Skip to main content
NCBI home page
Protein & Cell logoLink to Protein & Cell
. 2011 Sep 9;2(8):631–646. doi: 10.1007/s13238-011-1081-7

Quantitative proteomics analysis of parthenogenetically induced pluripotent stem cells

Zhe Hu 1, Lei Wang 1, Zhensheng Xie 2, Xinlei Zhang 3, Du Feng 1, Fang Wang 1, Bingfeng Zuo 1, Lingling Wang 1, Zhong Liu 1, Zhisheng Chen 1, Fuquan Yang 2,✉, Lin Liu 1,✉
PMCID: PMC4875327  PMID: 21904979

Abstract

Parthenogenetic embryonic stem (pES) cells isolated from parthenogenetic activation of oocytes and embryos, also called parthenogenetically induced pluripotent stem cells, exhibit pluripotency evidenced by both in vitro and in vivo differentiation potential. Differential proteomic analysis was performed using differential in-gel electrophoresis and isotope-coded affinity tag-based quantitative proteomics to investigate the molecular mechanisms underlying the developmental pluripotency of pES cells and to compare the protein expression of pES cells generated from either the in vivo-matured ovulated (IVO) oocytes or from the in vitro-matured (IVM) oocytes with that of fertilized embryonic stem (fES) cells derived from fertilized embryos. A total of 76 proteins were upregulated and 16 proteins were downregulated in the IVM pES cells, whereas 91 proteins were upregulated and 9 were downregulated in the IVO pES cells based on a minimal 1.5-fold change as the cutoff value. No distinct pathways were found in the differentially expressed proteins except for those involved in metabolism and physiological processes. Notably, no differences were found in the protein expression of imprinted genes between the pES and fES cells, suggesting that genomic imprinting can be corrected in the pES cells at least at the early passages. The germline competent IVM pES cells may be applicable for germ cell renewal in aging ovaries if oocytes are retrieved at a younger age.

Electronic Supplementary Material

Supplementary material is available for this article at 10.1007/s13238-011-1081-7 and is accessible for authorized users.

Keywords: parthenogenetic embryonic stem cell, proteome, fluorescent two-dimensional difference in-gel electrophoresis, isotope-coded affinity tag

Electronic supplementary material

13238_2011_1081_MOESM1_ESM.pdf (192.4KB, pdf)

Supplementary material, approximately 192 KB.

Footnotes

Electronic Supplementary Material

Supplementary material is available for this article at 10.1007/s13238-011-1081-7 and is accessible for authorized users.

Contributor Information

Fuquan Yang, Email: fqyang@ibp.ac.cn.

Lin Liu, Email: liulin@nankai.edu.cn.

References

  1. Aebersold R., Rist B., Gygi S.P. Quantitative proteome analysis: methods and applications. Ann N Y Acad Sci. 2000;919:33–47. doi: 10.1111/j.1749-6632.2000.tb06865.x. [DOI] [PubMed] [Google Scholar]
  2. Bartolomei M.S. Epigenetics: role of germ cell imprinting. Adv Exp Med Biol. 2003;518:239–245. doi: 10.1007/978-1-4419-9190-4_21. [DOI] [PubMed] [Google Scholar]
  3. Bradford M.M. A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding. Anal Biochem. 1976;72:248–254. doi: 10.1016/0003-2697(76)90527-3. [DOI] [PubMed] [Google Scholar]
  4. Brevini T.A., Gandolfi F. Parthenotes as a source of embryonic stem cells. Cell Prolif. 2008;41:20–30. doi: 10.1111/j.1365-2184.2008.00485.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Chen Z., Liu Z., Huang J., Amano T., Li C., Cao S., Wu C., Liu B., Zhou L., Carter M.G., et al. Birth of parthenote mice directly from parthenogenetic embryonic stem cells. Stem Cells. 2009;27:2136–2145. doi: 10.1002/stem.158. [DOI] [PubMed] [Google Scholar]
  6. Choi J., Koh E., Suzuki H., Maeda Y., Yoshida A., Namiki M. Alu sequence variants of the BPY2 gene in proven fertile and infertile men with Sertoli cell-only phenotype. Int J Urol. 2007;14:431–435. doi: 10.1111/j.1442-2042.2007.01741.x. [DOI] [PubMed] [Google Scholar]
  7. Cibelli J.B., Grant K.A., Chapman K.B., Cunniff K., Worst T., Green H.L., Walker S.J., Gutin P.H., Vilner L., Tabar V., et al. Parthenogenetic stem cells in nonhuman primates. Science. 2002;295:819. doi: 10.1126/science.1065637. [DOI] [PubMed] [Google Scholar]
  8. Cui X.S., Shen X.H., Lee C.K., Kang Y.K., Wakayama T., Kim N.H. Analysis of proteomic profiling of mouse embryonic stem cells derived from fertilized, parthenogenetic and androgenetic blastocysts. Stem Cell Discovery. 2011;1:1–15. doi: 10.4236/scd.2011.11001. [DOI] [Google Scholar]
  9. De Sousa P. A., Wilmut I. Human parthenogenetic embryo stem cells: appreciating what you have when you have it. Cell Stem Cell. 2007;1:243–244. doi: 10.1016/j.stem.2007.08.006. [DOI] [PubMed] [Google Scholar]
  10. Dighe V., Clepper L., Pedersen D., Byrne J., Ferguson B., Gokhale S., Penedo M.C., Wolf D., Mitalipov S. Heterozygous embryonic stem cell lines derived from nonhuman primate parthenotes. Stem Cells. 2008;26:756–766. doi: 10.1634/stemcells.2007-0869. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Donnay I., Knoops B. Peroxiredoxins in gametogenesis and embryo development. Subcell Biochem. 2007;44:345–355. doi: 10.1007/978-1-4020-6051-9_16. [DOI] [PubMed] [Google Scholar]
  12. Fang Z.F., Gai H., Huang Y.Z., Li S.G., Chen X.J., Shi J.J., Wu L., Liu A., Xu P., Sheng H.Z. Rabbit embryonic stem cell lines derived from fertilized, parthenogenetic or somatic cell nuclear transfer embryos. Exp Cell Res. 2006;312:3669–3682. doi: 10.1016/j.yexcr.2006.08.013. [DOI] [PubMed] [Google Scholar]
  13. Fortschegger K., Wagner B., Voglauer R., Katinger H., Sibilia M., Grillari J. Early embryonic lethality of mice lacking the essential protein SNEV. Mol Cell Biol. 2007;27:3123–3130. doi: 10.1128/MCB.01188-06. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Graumann J., Hubner N.C., Kim J.B., Ko K., Moser M., Kumar C., Cox J., Schöler H., Mann M. 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. Mol Cell Proteomics. 2008;7:672–683. doi: 10.1074/mcp.M700460-MCP200. [DOI] [PubMed] [Google Scholar]
  15. Gygi S.P., Rist B., Gerber S.A., Turecek F., Gelb M.H., Aebersold R. Quantitative analysis of complex protein mixtures using isotope-coded affinity tags. Nat Biotechnol. 1999;17:994–999. doi: 10.1038/13690. [DOI] [PubMed] [Google Scholar]
  16. Harris L.J., Abdollahi H., Zhang P., McIlhenny S., Tulenko T.N., DiMuzio P.J. Differentiation of adult stem cells into smooth muscle for vascular tissue engineering. J Surg Res. 2011;168:306–314. doi: 10.1016/j.jss.2009.08.001. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Haynes P.A., Yates J.R., 3rd Proteome profiling-pitfalls and progress. Yeast. 2000;17:81–87. doi: 10.1002/1097-0061(20000630)17:2<81::AID-YEA22>3.3.CO;2-Q. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. He L., Liu J., Collins I., Sanford S., O’Connell B., Benham C.J., Levens D. Loss of FBP function arrests cellular proliferation and extinguishes c-myc expression. EMBO J. 2000;19:1034–1044. doi: 10.1093/emboj/19.5.1034. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Horii T., Kimura M., Morita S., Nagao Y., Hatada I. Loss of genomic imprinting in mouse parthenogenetic embryonic stem cells. Stem Cells. 2008;26:79–88. doi: 10.1634/stemcells.2006-0635. [DOI] [PubMed] [Google Scholar]
  20. Huber P.A. Caldesmon. Int J Biochem Cell Biol. 1998;29:1047–1051. doi: 10.1016/S1357-2725(97)00004-6. [DOI] [PubMed] [Google Scholar]
  21. Jiang H., Sun B., Wang W., Zhang Z., Gao F., Shi G., Cui B., Kong X., He Z., Ding X., et al. Activation of paternally expressed imprinted genes in newly derived germline-competent mouse parthenogenetic embryonic stem cell lines. Cell Res. 2007;17:792–803. doi: 10.1038/cr.2007.70. [DOI] [PubMed] [Google Scholar]
  22. Kim K., Lerou P., Yabuuchi A., Lengerke C., Ng K., West J., Kirby A., Daly M.J., Daley G.Q. Histocompatible embryonic stem cells by parthenogenesis. Science. 2007;315:482–486. doi: 10.1126/science.1133542. [DOI] [PubMed] [Google Scholar]
  23. Levchenko A. Proteomics takes stem cell analyses to another level. Nat Biotechnol. 2005;23:828–830. doi: 10.1038/nbt0705-828. [DOI] [PubMed] [Google Scholar]
  24. Li C., Chen Z., Liu Z., Huang J., Zhang W., Zhou L., Keefe D.L., Liu L. Correlation of expression and methylation of imprinted genes with pluripotency of parthenogenetic embryonic stem cells. Hum Mol Genet. 2009;18:2177–2187. doi: 10.1093/hmg/ddp150. [DOI] [PubMed] [Google Scholar]
  25. Liu Z., Hu Z., Pan X., Li M., Togun T.A., Tuck D., Pelizzola M., Huang J., Ye X., Yin Y., et al. Germline competency of parthenogenetic embryonic stem cells from immature oocytes of adult mouse ovary. Hum Mol Genet. 2011;20:1339–1352. doi: 10.1093/hmg/ddr016. [DOI] [PMC free article] [PubMed] [Google Scholar]
  26. Lyakhovich A., Canals F., Nosov M., Surralles J. A DIGE-based approach to study interacting proteins. J Biochem Biophys Methods. 2007;70:693–695. doi: 10.1016/j.jbbm.2007.03.002. [DOI] [PubMed] [Google Scholar]
  27. Mai Q., Yu Y., Li T., Wang L., Chen M.J., Huang S.Z., Zhou C., Zhou Q. Derivation of human embryonic stem cell lines from parthenogenetic blastocysts. Cell Res. 2007;17:1008–1019. doi: 10.1038/cr.2007.102. [DOI] [PubMed] [Google Scholar]
  28. Mann J.R., Gadi I., Harbison M.L., Abbondanzo S.J., Stewart C.L. Androgenetic mouse embryonic stem cells are pluripotent and cause skeletal defects in chimeras: implications for genetic imprinting. Cell. 1990;62:251–260. doi: 10.1016/0092-8674(90)90363-J. [DOI] [PubMed] [Google Scholar]
  29. Marouga R., David S., Hawkins E. The development of the DIGE system: 2D fluorescence difference gel analysis technology. Anal Bioanal Chem. 2005;382:669–678. doi: 10.1007/s00216-005-3126-3. [DOI] [PubMed] [Google Scholar]
  30. Monk M. Genomic imprinting. Genes Dev. 1988;2:921–925. doi: 10.1101/gad.2.8.921. [DOI] [PubMed] [Google Scholar]
  31. Moseley M.A. Current trends in differential expression proteomics: isotopically coded tags. Trends Biotechnol. 2001;19:S10–S16. doi: 10.1016/S0167-7799(01)01793-0. [DOI] [PubMed] [Google Scholar]
  32. Nagano K., Taoka M., Yamauchi Y., Itagaki C., Shinkawa T., Nunomura K., Okamura N., Takahashi N., Izumi T., Isobe T. Large-scale identification of proteins expressed in mouse embryonic stem cells. Proteomics. 2005;5:1346–1361. doi: 10.1002/pmic.200400990. [DOI] [PubMed] [Google Scholar]
  33. Rabilloud T. Two-dimensional gel electrophoresis in proteomics: old, old fashioned, but it still climbs up the mountains. Proteomics. 2002;2:3–10. doi: 10.1002/1615-9861(200201)2:1<3::AID-PROT3>3.0.CO;2-R. [DOI] [PubMed] [Google Scholar]
  34. Sapienza C. Imprinted gene expression, transplantation medicine, and the “other” human embryonic stem cell. Proc Natl Acad Sci U S A. 2002;99:10243–10245. doi: 10.1073/pnas.172384299. [DOI] [PMC free article] [PubMed] [Google Scholar]
  35. Shao H., Wei Z., Wang L., Wen L., Duan B., Mang L., Bou S. Generation and characterization of mouse parthenogenetic embryonic stem cells containing genomes from non-growing and fully grown oocytes. Cell Biol Int. 2007;31:1336–1344. doi: 10.1016/j.cellbi.2007.05.008. [DOI] [PubMed] [Google Scholar]
  36. Skaletsky H., Kuroda-Kawaguchi T., Minx P.J., Cordum H.S., Hillier L., Brown L.G., Repping S., Pyntikova T., Ali J., Bieri T., et al. The male-specific region of the human Y chromosome is a mosaic of discrete sequence classes. Nature. 2003;423:825–837. doi: 10.1038/nature01722. [DOI] [PubMed] [Google Scholar]
  37. Sritanaudomchai H., Ma H., Clepper L., Gokhale S., Bogan R., Hennebold J., Wolf D., Mitalipov S. Discovery of a novel imprinted gene by transcriptional analysis of parthenogenetic embryonic stem cells. Hum Reprod. 2010;25:1927–1941. doi: 10.1093/humrep/deq144. [DOI] [PMC free article] [PubMed] [Google Scholar]
  38. Surani M.A. Imprinting and the initiation of gene silencing in the germ line. Cell. 1998;93:309–312. doi: 10.1016/S0092-8674(00)81156-3. [DOI] [PubMed] [Google Scholar]
  39. Vigé A., Gallou-Kabani C., Gross M.S., Fabre A., Junien C., Jais J.P. An oligonucleotide microarray for mouse imprinted genes profiling. Cytogenet Genome Res. 2006;113:253–261. doi: 10.1159/000090840. [DOI] [PubMed] [Google Scholar]
  40. Wang D., Gao L. Proteomic analysis of neural differentiation of mouse embryonic stem cells. Proteomics. 2005;5:4414–4426. doi: 10.1002/pmic.200401304. [DOI] [PubMed] [Google Scholar]
  41. Wang S., Tang X., Niu Y., Chen H., Li B., Li T., Zhang X., Hu Z., Zhou Q., Ji W. Generation and characterization of rabbit embryonic stem cells. Stem Cells. 2007;25:481–489. doi: 10.1634/stemcells.2006-0226. [DOI] [PubMed] [Google Scholar]
  42. Wong E.Y., Tse J.Y., Yao K.M., Tam P.C., Yeung W.S. VCY2 protein interacts with the HECT domain of ubiquitin-protein ligase E3A. Biochem Biophys Res Commun. 2002;296:1104–1111. doi: 10.1016/S0006-291X(02)02040-5. [DOI] [PubMed] [Google Scholar]
  43. Wu W.W., Wang G., Baek S.J., Shen R.F. Comparative study of three proteomic quantitative methods, DIGE, cICAT, and iTRAQ, using 2D gel- or LC-MALDI TOF/TOF. J Proteome Res. 2006;5:651–658. doi: 10.1021/pr050405o. [DOI] [PubMed] [Google Scholar]
  44. Zhang R., Sioma C.S., Wang S., Regnier F.E. Fractionation of isotopically labeled peptides in quantitative proteomics. Anal Chem. 2001;73:5142–5149. doi: 10.1021/ac010583a. [DOI] [PubMed] [Google Scholar]
  45. Zimmerman L., Parr B., Lendahl U., Cunningham M., McKay R., Gavin B., Mann J., Vassileva G., McMahon A. Independent regulatory elements in the nestin gene direct transgene expression to neural stem cells or muscle precursors. Neuron. 1994;12:11–24. doi: 10.1016/0896-6273(94)90148-1. [DOI] [PubMed] [Google Scholar]

Associated Data

This section collects any data citations, data availability statements, or supplementary materials included in this article.

Supplementary Materials

13238_2011_1081_MOESM1_ESM.pdf (192.4KB, pdf)

Supplementary material, approximately 192 KB.

Articles from Protein & Cell are provided here courtesy of Oxford University Press

RESOURCES