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.

13824Connections
30Hypotheses
4Analyses
50Outgoing
50Incoming
20Experiments
4Debates

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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AI portrait of AUTOPHAGY

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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 Connections7529 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 (6284)

TargetRelationTypeStr
Neurodegenerationtherapeutic_targetdisease1.00
Apoptosistherapeutic_targetpathway1.00
Inflammationtherapeutic_targetdisease1.00
Alzheimertherapeutic_targetdisease1.00
Diabetesactivatesdisease1.00

Incoming (7540)

SourceRelationTypeStr
P62regulatesgene1.00
AMPKactivatesgene1.00
AMPKregulatesgene1.00
Alsinhibitsdisease1.00
AKTactivatesgene1.00

Targeting Hypotheses (30)

Hypotheses where this entity is a therapeutic target

HypothesisScoreDiseaseAnalysis
Autophagy-Senescence Axis Therapeutic Window 0.921 - Senescent cell clearance as neurodegener
Transcriptional Autophagy-Lysosome Coupling 0.900 neurodegeneration Autophagy-lysosome pathway convergence a
APOE-Dependent Autophagy Restoration 0.863 neurodegeneration Mechanistic role of APOE in neurodegener
Gamma Oscillation Entrainment Enhances lncRNA-9969-Mediated 0.843 molecular neurobiology View
VCP-Mediated Autophagy Enhancement 0.787 neurodegeneration Tau propagation mechanisms and therapeut
Closed-loop tACS targeting entorhinal cortex layer II SST in 0.784 Alzheimer's disease Circuit-level neural dynamics in neurode
TBK1-OPTN-NDP52 Phospho-Cascade Coordinates Multi-Organelle 0.772 neurodegeneration How do different organelle-specific auto
Circadian Clock-Autophagy Synchronization 0.763 neurodegeneration Sleep disruption as cause and consequenc
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
p21^Cip1 Phospho-State as Autophagy Responsiveness Predictor 0.710 molecular biology What is the optimal therapeutic window t
Autophagy-Lysosomal Degradation of IBA1 in Stressed Microgli 0.706 neuroinflammation What causes IBA1 low/negative microglia
TFEB-Independent Autophagy Bypass 0.697 neurodegeneration Does TFEB dysfunction cause neurodegener
mTORC1 Reactivation as Autophagy-Senescence Divergence Point 0.685 molecular biology What is the optimal therapeutic window t
TDP-43 Pathology Disrupts the HGS-PYGB Autophagy Receptor Ca 0.678 neurodegeneration What mechanisms underlie neuronal resist
GDF15-GFRAL Axis as Systemic Autophagy-Senescence Integrator 0.653 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
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
FUS Mutations Alter Stress Granule Material Properties to Co 0.613 neurodegeneration How do pathological stress granules in n
P2RY12-mediated autophagy inhibition in cerebral VSMCs impai 0.605 neurodegeneration How does P2RY12-mediated VSMC dysfunctio
Autophagy Activation ULK1/VPS34 (H3): Lipid Routing to Lysos 0.600 neurodegeneration Does restoring neuronal AMPK activity re
VCP-Mediated Autophagy Enhancement 0.595 Alzheimer's Disease Tau propagation mechanisms and therapeut
P2RY12-driven autophagy impairment in cerebral VSMCs mediate 0.585 neurodegeneration How does P2RY12-mediated VSMC dysfunctio
Autophagy-Epigenetic Feedback Loop Creates a Compounding Bio 0.583 - Epigenetic clocks as biomarkers for Alzh
Selective c-Abl Inhibition Promotes α-Synuclein Clearance vi 0.580 neurodegeneration Test Hypothesis Fixtures

Mentioning Analyses (4)

Scientific analyses that reference this entity

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

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

Do tau-containing vesicles exhibit unique surface glycosylation patterns that di

neurodegeneration | 2026-04-09 | 0 hypotheses

Does TFEB dysfunction cause neurodegeneration or represent a compensatory respon

neurodegeneration | 2026-04-03 | 7 hypotheses Top: 0.697

Protein aggregation cross-seeding across neurodegenerative diseases

neurodegeneration | 2026-04-01 | 7 hypotheses Top: 0.639

Experiments (20)

Experimental studies targeting or related to this entity

ExperimentTypeDiseaseScoreFeasibilityModelStatusEst. Cost
Circadian gene expression effects of SD vs ketamine exploratory depression 0.950 0.00 C57BL/6J mice proposed N/A
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
CLOCK/BMAL1 regulation of ICC autophagy in GERD model exploratory gastroesophageal reflux diseas 0.900 0.00 primary esophageal interstitia 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
Proposed experiment from debate on Astrocytes adopt A1 (neurotoxic) an falsification Neurodegeneration 0.400 0.50 cell_line proposed $80,000
Proposed experiment from debate on Epigenetic clocks and biological ag falsification Neurodegeneration 0.400 0.50 cell_line proposed $100,000
Circadian-Vascular-Metabolic Syndrome (CVMS) Intervention Trial clinical Neurodegeneration 0.400 0.50 human proposed $3,900,000
Experiment Index validation Neurodegeneration 0.400 0.50 human proposed $2,280,000
N-of-1 Clinical Trial Design for CBS/PSP clinical ALS 0.400 0.50 human proposed $5,460,000

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
Improved T-cell Receptor Diversity Estimates Associate with Survival and Respons [PMID:33177107] Bortone DS, Woodcock MG, Parker JS, Vinc Cancer Immunol Res 2021 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
Spatiotemporal profile of postsynaptic interactomes integrates components of com [PMID:28671696] Li J, Zhang W, Yang H, Howrigan DP, Wilk Nat Neurosci 2017 1
Core Concept: The Internet of Things and the explosion of interconnectivity. [PMID:27702874] Ornes S Proc Natl Acad Sci U S A 2016 1
Precision Neurodegeneration: Integrating Molecular Mechanisms, Biomarkers, and T [PMID:41833042] ["Lyu G", "Li D"] CNS & neurological disorders d 2026 0
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
Epigenetics and the gut-brain axis: Insights into DNA methylation, aging, and Al [PMID:41886887] Kumar V, Shukla R, Gangani S, Joseph R, The Journal of pharmacology an 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
Effects of circadian rhythms on antimicrobial peptide concentrations in lactatin [PMID:41923233] Liang ZL, Nii T, Sugino T, Isobe N BMC veterinary research 2026 0
Circadian synchronization between diet and gut microbiota in modulating host's h [PMID:41914045] ["Ma J", "Zhen Y", "Weng Y", "Lin J", "Z Gut microbes 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
Randomized controlled trial of resistance exercise and brain aging clocks. [PMID:41665740] ["Gonzalez-Gomez R", "Demnitz N", "Coron GeroScience 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

Debates (4)

Multi-agent debates referencing this entity

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

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

Do tau-containing vesicles exhibit unique surface glycosylation patterns that di

closed · Rounds: 4 · Score: 0.95 · 2026-04-10

The debate highlighted TFEB's role in mitochondrial-lysosomal coupling but could

closed · Rounds: 4 · Score: 0.95 · 2026-04-03

What are the mechanisms underlying protein aggregation cross-seeding across neur

closed · Rounds: 4 · Score: 0.95 · 2026-04-01

Related Research

Hypotheses and analyses mentioning AUTOPHAGY in their description or question text

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

Score: 0.784 · Alzheimer's disease · 2026-04-05

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

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

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

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

p21^Cip1 Phospho-State as Autophagy Responsiveness Predictor

Score: 0.710 · molecular biology · 2026-04-21

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

Autophagy-Lysosomal Degradation of IBA1 in Stressed Microglia

Score: 0.706 · neuroinflammation · 2026-04-21

## Mechanistic Overview Autophagy-Lysosomal Degradation of IBA1 in Stressed Microglia starts from the claim that modulat

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: 0.685 · molecular biology · 2026-04-21

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

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

Score: 0.678 · neurodegeneration · 2026-04-26

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

GDF15-GFRAL Axis as Systemic Autophagy-Senescence Integrator

Score: 0.653 · molecular biology · 2026-04-21

## Mechanistic Overview GDF15-GFRAL Axis as Systemic Autophagy-Senescence Integrator starts from the claim that modulati

Radiation drives pericyte senescence through lysosome acidification failure and

Score: 0.652 · neurodegeneration · 2026-04-25

Autophagosomes still form after irradiation, but damaged lysosomes cannot clear cargo, sustaining ROS and SASP output.

p62 Liquid-Liquid Phase Separation Nucleates Cross-Organelle Cargo for Coordinat

Score: 0.649 · neurodegeneration · 2026-04-21

## Mechanistic Overview p62 Liquid-Liquid Phase Separation Nucleates Cross-Organelle Cargo for Coordinated Autophagy sta

H7: mTOR Hyperactivity Blocks Autophagy, Permitting Tau Seeding

Score: 0.640 · neurodegeneration · 2026-04-22

**Molecular Mechanism and Rationale** The mechanistic target of rapamycin complex 1 (mTORC1) serves as a critical cellu