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Immunomodulatory lysophosphatidylserines are regulated by ABHD16A and ABHD12 interplay

Nature Chemical Biology volume 11, pages 164–171 (2015)Cite this article

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Abstract

Lysophosphatidylserines (lyso-PSs) are a class of signaling lipids that regulate immunological and neurological processes. The metabolism of lyso-PSs remains poorly understood in vivo. Recently, we determined that ABHD12 is a major brain lyso-PS lipase, implicating lyso-PSs in the neurological disease polyneuropathy, hearing loss, ataxia, retinitis pigmentosa and cataract (PHARC), which is caused by null mutations in the ABHD12 gene. Here, we couple activity-based profiling with pharmacological and genetic methods to annotate the poorly characterized enzyme ABHD16A as a phosphatidylserine (PS) lipase that generates lyso-PS in mammalian systems. We describe a small-molecule inhibitor of ABHD16A that depletes lyso-PSs from cells, including lymphoblasts derived from subjects with PHARC. In mouse macrophages, disruption of ABHD12 and ABHD16A respectively increases and decreases both lyso-PSs and lipopolysaccharide-induced cytokine production. Finally, Abhd16a−/− mice have decreased brain lyso-PSs, which runs counter to the elevation in lyso-PS in Abhd12−/− mice. Our findings illuminate an ABHD16A-ABHD12 axis that dynamically regulates lyso-PS metabolism in vivo, designating these enzymes as potential targets for treating neuroimmunological disorders.

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Figure 1: Identification of ABHD16A as a PS lipase.
Figure 2: Identification of an ABHD16A inhibitor and a paired inactive control probe.
Figure 3: Disruption of ABHD16A reduces the lyso-PS content of human cells.
Figure 4: ABHD16A-ABHD12 interplay regulates lyso-PS and cytokine release from macrophages.
Figure 5: Generation and characterization of Abhd16a−/− mice.

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References

  1. Rivera, R. & Chun, J. Biological effects of lysophospholipids. Rev. Physiol. Biochem. Pharmacol. 160, 25–46 (2008).

    CAS  PubMed  Google Scholar 

  2. Makide, K. et al. Novel lysophospholipid receptors; their structure and function. J. Lipid Res. 55, 1986–1995 (2014).

    Article  CAS  Google Scholar 

  3. Rosen, H., Stevens, R.C., Hanson, M., Roberts, E. & Oldstone, M.B. Sphingosine-1-phosphate and its receptors: structure, signaling, and influence. Annu. Rev. Biochem. 82, 637–662 (2013).

    Article  CAS  Google Scholar 

  4. Lynch, K.R. & Macdonald, T.L. Sphingosine 1-phosphate chemical biology. Biochim. Biophys. Acta 1781, 508–512 (2008).

    Article  CAS  Google Scholar 

  5. van der Kleij, D. et al. A novel host-parasite lipid cross-talk. Schistosomal lyso-phosphatidylserine activates toll-like receptor 2 and affects immune polarization. J. Biol. Chem. 277, 48122–48129 (2002).

    Article  CAS  Google Scholar 

  6. Inoue, A. et al. TGFα shedding assay: an accurate and versatile method for detecting GPCR activation. Nat. Methods 9, 1021–1029 (2012).

    Article  CAS  Google Scholar 

  7. Sugita, K., Yamamura, C., Tabata, K. & Fujita, N. Expression of orphan G-protein coupled receptor GPR174 in CHO cells induced morphological changes and proliferation delay via increasing intracellular cAMP. Biochem. Biophys. Res. Commun. 430, 190–195 (2013).

    Article  CAS  Google Scholar 

  8. Chu, X. et al. An X chromosome-wide association analysis identifies variants in GPR174 as a risk factor for Graves' disease. J. Med. Genet. 50, 479–485 (2013).

    Article  CAS  Google Scholar 

  9. Szymański, K. et al. rs3827440, a nonsynonymous single nucleotide polymorphism within GPR174 gene in X chromosome, is associated with Graves' disease in Polish Caucasian population. Tissue Antigens 83, 41–44 (2014).

    Article  Google Scholar 

  10. Frasch, S.C. & Bratton, D.L. Emerging roles for lysophosphatidylserine in resolution of inflammation. Prog. Lipid Res. 51, 199–207 (2012).

    Article  CAS  Google Scholar 

  11. Park, K.S., Lee, H.Y., Kim, M.K., Shin, E.H. & Bae, Y.S. Lysophosphatidylserine stimulates leukemic cells but not normal leukocytes. Biochem. Biophys. Res. Commun. 333, 353–358 (2005).

    Article  CAS  Google Scholar 

  12. Lloret, S. & Moreno, J.J. Ca2+ influx, phosphoinositide hydrolysis, and histamine release induced by lysophosphatidylserine in mast cells. J. Cell. Physiol. 165, 89–95 (1995).

    Article  CAS  Google Scholar 

  13. Lee, S.Y. et al. Lysophosphatidylserine stimulates chemotactic migration in U87 human glioma cells. Biochem. Biophys. Res. Commun. 374, 147–151 (2008).

    Article  CAS  Google Scholar 

  14. Knowlden, S. & Georas, S.N. The autotaxin-LPA axis emerges as a novel regulator of lymphocyte homing and inflammation. J. Immunol. 192, 851–857 (2014).

    Article  CAS  Google Scholar 

  15. Billich, A. & Baumruker, T. Sphingolipid metabolizing enzymes as novel therapeutic targets. Subcell. Biochem. 49, 487–522 (2008).

    Article  Google Scholar 

  16. Blankman, J.L., Long, J.Z., Trauger, S.A., Siuzdak, G. & Cravatt, B.F. ABHD12 controls brain lysophosphatidylserine pathways that are deregulated in a murine model of the neurodegenerative disease PHARC. Proc. Natl. Acad. Sci. USA 110, 1500–1505 (2013).

    Article  CAS  Google Scholar 

  17. Fiskerstrand, T. et al. Mutations in ABHD12 cause the neurodegenerative disease PHARC: an inborn error of endocannabinoid metabolism. Am. J. Hum. Genet. 87, 410–417 (2010).

    Article  CAS  Google Scholar 

  18. Chen, D.H. et al. Two novel mutations in ABHD12: expansion of the mutation spectrum in PHARC and assessment of their functional effects. Hum. Mutat. 34, 1672–1678 (2013).

    Article  Google Scholar 

  19. Hosono, H. et al. Phosphatidylserine-specific phospholipase A1 stimulates histamine release from rat peritoneal mast cells through production of 2-acyl-1-lysophosphatidylserine. J. Biol. Chem. 276, 29664–29670 (2001).

    Article  CAS  Google Scholar 

  20. Aoki, J., Nagai, Y., Hosono, H., Inoue, K. & Arai, H. Structure and function of phosphatidylserine-specific phospholipase A1. Biochim. Biophys. Acta 1582, 26–32 (2002).

    Article  CAS  Google Scholar 

  21. Kelleher, J.A. & Sun, G.Y. Enzymic hydrolysis of arachidonoyl-phospholipids by rat brain synaptosomes. Neurochem. Int. 7, 825–831 (1985).

    Article  CAS  Google Scholar 

  22. Simon, G.M. & Cravatt, B.F. Activity-based proteomics of enzyme superfamilies: serine hydrolases as a case study. J. Biol. Chem. 285, 11051–11055 (2010).

    Article  CAS  Google Scholar 

  23. Borgström, B. Mode of action of tetrahydrolipstatin: a derivative of the naturally occurring lipase inhibitor lipstatin. Biochim. Biophys. Acta 962, 308–316 (1988).

    Article  Google Scholar 

  24. Hoover, H.S., Blankman, J.L., Niessen, S. & Cravatt, B.F. Selectivity of inhibitors of endocannabinoid biosynthesis evaluated by activity-based protein profiling. Bioorg. Med. Chem. Lett. 18, 5838–5841 (2008).

    Article  CAS  Google Scholar 

  25. Baggelaar, M.P. et al. Development of an activity-based probe and in silico design reveal highly selective inhibitors for diacylglycerol lipase-α in brain. Angew. Chem. Int. Edn. Engl. 52, 12081–12085 (2013).

    Article  CAS  Google Scholar 

  26. Pemble, C.W.T., Johnson, L.C., Kridel, S.J. & Lowther, W.T. Crystal structure of the thioesterase domain of human fatty acid synthase inhibited by Orlistat. Nat. Struct. Mol. Biol. 14, 704–709 (2007).

    Article  CAS  Google Scholar 

  27. Dekker, F.J. et al. Small-molecule inhibition of APT1 affects Ras localization and signaling. Nat. Chem. Biol. 6, 449–456 (2010).

    Article  CAS  Google Scholar 

  28. Ortar, G. et al. Tetrahydrolipstatin analogues as modulators of endocannabinoid 2-arachidonoylglycerol metabolism. J. Med. Chem. 51, 6970–6979 (2008).

    Article  CAS  Google Scholar 

  29. Ngai, M.H. et al. Click-based synthesis and proteomic profiling of lipstatin analogues. Chem. Commun. (Camb.) 46, 8335–8337 (2010).

    Article  CAS  Google Scholar 

  30. Camara, K., Kamat, S., Lasota, C.C., Cravatt, B.F. & Howell, A.R. Combining cross-metathesis and activity-based protein profiling: new β-lactone motifs for targeting serine hydrolases. Bioorg. Med. Chem. Lett. 25, 317–321 (2015).

    Article  CAS  Google Scholar 

  31. Jessani, N. et al. A streamlined platform for high-content functional proteomics of primary human specimens. Nat. Methods 2, 691–697 (2005).

    Article  CAS  Google Scholar 

  32. Adibekian, A. et al. Click-generated triazole ureas as ultrapotent in vivo–active serine hydrolase inhibitors. Nat. Chem. Biol. 7, 469–478 (2011).

    Article  CAS  Google Scholar 

  33. Liu, Y., Patricelli, M.P. & Cravatt, B.F. Activity-based protein profiling: the serine hydrolases. Proc. Natl. Acad. Sci. USA 96, 14694–14699 (1999).

    Article  CAS  Google Scholar 

  34. Blankman, J.L., Simon, G.S. & Cravatt, B.F. A comprehensive profile of brain enzymes that hydrolyze the endocannabinoid 2-arachidonoylglycerol. Chem. Biol. 14, 1347–1356 (2007).

    Article  CAS  Google Scholar 

  35. Hua, X., Sakai, J., Ho, Y.K., Goldstein, J.L. & Brown, M.S. Hairpin orientation of sterol regulatory element-binding protein-2 in cell membranes as determined by protease protection. J. Biol. Chem. 270, 29422–29427 (1995).

    Article  CAS  Google Scholar 

  36. Vance, J.E. & Tasseva, G. Formation and function of phosphatidylserine and phosphatidylethanolamine in mammalian cells. Biochim. Biophys. Acta 1831, 543–554 (2013).

    Article  CAS  Google Scholar 

  37. Rossol, M. et al. LPS-induced cytokine production in human monocytes and macrophages. Crit. Rev. Immunol. 31, 379–446 (2011).

    Article  CAS  Google Scholar 

  38. Boersema, P.J., Raijmakers, R., Lemeer, S., Mohammed, S. & Heck, A.J. Multiplex peptide stable isotope dimethyl labeling for quantitative proteomics. Nat. Protoc. 4, 484–494 (2009).

    Article  CAS  Google Scholar 

  39. Wilson-Grady, J.T., Haas, W. & Gygi, S.P. Quantitative comparison of the fasted and re-fed mouse liver phosphoproteomes using lower pH reductive dimethylation. Methods 61, 277–286 (2013).

    Article  CAS  Google Scholar 

  40. Kim, H.Y., Huang, B.X. & Spector, A.A. Phosphatidylserine in the brain: metabolism and function. Prog. Lipid Res. 56C, 1–18 (2014).

    Article  Google Scholar 

  41. Spies, T., Blanck, G., Bresnahan, M., Sands, J. & Strominger, J.L. A new cluster of genes within the human major histocompatibility complex. Science 243, 214–217 (1989).

    Article  CAS  Google Scholar 

  42. Spies, T., Bresnahan, M. & Strominger, J.L. Human major histocompatibility complex contains a minimum of 19 genes between the complement cluster and HLA-B. Proc. Natl. Acad. Sci. USA 86, 8955–8958 (1989).

    Article  CAS  Google Scholar 

  43. Frasch, S.C. et al. Neutrophils regulate tissue neutrophilia in inflammation via the oxidant-modified lipid lysophosphatidylserine. J. Biol. Chem. 288, 4583–4593 (2013).

    Article  CAS  Google Scholar 

  44. Ishii, I., Fukushima, N., Ye, X. & Chun, J. Lysophospholipid receptors: signaling and biology. Annu. Rev. Biochem. 73, 321–354 (2004).

    Article  CAS  Google Scholar 

  45. Swaney, J.S. et al. A novel, orally active LPA1 receptor antagonist inhibits lung fibrosis in the mouse bleomycin model. Br. J. Pharmacol. 160, 1699–1713 (2010).

    Article  CAS  Google Scholar 

  46. Inloes, J.M. et al. The hereditary spastic paraplegia-related enzyme DDHD2 is a principal brain triglyceride lipase. Proc. Natl. Acad. Sci. USA 111, 14924–14929 (2014).

    Article  CAS  Google Scholar 

  47. Hsu, K.L. et al. DAGLβ inhibition perturbs a lipid network involved in macrophage inflammatory responses. Nat. Chem. Biol. 8, 999–1007 (2012).

    Article  CAS  Google Scholar 

  48. Washburn, M.P., Wolters, D. & Yates, J.R. III. Large-scale analysis of the yeast proteome by multidimensional protein identification technology. Nat. Biotechnol. 19, 242–247 (2001).

    Article  CAS  Google Scholar 

  49. Weerapana, E. et al. Quantitative reactivity profiling predicts functional cysteines in proteomes. Nature 468, 790–795 (2010).

    Article  CAS  Google Scholar 

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Acknowledgements

We are grateful to K. Masuda, A. Viader and K.-L. Hsu for their helpful discussions, guidance and technical expertise in harvesting tissues; G. Simon and J. Blankman for helpful discussions; M. Niphakis for advice on the SAR studies on the β-lactone scaffolds; O. Ulanovskaya for advice on generating the shRNA knockdown cell lines; B. Correia for the guidance on using CIMAGE; C. Joslyn and T. Takei for technical assistance; and M. Lau for contributions to initial synthetic studies. This work was supported by the US National Institutes of Health (DA033760) and the ninth Irving S. Sigal postdoctoral fellowship from the American Chemical Society (to S.S.K.), a Hewitt Foundation for Medical Research fellowship (to W.H.P.), the Department of Veterans Affairs Research Funds (to T.D.B.) and the US National Science Foundation (CHE-0809753 and CHE-1048717 to A.R.H.).

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Authors and Affiliations

  1. Department of Chemical Physiology, The Scripps Research Institute, La Jolla, California

    Siddhesh S Kamat, William H Parsons, Melissa M Dix & Benjamin F Cravatt

  2. The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California

    Siddhesh S Kamat, William H Parsons, Melissa M Dix & Benjamin F Cravatt

  3. Department of Chemistry, University of Connecticut, Storrs, Connecticut

    Kaddy Camara & Amy R Howell

  4. Department of Neurology, University of Washington, Seattle, Washington

    Dong-Hui Chen & Thomas D Bird

  5. Department of Medicine, University of Washington, Seattle, Washington

    Thomas D Bird

  6. VA Puget Sound Health Care System, Seattle, Washington

    Thomas D Bird

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Contributions

S.S.K. and B.F.C. conceived the project and designed the experiments. S.S.K. performed the biochemical and cell biological experiments. K.C. and A.R.H. synthesized and chemically characterized all β-lactone compounds. D.-H.C. and T.D.B. generated the LCL lines from the patient and controls in this study. W.H.P. assisted with chemical and biochemical studies, and M.M.D. performed the ABPP-reductive dimethylation experiments. S.S.K. and B.F.C. wrote the manuscript.

Corresponding author

Correspondence to Benjamin F Cravatt.

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Competing interests

B.F.C. is a founder and advisor to Abide Therapeutics, a biotechnology company interested in developing serine hydrolase inhibitors and therapeutics.

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Kamat, S., Camara, K., Parsons, W. et al. Immunomodulatory lysophosphatidylserines are regulated by ABHD16A and ABHD12 interplay. Nat Chem Biol 11, 164–171 (2015). https://doi.org/10.1038/nchembio.1721

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