Repertoires of Autophagy in the Pathogenesis of Ocular Diseases

Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls

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AMPK and mTOR regulate autophagy through direct phosphorylation of Ulk1

Kim, J., Kundu, M., Viollet, B., & Guan, K.-L. (2011) · Nature Cell Biology · doi:10.1038/ncb2152 · Cited by 7,227

Autophagy in the Pathogenesis of Disease

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Targeting the DNA repair defect in BRCA mutant cells as a therapeutic strategy

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LC3, a mammalian homologue of yeast Apg8p, is localized in autophagosome membranes after processing.

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Autophagy fights disease through cellular self-digestion

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Cell Death

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p62/SQSTM1 Binds Directly to Atg8/LC3 to Facilitate Degradation of Ubiquitinated Protein Aggregates by Autophagy

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Release of chromatin protein HMGB1 by necrotic cells triggers inflammation

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Parkin is recruited selectively to impaired mitochondria and promotes their autophagy

Narendra, D., Tanaka, A., Suen, D.-F., & Youle, R. J. (2008) · The Journal of Cell Biology · doi:10.1083/jcb.200809125 · Cited by 4,026

Potential function for the Huntingtin protein as a scaffold for selective autophagy

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Dissecting the dynamic turnover of GFP-LC3 in the autolysosome

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Autoimmune diseases: insights from genome-wide association studies

Lettre, G., & Rioux, J. D. (2008) · Human Molecular Genetics · doi:10.1093/hmg/ddn246 · Cited by 317

Metformin protects against apoptosis and senescence in nucleus pulposus cells and ameliorates disc degeneration in vivo

Chen, D., Xia, D., Pan, Z., Xu, D., Zhou, Y., Wu, Y., Cai, N., Tang, Q., Wang, C., Yan, M., et al. (2016) · Cell Death & Disease · doi:10.1038/cddis.2016.334 · Cited by 314

The clearance of dying cells: table for two

Green, D. R., Oguin, T. H., & Martinez, J. (2016) · Cell Death & Differentiation · doi:10.1038/cdd.2015.172 · Cited by 314

The Autophagy Machinery Controls Cell Death Switching between Apoptosis and Necroptosis

Goodall, M. L., Fitzwalter, B. E., Zahedi, S., Wu, M., Rodriguez, D., Mulcahy-Levy, J. M., Green, D. R., Morgan, M., Cramer, S. D., & Thorburn, A. (2016) · Developmental Cell · doi:10.1016/j.devcel.2016.04.018 · Cited by 314

Whole-genome sequencing reveals important role for TBK1 and OPTN mutations in frontotemporal lobar degeneration without motor neuron disease

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microRNA‐101 is a potent inhibitor of autophagy

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The ATG1/ATG13 Protein Kinase Complex Is Both a Regulator and a Target of Autophagic Recycling in Arabidopsis

Suttangkakul, A., Li, F., Chung, T., & Vierstra, R. D. (2011) · The Plant Cell · doi:10.1105/tpc.111.090993 · Cited by 311

Pleiotropic Effects of GLP-1 and Analogs on Cell Signaling, Metabolism, and Function

Rowlands, J., Heng, J., Newsholme, P., & Carlessi, R. (2018) · Frontiers in Endocrinology · doi:10.3389/fendo.2018.00672 · Cited by 302

Compartment-Specific Regulation of Autophagy in Primary Neurons

Maday, S., & Holzbaur, E. L. F. (2016) · The Journal of Neuroscience · doi:10.1523/jneurosci.4401-15.2016 · Cited by 309

MiT/TFE transcription factors are activated during mitophagy downstream of Parkin and Atg5

Nezich, C. L., Wang, C., Fogel, A. I., & Youle, R. J. (2015) · Journal of Cell Biology · doi:10.1083/jcb.201501002 · Cited by 309

Mammalian/mechanistic target of rapamycin (mTOR) complexes in neurodegeneration

Querfurth, H., & Lee, H.-K. (2021) · Molecular Neurodegeneration · doi:10.1186/s13024-021-00428-5 · Cited by 288

Characterization of VPS34-IN1, a selective inhibitor of Vps34, reveals that the phosphatidylinositol 3-phosphate-binding SGK3 protein kinase is a downstream target of class III phosphoinositide 3-kinase

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Mechanism of arginine sensing by CASTOR1 upstream of mTORC1

Saxton, R. A., Chantranupong, L., Knockenhauer, K. E., Schwartz, T. U., & Sabatini, D. M. (2016) · Nature · doi:10.1038/nature19079 · Cited by 308

Acetylation in the regulation of autophagy

Xu, Y., & Wan, W. (2023) · Autophagy · doi:10.1080/15548627.2022.2062112 · Cited by 307

Increased Mammalian Lifespan and a Segmental and Tissue-Specific Slowing of Aging after Genetic Reduction of mTOR Expression

Wu, J. J., Liu, J., Chen, E. B., Wang, J. J., Cao, L., Narayan, N., Fergusson, M. M., Rovira, I. I., Allen, M., Springer, D. A., et al. (2013) · Cell Reports · doi:10.1016/j.celrep.2013.07.030 · Cited by 307

Autophagy in diabetic nephropathy

Ding, Y., & Choi, M. E. (2015) · Journal of Endocrinology · doi:10.1530/joe-14-0437 · Cited by 306

Skeletal muscle tissue engineering: methods to form skeletal myotubes and their applications

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AMPK activation protects cells from oxidative stress‐induced senescence via autophagic flux restoration and intracellular NAD + elevation

Han, X., Tai, H., Wang, X., Wang, Z., Zhou, J., Wei, X., Ding, Y., Gong, H., Mo, C., Zhang, J., et al. (2016) · Aging Cell · doi:10.1111/acel.12446 · Cited by 302

Posttranslational modification of autophagy-related proteins in macroautophagy

Xie, Y., Kang, R., Sun, X., Zhong, M., Huang, J., Klionsky, D. J., & Tang, D. (2015) · Autophagy · doi:10.4161/15548627.2014.984267 · Cited by 302

Autophagy receptors link myosin VI to autophagosomes to mediate Tom1-dependent autophagosome maturation and fusion with the lysosome

Tumbarello, D. A., Waxse, B. J., Arden, S. D., Bright, N. A., Kendrick-Jones, J., & Buss, F. (2012) · Nature Cell Biology · doi:10.1038/ncb2589 · Cited by 301

The role of mammalian target of rapamycin (mTOR) in insulin signaling

Yoon, M.-S. (2017) · Nutrients · doi:10.3390/nu9111176 · Cited by 300

Endothelial cell and podocyte autophagy synergistically protect from diabetes-induced glomerulosclerosis

Lenoir, O., Jasiek, M., Hénique, C., Guyonnet, L., Hartleben, B., Bork, T., Chipont, A., Flosseau, K., Bensaada, I., Schmitt, A., et al. (2015) · Autophagy · doi:10.1080/15548627.2015.1049799 · Cited by 296

The role of skeletal muscle mTOR in the regulation of mechanical load‐induced growth

Goodman, C. A., Frey, J. W., Mabrey, D. M., Jacobs, B. L., Lincoln, H. C., You, J., & Hornberger, T. A. (2011) · The Journal of Physiology · doi:10.1113/jphysiol.2011.218255 · Cited by 297

How to control self-digestion: transcriptional, post-transcriptional, and post-translational regulation of autophagy

Feng, Y., Yao, Z., & Klionsky, D. J. (2015) · Trends in Cell Biology · doi:10.1016/j.tcb.2015.02.002 · Cited by 296

Early glycolytic reprogramming controls microglial inflammatory activation

Cheng, J., Zhang, R., Xu, Z., Ke, Y., Sun, R., Yang, H., Zhang, X., Zhen, X., & Zheng, L.-T. (2021) · Journal of Neuroinflammation · doi:10.1186/s12974-021-02187-y · Cited by 295

Maintenance of metabolic homeostasis by Sestrin2 and Sestrin3

Lee, J. H., Budanov, A. V., Talukdar, S., Park, E. J., Park, H. L., Park, H.-W., Bandyopadhyay, G., Li, N., Aghajan, M., Jang, I., et al. (2012) · Cell Metabolism · doi:10.1016/j.cmet.2012.08.004 · Cited by 295

p62 and NDP52 Proteins Target Intracytosolic Shigella and Listeria to Different Autophagy Pathways

Mostowy, S., Sancho-Shimizu, V., Hamon, M. A., Simeone, R., Brosch, R., Johansen, T., & Cossart, P. (2011) · Journal of Biological Chemistry · doi:10.1074/jbc.m111.223610 · Cited by 294

Dual roles of autophagy in the survival of Caenorhabditis elegans during starvation

Kang, C., You, Y.-J., & Avery, L. (2007) · Genes & Development · doi:10.1101/gad.1573107 · Cited by 294

Characterization of LAMP1-labeled nondegradative lysosomal and endocytic compartments in neurons

Cheng, X.-T., Xie, Y.-X., Zhou, B., Huang, N., Farfel-Becker, T., & Sheng, Z.-H. (2018) · Journal of Cell Biology · doi:10.1083/jcb.201711083 · Cited by 294

6-Phosphogluconate dehydrogenase links oxidative PPP, lipogenesis and tumour growth by inhibiting LKB1–AMPK signalling

Lin, R., Elf, S., Shan, C., Kang, H.-B., Ji, Q., Zhou, L., Hitosugi, T., Zhang, L., Zhang, S., Seo, J. H., et al. (2015) · Nature Cell Biology · doi:10.1038/ncb3255 · Cited by 287

Trehalose inhibits solute carrier 2A (SLC2A) proteins to induce autophagy and prevent hepatic steatosis

DeBosch, B. J., Heitmeier, M. R., Mayer, A. L., Higgins, C. B., Crowley, J. R., Kraft, T. E., Chi, M., Newberry, E. P., Chen, Z., Finck, B. N., et al. (2016) · Science Signaling · doi:10.1126/scisignal.aac5472 · Cited by 280

AMPK: Regulating Energy Balance at the Cellular and Whole Body Levels

Hardie, D. G., & Ashford, M. L. J. (2014) · Physiology · doi:10.1152/physiol.00050.2013 · Cited by 280

mTOR inhibition prevents epithelial stem cell senescence and protects from radiation-induced mucositis

Iglesias-Bartolome, R., Patel, V., Cotrim, A., Leelahavanichkul, K., Molinolo, A. A., Mitchell, J. B., & Gutkind, J. S. (2012) · Cell Stem Cell · doi:10.1016/j.stem.2012.06.007 · Cited by 284

Autophagy and the hallmarks of aging

Kaushik, S., Tasset, I., Arias, E., Pampliega, O., Wong, E., Martinez-Vicente, M., & Cuervo, A. M. (2021) · Ageing Research Reviews · doi:10.1016/j.arr.2021.101468 · Cited by 285

Inhibition of mTOR induces a paused pluripotent state

Bulut-Karslioglu, A., Biechele, S., Jin, H., Macrae, T. A., Hejna, M., Gertsenstein, M., Song, J. S., & Ramalho-Santos, M. (2016) · Nature · doi:10.1038/nature20578 · Cited by 283

The lipofuscin component A2E selectively inhibits phagolysosomal degradation of photoreceptor phospholipid by the retinal pigment epithelium

Finnemann, S. C., Leung, L. W., & Rodriguez-Boulan, E. (2002) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.052025899 · Cited by 283

Induction of hypoxia and necrosis in multicellular tumor spheroids is associated with resistance to chemotherapy treatment

Däster, S., Amatruda, N., Calabrese, D., Ivanek, R., Turrini, E., Droeser, R. A., Zajac, P., Fimognari, C., Spagnoli, G. C., Iezzi, G., et al. (2017) · Oncotarget · doi:10.18632/oncotarget.13857 · Cited by 281

Calorie Restriction: Is AMPK a Key Sensor and Effector

Cantó, C., & Auwerx, J. (2011) · Physiology · doi:10.1152/physiol.00010.2011 · Cited by 282

PICALM modulates autophagy activity and tau accumulation

Moreau, K., Fleming, A., Imarisio, S., Lopez Ramirez, A., Mercer, J. L., Jimenez-Sanchez, M., Bento, C. F., Puri, C., Zavodszky, E., Siddiqi, F., et al. (2014) · Nature Communications · doi:10.1038/ncomms5998 · Cited by 281

PIKfyve inhibition increases exosome release and induces secretory autophagy

Hessvik, N. P., Øverbye, A., Brech, A., Torgersen, M. L., Jakobsen, I. S., Sandvig, K., & Llorente, A. (2016) · Cellular and Molecular Life Sciences · doi:10.1007/s00018-016-2309-8 · Cited by 269

Natural Antioxidants: Multiple Mechanisms to Protect Skin From Solar Radiation

Dunaway, S., Odin, R., Zhou, L., Ji, L., Zhang, Y., & Kadekaro, A. L. (2018) · Frontiers in Pharmacology · doi:10.3389/fphar.2018.00392 · Cited by 280

Herpes Simplex Virus Type 1 and Other Pathogens are Key Causative Factors in Sporadic Alzheimer’s Disease

Harris, S. A., & Harris, E. A. (2015) · Journal of Alzheimer's Disease · doi:10.3233/jad-142853 · Cited by 279

Live strong and prosper: the importance of skeletal muscle strength for healthy ageing

McLeod, M., Breen, L., Hamilton, D. L., & Philp, A. (2016) · Biogerontology · doi:10.1007/s10522-015-9631-7 · Cited by 274

Autophagy regulates selective HMGB1 release in tumor cells that are destined to die

Thorburn, J., Horita, H., Redzic, J., Hansen, K., Frankel, A. E., & Thorburn, A. (2009) · Cell Death & Differentiation · doi:10.1038/cdd.2008.143 · Cited by 268

Metformin as an Anticancer Agent

Vancura, A., Bu, P., Bhagwat, M., Zeng, J., & Vancurova, I. (2018) · Trends in Pharmacological Sciences · doi:10.1016/j.tips.2018.07.006 · Cited by 274

Regulation of Autophagy by the p300 Acetyltransferase

Lee, I. H., & Finkel, T. (2009) · Journal of Biological Chemistry · doi:10.1074/jbc.m807135200 · Cited by 277

A Critical Review of the Evidence That Metformin Is a Putative Anti-Aging Drug That Enhances Healthspan and Extends Lifespan

Mohammed, I., Hollenberg, M. D., Ding, H., & Triggle, C. R. (2021) · Frontiers in Endocrinology · doi:10.3389/fendo.2021.718942 · Cited by 278

Macroautophagy Regulates Energy Metabolism during Effector T Cell Activation

Hubbard, V. M., Valdor, R., Patel, B., Singh, R., Cuervo, A. M., & Macian, F. (2010) · The Journal of Immunology · doi:10.4049/jimmunol.1000576 · Cited by 275

BCL-2 family: integrating stress responses at the ER to control cell demise

Pihán, P., Carreras-Sureda, A., & Hetz, C. (2017) · Cell Death & Differentiation · doi:10.1038/cdd.2017.82 · Cited by 274

Molecular Mechanisms of Autophagy in the Cardiovascular System

Gatica, D., Chiong, M., Lavandero, S., & Klionsky, D. J. (2015) · Circulation Research · doi:10.1161/circresaha.114.303788 · Cited by 272

Nilotinib Effects in Parkinson’s disease and Dementia with Lewy bodies

Pagan, F., Hebron, M., Valadez, E. H., Torres-Yaghi, Y., Huang, X., Mills, R. R., Wilmarth, B. M., Howard, H., Dunn, C., Carlson, A., et al. (2016) · Journal of Parkinson’s Disease · doi:10.3233/jpd-160867 · Cited by 265

Retrograde Axonal Degeneration in Parkinson Disease

Tagliaferro, P., & Burke, R. E. (2016) · Journal of Parkinson’s Disease · doi:10.3233/jpd-150769 · Cited by 272

Autophagy as a new therapeutic target in Duchenne muscular dystrophy

De Palma, C., Morisi, F., Cheli, S., Pambianco, S., Cappello, V, Vezzoli, M., Rovere-Querini, P., Moggio, M., Ripolone, M., Francolini, M., et al. (2012) · Cell Death & Disease · doi:10.1038/cddis.2012.159 · Cited by 269

Nrf2 promotes the development of fibrosis and tumorigenesis in mice with defective hepatic autophagy

Ni, H.-M., Woolbright, B. L., Williams, J., Copple, B., Cui, W., Luyendyk, J. P., Jaeschke, H., & Ding, W.-X. (2014) · Journal of Hepatology · doi:10.1016/j.jhep.2014.04.043 · Cited by 270

AMP-activated protein kinase: maintaining energy homeostasis at the cellular and whole-body levels

Hardie, D. G. (2014) · Annual Review of Nutrition · doi:10.1146/annurev-nutr-071812-161148 · Cited by 281

Defective autophagy in vascular smooth muscle cells accelerates senescence and promotes neointima formation and atherogenesis

Grootaert, M. O., da Costa Martins, P. A., Bitsch, N., Pintelon, I., De Meyer, G. R., Martinet, W., & Schrijvers, D. M. (2015) · Autophagy · doi:10.1080/15548627.2015.1096485 · Cited by 267

The Cytoskeleton-Autophagy Connection

Kast, D. J., & Dominguez, R. (2017) · Current Biology · doi:10.1016/j.cub.2017.02.061 · Cited by 267

Physical exercise stimulates autophagy in normal skeletal muscles but is detrimental for collagen VI-deficient muscles

Grumati, P., Coletto, L., Schiavinato, A., Castagnaro, S., Bertaggia, E., Sandri, M., & Bonaldo, P. (2011) · Autophagy · doi:10.4161/auto.7.12.17877 · Cited by 267

The Role of AMPK in the Regulation of Skeletal Muscle Size, Hypertrophy, and Regeneration

Thomson, D. M. (2018) · International Journal of Molecular Sciences · doi:10.3390/ijms19103125 · Cited by 267

Distinct mechanisms of ferritin delivery to lysosomes in iron-depleted and iron-replete cells

Asano, T., Komatsu, M., Yamaguchi-Iwai, Y., Ishikawa, F., Mizushima, N., & Iwai, K. (2011) · Molecular and Cellular Biology · doi:10.1128/mcb.01437-10 · Cited by 265

Atg9 Cycles Between Mitochondria and the Pre-Autophagosomal Structure in Yeasts

Reggiori, F., Shintani, T., Chong, H., Nair, U., & Klionsky, D. J. (2005) · Autophagy · doi:10.4161/auto.1.2.1840 · Cited by 266

MTOR inhibitors in cancer therapy

Xie, J., Wang, X., & Proud, C. G. (2016) · F1000Research · doi:10.12688/f1000research.9207.1 · Cited by 266

Mitochondrial and lysosomal biogenesis are activated following PINK 1/parkin‐mediated mitophagy

Ivankovic, D., Chau, K., Schapira, A. H. V., & Gegg, M. E. (2016) · Journal of Neurochemistry · doi:10.1111/jnc.13412 · Cited by 264

Metabolomics of type 1 and type 2 diabetes

Arneth, B., Arneth, R., & Shams, M. (2019) · International Journal of Molecular Sciences · doi:10.3390/ijms20102467 · Cited by 262

Normal tension glaucoma: review of current understanding and mechanisms of the pathogenesis

Killer, H., & Pircher, A. (2018) · Eye · doi:10.1038/s41433-018-0042-2 · Cited by 262

Profiling of residual breast cancers after neoadjuvant chemotherapy identifies DUSP4 deficiency as a mechanism of drug resistance

Balko, J. M., Cook, R. S., Vaught, D. B., Kuba, M. G., Miller, T. W., Bhola, N. E., Sanders, M. E., Granja-Ingram, N. M., Smith, J. J., Meszoely, I. M., et al. (2012) · Nature Medicine · doi:10.1038/nm.2795 · Cited by 262

Genetic perspective on the role of the autophagy-lysosome pathway in Parkinson disease

Gan-Or, Z., Dion, P. A., & Rouleau, G. A. (2015) · Autophagy · doi:10.1080/15548627.2015.1067364 · Cited by 260

Chaperone-mediated autophagy. Molecular mechanisms and physiological relevance

Orenstein, S. J., & Cuervo, A. M. (2010) · Seminars in Cell & Developmental Biology · doi:10.1016/j.semcdb.2010.02.005 · Cited by 260

Autophagy in diabetic kidney disease: regulation, pathological role and therapeutic potential

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Linking diet to acne metabolomics, inflammation, and comedogenesis: an update

Melnik, B. (2015) · Clinical, Cosmetic and Investigational Dermatology · doi:10.2147/ccid.s69135 · Cited by 259

Fanconi Anemia Proteins Function in Mitophagy and Immunity

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A tuberous sclerosis complex signalling node at the peroxisome regulates mTORC1 and autophagy in response to ROS

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Mitochondrial Dysfunction in Alzheimer’s Disease and the Rationale for Bioenergetics Based Therapies

Onyango, I. G., Dennis, J., & Khan, S. M. (2016) · Aging and Disease · doi:10.14336/ad.2015.1007 · Cited by 260

Foam Cells in Atherosclerosis: Novel Insights Into Its Origins, Consequences, and Molecular Mechanisms

Gui, Y., Zheng, H., & Cao, R. Y. (2022) · Frontiers in Cardiovascular Medicine · doi:10.3389/fcvm.2022.845942 · Cited by 258

The complement system in age-related macular degeneration

Armento, A., Ueffing, M., & Clark, S. J. (2021) · Cellular and Molecular Life Sciences · doi:10.1007/s00018-021-03796-9 · Cited by 258

Telomere-driven diseases and telomere-targeting therapies

Martínez, P., & Blasco, M. A. (2017) · Journal of Cell Biology · doi:10.1083/jcb.201610111 · Cited by 257

Proteome-wide analysis of chaperone-mediated autophagy targeting motifs

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Autophagy is activated in systemic lupus erythematosus and required for plasmablast development

Clarke, A. J., Ellinghaus, U., Cortini, A., Stranks, A., Simon, A. K., Botto, M., & Vyse, T. J. (2015) · Annals of the Rheumatic Diseases · doi:10.1136/annrheumdis-2013-204343 · Cited by 252

AMP-Activated Protein Kinase (AMPK) Regulates Energy Metabolism through Modulating Thermogenesis in Adipose Tissue

Wu, L., Zhang, L., Li, B., Jiang, H., Duan, Y., Xie, Z., Shuai, L., Li, J., & Li, J. (2018) · Frontiers in Physiology · doi:10.3389/fphys.2018.00122 · Cited by 255

Telomere and its role in the aging pathways: telomere shortening, cell senescence and mitochondria dysfunction

Zhu, Y., Liu, X., Ding, X., Wang, F., & Geng, X. (2019) · Biogerontology · doi:10.1007/s10522-018-9769-1 · Cited by 255

Transcriptional Regulation of Autophagy: Mechanisms and Diseases

Di Malta, C., Cinque, L., & Settembre, C. (2019) · Frontiers in Cell and Developmental Biology · doi:10.3389/fcell.2019.00114 · Cited by 255

Redundancy of human ATG4 protease isoforms in autophagy and LC3/GABARAP processing revealed in cells

Agrotis, A., Pengo, N., Burden, J. J., & Ketteler, R. (2019) · Autophagy · doi:10.1080/15548627.2019.1569925 · Cited by 255

Nrf2-dependent persistent oxidative stress results in stress-induced vulnerability to depression

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Autophagy Impairment Induces Premature Senescence in Primary Human Fibroblasts

Kang, H. T., Lee, K. B., Kim, S. Y., Choi, H. R., & Park, S. C. (2011) · PLoS ONE · doi:10.1371/journal.pone.0023367 · Cited by 254

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