Stem Cell Reviews and Reports

, Volume 10, Issue 4, pp 561–572 | Cite as

New Proteomic Insights on the Role of NPR-A in Regulating Self-Renewal of Embryonic Stem Cells

  • Sameh Magdeldin
  • Tadashi Yamamoto
  • Ikuo Tooyama
  • Essam M. Abdelalim
Article

Abstract

Embryonic stem cells (ESCs) have the ability to self-renew indefinitely and they can give unlimited source of cells and tissues for cellular therapies. Recently, the natriuretic peptide receptor A (NPR-A) has been recognized as an important regulator for the self-renewal of ESCs. To gain insights into possible novel mechanisms involved in NPR-A pathway that presumably regulates self-renewal and survival of ESCs, we utilized a comprehensive label-free proteomics technology in our study. Targeting of NPR-A gene with small interfering RNA (siRNA) resulted in the inhibition of ESCs self-renewal. Coherently, quantitative label-free shotgun proteomic analysis identified differentially expressed proteins involved in several biological processes, including cell cycle regulation, cell proliferation, cell fate specification, and apoptosis. Interestingly, in addition to Oct4 Nanog, and Sox2, other proteins involved in ESCs self-renewal were down-regulated after NPR-A knockdown, such as heterogeneous nuclear ribonucleoprotein A2/B1 (ROA2), non-POU domain-containing octamer-binding protein (Nono), nucleoplasmin (Npm1), histone H2A type 1-B/E (histone H2A.2), SW1/SNF complex (Brg1), polycomb protein Suz12 (Suz12), and cyclin-dependent kinase 4 (Cdk4). Furthermore, several protein candidates involved in early differentiation and cell death were up-regulated or down-regulated as a result of NPR-A knockdown, including importin subunit alpha-4 (Impα4), importin-5 (Ipo5), H3 histones, core histone macro-H2A.1 (H2A.y), apurine/apyrimidine endonuclease 1 (Apex1), 78-kDa glucose-regulated protein (Grp78), and programmed cell death 5 (Pdcd5). Overall, these findings depict a comprehensive view to our understanding of the pathways involved in the role of NPR-A in maintaining ESC functions.

Keywords

ESCs Proteome Knockdown Natriuretic peptide receptor A Pluripotency Differentiation Label free quantification 

Supplementary material

12015_2014_9517_MOESM1_ESM.docx (3.7 mb)
Figure S1(DOCX 3,826 kb)
12015_2014_9517_MOESM2_ESM.docx (28 kb)
Figure S2(DOCX 27 kb)
12015_2014_9517_MOESM3_ESM.docx (348 kb)
Figure S3(DOCX 348 kb)
12015_2014_9517_MOESM4_ESM.docx (54 kb)
Figure S4(DOCX 54 kb)
12015_2014_9517_MOESM5_ESM.xlsx (146 kb)
Supplemental Table 1(XLSX 145 kb)
12015_2014_9517_MOESM6_ESM.xlsx (33 kb)
Supplemental Table 2(XLSX 33 kb)

References

  1. 1.
    Chen, L., & Daley, G. Q. (2008). Molecular basis of pluripotency. Human Molecular Genetics, 17(R1), R23–R27.PubMedCrossRefGoogle Scholar
  2. 2.
    Avilion, A. A., Nicolis, S. K., Pevny, L. H., Perez, L., Vivian, N., & Lovell-Badge, R. (2003). Multipotent cell lineages in early mouse development depend on SOX2 function. Genes and Development, 17(1), 126–140.PubMedCentralPubMedCrossRefGoogle Scholar
  3. 3.
    Boyer, L. A., Lee, T. I., Cole, M. F., Johnstone, S. E., Levine, S. S., Zucker, J. P., et al. (2005). Core transcriptional regulatory circuitry in human embryonic stem cells. Cell, 122(6), 947–956.PubMedCentralPubMedCrossRefGoogle Scholar
  4. 4.
    Loh, Y. H., Wu, Q., Chew, J. L., Vega, V. B., Zhang, W., Chen, X., et al. (2006). The Oct4 and Nanog transcription network regulates pluripotency in mouse embryonic stem cells. Nature Genetics, 38(4), 431–440.PubMedCrossRefGoogle Scholar
  5. 5.
    Abdelalim, E. M. (2013). Molecular mechanisms controlling the cell cycle in embryonic stem cells. Stem Cell Reviews, 9(6), 764–773.PubMedCrossRefGoogle Scholar
  6. 6.
    Niwa, H. (2007). How is pluripotency determined and maintained? Development, 134(4), 635–646.PubMedCrossRefGoogle Scholar
  7. 7.
    Pandey, K. N. (2005). Biology of natriuretic peptides and their receptors. Peptides, 26(6), 901–932.PubMedCrossRefGoogle Scholar
  8. 8.
    Abdelalim, E. M., & Tooyama, I. (2011). NPR-A regulates self-renewal and pluripotency of embryonic stem cells. Cell Death Diseases, 2, e127.CrossRefGoogle Scholar
  9. 9.
    Abdelalim, E. M., & Tooyama, I. (2009). BNP signaling is crucial for embryonic stem cell proliferation. PLoS ONE, 4(4), e5341.PubMedCentralPubMedCrossRefGoogle Scholar
  10. 10.
    Morishita, R., Gibbons, G. H., Pratt, R. E., Tomita, N., Kaneda, Y., Ogihara, T., et al. (1994). Autocrine and paracrine effects of atrial natriuretic peptide gene transfer on vascular smooth muscle and endothelial cellular growth. Journal of Clinical Investigation, 94(2), 824–829.PubMedCentralPubMedCrossRefGoogle Scholar
  11. 11.
    Levin, E. R., Gardner, D. G., & Samson, W. K. (1998). Natriuretic peptides. New England Journal of Medicine, 339(5), 321–328.PubMedCrossRefGoogle Scholar
  12. 12.
    Silberbach, M., & Roberts, C. T., Jr. (2001). Natriuretic peptide signalling: molecular and cellular pathways to growth regulation. Cellular Signalling, 13(4), 221–231.PubMedCrossRefGoogle Scholar
  13. 13.
    Scott, N. J., Ellmers, L. J., Lainchbury, J. G., Maeda, N., Smithies, O., Richards, A. M., et al. (2009). Influence of natriuretic peptide receptor-1 on survival and cardiac hypertrophy during development. Biochimica et Biophysica Acta, 1792(12), 1175–1184.PubMedCentralPubMedCrossRefGoogle Scholar
  14. 14.
    Abdelalim, E. M., & Tooyama, I. (2012). Regulation of self-renewal and pluripotency of embryonic stem cells: role of natriuretic peptide receptor A. In M. A. Hayat (Ed.), Stem cells and cancer stem cells; therapeutic applications in disease and injury (Vol. 8, pp. 123–131). Netherlands: Springer.Google Scholar
  15. 15.
    Graumann, J., Hubner, N. C., Kim, J. B., Ko, K., Moser, M., Kumar, C., et al. (2008). Stable isotope labeling by amino acids in cell culture (SILAC) and proteome quantitation of mouse embryonic stem cells to a depth of 5,111 proteins. Molecular and Cellular Proteomics, 7(4), 672–683.PubMedCrossRefGoogle Scholar
  16. 16.
    O’Brien, R. N., Shen, Z., Tachikawa, K., Lee, P. A., & Briggs, S. P. (2010). Quantitative proteome analysis of pluripotent cells by iTRAQ mass tagging reveals post-transcriptional regulation of proteins required for ES cell self-renewal. Molecular and Cellular Proteomics, 9(10), 2238–2251.PubMedCentralPubMedCrossRefGoogle Scholar
  17. 17.
    Collier, T. S., Sarkar, P., Rao, B., & Muddiman, D. C. (2010). Quantitative top-down proteomics of SILAC labeled human embryonic stem cells. Journal of the American Society for Mass Spectrometry, 21(6), 879–889.PubMedCrossRefGoogle Scholar
  18. 18.
    Novak, A., Amit, M., Ziv, T., Segev, H., Fishman, B., Admon, A., et al. (2012). Proteomics profiling of human embryonic stem cells in the early differentiation stage. Stem Cell Reviews, 8(1), 137–149.PubMedCrossRefGoogle Scholar
  19. 19.
    Magdeldin, S., K. Yamamoto, Y. Yoshida, B. Xu, Y. Zhang, H. Fujinaka, et al. (2014). Deep proteome mapping of mouse kidney based on OFFGel prefractionation reveals remarkable protein post-translational modifications. J Proteome Res, Google Scholar
  20. 20.
    Rappsilber, J., Mann, M., & Ishihama, Y. (2007). Protocol for micro-purification, enrichment, pre-fractionation and storage of peptides for proteomics using StageTips. Nature Protocols, 2(8), 1896–1906.PubMedCrossRefGoogle Scholar
  21. 21.
    Cociorva, D., L.T. D, and J.R. Yates. (2007). Validation of tandem mass spectrometry database search results using DTASelect. Curr Protoc Bioinformatics, Chapter 13, Unit 13 4.Google Scholar
  22. 22.
    Park, S. K., Venable, J. D., Xu, T., & Yates, J. R., 3rd. (2008). A quantitative analysis software tool for mass spectrometry-based proteomics. Nature Methods, 5(4), 319–322.PubMedCentralPubMedGoogle Scholar
  23. 23.
    Magdeldin, S., Yoshida, Y., Li, H., Maeda, Y., Yokoyama, M., Enany, S., et al. (2012). Murine colon proteome and characterization of the protein pathways. BioData Mining, 5(1), 11.PubMedCentralPubMedCrossRefGoogle Scholar
  24. 24.
    Abdelalim, E. M., & Tooyama, I. (2012). NPR-C protects embryonic stem cells from apoptosis by regulating p53 levels. Stem Cells and Development, 21(8), 1264–1271.PubMedCrossRefGoogle Scholar
  25. 25.
    Carvalho, P. C., Hewel, J., Barbosa, V. C., & Yates, J. R., 3rd. (2008). Identifying differences in protein expression levels by spectral counting and feature selection. Genetics and Molecular Research, 7(2), 342–356.PubMedCentralPubMedCrossRefGoogle Scholar
  26. 26.
    Jirmanova, L., Afanassieff, M., Gobert-Gosse, S., Markossian, S., & Savatier, P. (2002). Differential contributions of ERK and PI3-kinase to the regulation of cyclin D1 expression and to the control of the G1/S transition in mouse embryonic stem cells. Oncogene, 21(36), 5515–5528.PubMedCrossRefGoogle Scholar
  27. 27.
    Assou, S., Le Carrour, T., Tondeur, S., Strom, S., Gabelle, A., Marty, S., et al. (2007). A meta-analysis of human embryonic stem cells transcriptome integrated into a web-based expression atlas. Stem Cells, 25(4), 961–973.PubMedCentralPubMedCrossRefGoogle Scholar
  28. 28.
    Van Hoof, D., Munoz, J., Braam, S. R., Pinkse, M. W., Linding, R., Heck, A. J., et al. (2009). Phosphorylation dynamics during early differentiation of human embryonic stem cells. Cell Stem Cell, 5(2), 214–226.PubMedCrossRefGoogle Scholar
  29. 29.
    Choi, H.S., H.M. Lee, Y.J. Jang, C.H. Kim, and C.J. Ryu. (2013). Heterogeneous Nuclear Ribonucleoprotein A2/B1 Regulates the Selfrenewal and Pluripotency of Human Embryonic Stem Cells via the Control of the G1/S Transition. Stem Cells,Google Scholar
  30. 30.
    Park, Y., Lee, J. M., Hwang, M. Y., Son, G. H., & Geum, D. (2013). NonO binds to the CpG island of oct4 promoter and functions as a transcriptional activator of oct4 gene expression. Molecules and Cells, 35(1), 61–69.PubMedCentralPubMedCrossRefGoogle Scholar
  31. 31.
    Niwa, H., Miyazaki, J., & Smith, A. G. (2000). Quantitative expression of Oct-3/4 defines differentiation, dedifferentiation or self-renewal of ES cells. Nature Genetics, 24(4), 372–376.PubMedCrossRefGoogle Scholar
  32. 32.
    Xie, X., Shi, Z., & Gu, W. (2012). Late-stage Freiberg’s disease treated with dorsal wedge osteotomy and joint distraction arthroplasty: technique tip. Foot and Ankle International, 33(11), 1015–1017.PubMedCrossRefGoogle Scholar
  33. 33.
    Elliott, S. T., Crider, D. G., Garnham, C. P., Boheler, K. R., & Van Eyk, J. E. (2004). Two-dimensional gel electrophoresis database of murine R1 embryonic stem cells. Proteomics, 4(12), 3813–3832.PubMedCrossRefGoogle Scholar
  34. 34.
    Richards, M., Tan, S. P., Tan, J. H., Chan, W. K., & Bongso, A. (2004). The transcriptome profile of human embryonic stem cells as defined by SAGE. Stem Cells, 22(1), 51–64.PubMedCrossRefGoogle Scholar
  35. 35.
    Wang, B. B., Lu, R., Wang, W. C., & Jin, Y. (2006). Inducible and reversible suppression of Npm1 gene expression using stably integrated small interfering RNA vector in mouse embryonic stem cells. Biochemical and Biophysical Research Communications, 347(4), 1129–1137.PubMedCrossRefGoogle Scholar
  36. 36.
    Johansson, H., & Simonsson, S. (2010). Core transcription factors, Oct4, Sox2 and Nanog, individually form complexes with nucleophosmin (Npm1) to control embryonic stem (ES) cell fate determination. Aging (Albany NY), 2(11), 815–822.Google Scholar
  37. 37.
    Xu, B., & Huang, Y. (2009). Histone H2a mRNA interacts with Lin28 and contains a Lin28-dependent posttranscriptional regulatory element. Nucleic Acids Research, 37(13), 4256–4263.PubMedCentralPubMedCrossRefGoogle Scholar
  38. 38.
    Xu, B., Zhang, K., & Huang, Y. (2009). Lin28 modulates cell growth and associates with a subset of cell cycle regulator mRNAs in mouse embryonic stem cells. RNA, 15(3), 357–361.PubMedCentralPubMedCrossRefGoogle Scholar
  39. 39.
    Peric-Hupkes, D., Meuleman, W., Pagie, L., Bruggeman, S. W., Solovei, I., Brugman, W., et al. (2010). Molecular maps of the reorganization of genome-nuclear lamina interactions during differentiation. Molecular Cell, 38(4), 603–613.PubMedCrossRefGoogle Scholar
  40. 40.
    Chambers, I., Colby, D., Robertson, M., Nichols, J., Lee, S., Tweedie, S., et al. (2003). Functional expression cloning of Nanog, a pluripotency sustaining factor in embryonic stem cells. Cell, 113(5), 643–655.PubMedCrossRefGoogle Scholar
  41. 41.
    Yan, Z., Wang, Z., Sharova, L., Sharov, A. A., Ling, C., Piao, Y., et al. (2008). BAF250B-associated SWI/SNF chromatin-remodeling complex is required to maintain undifferentiated mouse embryonic stem cells. Stem Cells, 26(5), 1155–1165.PubMedCentralPubMedCrossRefGoogle Scholar
  42. 42.
    Chen, X., Xu, H., Yuan, P., Fang, F., Huss, M., Vega, V. B., et al. (2008). Integration of external signaling pathways with the core transcriptional network in embryonic stem cells. Cell, 133(6), 1106–1117.PubMedCrossRefGoogle Scholar
  43. 43.
    Kim, J., Chu, J., Shen, X., Wang, J., & Orkin, S. H. (2008). An extended transcriptional network for pluripotency of embryonic stem cells. Cell, 132(6), 1049–1061.PubMedCrossRefGoogle Scholar
  44. 44.
    Young, J. C., Major, A. T., Miyamoto, Y., Loveland, K. L., & Jans, D. A. (2011). Distinct effects of importin alpha2 and alpha4 on Oct3/4 localization and expression in mouse embryonic stem cells. FASEB Journal, 25(11), 3958–3965.PubMedCrossRefGoogle Scholar
  45. 45.
    Golob, J. L., Paige, S. L., Muskheli, V., Pabon, L., & Murry, C. E. (2008). Chromatin remodeling during mouse and human embryonic stem cell differentiation. Developmental Dynamics, 237(5), 1389–1398.PubMedCentralPubMedCrossRefGoogle Scholar
  46. 46.
    Lee, E. R., McCool, K. W., Murdoch, F. E., & Fritsch, M. K. (2006). Dynamic changes in histone H3 phosphoacetylation during early embryonic stem cell differentiation are directly mediated by mitogen-and stress-activated protein kinase 1 via activation of MAPK pathways. Journal of Biological Chemistry, 281(30), 21162–21172.PubMedCrossRefGoogle Scholar
  47. 47.
    Pasque, V., Radzisheuskaya, A., Gillich, A., Halley-Stott, R. P., Panamarova, M., Zernicka-Goetz, M., et al. (2012). Histone variant macroH2A marks embryonic differentiation in vivo and acts as an epigenetic barrier to induced pluripotency. Journal of Cell Science, 125(Pt 24), 6094–6104.PubMedCentralPubMedCrossRefGoogle Scholar
  48. 48.
    Unnikrishnan, A., Raffoul, J. J., Patel, H. V., Prychitko, T. M., Anyangwe, N., Meira, L. B., et al. (2009). Oxidative stress alters base excision repair pathway and increases apoptotic response in apurinic/apyrimidinic endonuclease 1/redox factor-1 haploinsufficient mice. Free Radical Biology and Medicine, 46(11), 1488–1499.PubMedCentralPubMedCrossRefGoogle Scholar
  49. 49.
    Kruta, M., Balek, L., Hejnova, R., Dobsakova, Z., Eiselleova, L., Matulka, K., et al. (2013). Decrease in abundance of apurinic/apyrimidinic endonuclease causes failure of base excision repair in culture-adapted human embryonic stem cells. Stem Cells, 31(4), 693–702.PubMedCrossRefGoogle Scholar
  50. 50.
    Chen, Y., Sun, R., Han, W., Zhang, Y., Song, Q., Di, C., et al. (2001). Nuclear translocation of PDCD5 (TFAR19): an early signal for apoptosis? FEBS Letters, 509(2), 191–196.PubMedCrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media New York 2014

Authors and Affiliations

  • Sameh Magdeldin
    • 1
    • 2
  • Tadashi Yamamoto
    • 1
  • Ikuo Tooyama
    • 3
  • Essam M. Abdelalim
    • 3
    • 4
    • 5
  1. 1.Department of Structural Pathology Institute of Nephrology, Graduate School of Medical and Dental SciencesNiigata UniversityTokyoJapan
  2. 2.Department of Physiology, Faculty of Veterinary MedicineSuez Canal UniversityIsmailiaEgypt
  3. 3.Molecular Neuroscience Research CenterShiga University of Medical ScienceOtsuJapan
  4. 4.Qatar Biomedical Research InstituteQatar Foundation, Education CityDohaQatar
  5. 5.Department of Cytology and Histology, Faculty of Veterinary MedicineSuez Canal UniversityIsmailiaEgypt

Personalised recommendations