradation, and autophagy substrate accumulation research
Mitophagy induction	CCCP	555-60-2	Mitochondrial depolarizing agent	PINK1/Parkin recruitment, mitophagy, and mitochondrial quality control research
Mitochondrial injury model	Rotenone	83-79-4	Mitochondrial complex I inhibitor	Mitochondrial injury, ROS, Parkinson’s disease models, and mitophagy research
Protein aggregate stress	MG132	133407-82-6	Proteasome inhibitor that induces protein aggregation stress	Aggrephagy, p62-mediated selective autophagy, and proteostasis research
ER stress/ER-phagy research	Thapsigargin	67526-95-8	SERCA inhibitor that induces ER calcium homeostasis disruption	ER stress, ER-phagy, and crosstalk between autophagy and cell death
AKT/PI3K pathway intervention	LY294002	154447-36-6	PI3K inhibitor	PI3K/AKT/mTOR pathway, autophagy regulation, and tumor cell survival research
Oxidative stress-related autophagy	N-Acetyl-L-cysteine	616-91-1	ROS scavenger and GSH precursor	Oxidative stress, source determination of autophagy induction, and mitochondrial injury research

Table 7 Product Lines Related to Autophagy and Application Directions

Research Direction	Product Line	Covered Object/Target	Applicable Research Direction
Overview of autophagy research	Autophagy	Autophagy-related proteins, detection reagents, and regulatory compounds	Autophagosome formation, lysosomal degradation, autophagic flux, and disease mechanism research
Autophagy initiation research	ULK	ULK1/2, ATG13, and initiation complex	mTOR/AMPK-ULK1 axis, autophagy initiation, and nutrient stress research
Autophagy nucleation research	Beclin1	Beclin1-VPS34 complex-related molecules	Isolation membrane nucleation, PI3P production, autophagy initiation, and apoptosis crosstalk research
LC3 lipidation research	Atg7	ATG7 and LC3/ATG8 conjugation system	LC3 lipidation, autophagosome elongation, and ATG-dependent autophagy research
LC3 processing research	Atg4	ATG4 family and LC3 processing/delipidation-related molecules	LC3 cycling, autophagic membrane dynamics, and autophagosome maturation research
Autophagosome marker research	Atg8/LC3	LC3/GABARAP family	Autophagosome formation, LC3 puncta, autophagic flux, and imaging analysis research
Selective autophagy receptor research	p62	p62/SQSTM1 and ubiquitinated substrate recognition	Aggrephagy, protein aggregate clearance, p62 degradation, and selective autophagy research
Mitochondrial quality control research	Mitophagy	Mitophagy-related proteins and detection tools	Damaged mitochondrial clearance, oxidative stress, neurodegenerative diseases, and metabolic homeostasis research
PINK1/Parkin pathway research	PINK1/Parkin	PINK1, Parkin, and mitochondrial ubiquitination regulation	Parkinson’s disease, mitochondrial depolarization, Parkin translocation, and mitophagy flux research
LRRK2-related research	LRRK2	LRRK2 and Parkinson’s disease-related autophagy/lysosomal regulatory molecules	Parkinson’s disease, autophagy-lysosome function, mitochondrial quality control, and neurodegeneration research
Targeted autophagic degradation research	AUTACs	Autophagy-targeting chimeric degradation molecules	Autophagic degradation of target proteins/organelles, proteostasis, and selective autophagy technology research
LC3-targeted degradation research	ATTECs	LC3-linking targeted autophagy degradation tools	Target protein delivery to autophagy, protein aggregation diseases, and targeted degradation mechanism research
Protein folding and autophagy crosstalk research	FKBP	FKBP family, mTOR-related complexes, and protein folding regulation	Rapamycin-FKBP-mTOR, autophagy induction, proteostasis, and drug mechanism research

The key to autophagy research is to distinguish whether autophagosome formation, autophagic flux, and lysosomal degradation change synchronously. Only by combining LC3, p62, lysosomal function, comparisons before and after flux inhibitors, and selective substrate degradation can the true role of autophagy in disease models, drug treatment, and cellular stress be accurately determined.

References

[1] Mizushima N. Genes Dev. 2007 Nov 15;21(22):2861-2873.

[2] Wesselborg S, et al. Cell Mol Life Sci. 2015 Dec;72(24):4721-4757.

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