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Neuronal ceroid lipofuscinosis with DNAJC5/CSPα mutation has PPT1 pathology and exhibit aberrant protein palmitoylation

Abstract

Neuronal ceroid lipofuscinoses (NCL) are a group of inherited neurodegenerative disorders with lysosomal pathology (CLN1-14). Recently, mutations in the DNAJC5/CLN4 gene, which encodes the presynaptic co-chaperone CSPα were shown to cause autosomal-dominant NCL. Although 14 NCL genes have been identified, it is unknown if they act in common disease pathways. Here we show that two disease-associated proteins, CSPα and the depalmitoylating enzyme palmitoyl-protein thioesterase 1 (PPT1/CLN1) are biochemically linked. We find that in DNAJC5/CLN4 patient brains, PPT1 is massively increased and mis-localized. Surprisingly, the specific enzymatic activity of PPT1 is dramatically reduced. Notably, we demonstrate that CSPα is depalmitoylated by PPT1 and hence its substrate. To determine the consequences of PPT1 accumulation, we compared the palmitomes from control and DNAJC5/CLN4 patient brains by quantitative proteomics. We discovered global changes in protein palmitoylation, mainly involving lysosomal and synaptic proteins. Our findings establish a functional link between two forms of NCL and serve as a springboard for investigations of NCL disease pathways.

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Acknowledgments

We thank Dr. Katherine Sims for contributing pathologic material from the Massachusetts General Hospital NCL Biorepository. We also thank Ted Voss, Jean Kanyo, and Kathrin Wilczak for assistance with sample prep, data collection, and LFQ analysis, respectively. We would like to thank Art Horwich, Shawn Ferguson, Pietro De Camilli, Thomas Biederer, and members of our laboratories for critical discussions related to this paper. We would also like to thank Zack Gomez for data analysis. This work was supported by the Battens Disease Research and Support Association Grant, NIH R01NS083846, R01NS064963 (to S.S.C.), NIDA Neuroproteomic Center Grant (5 P30 DA018343-07) and by a NRSA NS078861-02 (to M.X.H) as well as CTSA Grant UL1 RR024139 from the National Center for Research Resources (NCRR) and the National Center for Advancing Translational Science (NCATS).

Author contributions

M.X.H. and G.S.W. performed all immunohistochemical and immunoblot analyses; M.X.H. and G.S.W. maintained and lentivirally transduced primary mouse neuronal cultures; G.S.W. performed in vitro depalmitoylation assays, IPA and CELLO analyses of MS data; Y.Z. performed RT-PCR; A.F.R. and N.G.D. purified palmitoylated proteins for MS using AcylRAC; G.D. performed PPT1 activity assays; T.T.L. performed MS analyses; F.D. provided statistical analyses of MS data; M.V., N.D., J.F.S. and P.C.G.N. clinically characterized patients and provided control and patient tissue; S.D.G. provided additional samples; M.X.H., G.S.W., and S.S.C. were involved in study design, analyzed data, and wrote the paper. M.X.H. and G.S.W. contributed equally to this study. All authors discussed the results and commented on the manuscript.

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Correspondence to Sreeganga S. Chandra.

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The authors declare no competing financial interests.

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All procedures performed in studies involving animals were in accordance with the ethical standards of the institution or practice at which the studies were conducted.

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Michael X. Henderson and Gregory S. Wirak have contributed equally to this work.

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Henderson, M.X., Wirak, G.S., Zhang, Yq. et al. Neuronal ceroid lipofuscinosis with DNAJC5/CSPα mutation has PPT1 pathology and exhibit aberrant protein palmitoylation. Acta Neuropathol 131, 621–637 (2016). https://doi.org/10.1007/s00401-015-1512-2

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Keywords

  • Neuronal ceroid lipofuscinosis (NCL)
  • Cysteine-string protein alpha (CSPα)
  • Palmitoyl-protein thioesterase 1 (PPT1)
  • Palmitoylation
  • Neurodegeneration