Phosphoproteome-based kinase activity profiling reveals the critical role of MAP2K2 and PLK1 in neuronal autophagy

Autophagy. 2017;13(11):1969-1980. doi: 10.1080/15548627.2017.1371393. Epub 2017 Oct 4.

Abstract

Recent studies have demonstrated that dysregulation of macroautophagy/autophagy may play a central role in the pathogenesis of neurodegenerative disorders, and the induction of autophagy protects against the toxic insults of aggregate-prone proteins by enhancing their clearance. Thus, autophagy has become a promising therapeutic target against neurodegenerative diseases. In this study, quantitative phosphoproteomic profiling together with a computational analysis was performed to delineate the phosphorylation signaling networks regulated by 2 natural neuroprotective autophagy enhancers, corynoxine (Cory) and corynoxine B (Cory B). To identify key regulators, namely, protein kinases, we developed a novel network-based algorithm of in silico Kinome Activity Profiling (iKAP) to computationally infer potentially important protein kinases from phosphorylation networks. Using this algorithm, we observed that Cory or Cory B potentially regulated several kinases. We predicted and validated that Cory, but not Cory B, downregulated a well-documented autophagy kinase, RPS6KB1/p70S6K (ribosomal protein S6 kinase, polypeptide 1). We also discovered 2 kinases, MAP2K2/MEK2 (mitogen-activated protein kinase kinase 2) and PLK1 (polo-like kinase 1), to be potentially upregulated by Cory, whereas the siRNA-mediated knockdown of Map2k2 and Plk1 significantly inhibited Cory-induced autophagy. Furthermore, Cory promoted the clearance of Alzheimer disease-associated APP (amyloid β [A4] precursor protein) and Parkinson disease-associated SNCA/α-synuclein (synuclein, α) by enhancing autophagy, and these effects were dramatically diminished by the inhibition of the kinase activities of MAP2K2 and PLK1. As a whole, our study not only developed a powerful method for the identification of important regulators from the phosphoproteomic data but also identified the important role of MAP2K2 and PLK1 in neuronal autophagy.

Keywords: autophagy; corynoxine; kinase activity; phosphoproteome; phosphorylation; protein kinase.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amyloid beta-Peptides / metabolism*
  • Animals
  • Autophagy / drug effects
  • Autophagy / physiology*
  • Cell Cycle Proteins / metabolism*
  • Computer Simulation
  • Indoles / pharmacology
  • MAP Kinase Kinase 2 / metabolism
  • Mice
  • Neurodegenerative Diseases / metabolism
  • Neurons / drug effects
  • Neurons / metabolism
  • Neurons / pathology*
  • PC12 Cells
  • Phosphoproteins / metabolism*
  • Phosphorylation
  • Protein-Serine-Threonine Kinases / metabolism*
  • Proteome / metabolism
  • Proto-Oncogene Proteins / metabolism*
  • Rats
  • Ribosomal Protein S6 Kinases, 70-kDa / metabolism
  • Spiro Compounds / pharmacology
  • alpha-Synuclein / metabolism

Substances

  • Amyloid beta-Peptides
  • Cell Cycle Proteins
  • Indoles
  • Phosphoproteins
  • Proteome
  • Proto-Oncogene Proteins
  • Spiro Compounds
  • alpha-Synuclein
  • corynoxine
  • corynoxine B
  • Protein-Serine-Threonine Kinases
  • Ribosomal Protein S6 Kinases, 70-kDa
  • polo-like kinase 1
  • ribosomal protein S6 kinase, 70kD, polypeptide 1
  • MAP Kinase Kinase 2

Grant support

This work was supported by grants from the Special Project on Precision Medicine under the National Key R&D Program (SQ2017YFSF090210 to Y.XUE), the National Basic Research Program (973 project) (2013CB933900 to Y.XUE), and Natural Science Foundation of China (31671360 to Y. XUE). It was also supported by grants from Shenzhen Science, Technology & Innovation Foundation (2014/03/1857 to M.LI), the General Research Fund of Hong Kong Government (RGC/HKBU-121009/14 to M.LI), the Health and Medical Research Fund from Food and Health Bureau of Hong Kong Government (HMRF/12132091 to M.LI) and the Interdisciplinary Research Matching Scheme (IRMS) of Hong Kong Baptist University (RC-IRMS/15–16/04 to M.LI).