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Chemical modulation of chaperone-mediated autophagy by retinoic acid derivatives

A Corrigendum to this article was published on 18 October 2013

This article has been updated

Abstract

Chaperone-mediated autophagy (CMA) contributes to cellular quality control and the cellular response to stress through the selective degradation of cytosolic proteins in lysosomes. A decrease in CMA activity occurs in aging and in age-related disorders (for example, neurodegenerative diseases and diabetes). Although prevention of this age-dependent decline through genetic manipulation in mice has proven beneficial, chemical modulation of CMA is not currently possible, owing in part to the lack of information on the signaling mechanisms that modulate this pathway. In this work, we report that signaling through retinoic acid receptor α (RARα) inhibits CMA and apply structure-based chemical design to develop synthetic derivatives of all-trans-retinoic acid to specifically neutralize this inhibitory effect. We demonstrate that chemical enhancement of CMA protects cells from oxidative stress and from proteotoxicity, supporting a potential therapeutic opportunity when reduced CMA contributes to cellular dysfunction and disease.

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Figure 1: Effect of knockdown of RARα on intracellular turnover of long-lived proteins.
Figure 2: Effect of knockdown of RARα on autophagic pathways.
Figure 3: Effect of ATRA on autophagy.
Figure 4: Design, synthesis and molecular docking of RARα-targeting compounds.
Figure 5: Effect of the chemical activators of CMA on RARα activity.
Figure 6: Characterization of the effect of the retinoid derivatives on CMA.
Figure 7: Effect of the retinoid derivatives in the cellular response against different stressors.

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  • 28 June 2013

    In the version of this article initially published, one of the three gray bars in Figure 6a was not defined, and the asterisks for these bars were misaligned. The errors have been corrected in the HTML and PDF versions of the article.

References

  1. Mizushima, N., Levine, B., Cuervo, A.M. & Klionsky, D.J. Autophagy fights disease through cellular self-digestion. Nature 451, 1069–1075 (2008).

    Article  CAS  Google Scholar 

  2. Yang, Z. & Klionsky, D.J. An overview of the molecular mechanism of autophagy. Curr. Top. Microbiol. Immunol. 335, 1–32 (2009).

    CAS  PubMed  PubMed Central  Google Scholar 

  3. Mizushima, N. Autophagy in protein and organelle turnover. Cold Spring Harb. Symp. Quant. Biol. 76, 397–402 (2011).

    Article  CAS  Google Scholar 

  4. Wong, E. & Cuervo, A.M. Autophagy gone awry in neurodegenerative diseases. Nat. Neurosci. 13, 805–811 (2010).

    Article  CAS  Google Scholar 

  5. Arias, E. & Cuervo, A.M. Chaperone-mediated autophagy in protein quality control. Curr. Opin. Cell Biol. 23, 184–189 (2011).

    Article  CAS  Google Scholar 

  6. Dice, J.F. Peptide sequences that target cytosolic proteins for lysosomal proteolysis. Trends Biochem. Sci. 15, 305–309 (1990).

    Article  CAS  Google Scholar 

  7. Chiang, H.L., Terlecky, S., Plant, C. & Dice, J.F. A role for a 70-kilodalton heat shock protein in lysosomal degradation of intracellular proteins. Science 246, 382–385 (1989).

    Article  CAS  Google Scholar 

  8. Bandyopadhyay, U., Kaushik, S., Varticovski, L. & Cuervo, A.M. The chaperone-mediated autophagy receptor organizes in dynamic protein complexes at the lysosomal membrane. Mol. Cell Biol. 28, 5747–5763 (2008).

    Article  CAS  Google Scholar 

  9. Cuervo, A.M., Stefanis, L., Fredenburg, R., Lansbury, P.T. & Sulzer, D. Impaired degradation of mutant α-synuclein by chaperone-mediated autophagy. Science 305, 1292–1295 (2004).

    Article  CAS  Google Scholar 

  10. Mak, S.K., McCormack, A.L., Manning-Bog, A.B., Cuervo, A.M. & Di Monte, D.A. Lysosomal degradation of α-synuclein in vivo. J. Biol. Chem. 285, 13621–13629 (2010).

    Article  CAS  Google Scholar 

  11. Wang, Y. et al. Tau fragmentation, aggregation and clearance: the dual role of lysosomal processing. Hum. Mol. Genet. 18, 4153–4170 (2009).

    Article  CAS  Google Scholar 

  12. Sooparb, S., Price, S.R., Shaoguang, J. & Franch, H.A. Suppression of chaperone-mediated autophagy in the renal cortex during acute diabetes mellitus. Kidney Int. 65, 2135–2144 (2004).

    Article  CAS  Google Scholar 

  13. Venugopal, B. et al. Chaperone-mediated autophagy is defective in mucolipidosis type IV. J. Cell. Physiol. 219, 344–353 (2009).

    Article  CAS  Google Scholar 

  14. Cuervo, A.M. & Dice, J.F. Age-related decline in chaperone-mediated autophagy. J. Biol. Chem. 275, 31505–31513 (2000).

    Article  CAS  Google Scholar 

  15. Zhang, C. & Cuervo, A.M. Restoration of chaperone-mediated autophagy in aging liver improves cellular maintenance and hepatic function. Nat. Med. 14, 959–965 (2008).

    Article  CAS  Google Scholar 

  16. Finn, P.F., Mesires, N., Vine, M. & Dice, J.F. Effects of small molecules on chaperone-mediated autophagy. Autophagy 1, 141–145 (2005).

    Article  CAS  Google Scholar 

  17. Duong, V. & Rochette-Egly, C. The molecular physiology of nuclear retinoic acid receptors. From health to disease. Biochim. Biophys. Acta 1812, 1023–1031 (2011).

    Article  CAS  Google Scholar 

  18. Kon, M. et al. Chaperone-mediated autophagy is required for tumor growth. Sci. Transl. Med. 3, 109ra117 (2011).

    Article  Google Scholar 

  19. Frolik, C.A., Roller, P.P., Roberts, A.B. & Sporn, M.B. In vitro and in vivo metabolism of all-trans- and 13-cis-retinoic acid in hamsters. Identification of 13-cis-4-oxoretinoic acid. J. Biol. Chem. 255, 8057–8062 (1980).

    CAS  PubMed  Google Scholar 

  20. Rochette-Egly, C. & Germain, P. Dynamic and combinatorial control of gene expression by nuclear retinoic acid receptors (RARs). Nucl. Recept. Signal. 7, e005 (2009).

    Article  Google Scholar 

  21. de Lera, A.R., Bourguet, W., Altucci, L. & Gronemeyer, H. Design of selective nuclear receptor modulators: RAR and RXR as a case study. Nat. Rev. Drug Discov. 6, 811–820 (2007).

    Article  CAS  Google Scholar 

  22. Njar, V.C. et al. Retinoic acid metabolism blocking agents (RAMBAs) for treatment of cancer and dermatological diseases. Bioorg. Med. Chem. 14, 4323–4340 (2006).

    Article  CAS  Google Scholar 

  23. Das, B.C. et al. Design and synthesis of 3,5-disubstituted 1,2,4-oxadiazole containing retinoids from a retinoic acid receptor agonist. Tetrahedr. Lett. 52, 2433–2435 (2011).

    Article  CAS  Google Scholar 

  24. Das, B.C., McCartin, K., Liu, T.C., Peterson, R.T. & Evans, T. A forward chemical screen in zebrafish identifies a retinoic acid derivative with receptor specificity. PLoS ONE 5, e10004 (2010).

    Article  Google Scholar 

  25. Isakson, P., Bjoras, M., Boe, S.O. & Simonsen, A. Autophagy contributes to therapy-induced degradation of the PML/RARA oncoprotein. Blood 116, 2324–2331 (2010).

    Article  CAS  Google Scholar 

  26. Wang, Z. et al. Autophagy regulates myeloid cell differentiation by p62/SQSTM1–mediated degradation of PML-RARα oncoprotein. Autophagy 7, 401–411 (2011).

    Article  CAS  Google Scholar 

  27. Trocoli, A. et al. ATRA-induced upregulation of Beclin 1 prolongs the life span of differentiated acute promyelocytic leukemia cells. Autophagy 7, 1108–1114 (2011).

    Article  CAS  Google Scholar 

  28. Rajawat, Y., Hilioti, Z. & Bossis, I. Retinoic acid induces autophagosome maturation through redistribution of the cation-independent mannose-6-phosphate receptor. Antioxid. Redox Signal. 14, 2165–2177 (2011).

    Article  CAS  Google Scholar 

  29. Tanida, I., Minematsu-Ikeguchi, N., Ueno, T. & Kominami, E. Lysosomal turnover, but not a cellular level, of endogenous lc3 is a marker for autophagy. Autophagy 1, 84–91 (2005).

    Article  CAS  Google Scholar 

  30. Koga, H., Martinez-Vicente, M., Verkhusha, V.V. & Cuervo, A.M. A photoconvertible fluorescent reporter to track chaperone-mediated autophagy. Nat. Commun. 2, 386 (2011).

    Article  Google Scholar 

  31. Das, B.C., Anguiano, J. & Mahalingam, S.M. Design and synthesis of α-aminonitrile–functionalized novel retinoids. Tetrahedr. Lett. 50, 5670–5672 (2009).

    Article  CAS  Google Scholar 

  32. Das, B.C. et al. Design and synthesis of potential new apoptosis agents: hybrid compounds containing perillyl alcohol and new constrained retinoids. Tetrahedr. Lett. 51, 1462–1466 (2010).

    Article  CAS  Google Scholar 

  33. Das, B.C., Madhukumar, A.V., Anguiano, J. & Mani, S. Design, synthesis and biological evaluation of 2H-benzo[b][1,4] oxazine derivatives as hypoxia targeted compounds for cancer therapeutics. Bioorg. Med. Chem. Lett. 19, 4204–4206 (2009).

    Article  CAS  Google Scholar 

  34. Massey, A.C., Kaushik, S., Sovak, G., Kiffin, R. & Cuervo, A.M. Consequences of the selective blockage of chaperone-mediated autophagy. Proc. Natl. Acad. Sci. USA 103, 5805–5810 (2006).

    Article  CAS  Google Scholar 

  35. Ahlemeyer, B. et al. Retinoic acid reduces apoptosis and oxidative stress by preservation of SOD protein level. Free Radic. Biol. Med. 30, 1067–1077 (2001).

    Article  CAS  Google Scholar 

  36. Kiffin, R., Christian, C., Knecht, E. & Cuervo, A. Activation of chaperone-mediated autophagy during oxidative stress. Mol. Biol. Cell 15, 4829–4840 (2004).

    Article  CAS  Google Scholar 

  37. Eskelinen, E.L. et al. Role of LAMP-2 in lysosome biogenesis and autophagy. Mol. Biol. Cell 13, 3355–3368 (2002).

    Article  CAS  Google Scholar 

  38. Sardiello, M. et al. A gene network regulating lysosomal biogenesis and function. Science 325, 473–477 (2009).

    Article  CAS  Google Scholar 

  39. Delacroix, L. et al. Cell-specific interaction of retinoic acid receptors with target genes in mouse embryonic fibroblasts and embryonic stem cells. Mol. Cell Biol. 30, 231–244 (2010).

    Article  CAS  Google Scholar 

  40. Kaushik, S. & Cuervo, A.M. Methods to monitor chaperone-mediated autophagy. Methods Enzymol. 452, 297–324 (2009).

    Article  CAS  Google Scholar 

  41. Klionsky, D.J. et al. Guidelines for the use and interpretation of assays for monitoring autophagy. Autophagy 8, 445–544 (2012).

    Article  CAS  Google Scholar 

  42. Cuervo, A.M., Dice, J.F. & Knecht, E. A population of rat liver lysosomes responsible for the selective uptake and degradation of cytosolic proteins. J. Biol. Chem. 272, 5606–5615 (1997).

    Article  CAS  Google Scholar 

  43. Shridhar, D.R., Reddy, C.V., Sastry, O.P., Bansal, O.P. & Rao, P.P. A convenient one-step synthesis of 3-aryl-2H–1,4-benzoxazines. Synthesis 1981, 912–913 (1981).

    Article  Google Scholar 

  44. Friesner, R.A. et al. Extra precision glide: docking and scoring incorporating a model of hydrophobic enclosure for protein-ligand complexes. J. Med. Chem. 49, 6177–6196 (2006).

    Article  CAS  Google Scholar 

  45. Halgren, T.A. et al. Glide: a new approach for rapid, accurate docking and scoring. 2. Enrichment factors in database screening. J. Med. Chem. 47, 1750–1759 (2004).

    Article  CAS  Google Scholar 

  46. Friesner, R.A. et al. Glide: a new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy. J. Med. Chem. 47, 1739–1749 (2004).

    Article  CAS  Google Scholar 

  47. Shivakumar, D. et al. Prediction of Absolute solvation free energies using molecular dynamics free energy perturbation and the OPLS force field. J. Chem. Theory Comput. 6, 1509–1519 (2010).

    Article  CAS  Google Scholar 

  48. Guo, Z. et al. Probing the α-helical structural stability of stapled p53 peptides: molecular dynamics simulations and analysis. Chem. Biol. Drug Des. 75, 348–359 (2010).

    Article  CAS  Google Scholar 

  49. Bowers, K.J., Dror, R.O. & Shaw, D.E. The midpoint method for parallelization of particle simulations. J. Chem. Phys. 124, 184109 (2006).

    Article  Google Scholar 

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Acknowledgements

We thank R. Valdor for technical assistance with the luciferase assay, R. Kiffin for assistance with the quantitative RT-PCR, F. Macian for help with fluorescence-activated cell sorting procedures, T. Evans and I. Torregroza for advice with the RARα luciferase assay, C.-L. Towse for advice on the simulated annealing and molecular dynamics simulations and S. Kaushik for critically reviewing this manuscript. This work was supported by grants from the US National Institutes of Health (NIH)–National Institute on Aging (AG021904 and AG031782 to A.M.C.); Albert Einstein College of Medicine start-up funds (to E.G.); NIH–National Heart, Lung, and Blood Institute (HL095929 to E.G.); NIH–National Institute on Alcohol Abuse and Alcoholism (AA020630 to B.C.D.); and by the Rainwaters Foundation, the Beatrice and Roy Backus Foundation and a Robert and Renee Belfer gift (to A.M.C.).

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J.A. performed the experiments, analyzed the data and contributed to writing the paper; T.P.G. performed the in silico docking and molecular dynamics simulations; M.M. contributed to the synthesis of chemical compounds; B.C.D. designed the chemical compounds, analyzed the chemical data and revised the manuscript; E.G. designed and directed the in silico docking and molecular dynamics simulations and contributed to the interpretation of the chemical data and to the writing and revising of the manuscript; and A.M.C. designed the biological experiments, directed the study and wrote the manuscript.

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Correspondence to Bhaskar C Das, Evripidis Gavathiotis or Ana Maria Cuervo.

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The authors declare no competing financial interests.

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Anguiano, J., Garner, T., Mahalingam, M. et al. Chemical modulation of chaperone-mediated autophagy by retinoic acid derivatives. Nat Chem Biol 9, 374–382 (2013). https://doi.org/10.1038/nchembio.1230

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