gene

AUTOPHAGY

Entity Detail — Knowledge Graph Node

Understanding Entity Pages

This page aggregates everything SciDEX knows about AUTOPHAGY: its mechanistic relationships (Knowledge Graph edges), hypotheses targeting it, analyses mentioning it, and supporting scientific papers. The interactive graph below shows its immediate neighbors. All content is AI-synthesized from peer-reviewed literature.

13827Connections
30Hypotheses
20Analyses
50Outgoing
50Incoming
13Experiments
20Debates

Summary

Autophagy is an evolutionarily conserved cellular degradation pathway that removes damaged organelles and misfolded proteins through lysosomal degradation. In neurodegeneration, autophagy dysfunction contributes to accumulation of toxic protein aggregates including amyloid-beta, tau, alpha-synuclein, and TDP-43. Key regulators include mTOR, AMPK, Beclin-1, and TFEB. Enhancing autophagy is a major therapeutic strategy for neurodegenerative diseases.

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🧬 Gene Info
Gene SymbolAUTOPHAGY
AliasesAutophagy-lysosomal pathway, Cellular self-eating
FunctionProtein degradation; Organelle turnover; Quality control
PathwaysmTOR pathway, AMPK signaling, Beclin-1 complex
Autophagosome accumulationAccumulation of immature autophagosomes suggests block in fusion with lysosomes
Amyloid interactionAβ peptides impair autophagic flux, creating a vicious cycle
Mitophagy defectsReduced PINK1/Parkin-mediated mitophagy leads to mitochondrial dysfunction
LRRK2 mutationsG2019S LRRK2 impairs autophagosome formation
PINK1/Parkin pathwayLoss-of-function mutations cause mitophagy failure
GBA mutationsGlucocerebrosidase deficiency impairs lysosomal function
Associated DiseasesAging, Als, Alzheimer, Amyotrophic Lateral Sclerosis
Known Drugs/Compounds3-Methyladenine, BEVACIZUMAB, BPA, COENZYME Q10, CURCUMIN, Cyclocreatine
Interactions6-OHDA, ABCA1, ABCD3, ABCG1, ABCG2, ACC
KG Connections7512 knowledge graph edges
DatabasesGeneCardsUniProtNCBI GeneHPASTRING

Wiki Pages (2)

Knowledge base pages for this entity

Canonical Page

Autophagy Mechanisms

mechanism · 4866 words

AUTOPHAGY

pathway · 554 words

Pathway Diagram

graph TD
    subgraph Pathology["Pathology"]
        AUTOPHAGY["AUTOPHAGY"] -->|"associated with"| CANCER["CANCER"]
        AUTOPHAGY["AUTOPHAGY"] -->|"associated with"| AGING["AGING"]
        AUTOPHAGY["AUTOPHAGY"] -->|"associated with"| NEURON["NEURON"]
        AUTOPHAGY["AUTOPHAGY"] -->|"associated with"| MICROGLIA["MICROGLIA"]
        AUTOPHAGY["AUTOPHAGY"] -->|"associated with"| LYSOSOME["LYSOSOME"]
        AUTOPHAGY["AUTOPHAGY"] -->|"associated with"| MITOCHONDRIA["MITOCHONDRIA"]
    end
    subgraph Signaling["Signaling"]
        AUTOPHAGY["AUTOPHAGY"] -->|"regulates"| AGING_1["AGING"]
        AUTOPHAGY["AUTOPHAGY"] -.->|"inhibits"| P62["P62"]
        AUTOPHAGY["AUTOPHAGY"] -->|"regulates"| CANCER_2["CANCER"]
        MTORC1["MTORC1"] -.->|"inhibits"| AUTOPHAGY["AUTOPHAGY"]
        ULK1["ULK1"] -->|"regulates"| AUTOPHAGY["AUTOPHAGY"]
        AMPK["AMPK"] -->|"activates"| AUTOPHAGY["AUTOPHAGY"]
        SIRT1["SIRT1"] -->|"activates"| AUTOPHAGY["AUTOPHAGY"]
        ROS["ROS"] -->|"activates"| AUTOPHAGY["AUTOPHAGY"]
        P62_3["P62"] -->|"regulates"| AUTOPHAGY["AUTOPHAGY"]
    end
    style AUTOPHAGY fill:#4a1a6b,stroke:#4fc3f7,stroke-width:3px,color:#e0e0e0,font-weight:bold
    style CANCER fill:#ef5350,stroke:#4fc3f7,stroke-width:1px,color:#e0e0e0
    style AGING fill:#5d4400,stroke:#4fc3f7,stroke-width:1px,color:#e0e0e0
    style AGING_1 fill:#5d4400,stroke:#4fc3f7,stroke-width:1px,color:#e0e0e0
    style P62 fill:#4a1a6b,stroke:#4fc3f7,stroke-width:1px,color:#e0e0e0
    style CANCER_2 fill:#4a1a6b,stroke:#4fc3f7,stroke-width:1px,color:#e0e0e0
    style NEURON fill:#4a1a6b,stroke:#4fc3f7,stroke-width:1px,color:#e0e0e0
    style MICROGLIA fill:#4a1a6b,stroke:#4fc3f7,stroke-width:1px,color:#e0e0e0
    style LYSOSOME fill:#4a1a6b,stroke:#4fc3f7,stroke-width:1px,color:#e0e0e0
    style MITOCHONDRIA fill:#4a1a6b,stroke:#4fc3f7,stroke-width:1px,color:#e0e0e0
    style MTORC1 fill:#006494,stroke:#4fc3f7,stroke-width:1px,color:#e0e0e0
    style ULK1 fill:#006494,stroke:#4fc3f7,stroke-width:1px,color:#e0e0e0
    style AMPK fill:#006494,stroke:#4fc3f7,stroke-width:1px,color:#e0e0e0
    style SIRT1 fill:#006494,stroke:#4fc3f7,stroke-width:1px,color:#e0e0e0
    style ROS fill:#5d4400,stroke:#4fc3f7,stroke-width:1px,color:#e0e0e0
    style P62_3 fill:#006494,stroke:#4fc3f7,stroke-width:1px,color:#e0e0e0

Outgoing (6280)

TargetRelationTypeStr
PINK1associated_withgene1.00
Mitochondrial Functionactivatespathway1.00
AMPKregulatesgene1.00
APOPTOSISactivatesgene1.00
MITOPHAGYregulatesgene1.00

Incoming (7547)

SourceRelationTypeStr
LC3inhibitsgene1.00
Diabetesactivatesdisease1.00
Agingactivatesdisease1.00
Obesityactivatesdisease1.00
ERKactivatesgene1.00

Targeting Hypotheses (30)

Hypotheses where this entity is a therapeutic target

HypothesisScoreDiseaseAnalysis
APOE-Dependent Autophagy Restoration 0.895 neurodegeneration Survival Analysis of AD Patient Cohorts:
Gamma Oscillation Entrainment Enhances lncRNA-9969-Mediated 0.865 molecular-neurobiology How does lncRNA-0021 achieve sequence-sp
J-protein co-chaperone system mediates selective autophagy t 0.831 protein-biochemistry Do chaperones selectively recognize path
Autophagy-Lysosomal Pathway Dysfunction as a Unifying Proteo 0.820 neurodegeneration Cross-disease neurodegeneration mechanis
C9ORF72 autophagy-lysosome collapse across ALS and FTD 0.816 multi Cross-disease neurodegeneration mechanis
VCP-Mediated Autophagy Enhancement 0.787 neurodegeneration Tau propagation mechanisms and therapeut
Closed-loop tACS targeting entorhinal cortex layer II SST in 0.784 alzheimers Circuit-level neural dynamics in neurode
Transcriptional Autophagy-Lysosome Coupling 0.777 neurodegeneration Autophagy-lysosome pathway convergence a
TBK1-OPTN-p62 selective autophagy failure across ALS, FTD, a 0.776 multi Cross-disease neurodegeneration mechanis
TBK1-OPTN-NDP52 Phospho-Cascade Coordinates Multi-Organelle 0.772 neurodegeneration How do different organelle-specific auto
p21^Cip1 Phospho-State as Autophagy Responsiveness Predictor 0.768 molecular-biology What is the optimal therapeutic window t
Circadian Clock-Autophagy Synchronization 0.763 neurodegeneration Sleep disruption as cause and consequenc
LAMP2A-Mediated Autophagy Enhancement Blocks Alpha-Synuclein 0.745 neurodegeneration Test
H2: Impaired Autophagy Receptor Recruitment Traps G3BP1 Gran 0.737 neurodegeneration How do pathological stress granules tran
VCP/p97 ATPase mutations impair extraction of ubiquitinated 0.720 neurodegeneration What are the neuron-specific effects of
C9orf72 DPRs Impair Autophagy Receptor Docking on Stress Gra 0.717 neurodegeneration How do pathological stress granules in n
TDP-43 Pathology Disrupts the HGS-PYGB Autophagy Receptor Ca 0.703 neurodegeneration What mechanisms underlie neuronal resist
Lysosomal Acidification Failure: Convergent GBA1/LAMP2A–medi 0.700 neurodegeneration -
TFEB-Independent Autophagy Bypass 0.697 neurodegeneration Does TFEB dysfunction cause neurodegener
mTORC1 Reactivation as Autophagy-Senescence Divergence Point 0.682 molecular-biology What is the optimal therapeutic window t
Autophagy-Lysosomal Degradation of IBA1 in Stressed Microgli 0.681 neuroinflammation What causes IBA1 low/negative microglia
GDF15-GFRAL Axis as Systemic Autophagy-Senescence Integrator 0.659 molecular-biology What is the optimal therapeutic window t
Radiation drives pericyte senescence through lysosome acidif 0.652 neurodegeneration What specific autophagy pathways are def
p62 Liquid-Liquid Phase Separation Nucleates Cross-Organelle 0.649 neurodegeneration How do different organelle-specific auto
H7: mTOR Hyperactivity Blocks Autophagy, Permitting Tau Seed 0.640 neurodegeneration Entorhinal cortex layer II vulnerability
G3BP1 NTF2L Domain-Mediated mRNP Scaffold Creates Core Exclu 0.633 neurodegeneration What determines the spatial organization
Autophagy-Senescence Axis Therapeutic Window 0.624 - Senescent cell clearance as neurodegener
Glial-Autophagy-Senescence Coupling Defines CNS Therapeutic 0.614 molecular-biology What is the optimal therapeutic window t
Mitophagy collapse via PINK1-PRKN is the primary autophagy l 0.614 neurodegeneration What specific autophagy pathways are def
LAMP2A Upregulation to Enhance Chaperone-Mediated Autophagy 0.000 proteomics Quantitative proteomics of the aging syn

Mentioning Analyses (20)

Scientific analyses that reference this entity

Epigenetic clocks as biomarkers for Alzheimer disease and neurodegeneration

neurodegeneration | 2026-04-25 | 6 hypotheses Top: 0.387

Clinical Trial Landscaping for Alzheimer's Disease Therapeutics

neurodegeneration | 2026-04-16 | 1 hypotheses Top: 0.629

Does LRRK2's role as a lysosomal volume sensor explain the pathogenic mechanism

neurodegeneration | 2026-04-16 | 1 hypotheses Top: 0.666

Does APOE4 drive tau propagation

neurodegeneration | 2026-04-15 | 0 hypotheses

What are the molecular mechanisms by which GLP-1RAs provide neuroprotective effe

neurodegeneration | 2026-04-14 | 0 hypotheses

Experiments (13)

Experimental studies targeting or related to this entity

ExperimentTypeDiseaseScoreFeasibilityModelStatusEst. Cost
iPSC-NPC effects on astrocytes in vitro ICH model exploratory intracerebral hemorrhage 0.900 0.00 in vitro ICH cell culture mode completed N/A
Autophagy receptor identification for stress granule elimination exploratory neurodegenerative diseases 0.900 0.00 cultured cells under arsenite proposed N/A
AMPK knockdown validation experiment exploratory intracerebral hemorrhage 0.880 0.00 astrocyte cell culture proposed N/A
P2RY12-MTOR pathway interaction in VSMCs exploratory atherosclerosis 0.850 0.00 cultured VSMCs proposed N/A
iPSC-NPC transplantation in ICH animal model validation intracerebral hemorrhage 0.850 0.00 animal ICH model proposed N/A
Autophagy Enhancement Drug Screening for Neurodegeneration clinical Alzheimer's Disease 0.400 0.50 human proposed $6,550,000
Chaperone-Mediated Autophagy Dysfunction in PD - Experiment Design clinical Parkinson's Disease 0.400 0.50 human proposed $5,460,000
Macroautophagy Dysfunction in PD - Experiment Design clinical Parkinson's Disease 0.400 0.50 human proposed $5,460,000
Validate Mitochondria-Lysosome Contact Site Dysfunction in PD validation Parkinson's Disease 0.400 0.50 human proposed $2,730,000
Mutant Huntingtin (mHTT) Clearance Mechanisms — Therapeutic Target Val validation Neurodegeneration 0.400 0.50 human proposed $3,000,000
MLCS Quantification in Parkinson's Disease validation Parkinson's Disease 0.400 0.50 human proposed $2,730,000
Presymptomatic GRN Carrier Intervention Timing — Biomarker-Guided Ther clinical Neurodegeneration 0.400 0.50 human proposed $5,460,000
TMEM106B Haplotype as Genetic Modifier in FTD — Mechanism and Therapeu validation Neurodegeneration 0.400 0.50 human proposed $2,730,000

Related Papers (20)

Scientific publications cited in analyses involving this entity

Title & PMIDAuthorsJournalYearCitations
Hepatocyte FoxO1 Deficiency Protects From Liver Fibrosis via Reducing Inflammati [PMID:37678798] Pan Q, Gao M, Kim D, Ai W, Yang W, Jiang Cell Mol Gastroenterol Hepatol 2024 1
Metabolic orchestration of cell death by AMPK-mediated phosphorylation of RIPK1. [PMID:37384704] Zhang T, Xu D, Trefts E, Lv M, Inuzuka H Science 2023 1
Cinobufagin induces FOXO1-regulated apoptosis, proliferation, migration, and inv [PMID:35176466] Zhang L, Liang B, Xu H, Gong Y, Hu W, Ji J Ethnopharmacol 2022 1
Metformin Improves Mitochondrial Respiratory Activity through Activation of AMPK [PMID:31693892] Wang Y, An H, Liu T, Qin C, Sesaki H, Gu Cell Rep 2019 1
AMPK-Mediated BECN1 Phosphorylation Promotes Ferroptosis by Directly Blocking Sy [PMID:30057310] Song X, Zhu S, Chen P, Hou W, Wen Q, Liu Curr Biol 2018 1
Obestatin controls the ubiquitin-proteasome and autophagy-lysosome systems in gl [PMID:28675664] Cid-Díaz T, Santos-Zas I, González-Sánch J Cachexia Sarcopenia Muscle 2017 1
PTEN loss drives B7H3 upregulation via the mTORC2/FOXO/c-Myc axis to promote tum [PMID:41920736] Wang Z, Jin N, Li X, Ma X, Feng Y, Yin K Cell reports 2026 0
Replating Induces mTOR-Dependent Rescue of Protein Synthesis in Charcot-Marie-To [PMID:41876253] Koenig J, McGuire A, Homedan Y, Alberhas eNeuro 2026 0
S-equol promotes ferroptosis in triple negative breast cancer by coordinating NC [PMID:41925800] Ni F, Huang Z, Cui Y, Huang P, Xue Z, Hu Molecular and cellular biochem 2026 0
Mammalian lipophagy: process and function. [PMID:41681129] Zhao R, Dai E, Kang R, Liu J, Klionsky D Autophagy 2026 0
TAZ alleviates ischemic stroke injury by activating Foxo1: Usp1-mediated deubiqu [PMID:41921828] ["Xin Y", "Sun Y", "Pan E", "Li M", "Che Free radical biology & medicin 2026 0
Evaluation of Copathology and Clinical Trajectories in Individuals With Tau-Clin [PMID:41396614] Brown CA, Mundada NS, Cousins KAQ, Sadeg JAMA neurology 2026 0
Membralin Assembles a MAN1B1-VCP Complex to Target Foreign Glycoproteins from th [PMID:41324484] Zhang J, Lu X, Li S, Wang T, Ahmad I et Adv Sci (Weinh) 2026 0
Viscum coloratum polysaccharide ameliorates hyperuricemic nephropathy by upregul [PMID:41325866] Zhang K, Sun S, Qiu H, Zhao H, Zhao H et J Ethnopharmacol 2026 0
Evaluation of Copathology and Clinical Trajectories in Individuals With Tau-Clin [PMID:41396614] Brown CA, Mundada NS, Cousins KAQ, Sadeg JAMA Neurol 2026 0
Metabolic dysregulation reshapes the immune landscape: The gut microbiota-mTOR a [PMID:41445190] Li J, Li J, Chen K Mol Ther 2026 0
Aberrant nuclear pore complex degradation contributes to neurodegeneration in VC [PMID:41475349] Dubey SK, Chaubey D, Ikenaga C, Lin WW, Neuron 2026 0
Senecavirus a VP2 protein orchestrates PRDX1 degradation through dual autophagy [PMID:41479169] Li Z, Yang X, Mao J, Zeng P, Qi Y et al. Autophagy 2026 0
Inhibition of mTOR Enhances the Efficacy of Proteasome-Dependent Targeted Protei [PMID:41529091] Liu Y, Sun Y, Song TY, Ni SY, Pu YS et a Cancer Res 2026 0
Genetic commonalities between rare subtypes of ALS and CMT: insights into molecu [PMID:41621017] Aynaashe A, Kursula P Amino Acids 2026 0

Debates (20)

Multi-agent debates referencing this entity

Epigenetic clocks as biomarkers for Alzheimer disease and neurodegeneration

completed · Rounds: 5 · Score: 0.50 · 2026-04-25

The study shows trehalose causes lysosomal membrane permeabilization (LMP) that

closed · Rounds: 4 · Score: 0.61 · 2026-04-21

The abstract describes IBA1 low/negative microglia in individuals with liver dis

closed · Rounds: 4 · Score: 0.76 · 2026-04-21

The core debate question remains unresolved - whether intrinsic tau conformation

closed · Rounds: 4 · Score: 0.30 · 2026-04-21

The debate identified glycolytic shifts and mTOR disruption but couldn't disting

closed · Rounds: 4 · Score: 0.48 · 2026-04-21

What is the current clinical trial landscape for AD therapeutics, and which mech

closed · Rounds: 4 · Score: 0.70 · 2026-04-21

The debate assumed that correcting APOE4's aberrant domain interactions would re

closed · Rounds: 4 · Score: 0.43 · 2026-04-20

The debate highlighted major safety concerns about blocking CXCL10, particularly

closed · Rounds: 4 · Score: 1.00 · 2026-04-20

Is the amyloid concentration in AD clinical trials rational given lecanemab's ap

closed · Rounds: 4 · Score: 0.70 · 2026-04-16

While the study establishes LRRK2 as a lysosomal swelling sensor and notes that

closed · Rounds: 4 · Score: 0.85 · 2026-04-16

Related Research

Hypotheses and analyses mentioning AUTOPHAGY in their description or question text

VCP-Mediated Autophagy Enhancement

Score: 0.787 · neurodegeneration · 2026-04-16

## Mechanistic Overview VCP-Mediated Autophagy Enhancement starts from the claim that modulating VCP within the disease

Closed-loop tACS targeting entorhinal cortex layer II SST interneurons to activa

Score: 0.784 · alzheimers · 2026-04-05

## Mechanistic Overview Closed-loop tACS targeting entorhinal cortex layer II SST interneurons to activate AMPK-autophag

Transcriptional Autophagy-Lysosome Coupling

Score: 0.777 · neurodegeneration · 2026-04-02

## Mechanistic Overview Transcriptional Autophagy-Lysosome Coupling starts from the claim that modulating FOXO1 within t

TBK1-OPTN-p62 selective autophagy failure across ALS, FTD, and PD-like proteotox

Score: 0.776 · multi · 2026-04-28

Shared mechanism across ALS, FTD, PD: TBK1 coordinates selective autophagy adaptors and innate immune tone. TBK1 haploin

TBK1-OPTN-NDP52 Phospho-Cascade Coordinates Multi-Organelle Autophagy

Score: 0.772 · neurodegeneration · 2026-04-21

## Mechanistic Overview TBK1-OPTN-NDP52 Phospho-Cascade Coordinates Multi-Organelle Autophagy starts from the claim that

p21^Cip1 Phospho-State as Autophagy Responsiveness Predictor

Score: 0.768 · molecular-biology · 2026-04-21

**Molecular Mechanism and Rationale** The p21^Cip1 protein, encoded by the CDKN1A gene, functions as a critical molecul

Circadian Clock-Autophagy Synchronization

Score: 0.763 · neurodegeneration · 2026-04-02

## Mechanistic Overview Circadian Clock-Autophagy Synchronization starts from the claim that modulating CLOCK within the

LAMP2A-Mediated Autophagy Enhancement Blocks Alpha-Synuclein Propagation in Park

Score: 0.745 · neurodegeneration · 2026-05-10

AAV9-mediated overexpression of LAMP2A enhances chaperone-mediated autophagy to selectively degrade pathological alpha-s

H2: Impaired Autophagy Receptor Recruitment Traps G3BP1 Granules

Score: 0.737 · neurodegeneration · 2026-04-22

**Molecular Mechanism and Rationale** The central molecular mechanism underlying this hypothesis involves the intricate

VCP/p97 ATPase mutations impair extraction of ubiquitinated autophagy substrates

Score: 0.720 · neurodegeneration · 2026-04-21

## Mechanistic Overview VCP/p97 ATPase mutations impair extraction of ubiquitinated autophagy substrates, causing protea

C9orf72 DPRs Impair Autophagy Receptor Docking on Stress Granules

Score: 0.717 · neurodegeneration · 2026-04-22

## **Molecular Mechanism and Rationale** The hexanucleotide repeat expansion (GGGGCC) in the C9orf72 gene represents th

TDP-43 Pathology Disrupts the HGS-PYGB Autophagy Receptor Cascade in Motor Neuro

Score: 0.703 · neurodegeneration · 2026-04-26

TDP-43 aggregates sequester hepatocyte growth factor-regulated tyrosine kinase substrate (HGS), a critical hub coordinat

TFEB-Independent Autophagy Bypass

Score: 0.697 · neurodegeneration · 2026-04-04

## Mechanistic Overview TFEB-Independent Autophagy Bypass starts from the claim that modulating ULK1 within the disease

mTORC1 Reactivation as Autophagy-Senescence Divergence Point Marker

Score: 0.682 · molecular-biology · 2026-04-21

## Mechanistic Overview mTORC1 Reactivation as Autophagy-Senescence Divergence Point Marker starts from the claim that m