Phosphoproteome and drug-response effects mediated by the three protein phosphatase 2A inhibitor proteins CIP2A, SET, and PME-1

J Biol Chem. 2020 Mar 27;295(13):4194-4211. doi: 10.1074/jbc.RA119.011265. Epub 2020 Feb 18.


Protein phosphatase 2A (PP2A) critically regulates cell signaling and is a human tumor suppressor. PP2A complexes are modulated by proteins such as cancerous inhibitor of protein phosphatase 2A (CIP2A), protein phosphatase methylesterase 1 (PME-1), and SET nuclear proto-oncogene (SET) that often are deregulated in cancers. However, how they impact cellular phosphorylation and how redundant they are in cellular regulation is poorly understood. Here, we conducted a systematic phosphoproteomics screen for phosphotargets modulated by siRNA-mediated depletion of CIP2A, PME-1, and SET (to reactivate PP2A) or the scaffolding A-subunit of PP2A (PPP2R1A) (to inhibit PP2A) in HeLa cells. We identified PP2A-modulated targets in diverse cellular pathways, including kinase signaling, cytoskeleton, RNA splicing, DNA repair, and nuclear lamina. The results indicate nonredundancy among CIP2A, PME-1, and SET in phosphotarget regulation. Notably, PP2A inhibition or reactivation affected largely distinct phosphopeptides, introducing a concept of nonoverlapping phosphatase inhibition- and activation-responsive sites (PIRS and PARS, respectively). This phenomenon is explained by the PPP2R1A inhibition impacting primarily dephosphorylated threonines, whereas PP2A reactivation results in dephosphorylation of clustered and acidophilic sites. Using comprehensive drug-sensitivity screening in PP2A-modulated cells to evaluate the functional impact of PP2A across diverse cellular pathways targeted by these drugs, we found that consistent with global phosphoproteome effects, PP2A modulations broadly affect responses to more than 200 drugs inhibiting a broad spectrum of cancer-relevant targets. These findings advance our understanding of the phosphoproteins, pharmacological responses, and cellular processes regulated by PP2A modulation and may enable the development of combination therapies.

Keywords: AURK inhibitor; LMNA; cancer; drug screening; nucleophosmin; phosphatase activation-responsive site (PARS); phosphatase inhibition-responsive site (PIRS); phosphoproteomics; protein phosphatase 2 (PP2A); systems biology.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Apoptosis / drug effects
  • Autoantigens / genetics*
  • Carboxylic Ester Hydrolases / genetics*
  • Cell Proliferation / drug effects
  • DNA-Binding Proteins / genetics*
  • Enzyme Inhibitors / chemistry
  • Gene Expression Regulation, Neoplastic / drug effects
  • HeLa Cells
  • Histone Chaperones / genetics*
  • Humans
  • Intracellular Signaling Peptides and Proteins / genetics*
  • Membrane Proteins / genetics*
  • Neoplasms / genetics
  • Neoplasms / pathology
  • Neoplasms / therapy
  • Nuclear Lamina / drug effects
  • Nuclear Lamina / genetics
  • Phosphoproteins / antagonists & inhibitors
  • Phosphoproteins / genetics
  • Phosphorylation / drug effects
  • Protein Phosphatase 2 / antagonists & inhibitors*
  • Protein Phosphatase 2 / genetics
  • Proteome / drug effects
  • RNA, Small Interfering / genetics
  • Systems Biology


  • Autoantigens
  • CIP2A protein, human
  • DNA-Binding Proteins
  • Enzyme Inhibitors
  • Histone Chaperones
  • Intracellular Signaling Peptides and Proteins
  • Membrane Proteins
  • PPP2R1A protein, human
  • Phosphoproteins
  • Proteome
  • RNA, Small Interfering
  • SET protein, human
  • Carboxylic Ester Hydrolases
  • protein phosphatase methylesterase-1
  • Protein Phosphatase 2