Monitoring Autophagy in the Treatment of Protein Aggregate Diseases: Steps Toward Identifying Autophagic Biomarkers

Neurotherapeutics

Volumn 10, Issue 3, 2013, Pages 383-390

  Weihl, Conrad C ^a  

^a WASHINGTON UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

Autophagy; Biomarkers; Neurodegeneration

Indexed keywords

BIOLOGICAL MARKER;

ALZHEIMER DISEASE; AUTOPHAGY; DEGENERATIVE DISEASE; HUMAN; HUNTINGTON CHOREA; IN VIVO STUDY; MACROAUTOPHAGY; NERVE DEGENERATION; NONHUMAN; PARKINSON DISEASE; PRIORITY JOURNAL; PROTEIN AGGREGATION; PROTEIN DEGRADATION; PROTEIN FOLDING; REVIEW;

AUTOPHAGY; BIOLOGICAL MARKERS; HUMANS; NERVE TISSUE PROTEINS; NEURODEGENERATIVE DISEASES; PROTEIN FOLDING;

EID: 84879950983     PISSN: 19337213     EISSN: 18787479     Source Type: Journal    
DOI: 10.1007/s13311-013-0180-y     Document Type: Review

References (54)

1. Banerjee R, Beal MF, Thomas B. Autophagy in neurodegenerative disorders: pathogenic roles and therapeutic implications. Trends Neurosci 2010;33: 541-549.
2. Rubinsztein DC, Codogno P, Levine B. Autophagy modulation as a potential therapeutic target for diverse diseases. Nat Rev Drug Discov 2012;11: 709-730.
3. Klionsky DJ. Autophagy: from phenomenology to molecular understanding in less than a decade. Nat Rev Mol Cell Biol 2007;8: 931-937.
4. Komatsu M, Waguri S, Chiba T, et al. Loss of autophagy in the central nervous system causes neurodegeneration in mice. Nature 2006;441: 880-884.
5. Hara T, Nakamura K, Matsui, M, et al. Suppression of basal autophagy in neural cells causes neurodegenerative disease in mice. Nature 2006;441: 885-889.
6. Komatsu M, Ichimura Y. Selective autophagy regulates various cellular functions. Genes Cells 2010;15: 923-933.
7. Youle RJ, Narendra DP. Mechanisms of mitophagy. Nat Rev Mol Cell Biol 2011;12: 9-14.
8. Pandey UB, Nie Z, Batlevi Y, et al. HDAC6 rescues neurodegeneration and provides an essential link between autophagy and the UPS. Nature 2007;447: 859-863.
9. Komatsu M, Waguri S, Koike M, et al. Homeostatic levels of p62 control cytoplasmic inclusion body formation in autophagy-deficient mice. Cell 2007;131: 1149-1163.
10. Ying Z, Wang H, Wang G. The Ubiquitin proteasome system as a potential target for the treatment of neurodegenerative diseases. Curr Pharm Des 2012 Nov 2 [Epub ahead of print].
11. Yarasheski KE, et al., Whole-body and muscle protein metabolism are not affected by acute deviations from habitual protein intake in older men: the Hormonal Regulators of Muscle and Metabolism in Aging (HORMA) Study. Am J Clin Nutr 2011;94: 172-181.
12. Kabeya Y, Mizushima N, Ueno T, et al. LC3, a mammalian homologue of yeast Apg8p, is localized in autophagosome membranes after processing. EMBO J 2000;19: 5720-5728.
13. Pankiv S, Clausen TH, Lamark T, et al. p62/SQSTM1 binds directly to Atg8/LC3 to facilitate degradation of ubiquitinated protein aggregates by autophagy. J Biol Chem 2007;282: 24131-24145.
14. Klionsky DJ, Abdalla FC, Abeliovich H, et al. Guidelines for the use and interpretation of assays for monitoring autophagy. Autophagy 2012;8: 445-544.
15. Zhang L, Yu J, Pan H, et al. Small molecule regulators of autophagy identified by an image-based high-throughput screen. Proc Natl Acad Sci U S A 2007;104: 19023-19028.
16. Farkas T, Hoyer-Hansen M, Jaattela M. Identification of novel autophagy regulators by a luciferase-based assay for the kinetics of autophagic flux. Autophagy 2009;5: 1018-1025.
17. Tsvetkov AS, Miller J, Arrasate M, et al. A small-molecule scaffold induces autophagy in primary neurons and protects against toxicity in a Huntington disease model. Proc Natl Acad Sci U S A 2010;107: 16982-16987.
18. Williams A, Sarkar S, Cuddon P, et al. Novel targets for Huntington's disease in an mTOR-independent autophagy pathway. Nat Chem Biol 2008;4: 295-305.
19. Ravikumar B, Vacher C, Berger Z, et al. Inhibition of mTOR induces autophagy and reduces toxicity of polyglutamine expansions in fly and mouse models of Huntington disease. Nat Genet 2004;36: 585-595.
20. Rose C, Menzie FM, Renna M, et al. Rilmenidine attenuates toxicity of polyglutamine expansions in a mouse model of Huntington's disease. Hum Mol Genet 2010;19: 2144-2153.
21. Fornai F, Longone P, Cafaro L, et al. Lithium delays progression of amyotrophic lateral sclerosis. Proc Natl Acad Sci U S A 2008;105: 2052-2057.
22. Hidvegi T, Ewing M, Hale P, et al. An autophagy-enhancing drug promotes degradation of mutant alpha1-antitrypsin Z and reduces hepatic fibrosis. Science 2010;329: 229-232.
23. Schaeffer V, Lavenir I, Ozcelik S, Tolnay M, Winker DT, Goedert M. Stimulation of autophagy reduces neurodegeneration in a mouse model of human tauopathy. Brain 2012;135: 2169-2177.
24. Jung CH, Ro SH, Cao J, Otto NM, Kim DH. mTOR regulation of autophagy. FEBS Lett 2010;584: 1287-1295.
25. Sengupta S, Peterson TR, Sabatini DM. Regulation of the mTOR complex 1 pathway by nutrients, growth factors, and stress. Mol Cell 2010;40: 310-322.
26. King MA, Hands S, Hafiz F, et al. Rapamycin inhibits polyglutamine aggregation independently of autophagy by reducing protein synthesis. Mol Pharmacol 2008;73: 1052-1063.
27. Lee BH, Lee MJ, Park S, et al. Enhancement of proteasome activity by a small-molecule inhibitor of USP14. Nature 2010;467: 179-184.
28. Rujano MA, Kampinga HH, Salomons FA. Modulation of polyglutamine inclusion formation by the Hsp70 chaperone machine. Exp Cell Res 2007;313: 3568-3578.
29. Zhao J, Brault JJ, Schild A, et al. FoxO3 coordinately activates protein degradation by the autophagic/lysosomal and proteasomal pathways in atrophying muscle cells. Cell Metab 2007; 6: 472-483.
30. Mammucari C, Milan G, Romanello V, et al. FoxO3 controls autophagy in skeletal muscle in vivo. Cell Metab 2007;6: 458-471.
31. Martinez-Vicente M, Talloczy Z, Wong E, et al. Cargo recognition failure is responsible for inefficient autophagy in Huntington's disease. Nat Neurosci 2010;13: 567-576.
32. Butler D, Nixon RA, Bahr BA. Potential compensatory responses through autophagic/lysosomal pathways in neurodegenerative diseases. Autophagy 2006;2: 234-237.
33. Mizushima N, Yamamoto A, Matsui M, Yoshimori T, Ohsumi Y. In vivo analysis of autophagy in response to nutrient starvation using transgenic mice expressing a fluorescent autophagosome marker. Mol Biol Cell 2004;15: 1101-1111.
34. Kuma A, Matsui M, Mizushima N. LC3, an autophagosome marker, can be incorporated into protein aggregates independent of autophagy: caution in the interpretation of LC3 localization. Autophagy 2007;3: 323-328.
35. Ju JS, Fuentealba RA, Miller SE, et al. Valosin-containing protein (VCP) is required for autophagy and is disrupted in VCP disease. J Cell Biol 2009;187: 875-888.
36. Lamark T, Kirkin V, Dikic I, Johansen T. NBR1 and p62 as cargo receptors for selective autophagy of ubiquitinated targets. Cell Cycle 2009;8: 1986-1990.
37. Babu JR, Geetha T, Wooten MW. Sequestosome 1/p62 shuttles polyubiquitinated tau for proteasomal degradation. J Neurochem 2005;94: 192-203.
38. Shaid S, Brandts CH, Serve H, Dikic I, Ubiquitination and selective autophagy. Cell Death Differ 2012;20: 21-30.
39. Dammer EB, Na CH, Xu P, et al. Polyubiquitin linkage profiles in three models of proteolytic stress suggest the etiology of Alzheimer disease. J Biol Chem 2011;286: 10457-10465.
40. Klionsky DJ, Abeliovich H, Agostinis P, et al. Guidelines for the use and interpretation of assays for monitoring autophagy in higher eukaryotes. Autophagy 2008;4: 151-175.
41. Ju JS, Varadhachary AS, Miller SE, Weihl CC. Quantitation of "autophagic flux" in mature skeletal muscle. Autophagy 2010;6: 929-935.
42. Iwai-Kanai E, Yuan H, Huang C, et al. A method to measure cardiac autophagic flux in vivo. Autophagy 2008;4: 322-329.
43. Haspel J, Shaik RS, Ifedigbo E, et al. Characterization of macroautophagic flux in vivo using a leupeptin-based assay. Autophagy 2011;7: 629-642.
44. Wildsmith KR, Basak JM, Patterson BW, et al. In vivo human apolipoprotein E isoform fractional turnover rates in the CNS. PLoS ONE 2012l7: e38013.
45. Bateman RJ, Munsell LY, Chen X, et al. Stable isotope labeling tandem mass spectrometry (SILT) to quantify protein production and clearance rates. J Am Soc Mass Spectrom 2007;18: 997-1006.
46. Bateman RJ, Munsell LY, Morris JC, Swarm R, Yarasheski KE, Holtzman DM. Human amyloid-beta synthesis and clearance rates as measured in cerebrospinal fluid in vivo. Nat Med 2006;12: 856-861.
47. Fagan AM, Roe CM, Xiong C, Mintun MA, Morris JC, Holtzman DM. Cerebrospinal fluid tau/beta-amyloid(42) ratio as a prediction of cognitive decline in nondemented older adults. Arch Neurol 2007; 64: 343-349.
48. Winer L, Srinivasan D, Chun S, et al. SOD1 in cerebral spinal fluid as a pharmacodynamic marker for antisense oligonucleotide therapy. Arch Neurol 2012 Nov 12 [Epub ahead of print].
49. Kasai T, Tokuda T, Ishigami N, et al. Increased TDP-43 protein in cerebrospinal fluid of patients with amyotrophic lateral sclerosis. Acta Neuropathol 2009;117: 55-62.
50. Bateman RJ Klunk WE. Measuring target effect of proposed disease-modifying therapies in Alzheimer's disease. Neurotherapeutics 2008;5: 381-390.
51. Balagopal P, Rooyackers OE, Adey DB, Ades PA, Nair KS. Effects of aging on in vivo synthesis of skeletal muscle myosin heavy-chain and sarcoplasmic protein in humans. Am J Physiol 1997;273: E790-800.
52. O'Sullivan U, Gluckman PD, Breir BH, Woodall S, Siddiqui RA, McCutcheon SN. Insulin-like growth factor-1 (IGF-1) in mice reduces weight loss during starvation. Endocrinology 1989;125: 2793-2794.
53. Zhang X, et al. Rapamycin treatment augments motor neuron degeneration in SOD1(G93A) mouse model of amyotrophic lateral sclerosis. Autophagy 2011;7: 412-425.
54. Ching JK, Elizabeth SV, Ju JS, Lusk C, Pittman SK, Weihl CC. mTOR dysfunction contributes to vacuolar pathology and weakness in valosin-containing protein associated inclusion body myopathy. Hum Mol Genet 2013 Jan 10 [Epub ahead of print].