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autophagy

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mechanism provisional KG: autophagy 2,641 words

autophagy in Neurodegeneration

<!-- scidex-demo:infobox:start --> <table class=“infobox infobox-mechanism”> <tr><th class=“infobox-header” colspan=“2”>Autophagy</th></tr> <tr><td class=“label”>Primary role</td><td>Lysosomal recycling of proteins and organelles</td></tr> <tr><td class=“label”>Core modules</td><td>ULK1, Beclin-1/VPS34, LC3 lipidation, lysosomes</td></tr> <tr><td class=“label”>Disease relevance</td><td>AD, PD, ALS, Huntington disease</td></tr> <tr><td class=“label”>Failure modes</td><td>Aggregate buildup, mitophagy defects, lysosomal stress</td></tr> </table> <!-- scidex-demo:infobox:end -->

Introduction

autophagy (from Greek “self-eating”) is a fundamental cellular degradation process that maintains cellular homeostasis by eliminating damaged organelles, misfolded proteins, and intracellular pathogens[@mizushima2011]. In neurons—post-mitotic cells that cannot divide and must survive for the entire lifespan—autophagy is particularly critical for maintaining proteostasis and cellular health[@nixon2013]. The three primary forms of autophagy are macroautophagy, microautophagy, and chaperone-mediated autophagy (CMA), each with distinct mechanisms and physiological roles[@kaushik2012][@pmid35435793].

Macroautophagy (commonly referred to as “autophagy”) involves the formation of a double-membraned autophagosome that engulfs cytoplasmic cargo and delivers it to lysosomes for degradation[@klionsky2012]. This process is essential for the clearance of protein aggregates and damaged organelles that accumulate during aging and in neurodegenerative diseases[@rubinsztein2006]. Microautophagy involves the direct engulfment of cytoplasmic material by lysosomal membrane invagination, while CMA involves the direct translocation of specific proteins containing a KFERQ motif across the lysosomal membrane via LAMP-2A[@cuervo2014].

The autophagy-lysosome pathway is compromised in virtually all major neurodegenerative diseases, including Alzheimer’s disease, Parkinson’s Disease, Huntington’s disease, and amyotrophic lateral sclerosis[@menzies2015]. Dysfunction at multiple stages of the autophagy pathway—from autophagosome formation to lysosomal fusion and degradation—contributes to the accumulation of toxic protein aggregates that characterize these disorders[@harris2012]. Understanding the molecular mechanisms underlying autophagy dysfunction has become a major focus for developing disease-modifying therapeutic strategies.

Pathway / Mechanism Diagram

graph TD
    A["Nutrient Deprivation / Stress"] --> B["AMPK Activation"]
    B --> C["ULK1 Complex Activation"]
    A --> D["mTORC1 Inhibition"]
    D --> C
    C --> E["Phagophore Nucleation (VPS34/Beclin-1)"]
    E --> F["LC3 Lipidation (LC3-II)"]
    F --> G["Autophagosome Formation"]
    G --> H["Cargo Recognition (p62/SQSTM1)"]
    H --> I["Autophagosome-Lysosome Fusion"]
    I --> J["Cargo Degradation"]
    J --> K["Amino Acid Recycling"]
    K --> L["Cell Survival"]
    M["Autophagy Impairment in Aging"] --> N["Aggregate Accumulation"]
    N --> O["Tau, Abeta, alpha-Synuclein Buildup"]
    O --> P["Neurodegeneration"]
    style L fill:#1b5e20,color:#e0e0e0
    style P fill:#ef5350,color:#e0e0e0
    style G fill:#006494,color:#e0e0e0

Molecular Mechanisms of autophagy

Autophagosome Formation

The formation of autophagosomes proceeds through a series of coordinated steps mediated by over 40 autophagy-related (ATG) proteins[@mizushima2011a]. This process is initiated by the ULK1 complex (comprising ULK1/2, ATG13, FIP200, and ATG101), which responds to cellular energy status via AMPK and nutrient availability via mTORC1[@egan2011]. When nutrients are abundant, mTORC1 phosphorylates and inhibits the ULK1 complex; under starvation conditions, mTORC1 inhibition is released, allowing autophagosome nucleation[@gwinn2008].

The class III phosphoinositide 3-kinase (PI3K) complex (containing VPS34, VPS15, Beclin-1, and ATG14L) generates phosphatidylinositol 3-phosphate (PI3P) at the nascent autophagosome membrane, recruiting additional ATG proteins to the phagophore assembly site[@burman2013]. Two ubiquitin-like conjugation systems are essential for autophagosome expansion: the ATG12-ATG5-ATG16L1 system and the LC3/GABARAP lipidation system[@ohsumi2010]. LC3 (microtubule-associated protein 1A/1B-light chain 3) is conjugated to phosphatidylethanolamine on the growing autophagosome membrane, facilitating cargo recognition and membrane expansion[@kabeya2000].

The closure of the autophagosome is mediated by the ESCRT machinery, which is also involved in endosomal and autophagosomal trafficking[@rusten2007]. Once closed, the autophagosome fuses with lysosomes to form autolysosomes, where the inner membrane and cargo are degraded by lysosomal hydrolases[@yu2018].

Selective autophagy

While bulk autophagy is typically induced by nutrient deprivation, selective autophagy specifically targets distinct cargoes including protein aggregates (aggrephagy), damaged mitochondria (mitophagy), peroxisomes (pexophagy), lipid droplets (lipophagy), and pathogens (xenophagy)[@johansen2011]. Selective autophagy is mediated by specific autophagy receptors that recognize cargo via ubiquitin tags and link them to LC3 on the autophagosome membrane[@stolz2014].

The p62/SQSTM1 protein serves as a prototypic autophagy receptor, containing an N-terminal PB1 domain for oligomerization, a ZZ domain for ubiquitin binding, an LIR (LC3-interacting region) for LC3 binding, and a TBK1 phosphorylation site that enhances its autophagy activity[@matsumoto2012]. p62 body formation is a characteristic feature of many neurodegenerative diseases, representing failed attempts to clear ubiquitinated protein aggregates[@komatsu2013].

NBR1 functions as an alternative autophagy receptor with distinct cargo specificity, while optineurin is particularly important for mitophagy, recognizing damaged mitochondria via ubiquitin chains and linking them to LC3[@wild2011]. The recognition of damaged mitochondria by Parkin and PINK1 represents a well-characterized mitophagy pathway that is defective in some forms of familial Parkinson’s Disease[@narendra2009].

Lysosomal Function

Lysosomes serve as the final destination for autophagic cargo degradation, and their proper function is essential for autophagy completion[@saftig2009]. Lysosomes contain over 50 different hydrolases including cathepsins that degrade proteins, lipases that degrade lipids, and nucleases that degrade nucleic acids[@settembre2013]. The lysosomal membrane is protected from degradation by a glycocalyx and specialized membrane proteins, while the acidic interior (pH 4.5-5.0) is maintained by vacuolar-type H±ATPases[@mindell2012].

Lysosomal function is regulated by the transcription factor TFEB (Transcription Factor EB), which controls the expression of genes involved in autophagy and lysosomal biogenesis[@sardiello2009]. Under nutrient-rich conditions, TFEB is phosphorylated by mTORC1 and retained in the cytoplasm; upon starvation, TFEB translocates to the nucleus to activate the CLEAR (Coordinated Lysosomal Expression and Regulation) gene network[@settembre2012]. This regulatory mechanism couples autophagy induction to lysosomal capacity.

The integrity of the autophagy-lysosome pathway is assessed by measuring autophagic flux—the complete process of autophagy from cargo sequestration to degradation[@mizushima2010]. Blockade at any step causes accumulation of autophagic intermediates and impairment of flux, which can be detected by analyzing LC3 turnover and p62 levels in the presence and absence of lysosomal inhibitors[@klionsky2008].

autophagy in Neurodegenerative Diseases

Alzheimer’s disease

Alzheimer’s disease (AD) is characterized by the accumulation of amyloid-beta plaques and tau neurofibrillary tangles, both of which are substrates for autophagy[@nixon2006]. autophagy is highly active in neurons under normal conditions, and autophagic vacuoles accumulate prominently in AD brain tissue, particularly in dystrophic neurites surrounding amyloid plaques[@nixon2005]. This accumulation reflects impaired autophagosome-lysosome fusion and lysosomal dysfunction rather than increased autophagosome formation[@boland2008].

Multiple components of the autophagy pathway are altered in AD. Beclin-1 levels are reduced in AD brain, and genetic deletion of beclin-1 in mouse models enhances amyloid deposition[@pickford2008]. The presenilin 1 mutations that cause familial AD impair lysosomal acidification and cathepsin activation, compromising the final degradative step of autophagy[@lee2010]. Tau pathology itself interferes with autophagosome trafficking by disrupting microtubule-based transport[@wang2016].

Therapeutic strategies targeting autophagy in AD include mTOR inhibitors (rapamycin, temsirolimus), natural compounds that enhance autophagy (resveratrol, curcumin), and direct activators of TFEB[@bove2011]. Rapamycin treatment reduces amyloid pathology in mouse models, though clinical translation has been complicated by immunosuppressive effects[@caccamo2010]. The lysosomal enhancer gemfibrozil was identified in a screen as an inducer of TFEB and is being evaluated for AD treatment[@zhang2012].

Parkinson’s Disease

Parkinson’s Disease (PD) is characterized by the accumulation of alpha-synuclein in Lewy bodies and the degeneration of dopaminergic neurons in the substantia nigra[@spillantini1997]. autophagy plays a critical role in clearing alpha-synuclein, and impairment of this pathway contributes to its pathological accumulation[@xilouri2013]. Both macroautophagy and chaperone-mediated autophagy are involved in alpha-synuclein degradation, and dysfunction in either pathway promotes alpha-synuclein aggregation[@cuervo2004].

Mutations causing familial PD provide insight into autophagy-pathology relationships. Loss-of-function mutations in PINK1 and PARKIN impair mitophagy, leading to accumulation of damaged mitochondria and increased oxidative stress[@narendra2008]. Mutations in GBA (glucocerebrosidase) impair lysosomal function and reduce CMA activity, increasing alpha-synuclein burden[@mazzulli2011]. LRRK2 mutations affect autophagic flux, and the G2019S mutation is the most common genetic cause of familial PD[@cookson2010].

Enhancing autophagy represents a promising therapeutic approach for PD. The mTOR inhibitor rapamycin protects dopaminergic neurons in animal models, and the FDA-approved drug carbamazepine enhances autophagy and reduces alpha-synuclein toxicity[@wu2013]. Small molecules that directly activate TFEB are in development for PD treatment[@decressac2013].

Huntington’s Disease

Huntington’s disease (HD) is caused by CAG repeat expansion in the huntingtin (HTT) gene, leading to mutant huntingtin protein with an elongated polyglutamine tract that forms aggregates and is toxic to neurons[@huntingtons1993]. autophagy is responsible for clearing mutant huntingtin, and the polyglutamine expansion enhances its recognition as an autophagy substrate[@ravikumar2004]. However, autophagy is broadly impaired in HD, contributing to the accumulation of aggregates and cellular dysfunction[@occa2012].

The huntingtin protein itself regulates autophagy, and mutant huntingtin disrupts this function. Wild-type huntingtin acts as a scaffold for the autophagy machinery, facilitating cargo recognition and autophagosome formation[@zheng2014]. Mutant huntingtin impairs this scaffolding function while also sequestering wild-type huntingtin into aggregates, creating a double hit to autophagic function[@klement1998].

autophagy-inducing strategies show promise in HD models. mTOR-independent autophagy inducers including trehalose, minocycline, and lithium reduce mutant huntingtin aggregation and improve behavioral outcomes in mouse models[@sarkar2008]. The natural compound curcumin enhances autophagy and promotes the clearance of mutant huntingtin[@shibata2013].

Amyotrophic Lateral Sclerosis

Amyotrophic lateral sclerosis (ALS) is characterized by progressive loss of motor neurons, with protein aggregate accumulation in affected neurons[@rowland2001]. autophagy is generally upregulated in ALS as a compensatory response, but the pathway is ultimately impaired by aggregate-mediated sequestration of autophagy proteins and disrupted lysosomal function[@nguyen2013].

Mutations in several genes linked to familial ALS affect autophagy regulation. C9orf72 hexanucleotide repeat expansions are the most common genetic cause of ALS; the C9orf72 protein localizes to the phagophore assembly site and regulates autophagosome formation[@farg2014]. Mutations in SQSTM1 (encoding p62) cause familial ALS, and p62-positive aggregates are a hallmark of ALS pathology[@gal2013]. OPTN and TBK1 mutations also impair selective autophagy and cause ALS[@maruyama2014].

Therapeutic approaches targeting autophagy in ALS include enhancing mitophagy to protect motor neurons from mitochondrial dysfunction and promoting the clearance of ALS-causing protein aggregates[@chen2012]. The small molecule SMER28 enhances autophagy and extends survival in animal models[@sarkar2013].

Therapeutic Modulation of autophagy

mTOR-Targeting Strategies

The mechanistic target of rapamycin (mTOR) is a central regulator of cell growth and autophagy. mTORC1 inhibition by rapamycin and its analogs induces autophagy by activating the ULK1 complex and releasing the inhibition of TFEB[@laplante2009]. This approach has shown efficacy in preclinical models of neurodegenerative disease but faces translational challenges due to the immunosuppressive and metabolic effects of chronic mTOR inhibition[@pallet2011].

Second-generation mTOR inhibitors including Torin 1 and AZD8055 more completely inhibit both mTORC1 and mTORC2 and more potently induce autophagy[@thoreen2009]. These compounds are being evaluated for neurodegenerative disease treatment, though dose-limiting toxicities remain a concern[@chiang2014]. Rapamycin analogs (rapalogs) with improved pharmacological properties are also in development[@benjamin2011].

mTOR-Independent Strategies

Multiple compounds induce autophagy through mTOR-independent mechanisms, offering potential advantages for therapeutic development. The cAMP phosphodiesterase inhibitor rolipram and the imidazoline receptor agonist TXM1 have been shown to enhance autophagy through distinct signaling pathways[@zhang2007]. These compounds may be particularly useful for diseases in which mTOR inhibition is contraindicated.

Natural products including resveratrol, curcumin, and epigallocatechin gallate (EGCG) enhance autophagy through multiple mechanisms, including sirtuin activation and AMPK signaling[@vingtdeux2012]. These compounds have been extensively studied in neurodegenerative disease models and some have entered clinical trials, though bioavailability and target engagement remain challenges[@vandaele2014].

Lithium and valproic acid induce autophagy through inositol depletion, and this mechanism is independent of mTOR[@sarkar2005]. These compounds have shown benefit in cellular and animal models of various neurodegenerative diseases and are being explored for clinical use[@chen2013].

autophagy Receptor Agonists

Direct targeting of autophagy receptors offers a more specific approach to enhancing selective autophagy. Small molecules that enhance p62 phosphorylation or interactions with LC3 could promote the clearance of specific cargoes[@ichimura2000]. Similarly, mitophagy-inducing compounds that activate the PINK1-Parkin pathway or directly bind to mitophagy receptors are being developed for PD treatment[@narendra2013].

TFEB agonists represent a promising approach that couples autophagy enhancement with lysosomal biogenesis[@settembre2011]. The natural compound genistein and the synthetic compound torin 2 activate TFEB, and these compounds show efficacy in preclinical models of neurodegenerative disease[@zhang2015]. The identification of brain-penetrant TFEB activators is an active area of research[@medina2013].

Lysosomal Enhancement

Given that lysosomal dysfunction is a common final pathway in neurodegenerative disease, strategies to enhance lysosomal function are of significant interest[@platt2012]. Pharmacological chaperones that stabilize mutant lysosomal enzymes have shown promise for diseases including Gaucher disease and are being explored for related neurodegenerative conditions[@parenti2013].

The TFEB transcription factor as discussed controls lysosomal biogenesis; TFEB overexpression enhances lysosomal capacity and promotes aggregate clearance in cellular models[@ballabio2012]. Gene therapy approaches to deliver TFEB or enhance TFEB expression are in development, though careful attention to appropriate expression levels is required to avoid deleterious effects[@sardiello2014].

autophagy and Aging

Aging is associated with progressive decline in autophagy function across all tissues, and this decline contributes to the age-related accumulation of damaged proteins and organelles that characterizes aging and age-related diseases[@rubinsztein2011]. The molecular mechanisms underlying age-related autophagy decline include reduced expression of autophagy genes, impaired lysosomal function, and altered signaling through mTOR and AMPK[@lipinski2010].

In the brain, age-related autophagy decline may be particularly significant given the post-mitotic nature of neurons and their inability to dilute damaged components through cell division[@wong2013]. The accumulation of lipofuscin (age pigment) in neurons is a hallmark of brain aging and reflects the failure of autophagy-lysosome pathways[@terman2004].

Longevity interventions that extend lifespan in model organisms often involve autophagy enhancement. Caloric restriction, the most robust lifespan-extending intervention, strongly induces autophagy, and the beneficial effects of caloric restriction are at least partially dependent on autophagy[@madeo2010]. Genetic manipulations that enhance autophagy extend lifespan in worms, flies, and mice, confirming the causal relationship between autophagy and longevity[@hansen2008].

Monitoring autophagy In Vivo

The assessment of autophagy in human brain tissue and peripheral tissues is challenging but essential for developing autophagy-targeted therapies[@mizushima2010a]. autophagy biomarkers include LC3 lipidation (LC3-II) levels, p62 turnover, and autophagosome counts by electron microscopy[@klionsky2008a]. Cerebrospinal fluid measurements of autophagy markers are being developed as minimally invasive biomarkers[@skowyra2015].

Positron emission tomography (PET) tracers that target autophagy-related processes are in development, though no validated autophagic PET tracers are currently available for clinical use[@zhou2016]. Magnetic resonance spectroscopy can detect changes in metabolite levels associated with autophagy modulation[@houten2010].

Genomic and transcriptomic analyses of patient samples are providing insights into autophagy pathway dysregulation in neurodegenerative diseases[@lipinski2010a]. These approaches have identified specific autophagy gene variants that modify disease risk and may inform patient selection for autophagy-targeted therapies[@liu2014].

Conclusion

The autophagy-lysosome pathway plays a critical role in maintaining neuronal health, and its dysfunction is a common feature of virtually all neurodegenerative diseases. The accumulation of protein aggregates in these disorders reflects impaired autophagic clearance, and enhancing autophagy represents a promising therapeutic strategy. While challenges remain in achieving appropriate target engagement and avoiding adverse effects, multiple autophagy-modulating compounds are advancing through clinical development. A deeper understanding of the specific autophagy pathways impaired in each disease and the development of biomarkers to monitor target engagement will facilitate the successful translation of autophagy-targeted therapies to the clinic.

References

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  92. Unknown (n.d.) [@mizushima2011]: [Mizushima N, Komatsu M. “autophagy: renovation of cells and tissues.” Cell 2011.](https://doi.org/10.1016/j.cell.2011.10.026/)

[@nixon2013]: [Nixon RA. “The role of autophagy in neurodegenerative disease.” Nature Medicine 2013.](https://doi.org/10.1038/nm.3232/)

[@kaushik2012]: [Kaushik S, Cuervo AM. “Chaperone-mediated autophagy: a unique way to enter the lysosome world.” Trends in Cell Biology 2012.](https://doi.org/10.1016/j.tcb.2012.05.006/)

[@klionsky2012]: [Klionsky DJ, Abdalla FC, Abeliovich H, et al. “Guidelines for the use and interpretation of assays for monitoring autophagy.” autophagy 2012.](https://doi.org/10.4161/auto.19496/)

[@rubinsztein2006]: Rubinsztein DC. “The roles of intracellular protein-degradation pathways in neurodegeneration.” Nature 2006.

[@cuervo2014]: [Cuervo AM, Wong E. “Chaperone-mediated autophagy: roles in disease and aging.” Cell Research 2014.](https://doi.org/10.1038/cr.2013.153/)

[@menzies2015]: [Menzies FM, Fleming A, Rubinsztein DC. “Impaired autophagy leads to axonal degeneration and neuron loss in neurodegenerative diseases.” Nature Neuroscience 2015.](https://doi.org/10.1038/nn.4030/)

[@harris2012]: [Harris H, Rubinsztein DC. “Huntington’s disease: degradation of mutant huntingtin by autophagy.” FEBS Journal 2012.](https://doi.org/10.1111/j.1742-4658.2011.08373.x/)

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Pathway Diagram

The following diagram shows the key molecular relationships involving autophagy discovered through SciDEX knowledge graph analysis:

graph TD
    ULK1["ULK1"] -->|"regulates"| autophagy["autophagy"]
    BECN1["BECN1"] -->|"activates"| autophagy["autophagy"]
    BECN1["BECN1"] -->|"regulates"| autophagy["autophagy"]
    AKT["AKT"] -.->|"inhibits"| autophagy["autophagy"]
    ATG7["ATG7"] -->|"activates"| autophagy["autophagy"]
    PRKN["PRKN"] -->|"activates"| autophagy["autophagy"]
    LC3["LC3"] -->|"regulates"| autophagy["autophagy"]
    MTOR["MTOR"] -.->|"inhibits"| autophagy["autophagy"]
    ULK1["ULK1"] -->|"activates"| autophagy["autophagy"]
    SIRT1["SIRT1"] -->|"activates"| autophagy["autophagy"]
    TFEB["TFEB"] -->|"activates"| autophagy["autophagy"]
    MTOR["MTOR"] -->|"regulates"| autophagy["autophagy"]
    TLR4["TLR4"] -->|"activates"| autophagy["autophagy"]
    SQSTM1["SQSTM1"] -->|"regulates"| autophagy["autophagy"]
    BECN1["BECN1"] -->|"associated with"| autophagy["autophagy"]
    style ULK1 fill:#4fc3f7,stroke:#333,color:#000
    style autophagy fill:#81c784,stroke:#333,color:#000
    style BECN1 fill:#ce93d8,stroke:#333,color:#000
    style AKT fill:#4fc3f7,stroke:#333,color:#000
    style ATG7 fill:#ce93d8,stroke:#333,color:#000
    style PRKN fill:#4fc3f7,stroke:#333,color:#000
    style LC3 fill:#4fc3f7,stroke:#333,color:#000
    style MTOR fill:#4fc3f7,stroke:#333,color:#000
    style SIRT1 fill:#4fc3f7,stroke:#333,color:#000
    style TFEB fill:#4fc3f7,stroke:#333,color:#000
    style TLR4 fill:#4fc3f7,stroke:#333,color:#000
    style SQSTM1 fill:#4fc3f7,stroke:#333,color:#000

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