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

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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

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Guidelines for the use and interpretation of assays for monitoring autophagy

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Autophagy regulates lipid metabolism

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mTOR: from growth signal integration to cancer, diabetes and ageing

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Suppression of basal autophagy in neural cells causes neurodegenerative disease in mice

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Loss of autophagy in the central nervous system causes neurodegeneration in mice

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Induction of autophagy and inhibition of tumorigenesis by beclin 1

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Mechanisms of mitophagy

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Calreticulin exposure dictates the immunogenicity of cancer cell death

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Toll-like receptor 4–dependent contribution of the immune system to anticancer chemotherapy and radiotherapy

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Functions of Lysosomes

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PINK1 Is Selectively Stabilized on Impaired Mitochondria to Activate Parkin

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The AMPK signalling pathway coordinates cell growth, autophagy and metabolism

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The role of autophagy during the early neonatal starvation period

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IKKβ Links Inflammation and Tumorigenesis in a Mouse Model of Colitis-Associated Cancer

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Impairment of starvation-induced and constitutive autophagy in Atg7 -deficient mice

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Promotion of tumorigenesis by heterozygous disruption of the beclin 1 autophagy gene

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Dissection of the Autophagosome Maturation Process by a Novel Reporter Protein, Tandem Fluorescent-Tagged LC3

Kimura, S., Noda, T., & Yoshimori, T. (2007) · Autophagy · doi:10.4161/auto.4451 · Cited by 2,278

Autophagy Is a Defense Mechanism Inhibiting BCG and Mycobacterium tuberculosis Survival in Infected Macrophages

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Bcl-2 family proteins regulate the release of apoptogenic cytochrome c by the mitochondrial channel VDAC

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Beclin 1, an autophagy gene essential for early embryonic development, is a haploinsufficient tumor suppressor

Yue, Z., Jin, S., Yang, C., Levine, A. J., & Heintz, N. (2003) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2436255100 · Cited by 2,116

Direct Activation of Bax by p53 Mediates Mitochondrial Membrane Permeabilization and Apoptosis

Chipuk, J. E., Kuwana, T., Bouchier-Hayes, L., Droin, N. M., Newmeyer, D. D., Schuler, M., & Green, D. R. (2004) · Science · doi:10.1126/science.1092734 · Cited by 2,108

Reactive oxygen species are essential for autophagy and specifically regulate the activity of Atg4

Scherz‐Shouval, R., Shvets, E., Fass, E., Shorer, H., Gil, L., & Elazar, Z. (2007) · The EMBO Journal · doi:10.1038/sj.emboj.7601623 · Cited by 2,101

Innate immune recognition of viral infection

Kawai, T., & Akira, S. (2006) · Nature Immunology · doi:10.1038/ni1303 · Cited by 1,899

Role of autophagy in cancer

Mathew, R., Karantza-Wadsworth, V., & White, E. (2007) · Nature Reviews Cancer · doi:10.1038/nrc2254 · Cited by 1,798

Genome-wide association study identifies new susceptibility loci for Crohn disease and implicates autophagy in disease pathogenesis

Rioux, J. D., Xavier, R. J., Taylor, K. D., Silverberg, M. S., Goyette, P., Huett, A., Green, T., Kuballa, P., Barmada, M. M., Datta, L. W., et al. (2007) · Nature Genetics · doi:10.1038/ng2032 · Cited by 1,769

Distinct BH3 domains either sensitize or activate mitochondrial apoptosis, serving as prototype cancer therapeutics

Letai, A., Bassik, M. C., Walensky, L. D., Sorcinelli, M. D., Weiler, S., & Korsmeyer, S. J. (2002) · Cancer Cell · doi:10.1016/s1535-6108(02)00127-7 · Cited by 1,677

The roles of intracellular protein-degradation pathways in neurodegeneration

Rubinsztein, D. C. (2006) · Nature · doi:10.1038/nature05291 · Cited by 1,625

Selective degradation of mitochondria by mitophagy

Kim, I., Rodriguez-Enriquez, S., & Lemasters, J. J. (2007) · Archives of Biochemistry and Biophysics · doi:10.1016/j.abb.2007.03.034 · Cited by 1,558

The role of autophagy in cardiomyocytes in the basal state and in response to hemodynamic stress

Nakai, A., Yamaguchi, O., Takeda, T., Higuchi, Y., Hikoso, S., Taniike, M., Omiya, S., Mizote, I., Matsumura, Y., Asahi, M., et al. (2007) · Nature Medicine · doi:10.1038/nm1574 · Cited by 1,520

Growth factor regulation of autophagy and cell survival in the absence of apoptosis

Lum, J. J., Bauer, D. E., Kong, M., Harris, M. H., Li, C., Lindsten, T., & Thompson, C. B. (2005) · Cell · doi:10.1016/j.cell.2004.11.046 · Cited by 1,487

Akt Stimulates Aerobic Glycolysis in Cancer Cells

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DRAM, a p53-Induced Modulator of Autophagy, Is Critical for Apoptosis

Crighton, D., Wilkinson, S., O'Prey, J., Syed, N., Smith, P., Harrison, P. R., Gasco, M., Garrone, O., Crook, T., & Ryan, K. M. (2006) · Cell · doi:10.1016/j.cell.2006.05.034 · Cited by 1,380

Role of Bcl-2 family proteins in a non-apoptotic programmed cell death dependent on autophagy genes

Shimizu, S., Kanaseki, T., Mizushima, N., Mizuta, T., Arakawa-Kobayashi, S., Thompson, C. B., & Tsujimoto, Y. (2004) · Nature Cell Biology · doi:10.1038/ncb1192 · Cited by 1,358

Autophagy-deficient mice develop multiple liver tumors

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The plasticity of aging: insights from long-lived mutants

Kenyon, C. (2005) · Cell · doi:10.1016/j.cell.2005.02.002 · Cited by 1,338

Superoxide Anion Radical (O·̄2), Superoxide Dismutases, and Related Matters

Fridovich, I. (1997) · Journal of Biological Chemistry · doi:10.1074/jbc.272.30.18515 · Cited by 1,337

Mutant p53 gain of function in two mouse models of Li-Fraumeni syndrome

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Defective Hepatic Autophagy in Obesity Promotes ER Stress and Causes Insulin Resistance

Yang, L., Li, P., Fu, S., Calay, E. S., & Hotamisligil, G. S. (2010) · Cell Metabolism · doi:10.1016/j.cmet.2010.04.005 · Cited by 1,274

Molecular dissection of autophagy: two ubiquitin-like systems

Ohsumi, Y. (2001) · Nature Reviews Molecular Cell Biology · doi:10.1038/35056522 · Cited by 1,240

HDAC6 rescues neurodegeneration and provides an essential link between autophagy and the UPS.

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Proteolysis: from the lysosome to ubiquitin and the proteasome

Ciechanover, A. (2005) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm1552 · Cited by 1,133

LKB1 modulates lung cancer differentiation and metastasis

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The role of the Atg1/ULK1 complex in autophagy regulation

Mizushima, N. (2010) · Current Opinion in Cell Biology · doi:10.1016/j.ceb.2009.12.004 · Cited by 1,062

Reactions of oxyl radicals with DNA

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Lithium induces autophagy by inhibiting inositol monophosphatase

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Macroautophagy—a novel β-amyloid peptide-generating pathway activated in Alzheimer's disease

Yu, W. H., Cuervo, A. M., Kumar, A., Peterhoff, C. M., Schmidt, S. D., Lee, J.-H., Mohan, P. S., Mercken, M., Farmery, M. R., Tjernberg, L. O., et al. (2005) · The Journal of Cell Biology · doi:10.1083/jcb.200505082 · Cited by 967

Oxygen poisoning and x-irradiation: a mechanism in common

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Inhibition of early apoptotic events by Akt/PKB is dependent on the first committed step of glycolysis and mitochondrial hexokinase

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Age-related macular degeneration: etiology, pathogenesis, and therapeutic strategies

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Lipofuscin: mechanisms of age-related accumulation and influence on cell function12 1Guest Editor: Rajindar S. Sohal 2This article is part of a series of reviews on “Oxidative Stress and Aging.” The full list of papers may be found on the homepage of the journal.

Brunk, U. T., & Terman, A. (2002) · Free Radical Biology and Medicine · doi:10.1016/s0891-5849(02)00959-0 · Cited by 919

Microautophagy of Cytosolic Proteins by Late Endosomes

Sahu, R., Kaushik, S., Clement, C. C., Cannizzo, E. S., Scharf, B., Follenzi, A., Potolicchio, I., Nieves, E., Cuervo, A. M., & Santambrogio, L. (2011) · Developmental Cell · doi:10.1016/j.devcel.2010.12.003 · Cited by 902

HSV-1 ICP34.5 Confers Neurovirulence by Targeting the Beclin 1 Autophagy Protein

Orvedahl, A., Alexander, D., Tallóczy, Z., Sun, Q., Wei, Y., Zhang, W., Burns, D., Leib, D. A., & Levine, B. (2007) · Cell Host & Microbe · doi:10.1016/j.chom.2006.12.001 · Cited by 857

Axon degeneration mechanisms: Commonality amid diversity

Coleman, M. (2005) · Nature reviews. Neuroscience · doi:10.1038/nrn1788 · Cited by 819

Beclin–phosphatidylinositol 3‐kinase complex functions at the trans‐Golgi network

Kihara, A., Kabeya, Y., Ohsumi, Y., & Yoshimori, T. (2001) · The EMBO Reports · doi:10.1093/embo-reports/kve061 · Cited by 813

HDAC6 and microtubules are required for autophagic degradation of aggregated huntingtin.

Iwata, A., Riley, B. E., Johnston, J. A., & Kopito, R. R. (2005) · Journal of Biological Chemistry · doi:10.1074/jbc.m508786200 · Cited by 719

Autophagy Controls Salmonella Infection in Response to Damage to the Salmonella-containing Vacuole

Birmingham, C. L., Smith, A. C., Bakowski, M. A., Yoshimori, T., & Brumell, J. H. (2006) · Journal of Biological Chemistry · doi:10.1074/jbc.m509157200 · Cited by 658

RPE lipofuscin and its role in retinal pathobiology

Sparrow, J. R., & Boulton, M. (2005) · Experimental Eye Research · doi:10.1016/j.exer.2005.01.007 · Cited by 644

A critical role for the autophagy gene Atg5 in T cell survival and proliferation

Pua, H. H., Dzhagalov, I., Chuck, M., Mizushima, N., & He, Y.-W. (2007) · The Journal of Experimental Medicine · doi:10.1084/jem.20061303 · Cited by 622

Risk factors for incident age-related macular degeneration

Tomany, S. C., Wang, J. J., van Leeuwen, R., Klein, R., Mitchell, P., Vingerling, J. R., Klein, B. E. K., Smith, W., & de Jong, P. T. V. M. (2004) · Ophthalmology · doi:10.1016/j.ophtha.2003.11.010 · Cited by 621

Essential role for autophagy protein Atg7 in the maintenance of axonal homeostasis and the prevention of axonal degeneration

Komatsu, M., Wang, Q. J., Holstein, G. R., Friedrich, V. L., Iwata, J.-I., Kominami, E., Chait, B. T., Tanaka, K., & Yue, Z. (2007) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0701311104 · Cited by 614

Autophagy: Basic Principles and Relevance to Disease

Kundu, M., & Thompson, C. B. (2008) · Annual Review of Pathology: Mechanisms of Disease · doi:10.1146/annurev.pathmechdis.2.010506.091842 · Cited by 523

Mitochondria—A Nexus for Aging, Calorie Restriction, and Sirtuins?

Guarente, L. (2008) · Cell · doi:10.1016/j.cell.2008.01.007 · Cited by 513

Isolation and one-step preparation of A2E and iso -A2E, fluorophores from human retinal pigment epithelium

Parish, C. A., Hashimoto, M., Nakanishi, K., Dillon, J., & Sparrow, J. (1998) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.95.25.14609 · Cited by 474

Regulation of intracellular accumulation of mutant Huntingtin by Beclin 1

Shibata, M., Lu, T., Furuya, T., Degterev, A., Mizushima, N., Yoshimori, T., MacDonald, M., Yankner, B., & Yuan, J. (2006) · Journal of Biological Chemistry · doi:10.1074/jbc.m600364200 · Cited by 458

Mitochondrial alterations of retinal pigment epithelium in age-related macular degeneration

Feher, J., Kovacs, I., Artico, M., Cavallotti, C., Papale, A., & Balacco Gabrieli, C. (2006) · Neurobiology of Aging · doi:10.1016/j.neurobiolaging.2005.05.012 · Cited by 388

Major histocompatibility complex class II‐restricted presentation of a cytosolic antigen by autophagy

Nimmerjahn, F., Milosevic, S., Behrends, U., Jaffee, E. M., Pardoll, D. M., Bornkamm, G. W., & Mautner, J. (2003) · European Journal of Immunology · doi:10.1002/eji.200323730 · Cited by 359

Autophagy is Required for Dietary Restriction-Mediated Life Span Extension in C. elegans

Jia, K., & Levine, B. (2007) · Autophagy · doi:10.4161/auto.4989 · Cited by 341

Neuronal loss and brain atrophy in mice lacking cathepsins B and L

Felbor, U., Kessler, B., Mothes, W., Goebel, H. H., Ploegh, H. L., Bronson, R. T., & Olsen, B. R. (2002) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.112632299 · Cited by 334

Oxidative Damage in the Retinal Mitochondria of Diabetic Mice: Possible Protection by Superoxide Dismutase

Kanwar, M., Chan, P.-S., Kern, T. S., & Kowluru, R. A. (2007) · Investigative Opthalmology & Visual Science · doi:10.1167/iovs.06-1280 · Cited by 333

Participation of Autophagy in Storage of Lysosomes in Neurons from Mouse Models of Neuronal Ceroid-Lipofuscinoses (Batten Disease)

Koike, M., Shibata, M., Waguri, S., Yoshimura, K., Tanida, I., Kominami, E., Gotow, T., Peters, C., von Figura, K., Mizushima, N., et al. (2005) · The American Journal of Pathology · doi:10.1016/s0002-9440(10)61253-9 · Cited by 330

Autophagy and heterophagy dysregulation leads to retinal pigment epithelium dysfunction and development of age-related macular degeneration

Kaarniranta, K., Sinha, D., Blasiak, J., Kauppinen, A., Veréb, Z., Salminen, A., Boulton, M. E., & Petrovski, G. (2013) · Autophagy · doi:10.4161/auto.24546 · Cited by 326

Induction of Autophagy in Axonal Dystrophy and Degeneration

Wang, Q. J., Ding, Y., Kohtz, S., Mizushima, N., Cristea, I. M., Rout, M. P., Chait, B. T., Zhong, Y., Heintz, N., & Yue, Z. (2006) · The Journal of Neuroscience · doi:10.1523/jneurosci.2261-06.2006 · Cited by 308

A Novel Protein Complex Linking the δ2 Glutamate Receptor and Autophagy

Yue, Z., Horton, A., Bravin, M., DeJager, P. L., Selimi, F., & Heintz, N. (2002) · Neuron · doi:10.1016/s0896-6273(02)00861-9 · Cited by 306

Thyroid hormone stimulates hepatic lipid catabolism via activation of autophagy

Sinha, R. A., You, S.-H., Zhou, J., Siddique, M. M., Bay, B.-H., Zhu, X., Privalsky, M. L., Cheng, S.-Y., Stevens, R. D., Summers, S. A., et al. (2012) · Journal of Clinical Investigation · doi:10.1172/jci60580 · Cited by 303

DNA Polymerase γ in Mitochondrial DNA Replication and Repair

Graziewicz, M. A., Longley, M. J., & Copeland, W. C. (2006) · Chemical Reviews · doi:10.1021/cr040463d · Cited by 301

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

Regulation of the aging process by autophagy.

Salminen, A., & Kaarniranta, K. (2009) · Trends in Molecular Medicine · doi:10.1016/j.molmed.2009.03.004 · Cited by 270

Intracellular Inclusions Containing Mutant α1-Antitrypsin Z Are Propagated in the Absence of Autophagic Activity

Kamimoto, T., Shoji, S., Hidvegi, T., Mizushima, N., Umebayashi, K., Perlmutter, D. H., & Yoshimori, T. (2006) · Journal of Biological Chemistry · doi:10.1074/jbc.m509409200 · Cited by 259

Mitochondrial disorders: prevalence, myths and advances

Thorburn, D. R. (2004) · Journal of Inherited Metabolic Disease · doi:10.1023/b:boli.0000031098.41409.55 · Cited by 258

Involvement of All-trans-retinal in Acute Light-induced Retinopathy of Mice

Maeda, A., Maeda, T., Golczak, M., Chou, S., Desai, A., Hoppel, C. L., Matsuyama, S., & Palczewski, K. (2009) · Journal of Biological Chemistry · doi:10.1074/jbc.m900322200 · Cited by 248

Mutations That Increase the Life Span of C. elegans Inhibit Tumor Growth

Pinkston, J. M., Garigan, D., Hansen, M., & Kenyon, C. (2006) · Science · doi:10.1126/science.1121908 · Cited by 242

Overexpression of mitochondrial superoxide dismutase in mice protects the retina from diabetes-induced oxidative stress

Kowluru, R. A., Kowluru, V., Xiong, Y., & Ho, Y.-S. (2006) · Free Radical Biology and Medicine · doi:10.1016/j.freeradbiomed.2006.01.012 · Cited by 233

Mechanism of All-trans-retinal Toxicity with Implications for Stargardt Disease and Age-related Macular Degeneration

Chen, Y., Okano, K., Maeda, T., Chauhan, V., Golczak, M., Maeda, A., & Palczewski, K. (2012) · Journal of Biological Chemistry · doi:10.1074/jbc.m111.315432 · Cited by 229

Metabolic catastrophe as a means to cancer cell death

Jin, S., DiPaola, R. S., Mathew, R., & White, E. (2007) · Journal of Cell Science · doi:10.1242/jcs.03349 · Cited by 229

The Role of Oxidative Stress in Diabetic Vascular and Neural Disease

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Autophagy promotes survival of retinal ganglion cells after optic nerve axotomy in mice

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