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A drug-like molecule engages nuclear hormone receptor DAF-12/FXR to regulate mitophagy and extend lifespan

Nature Aging volume 3, pages 1529–1543 (2023)Cite this article

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Abstract

Autophagy–lysosomal function is crucial for maintaining healthy lifespan and preventing age-related diseases. The transcription factor TFEB plays a key role in regulating this pathway. Decreased TFEB expression is associated with various age-related disorders, making it a promising therapeutic target. In this study, we screened a natural product library and discovered mitophagy-inducing coumarin (MIC), a benzocoumarin compound that enhances TFEB expression and lysosomal function. MIC robustly increases the lifespan of Caenorhabditis elegans in an HLH-30/TFEB-dependent and mitophagy-dependent manner involving DCT-1/BNIP3 while also preventing mitochondrial dysfunction in mammalian cells. Mechanistically, MIC acts by inhibiting ligand-induced activation of the nuclear hormone receptor DAF-12/FXR, which, in turn, induces mitophagy and extends lifespan. In conclusion, our study uncovers MIC as a promising drug-like molecule that enhances mitochondrial function and extends lifespan by targeting DAF-12/FXR. Furthermore, we discovered DAF-12/FXR as a previously unknown upstream regulator of HLH-30/TFEB and mitophagy.

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Fig. 1: MIC enhances TFEB/HLH-30 expression and lysosomal activity.
Fig. 2: MIC modulates activity of the NHR DAF-12/FXR.
Fig. 3: MIC-induced mitophagy enhances mitochondrial health.
Fig. 4: MIC extends lifespan and reduces neuropathologies in C. elegans.
Fig. 5: Conserved therapeutic potential of MIC in mammalian cells.

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References

  1. Aman, Y. et al. Autophagy in healthy aging and disease. Nat. Aging 1, 634–650 (2021).

    Article  PubMed  PubMed Central  Google Scholar 

  2. Kaushik, S. et al. Autophagy and the hallmarks of aging. Ageing Res. Rev. 72, 101468 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  3. Siddiqui, A. et al. Mitochondrial quality control via the PGC1α-TFEB signaling pathway is compromised by parkin Q311X mutation but independently restored by rapamycin. J. Neurosci. 35, 12833–12844 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  4. Abdrakhmanov, A., Gogvadze, V. & Zhivotovsky, B. To eat or to die: deciphering selective forms of autophagy. Trends Biochem. Sci 45, 347–364 (2020).

    Article  CAS  PubMed  Google Scholar 

  5. Lopez-Otin, C., Blasco, M. A., Partridge, L., Serrano, M. & Kroemer, G. The hallmarks of aging. Cell 153, 1194–1217 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  6. Lou, G. et al. Mitophagy and neuroprotection. Trends Mol. Med. 26, 8–20 (2020).

    Article  CAS  PubMed  Google Scholar 

  7. Singh, A. et al. Urolithin A improves muscle strength, exercise performance, and biomarkers of mitochondrial health in a randomized trial in middle-aged adults. Cell Rep. Med. 3, 100633 (2022).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  8. Ryu, D. et al. Urolithin A induces mitophagy and prolongs lifespan in C. elegans and increases muscle function in rodents. Nat. Med. 22, 879–888 (2016).

    Article  CAS  PubMed  Google Scholar 

  9. Fang, E. F. et al. Mitophagy inhibits amyloid-β and tau pathology and reverses cognitive deficits in models of Alzheimer’s disease. Nat. Neurosci. 22, 401–412 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  10. Palikaras, K., Princz, A. & Tavernarakis, N. In Encyclopedia of Biomedical Gerontology (ed Rattan, S. I. S.) 433–446 (Academic Press, 2020).

  11. Dong, Y. et al. Chemical mitophagy modulators: drug development strategies and novel regulatory mechanisms. Pharmacol. Res. 194, 106835 (2023).

    Article  CAS  PubMed  Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

  13. Settembre, C. et al. TFEB links autophagy to lysosomal biogenesis. Science 332, 1429–1433 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  14. Martini-Stoica, H., Xu, Y., Ballabio, A. & Zheng, H. The autophagy-lysosomal pathway in neurodegeneration: a TFEB perspective. Trends Neurosci. 39, 221–234 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  15. Cortes, C. J. & La Spada, A. R. TFEB dysregulation as a driver of autophagy dysfunction in neurodegenerative disease: molecular mechanisms, cellular processes, and emerging therapeutic opportunities. Neurobiol. Dis. 122, 83–93 (2019).

    Article  CAS  PubMed  Google Scholar 

  16. Lapierre, L. R. et al. The TFEB orthologue HLH-30 regulates autophagy and modulates longevity in Caenorhabditis elegans. Nat. Commun. 4, 2267 (2013).

    Article  PubMed  Google Scholar 

  17. O’Rourke, E. J. & Ruvkun, G. MXL-3 and HLH-30 transcriptionally link lipolysis and autophagy to nutrient availability. Nat. Cell Biol. 15, 668–676 (2013).

    Article  PubMed  PubMed Central  Google Scholar 

  18. Visvikis, O. et al. Innate host defense requires TFEB-mediated transcription of cytoprotective and antimicrobial genes. Immunity 40, 896–909 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  19. Nakamura, S. et al. Mondo complexes regulate TFEB via TOR inhibition to promote longevity in response to gonadal signals. Nat. Commun. 7, 10944 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  20. Gerisch, B. et al. HLH-30/TFEB is a master regulator of reproductive quiescence. Dev. Cell 53, 316–329 (2020).

    Article  CAS  PubMed  Google Scholar 

  21. Silvestrini, M. J. et al. Nuclear export inhibition enhances HLH-30/TFEB activity, autophagy, and lifespan. Cell Rep. 23, 1915–1921 (2018).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  22. Song, J. X. et al. A novel curcumin analog binds to and activates TFEB in vitro and in vivo independent of MTOR inhibition. Autophagy 12, 1372–1389 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  23. Wang, C. et al. Small-molecule TFEB pathway agonists that ameliorate metabolic syndrome in mice and extend C. elegans lifespan. Nat. Commun. 8, 2270 (2017).

    Article  PubMed  PubMed Central  Google Scholar 

  24. da Costa, A., Picoli, C., Mouthon, F. & Charveriat, M. Automated assays to identify modulators of transcription factor EB translocation and autophagy. Assay Drug Dev. Technol. 20, 67–74 (2022).

    Article  PubMed  Google Scholar 

  25. Martina, J. A., Diab, H. I., Brady, O. A. & Puertollano, R. TFEB and TFE3 are novel components of the integrated stress response. EMBO J. 35, 479–495 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  26. Settembre, C. et al. A lysosome-to-nucleus signalling mechanism senses and regulates the lysosome via mTOR and TFEB. EMBO J. 31, 1095–1108 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  27. Palmieri, M. et al. Characterization of the CLEAR network reveals an integrated control of cellular clearance pathways. Hum Mol. Genet. 20, 3852–3866 (2011).

    Article  CAS  PubMed  Google Scholar 

  28. Chang, J. T., Kumsta, C., Hellman, A. B., Adams, L. M. & Hansen, M. Spatiotemporal regulation of autophagy during Caenorhabditis elegans aging. eLife 6, e18459 (2017).

  29. Kimura, S., Noda, T. & Yoshimori, T. Dissection of the autophagosome maturation process by a novel reporter protein, tandem fluorescent-tagged LC3. Autophagy 3, 452–460 (2007).

    Article  CAS  PubMed  Google Scholar 

  30. Saftig, P. & Klumperman, J. Lysosome biogenesis and lysosomal membrane proteins: trafficking meets function. Nat. Rev. Mol. Cell Biol. 10, 623–635 (2009).

    Article  CAS  PubMed  Google Scholar 

  31. Guo, P., Hu, T., Zhang, J., Jiang, S. & Wang, X. Sequential action of Caenorhabditis elegans Rab GTPases regulates phagolysosome formation during apoptotic cell degradation. Proc. Natl Acad. Sci. USA 107, 18016–18021 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  32. Miao, R., Li, M., Zhang, Q., Yang, C. & Wang, X. An ECM-to-nucleus signaling pathway activates lysosomes for C. elegans larval development. Dev. Cell 52, 21–35 (2020).

    Article  CAS  PubMed  Google Scholar 

  33. Sun, Y. et al. Lysosome activity is modulated by multiple longevity pathways and is important for lifespan extension in C. elegans. eLife 9, e55745 (2020).

  34. Baxi, K., Ghavidel, A., Waddell, B., Harkness, T. A. & de Carvalho, C. E. Regulation of lysosomal function by the DAF-16 forkhead transcription factor couples reproduction to aging in Caenorhabditis elegans. Genetics 207, 83–101 (2017).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  35. Seok, S. et al. Transcriptional regulation of autophagy by an FXR–CREB axis. Nature 516, 108–111 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  36. Wang, Z. et al. The nuclear receptor DAF-12 regulates nutrient metabolism and reproductive growth in nematodes. PLoS Genet. 11, e1005027 (2015).

    Article  PubMed  PubMed Central  Google Scholar 

  37. Musa, M. A., Cooperwood, J. S. & Khan, M. O. A review of coumarin derivatives in pharmacotherapy of breast cancer. Curr. Med. Chem. 15, 2664–2679 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  38. Hochbaum, D. et al. DAF-12 regulates a connected network of genes to ensure robust developmental decisions. PLoS Genet. 7, e1002179 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  39. Motola, D. L. et al. Identification of ligands for DAF-12 that govern dauer formation and reproduction in C. elegans. Cell 124, 1209–1223 (2006).

    Article  CAS  PubMed  Google Scholar 

  40. Ao, W., Gaudet, J., Kent, W. J., Muttumu, S. & Mango, S. E. Environmentally induced foregut remodeling by PHA-4/FoxA and DAF-12/NHR. Science 305, 1743–1746 (2004).

    Article  CAS  PubMed  Google Scholar 

  41. Luciani, G. M. et al. Dafadine inhibits DAF-9 to promote dauer formation and longevity of Caenorhabditis elegans. Nat. Chem. Biol. 7, 891–893 (2011).

    Article  CAS  PubMed  Google Scholar 

  42. Otera, H. & Mihara, K. Discovery of the membrane receptor for mitochondrial fission GTPase Drp1. Small GTPases 2, 167–172 (2011).

    Article  PubMed  PubMed Central  Google Scholar 

  43. Benz, R. & McLaughlin, S. The molecular mechanism of action of the proton ionophore FCCP (carbonylcyanide ptrifluoromethoxyphenylhydrazone. Biophys. J. 41, 381–398 (1983).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  44. Heinz, S. et al. Mechanistic investigations of the mitochondrial complex I inhibitor rotenone in the context of pharmacological and safety evaluation. Sci Rep. 7, 45465 (2017).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  45. Benedetti, C., Haynes, C. M., Yang, Y., Harding, H. P. & Ron, D. Ubiquitin-like protein 5 positively regulates chaperone gene expression in the mitochondrial unfolded protein response. Genetics 174, 229–239 (2006).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  46. Miedel, M. T. et al. A pro-cathepsin L mutant is a luminal substrate for endoplasmic-reticulum-associated degradation in C. elegans. PLoS ONE 7, e40145 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  47. Palikaras, K. & Tavernarakis, N. In vivo mitophagy monitoring in Caenorhabditis elegans to determine mitochondrial homeostasis. Bio. Protoc. 7, e2215 (2017).

  48. Chapin, H. C., Okada, M., Merz, A. J. & Miller, D. L. Tissue-specific autophagy responses to aging and stress in C. elegans. Aging (Albany NY) 7, 419–434 (2015).

    Article  CAS  PubMed  Google Scholar 

  49. Palikaras, K., Lionaki, E. & Tavernarakis, N. Coordination of mitophagy and mitochondrial biogenesis during ageing in C. elegans. Nature 521, 525–528 (2015).

    Article  CAS  PubMed  Google Scholar 

  50. Kayser, E. B., Morgan, P. G., Hoppel, C. L. & Sedensky, M. M. Mitochondrial expression and function of GAS-1 in Caenorhabditis elegans. J. Biol. Chem. 276, 20551–20558 (2001).

    Article  CAS  PubMed  Google Scholar 

  51. Ishii, N. et al. A mutation in succinate dehydrogenase cytochrome b causes oxidative stress and ageing in nematodes. Nature 394, 694–697 (1998).

    Article  CAS  PubMed  Google Scholar 

  52. Lin, M. T. & Beal, M. F. Mitochondrial dysfunction and oxidative stress in neurodegenerative diseases. Nature 443, 787–795 (2006).

    Article  CAS  PubMed  Google Scholar 

  53. Link, C. D. et al. Gene expression analysis in a transgenic Caenorhabditis elegans Alzheimer’s disease model. Neurobiol Aging 24, 397–413 (2003).

    Article  CAS  PubMed  Google Scholar 

  54. van Ham, T. J. et al. C. elegans model identifies genetic modifiers of α-synuclein inclusion formation during aging. PLoS Genet. 4, e1000027 (2008).

    Article  PubMed  PubMed Central  Google Scholar 

  55. Ash, P. E. et al. Neurotoxic effects of TDP-43 overexpression in C. elegans. Hum. Mol. Genet. 19, 3206–3218 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  56. Poot, M. et al. Analysis of mitochondrial morphology and function with novel fixable fluorescent stains. J. Histochem. Cytochem. 44, 1363–1372 (1996).

    Article  CAS  PubMed  Google Scholar 

  57. Urizar, N. L. et al. A natural product that lowers cholesterol as an antagonist ligand for FXR. Science 296, 1703–1706 (2002).

    Article  CAS  PubMed  Google Scholar 

  58. Yang, J. F. et al. Guggulsterone inhibits migration and invasion through proteasomal and lysosomal degradation in human glioblastoma cells. Eur. J. Pharmacol. 938, 175411 (2023).

    Article  CAS  PubMed  Google Scholar 

  59. Wu, K. et al. FXR-mediated inhibition of autophagy contributes to FA-induced TG accumulation and accordingly reduces FA-induced lipotoxicity. Cell Commun. Signal. 18, 47 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  60. Deng, R. Therapeutic effects of guggul and its constituent guggulsterone: cardiovascular benefits. Cardiovasc. Drug Rev. 25, 375–390 (2007).

    Article  CAS  PubMed  Google Scholar 

  61. Chen, G., Kroemer, G. & Kepp, O. Mitophagy: an emerging role in aging and age-associated diseases. Front. Cell Dev. Biol. 8, 200 (2020).

    Article  PubMed  PubMed Central  Google Scholar 

  62. Leeman, D. S. et al. Lysosome activation clears aggregates and enhances quiescent neural stem cell activation during aging. Science 359, 1277–1283 (2018).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  63. Hughes, A. L. & Gottschling, D. E. An early age increase in vacuolar pH limits mitochondrial function and lifespan in yeast. Nature 492, 261–265 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  64. Ramachandran, P. V. et al. Lysosomal signaling promotes longevity by adjusting mitochondrial activity. Dev. Cell 48, 685–696 e685 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  65. Kennedy, B. K. et al. Geroscience: linking aging to chronic disease. Cell 159, 709–713 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  66. Fisher, A. L. & Lithgow, G. J. The nuclear hormone receptor DAF-12 has opposing effects on Caenorhabditis elegans lifespan and regulates genes repressed in multiple long-lived worms. Aging Cell 5, 127–138 (2006).

    Article  CAS  PubMed  Google Scholar 

  67. Panzitt, K. et al. FXR-dependent Rubicon induction impairs autophagy in models of human cholestasis. J. Hepatol. 72, 1122–1131 (2020).

    Article  CAS  PubMed  Google Scholar 

  68. Fonseca, I. et al. Tauroursodeoxycholic acid protects against mitochondrial dysfunction and cell death via mitophagy in human neuroblastoma cells. Mol. Neurobiol. 54, 6107–6119 (2017).

    Article  CAS  PubMed  Google Scholar 

  69. Fiorucci, S. & Distrutti, E. Bile acid-activated receptors, intestinal microbiota, and the treatment of metabolic disorders. Trends Mol. Med. 21, 702–714 (2015).

    Article  CAS  PubMed  Google Scholar 

  70. Mancin, L., Wu, G. D. & Paoli, A. Gut microbiota–bile acid–skeletal muscle axis. Trends Microbiol. 31, 254–269 (2023).

    Article  CAS  PubMed  Google Scholar 

  71. Monteiro-Cardoso, V. F., Corliano, M. & Singaraja, R. R. Bile acids: a communication channel in the gut–brain axis. Neuromolecular Med. 23, 99–117 (2021).

    Article  CAS  PubMed  Google Scholar 

  72. Muku, G. E., Murray, I. A., Espin, J. C. & Perdew, G. H. Urolithin A is a dietary microbiota-derived human aryl hydrocarbon receptor antagonist. Metabolites 8, 86 (2018).

  73. Livingston, S. et al. Pomegranate derivative urolithin A enhances vitamin D receptor signaling to amplify serotonin-related gene induction by 1,25-dihydroxyvitamin D. Biochem. Biophys. Rep. 24, 100825 (2020).

    PubMed  PubMed Central  Google Scholar 

  74. Vini, R. et al. Urolithins: the colon microbiota metabolites as endocrine modulators: prospects and perspectives. Front. Nutr. 8, 800990 (2021).

    Article  PubMed  Google Scholar 

  75. Niinivehmas, S. & Pentikainen, O. T. Coumarins as tool compounds to aid the discovery of selective function modulators of steroid hormone binding proteins. Molecules 26, 5142 (2021).

  76. Mark, K. A. et al. Vitamin D promotes protein homeostasis and longevity via the stress response pathway genes skn-1, ire-1, and xbp-1. Cell Rep. 17, 1227–1237 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  77. Thondamal, M., Witting, M., Schmitt-Kopplin, P. & Aguilaniu, H. Steroid hormone signalling links reproduction to lifespan in dietary-restricted Caenorhabditis elegans. Nat. Commun. 5, 4879 (2014).

    Article  CAS  PubMed  Google Scholar 

  78. Manley, S. et al. Farnesoid X receptor regulates forkhead BoxO3a activation in ethanol-induced autophagy and hepatotoxicity. Redox Biol. 2, 991–1002 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  79. Ding, W. X. et al. Parkin and mitofusins reciprocally regulate mitophagy and mitochondrial spheroid formation. J. Biol. Chem. 287, 42379–42388 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  80. Schmid, E. T., Pyo, J. H. & Walker, D. W. Neuronal induction of BNIP3-mediated mitophagy slows systemic aging in Drosophila. Nat Aging. 2, 494–507 (2022).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  81. Deng, H., Dodson, M. W., Huang, H. & Guo, M. The Parkinson’s disease genes pink1 and parkin promote mitochondrial fission and/or inhibit fusion in Drosophila. Proc. Natl Acad. Sci. USA. 105, 14503–14508 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  82. Lemasters, J. J. Variants of mitochondrial autophagy: types 1 and 2 mitophagy and micromitophagy (type 3).Redox Biol. 2, 749–754 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  83. Stefanachi, A., Leonetti, F., Pisani, L., Catto, M. & Carotti, A. Coumarin: a natural, privileged and versatile scaffold for bioactive compounds. Molecules 23, 250 (2018).

  84. Mishra, S., Pandey, A. & Manvati, S. Coumarin: an emerging antiviral agent. Heliyon 6, e03217 (2020).

    Article  PubMed  PubMed Central  Google Scholar 

  85. Andreux, P. A. et al. The mitophagy activator urolithin A is safe and induces a molecular signature of improved mitochondrial and cellular health in humans. Nat. Metab. 1, 595–603 (2019).

    Article  CAS  PubMed  Google Scholar 

  86. Stiernagle, T. Maintenance of C. elegans. WormBook 1–11 https://doi.org/10.1895/wormbook.1.101.1 (2006).

  87. Gelino, S. et al. Intestinal autophagy improves healthspan and longevity in C. elegans during dietary restriction. PLoS Genet. 12, e1006135 (2016).

    Article  PubMed  PubMed Central  Google Scholar 

  88. Kumsta, C. et al. The autophagy receptor p62/SQST-1 promotes proteostasis and longevity in C. elegans by inducing autophagy. Nat. Commun. 10, 5648 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  89. Lucanic, M. et al. Impact of genetic background and experimental reproducibility on identifying chemical compounds with robust longevity effects. Nat. Commun. 8, 14256 (2017).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  90. Anand, N. et al. Dysregulated iron metabolism in C. elegans catp-6/ATP13A2 mutant impairs mitochondrial function. Neurobiol. Dis. 139, 104786 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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Acknowledgements

The authors thank past and present members of the Lithgow and Andersen laboratories and Q. T. Le (Stanford University), D. Bhaumik, D. Tailor and S. Rajagopalan for help with laboratory resources. The authors also thank N. Tavernarakis (University of Crete Medical School) and C. E. de Carvalho (University of Saskatchewan) for the C. elegans reporter strains. C. elegans strains used in this work were provided by the Caenorhabditis Genetics Center (CGC), funded by the National Institutes of Health (NIH) Office of Research Infrastructure Programs (P40OD010440), and the Japanese National BioResource Project. This work was supported by NIH RF1 AG057358 to J.K.A. and R01 AG067325 to G.J.L. M.C. was supported by a postdoctoral fellowship from the Larry L. Hillblom Foundation. M.H. was supported by NIH AG 038664. The Lithgow and Andersen laboratories are also supported by the Larry L. Hillblom Foundation Center Grant. Figures were created using BioRender. The funders had no role in study design, data collection and analysis, decision to publish or preparation of the manuscript.

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Authors and Affiliations

  1. Buck Institute for Research on Aging, Novato, CA, USA

    Manish Chamoli, Anand Rane, Anna Foulger, Shankar J. Chinta, Azar Asadi Shahmirzadi, David Hall, Angelina Holcom, Suzanne Angeli, Minna Schmidt, Malene Hansen, Gordon J. Lithgow & Julie K. Andersen

  2. Touro University California, Vallejo, CA, USA

    Shankar J. Chinta

  3. University of Southern California, Los Angeles, CA, USA

    Azar Asadi Shahmirzadi, Angelina Holcom & Minna Schmidt

  4. Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA

    Caroline Kumsta & Malene Hansen

  5. Stanford University, Stanford, CA, USA

    Dhanya K. Nambiar & Sharon Pitteri

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  1. Manish Chamoli
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Contributions

Conceptualization: M.C., S.J.C., G.J.L. and J.K.A. Investigation: M.C., A.R., A.F., S.J.C., A.A.S., C.K., D.K.N., A.H., S.A., D.H. and M.S. Methodology: M.C., A.R., A.F., S.J.C., A.A.S., C.K., D.K.N., A.H. and S.A. Validation: M.C., A.R., A.F., A.A.S., C.K., D.K.N., S.A. and D.H. Visualization: M.C., A.R., C.K. and S.A. Resources: D.K.N. and S.P. Writing—original draft: MC. Writing—review and editing: M.C., M.H., G.J.L. and J.K.A. Supervision: M.C., G.J.L. and J.K.A. Funding acquisition: G.J.L. and J.K.A.

Corresponding authors

Correspondence to Manish Chamoli, Gordon J. Lithgow or Julie K. Andersen.

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Competing interests

The Buck Institute has filed a provisional patent application on which M.C., S.J.C., G.J.L. and J.K.A. are listed as an inventor. G.J.L. is a co-founder of Gerostate Alpha and declares no financial interests related to this work. M.C., G.J.L. and J.K.A. are co-founders of Symbiont Bio and declare no financial interests related to this work. The remaining authors declare no competing interests.

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Nature Aging thanks Javier Irazoqui and the other, anonymous, reviewer(s) for their contribtiuon to the peer review of this work.

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Extended data

Extended Data Fig. 1 MIC enhances TFEB/HLH-30 expression and lysosomal activity.

a, Day-2 HLH-30::GFP (MAH235) images 24 h post-treatment (20 °C) with DMSO or MIC. On 5 min starvation, animals show 100% nuclear localization (arrowheads). Assay was independently repeated three times (n ≥ 30 animals). Scale: 10 µm. b, Punctae count (muscles) of day-2 lgg-1p::gfp::lgg-1 (DA2123) post 24 h DMSO/MIC treatment (20 °C). Image highlighting LGG-1 punctae (arrow). Assay was independently repeated three times (n = 48 and 32 animals). Graph show mean ± s.d. (p-values via two-tailed unpaired t-test). Scale: 10 µm. c, Punctae count (pharynx) of day-2 lgg-1p::gfp::lgg-1 (DA2123) post 24 h DMSO/MIC treatment (20 °C). Image highlighting LGG-1 punctae (arrow). Assay was independently repeated three times (n = 28 and 32 animals). Graph show mean ± s.d. ns ≥ 0.05 (p-values via two-tailed unpaired t-test). Scale: 10 µm. d, Punctae count (neurons) in day-2 rgef-1p::gfp::lgg-1 (MAH242) post 24 h DMSO/MIC treatment (20 °C). Image highlighting LGG-1 punctae (arrow). Assay was independently repeated three times (n = 30 and 31 animals). Graph show mean ± s.d. (p-values via two-tailed unpaired t-test). Scale: 10 µm. e, Lysosomal area changes in day-2 WT(N2) 24 h post-treatment (20 °C) via lysotracker red. Assay was independently repeated three times with ≥15 animals/repeat (n = 311 and 571 lysosomes). The box plot shows the 25th–75th percentiles, median line, and min–max whiskers. p = 0.0004, (p-values via two-tailed unpaired t-test). f, Day-2 plmp1::lmp-1::GFP (RT258) images 24 h post-treatment (20 °C). Assay was independently repeated three times (n = 19 and 22 animals). The box plot shows the 25th–75th percentiles, median line, and min–max whiskers. p < 0.0001, (p-values via two-tailed unpaired t-test). Scale: 10 µm. g, Day-2 unc-54p: SEP::mCherry::laat-1 (arrow) images 24 h post-treatment (20 °C). Graph show mean ± s.d. Assay was independently repeated three times (n = 9 and 7 animals). p = 0.0066, (p-values via two-tailed unpaired t-test). Scale: 10 µm.

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Extended Data Fig. 2 MIC modulates activity of a nuclear hormone receptor DAF-12/FXR.

a, mRNA of lysosomal and mitophagy genes, day-1 WT(N2) and daf-12(rh61rh411) (20 °C). Assay was independently repeated four times. Graph show mean ± s.d. (p-values via two-tailed unpaired t-test). b, WT(N2) and daf-12(rh61rh411), day-1 (20 °C); Left: lysotracker intensity, (n = 311 and n = 325 lysosomes), p < 0.0001. Right: lysosomal area, (n = 311 and n = 321 lysosomes), p = 0.0013. Assay was independently repeated three times with ≥15 animals/repeat. (P-value via two-tailed unpaired t-test). Scale: 10 µm. c, WT(N2) and daf-12(rh61rh411) 24 h post-DMSO/MIC treatment, day-2 (20 °C); lysotracker intensity, Left: (n = 272 and n = 617 lysosomes), p < 0.0001; Right: (n = 325 and n = 477 lysosomes), p < 0.0001. Assay was independently repeated three times with ≥15 animals/repeat. (p-value via two-tailed unpaired t-test). d. mRNA of lysosomal genes, day-2 WT(N2) and hlh-30(tm1978) (20 °C). Assay was independently repeated five times. Graph show mean ± s.e.m. (p-values via two-tailed unpaired t-test). Right: lysotracker intensity, hlh-30(tm1978) 24 h post-DMSO/MIC treatment, day-2 (20 °C), (n = 447 and n = 156 lysosomes), p < 0.0001. Assay was independently repeated three times with ≥15 animals/repeat. (P-value via two-tailed unpaired t-test). The box plots (b, c and d) represent the 25th–75th percentiles, the line depicts the median and the whiskers show the min–max values. e, DAF-12 activity post-dafachronic acid (ligand) doses quantified by one-hybrid reporter assay. Graph show mean ± s.d. Assay was independently repeated four times, except for ligand 50 nM that is, two, Ligand200 (p = 0.0045) and Ligand500 (p = 0.0003), (P-value via one-way ANOVA with Tukey’s multiple comparisons test). f, Schematic depicts dafadine A (DFA) action. DFA induces HLH-30 expression. HLH-30::GFP (MAH235), day-2 animals post-DFA/DMSO treatment (20 °C) probed with GFP antibody, Actin (ACT) as loading control. Assay was independently repeated two times. g, mRNA of lysosomal genes, day-2 WT(N2) and daf-12(rh61rh411) (20 °C). Assay was independently repeated two times. (p-values via two-tailed unpaired t-test).

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Extended Data Fig. 3 MIC-induced mitophagy enhances mitochondrial health.

a. Image depicts co-localization (arrowheads) in day-2 reporter animals treated with DMSO, MIC, or FCCP at 20 °C, expressing mCherry::LGG-1 and mitochondrial GFP. FCCP is used as positive control. Right: Spearman’s co-localization coefficient. Assay was independently repeated four times. Graph show mean ± s.d. MIC (p = 0.0464) and FCCP (p = 0.0003), (p-value via two-tailed unpaired t-test). Scale: 10 µm. b. mRNA of mitophagy genes in day-2 WT(N2) and daf-12(rh61rh411) mutants 24 h post DMSO or MIC (20 °C). Assay was independently repeated four times. Graph show mean ± s.d. daf-12 vs WT, for dct-1 (p = 0.0059) and drp-1, (p = 0.0476), WT (DMSO vs MIC), for dct-1 (p = 0.0071) and for drp-1 (p = 0.0326), (p-value by unpaired t-test). c. mRNA of mitophagy genes in day-2 WT(N2) and hlh-30(tm1978) mutants 24 h post DMSO or MIC (20 °C). hlh-30 vs WT, for dct-1 (p = 0.0099), pink-1 (p = 0.0277). WT (DMSO vs MIC), for dct-1 (p = 0.0004) and hlh-30 (DMSO vs MIC) for pink-1 (p = 0.0163). Assay was independently repeated three times. Graph show mean ± s.d., (p-value by unpaired t-test). d. Quantification of mitophagy in muscle-specific mito-rosella reporter upon RNAi treatment, performed at day-2, 24 h post DMSO/MIC (20 °C). Assay was independently repeated three times (n = 45, 44, 34 and 26 animals). Graph show mean ± s.d. control RNAi, MIC vs DMSO (p = 0.0020), (p-value via one-way ANOVA with Tukey’s multiple comparison test). e. Survival of DMSO/MIC treated day-5 pdr-1(gk448) mutants 5 h (20 °C) post-rotenone. Assay was independently repeated three times. Graph show mean ± s.d., p = 0.0226 (p-value via two-tailed unpaired t-test). f. Oxygen consumption rate, basal (B) and max (M) of day-2 WT(N2) and hlh-30(tm1978) mutants 24 h post DMSO/MIC (20 °C). Assay was independently repeated four times. Graph show mean ± s.e.m. (B vs M) for; WT-DMSO (p = 0.0169), WT-MIC (p < 0.0001), hlh-30-DMSO (p = 0.0269), hlh-30-MIC (p = 0.0005); (max-WT-DMSO vs max-WT-MIC, p < 0.0001), (max-WT-MIC vs max-hlh-30-MIC, p < 0.0001), (p-value via two-way ANOVA with Sidak’s multiple comparison test).

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Extended Data Fig. 4 Lifespan extending effect of MIC.

a, Survival curve of WT(N2) animals, treatment (median days); N2-DMSO (22) and N2-MIC (29), ****p < 0.0001 (p-value via Mantel-Cox long-rank test). MIC exposure from days 1–12 (15 °C) of adulthood. Detailed statistical information for all lifespans is presented in Supplementary Table 1. b, Survival curve of WT(N2) animals, treatment (median days); N2-DMSO (17) and N2-MIC (17), MIC exposure (15 °C) during development only (egg to young adult). c, Left: Survival curve of WT(N2) and hlh-30(tm1978) animals on dafadine A (DFA) post-development, N2-DMSO (17) and N2-DFA (19); p = 0.0021, hlh-30-DMSO (15) and hlh-30-DFA (12); p < 0.0001, (p-value via Mantel-Cox long-rank test). Assay was independently repeated three times. Right: Survival of day-2 WT(N2) and hlh-30(tm1978), 3 h post-FCCP (20 °C). Assay was independently repeated two times, ≥30 animals/repeat. WT-DMSO vs WT-DFA 20 μM; (p = 0.0113), hlh-30-DMSO vs WT-DFA 40 μM; (p = 0.0116), (p-values via two-way ANOVA with Sidak’s multiple comparisons test). d, Survival curve of pdr-1(gk448) animals, pdr-1-DMSO (15) and pdr-1-MIC (17), (p = 0.0009) (p-value via Mantel-Cox long-rank test). Assay was independently repeated two times. MIC exposure from days 1–7 (20 °C) of adulthood. e, Median lifespan shown for conditions/genotypes post treatment. N2 (D-20 °C) indicates MIC treatment only during development. ‘Life-long’ means exposure throughout the life starting from day-of adulthood. Each dot depicts median lifespan from a plate of ~50 animals. Lifespan change is averaged across trials. DMSO vs MIC for N2(15 °C)-life-long; (p = 0.0149), N2(20 °C)-life-long; (p = 0.0400), N2(15 °C)-day1–15; (p < 0.0001), N2(20 °C)-day1–7; (<0.0001) and mev-1(20 °C)-day1–7; (p = 0.0020), (p-value via two-tailed unpaired t-test). Detailed statistical information for all lifespans is presented in Supplementary Table 1.

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Extended Data Fig. 5 Mitophagy inducer urolithin A modulates DAF-12/FXR activity.

a, Human FXR activity was measured post-treatment with GW4064 and MIC. Assay was independently repeated four times. Graph show mean ± s.d. GW4064 (p < 0.0001), (P-value via one-way ANOVA with Tukey’s multiple comparisons test). b, left: UA and MIC structure is shown with benzocoumarin rings depicted in grey. Right: Human FXR activity was measured post-treatment with GW4064 and (+/− UA). Assay was independently repeated four times. Graph show mean ± s.d. GW4064 vs ctrl (p < 0.0001) and GW4064-UA50 (p = 0.0012). (p-value via two-way ANOVA with Tukey’s multiple comparisons test). c, DAF-12 activity post-dafachronic acid treatment, alone or with UA, was quantified by one-hybrid reporter assay. Graph show mean ± s.d. Assay was independently repeated three times. DMSO + Ligand (p = 0.0005), Ligand+ UA30 (p = 0.0076) Ligand +UA50 (p = 0.0069), (P-value via one-way ANOVA with Tukey’s multiple comparisons test).

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Supplementary information

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Supplementary Figs. 1 and 2 and Supplementary Tables 1–3

Reporting Summary

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Chamoli, M., Rane, A., Foulger, A. et al. A drug-like molecule engages nuclear hormone receptor DAF-12/FXR to regulate mitophagy and extend lifespan. Nat Aging 3, 1529–1543 (2023). https://doi.org/10.1038/s43587-023-00524-9

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