Structural mechanism for inhibition of PP2A-B56α and oncogenicity by CIP2A.

Humans; Amino Acids; Carcinogenesis/genetics/metabolism; Catalytic Domain; Phosphorylation; Protein Phosphatase 2/genetics/ultrastructure; Protein Processing, Post-Translational; Triple Negative Breast Neoplasms/metabolism

Abstract :

[en] The protein phosphatase 2A (PP2A) heterotrimer PP2A-B56α is a human tumour suppressor. However, the molecular mechanisms inhibiting PP2A-B56α in cancer are poorly understood. Here, we report molecular level details and structural mechanisms of PP2A-B56α inhibition by an oncoprotein CIP2A. Upon direct binding to PP2A-B56α trimer, CIP2A displaces the PP2A-A subunit and thereby hijacks both the B56α, and the catalytic PP2Ac subunit to form a CIP2A-B56α-PP2Ac pseudotrimer. Further, CIP2A competes with B56α substrate binding by blocking the LxxIxE-motif substrate binding pocket on B56α. Relevant to oncogenic activity of CIP2A across human cancers, the N-terminal head domain-mediated interaction with B56α stabilizes CIP2A protein. Functionally, CRISPR/Cas9-mediated single amino acid mutagenesis of the head domain blunted MYC expression and MEK phosphorylation, and abrogated triple-negative breast cancer in vivo tumour growth. Collectively, we discover a unique multi-step hijack and mute protein complex regulation mechanism resulting in tumour suppressor PP2A-B56α inhibition. Further, the results unfold a structural determinant for the oncogenic activity of CIP2A, potentially facilitating therapeutic modulation of CIP2A in cancer and other diseases.

Disciplines :

Biochemistry, biophysics & molecular biology

Author, co-author :

PAVIC, Karolina ; University of Luxembourg > Faculty of Science, Technology and Medicine (FSTM) > Department of Life Sciences and Medicine (DLSM)

Gupta, Nikhil

Omella, Judit Domènech

Derua, Rita

Aakula, Anna

Huhtaniemi, Riikka

Määttä, Juha A.

Höfflin, Nico

Okkeri, Juha

Wang, Zhizhi

More authors (12 more)

External co-authors :

yes

Language :

English

Title :

Structural mechanism for inhibition of PP2A-B56α and oncogenicity by CIP2A.

Publication date :

2023

Journal title :

Nature Communications

eISSN :

2041-1723

Publisher :

Nature Publishing Group, London, United Kingdom

Volume :

Issue :

Pages :

1143

Peer reviewed :

Peer Reviewed verified by ORBi

Commentary :

Available on ORBilu :

since 06 July 2023

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Bibliography

Fowle, H., Zhao, Z. & Grana, X. PP2A holoenzymes, substrate specificity driving cellular functions and deregulation in cancer. Adv. Cancer Res. 144, 55–93 (2019).
Reynhout, S. & Janssens, V. Physiologic functions of PP2A: lessons from genetically modified mice. Biochim. Biophys. Acta Mol. Cell Res. 1866, 31–50 (2019).
Virshup, D. M. & Shenolikar, S. From promiscuity to precision: protein phosphatases get a makeover. Mol. Cell 33, 537–545 (2009).
Lambrecht, C. et al. Loss of protein phosphatase 2A regulatory subunit B56delta promotes spontaneous tumorigenesis in vivo. Oncogene 37, 544–552 (2018).
Mao, Z., Liu, C., Lin, X., Sun, B. & Su, C. PPP2R5A: a multirole protein phosphatase subunit in regulating cancer development. Cancer Lett. 414, 222–229 (2018).
Sablina, A. A., Hector, M., Colpaert, N. & Hahn, W. C. Identification of PP2A complexes and pathways involved in cell transformation. Cancer Res. 70, 10474–10484 (2010).
Chen, W. et al. Identification of specific PP2A complexes involved in human cell transformation. Cancer Cell 5, 127–136 (2004).
Liu, Z. et al. Mutations in the RNA splicing factor SF3B1 promote tumorigenesis through MYC stabilization. Cancer Discov. 10, 806–821 (2020).
Chuang, E. et al. The CD28 and CTLA-4 receptors associate with the serine/threonine phosphatase PP2A. Immunity 13, 313–322 (2000).
Hertz, E. P. et al. A conserved motif provides binding specificity to the PP2A-B56 phosphatase. Mol. Cell 63, 686–695 (2016).
Kruse, T. et al. Mechanisms of site-specific dephosphorylation and kinase opposition imposed by PP2A regulatory subunits. EMBO J. 39, e103695 (2020).
Arnold, H. K. & Sears, R. C. Protein phosphatase 2A regulatory subunit B56alpha associates with c-myc and negatively regulates c-myc accumulation. Mol. Cell Biol. 26, 2832–2844 (2006).
Arnold, H. K. & Sears, R. C. A tumor suppressor role for PP2A-B56alpha through negative regulation of c-Myc and other key oncoproteins. Cancer Metastasis Rev. 27, 147–158 (2008).
Wang, X., Bajaj, R., Bollen, M., Peti, W. & Page, R. Expanding the PP2A interactome by defining a B56-specific SLiM. Structure 24, 2174–2181 (2016).
Wang, J. et al. Crystal structure of a PP2A B56-BubR1 complex and its implications for PP2A substrate recruitment and localization. Protein Cell 7, 516–526 (2016).
Wu, C. G. et al. PP2A-B’ holoenzyme substrate recognition, regulation and role in cytokinesis. Cell Discov. 3, 17027 (2017).
Kauko, O. & Westermarck, J. Non-genomic mechanisms of protein phosphatase 2A (PP2A) regulation in cancer. Int. J. Biochem. Cell Biol. 96, 157–164 (2018).
Laine, A. et al. Senescence sensitivity of breast cancer cells is defined by positive feedback loop between CIP2A and E2F1. Cancer Discov. 3, 182–197 (2013).
Khanna A. & Pimanda J. E. Clinical significance of cancerous inhibitor of protein phosphatase 2A (CIP2A) in human cancers. Int. J. Cancer 138, 525–32 (2015).
Lucas, C. M. et al. Cancerous inhibitor of PP2A (CIP2A) at diagnosis of chronic myeloid leukemia is a critical determinant of disease progression. Blood 117, 6660–6668 (2011).
Junttila, M. R. et al. CIP2A inhibits PP2A in human malignancies. Cell 130, 51–62 (2007).
Janghorban, M. et al. Targeting c-MYC by antagonizing PP2A inhibitors in breast cancer. Proc. Natl Acad. Sci. USA 111, 9157–9162 (2014).
Elgendy, M. et al. Combination of hypoglycemia and metformin impairs tumor metabolic plasticity and growth by modulating the PP2A-GSK3beta-MCL-1 axis. Cancer Cell 35, 798–815 e795 (2019).
Laine, A. et al. CIP2A interacts with TopBP1 and drives basal-like breast cancer tumorigenesis. Cancer Res. 81, 4319–4331 (2021).
Myant, K. et al. Serine 62-phosphorylated MYC associates with nuclear lamins and its regulation by CIP2A is essential for regenerative proliferation. Cell Rep. 12, 1019–1031 (2015).
Adam, S. et al. The CIP2A-TOPBP1 axis safeguards chromosome stability and is a synthetic lethal target for BRCA-mutated cancer. Nat. Cancer 2, 1357–1371 (2021).
Kauko, O. et al. Phosphoproteome and drug-response effects mediated by the three protein phosphatase 2A inhibitor proteins CIP2A, SET, and PME-1. J. Biol. Chem. 295, 4194–4211 (2020).
Kauko O. et al. PP2A inhibition is a druggable MEK inhibitor resistance mechanism in KRAS-mutant lung cancer cells. Sci. Transl. Med. 10, eaaq1093 (2018).
Lucas, C. M. et al. Second generation tyrosine kinase inhibitors prevent disease progression in high-risk (high CIP2A) chronic myeloid leukaemia patients. Leukemia 29, 1514–1523 (2015).
Choi Y. A. et al. Increase in CIP2A expression is associated with doxorubicin resistance. FEBS Lett. 585, 755–60 (2011).
Wang, J. et al. Oncoprotein CIP2A is stabilized via interaction with tumor suppressor PP2A/B56. EMBO Rep. 18, 437–450 (2017).
Shentu, Y. P. et al. CIP2A causes tau/APP phosphorylation, synaptopathy, and memory deficits in Alzheimer’s disease. Cell Rep. 24, 713–723 (2018).
Soofiyani, S. R., Hejazi, M. S. & Baradaran, B. The role of CIP2A in cancer: a review and update. Biomed. Pharmacother. 96, 626–633 (2017).
Come, C. et al. CIP2A is associated with human breast cancer aggressivity. Clin. Cancer Res. 15, 5092–5100 (2009).
Liu, Z. et al. Cancerous inhibitor of PP2A is targeted by natural compound celastrol for degradation in non-small-cell lung cancer. Carcinogenesis 35, 905–914 (2014).
Nguyen, D. N. et al. Polymer-stabilized Cas9 nanoparticles and modified repair templates increase genome editing efficiency. Nat. Biotechnol. 38, 44–49 (2020).
McFall, A. et al. Oncogenic Ras blocks anoikis by activation of a novel effector pathway independent of phosphatidylinositol 3-kinase. Mol. Cell Biol. 21, 5488–5499 (2001).
Eriksson, J. E. et al. Specific in vivo phosphorylation sites determine the assembly dynamics of vimentin intermediate filaments. J. Cell Sci. 117, 919–932 (2004).
Dmello, C. et al. Vimentin-mediated regulation of cell motility through modulation of beta4 integrin protein levels in oral tumor derived cells. Int. J. Biochem. Cell Biol. 70, 161–172 (2016).
Xu, Y. et al. Structure of the protein phosphatase 2A holoenzyme. Cell 127, 1239–1251 (2006).
Cho, U. S. & Xu, W. Crystal structure of a protein phosphatase 2A heterotrimeric holoenzyme. Nature 445, 53–57 (2007).
Wang X. et al. A dynamic charge-charge interaction modulates PP2A:B56 substrate recruitment. Elife 9, e55966 (2020).
Cordeiro M. H., Smith R. J. & Saurin A. T. A fine balancing act: a delicate kinase-phosphatase equilibrium that protects against chromosomal instability and cancer. Int. J. Biochem. Cell Biol. 96, 148–156 (2017).
Kruse, T. et al. Direct binding between BubR1 and B56-PP2A phosphatase complexes regulate mitotic progression. J. Cell Sci. 126, 1086–1092 (2013).
Bludau, I. & Aebersold, R. Proteomic and interactomic insights into the molecular basis of cell functional diversity. Nat. Rev. Mol. Cell Biol. 21, 327–340 (2020).
Kruse, T. et al. The Ebola virus nucleoprotein recruits the host PP2A-B56 phosphatase to activate transcriptional support activity of VP30. Mol. Cell 69, 136–145 e136 (2018).
Du, Y. et al. PINA 3.0: mining cancer interactome. Nucleic Acids Res. 49, D1351–D1357 (2021).
Smith, R. J. et al. PP1 and PP2A use opposite phospho-dependencies to control distinct processes at the kinetochore. Cell Rep. 28, 2206–2219 e2208 (2019).
Hoermann, B. & Kohn, M. Evolutionary crossroads of cell signaling: PP1 and PP2A substrate sites in intrinsically disordered regions. Biochem. Soc. Trans. 49, 1065–1074 (2021).
Hatting, M. et al. Adipose tissue CLK2 promotes energy expenditure during high-fat diet intermittent fasting. Cell Metab. 25, 428–437 (2017).
Bidinosti, M. et al. CLK2 inhibition ameliorates autistic features associated with SHANK3 deficiency. Science 351, 1199–1203 (2016).
Wu, J. Q. et al. Control of Emi2 activity and stability through Mos-mediated recruitment of PP2A. Proc. Natl Acad. Sci. USA 104, 16564–16569 (2007).
Isoda, M. et al. Dynamic regulation of Emi2 by Emi2-bound Cdk1/Plk1/CK1 and PP2A-B56 in meiotic arrest of Xenopus eggs. Dev. Cell 21, 506–519 (2011).
Kurppa, K. J. & Westermarck, J. Good Guy in Bad Company: How STRNs Convert PP2A into an Oncoprotein. Cancer Cell 38, 20–22 (2020).
Fowle, H. et al. PP2A/B55alpha substrate recruitment as defined by the retinoblastoma-related protein p107. Elife 10, e63181 (2021).
Wu, C. G. et al. Methylation-regulated decommissioning of multimeric PP2A complexes. Nat. Commun. 8, 2272 (2017).
Makela, E. et al. Discovery of a Novel CIP2A Variant (NOCIVA) with Clinical Relevance in Predicting TKI Resistance in Myeloid Leukemias. Clin. Cancer Res. 27, 2848–2860 (2021).
Shentu, Y. P. et al. CIP2A-promoted astrogliosis induces AD-like synaptic degeneration and cognitive deficits. Neurobiol. Aging 75, 198–208 (2019).
Leitner, A. et al. Chemical cross-linking/mass spectrometry targeting acidic residues in proteins and protein complexes. Proc. Natl Acad. Sci. USA 111, 9455–9460 (2014).
Leitner, A., Walzthoeni, T. & Aebersold, R. Lysine-specific chemical cross-linking of protein complexes and identification of cross-linking sites using LC-MS/MS and the xQuest/xProphet software pipeline. Nat. Protoc. 9, 120–137 (2014).
Law, A. M. K. et al. Andy’s Algorithms: new automated digital image analysis pipelines for FIJI. Sci. Rep. 7, 15717 (2017).
Perez-Riverol, Y. et al. The PRIDE database and related tools and resources in 2019: improving support for quantification data. Nucleic Acids Res. 47, D442–D450 (2019).
Horn, H. et al. KinomeXplorer: an integrated platform for kinome biology studies. Nat. Methods 11, 603–604 (2014).
Laajala, T. D. et al. Optimized design and analysis of preclinical intervention studies in vivo. Sci. Rep. 6, 30723 (2016).
Leonard, D. et al. Selective PP2A enhancement through biased heterotrimer stabilization. Cell 181, 688–701 e616 (2020).