Molecular profiling of stem cells

Clinica Chimica Acta

Volumn 378, Issue 1-2, 2007, Pages 24-32

  Ma, Li ^a   Sun, Bingyun ^a   Hood, Leroy ^a   Tian, Qiang ^a  

^a INSTITUTE FOR SYSTEMS BIOLOGY   (United States)

Author keywords

ChIP chip; mass spectrometry; microarray; proteome; Stem Cell; transcriptome

Indexed keywords

PROTEOME; TRANSCRIPTOME;

EMBRYONIC STEM CELL; GENE EXPRESSION PROFILING; GENE LOCATION; GENOME ANALYSIS; HEMATOPOIETIC STEM CELL; HUMAN; NEURAL STEM CELL; NONHUMAN; NUCLEIC ACID ANALYSIS; PRIORITY JOURNAL; PROTEOMICS; REVIEW; STEM CELL; TRANSCRIPTOMICS;

ANIMALS; EMBRYONIC STEM CELLS; GENE EXPRESSION PROFILING; HEMATOPOIETIC STEM CELLS; HUMANS; NEURONS; PROTEOMICS; STEM CELLS; TRANSCRIPTION, GENETIC;

EID: 33846997588     PISSN: 00098981     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.cca.2006.12.016     Document Type: Review

References (98)

1. Eckfeldt C.E., Mendenhall E.M., and Verfaillie C.M. The molecular repertoire of the 'almighty' stem cell. Nat Rev Mol Cell Biol 6 (2005) 726-737
2. Li L., and Akashi K. Unraveling the molecular components and genetic blueprints of stem cells. Biotechniques 35 (2003) 1233-1239
3. Ideker T., et al. Integrated genomic and proteomic analyses of a systematically perturbed metabolic network. Science 292 (2001) 929-934
4. Tian Q., et al. Integrated genomic and proteomic analyses of gene expression in Mammalian cells. Mol Cell Proteomics 3 (2004) 960-969
5. Van Hoof D., et al. A quest for human and mouse embryonic stem cell-specific proteins. Mol Cell Proteomics 5 (2006) 1261-1273
6. Park I.K., et al. Differential gene expression profiling of adult murine hematopoietic stem cells. Blood 99 (2002) 488-498
7. Brandenberger R., et al. Transcriptome characterization elucidates signaling networks that control human ES cell growth and differentiation. Nat Biotechnol 22 (2004) 707-716
8. Richards M., Tan S.P., Tan J.H., Chan W.K., and Bongso A. The transcriptome profile of human embryonic stem cells as defined by SAGE. Stem Cells 22 (2004) 51-64
9. Akashi K., et al. Transcriptional accessibility for genes of multiple tissues and hematopoietic lineages is hierarchically controlled during early hematopoiesis. Blood 101 (2003) 383-389
10. Ivanova N.B., et al. A stem cell molecular signature. Science 298 (2002) 601-604
11. Ramalho-Santos M., Yoon S., Matsuzaki Y., Mulligan R.C., and Melton D.A. "Stemness": transcriptional profiling of embryonic and adult stem cells. Science 298 (2002) 597-600
12. Wei C.L., et al. Transcriptome profiling of human and murine ESCs identifies divergent paths required to maintain the stem cell state. Stem Cells 23 (2005) 166-185
13. Brandenberger R., et al. MPSS profiling of human embryonic stem cells. BMC Dev Biol 4 (2004) 10
14. Brenner S., et al. Gene expression analysis by massively parallel signature sequencing (MPSS) on microbead arrays. Nat Biotechnol 18 (2000) 630-634
15. Tanaka T.S., et al. Gene expression profiling of embryo-derived stem cells reveals candidate genes associated with pluripotency and lineage specificity. Genome Res 12 (2002) 1921-1928
16. Sharov A.A., et al. Transcriptome analysis of mouse stem cells and early embryos. PLoS Biol 1 (2003) E74
17. Thomson J.A., et al. Embryonic stem cell lines derived from human blastocysts. Science 282 (1998) 1145-1147
18. Sperger J.M., et al. Gene expression patterns in human embryonic stem cells and human pluripotent germ cell tumors. Proc Natl Acad Sci U S A 100 (2003) 13350-13355
19. Bhattacharya B., et al. Gene expression in human embryonic stem cell lines: unique molecular signature. Blood 103 (2004) 2956-2964
20. Bhattacharya B., et al. Comparison of the gene expression profile of undifferentiated human embryonic stem cell lines and differentiating embryoid bodies. BMC Dev Biol 5 (2005) 22
21. Abeyta M.J., et al. Unique gene expression signatures of independently-derived human embryonic stem cell lines. Hum Mol Genet 13 (2004) 601-608
22. Kielman M.F., et al. Apc modulates embryonic stem-cell differentiation by controlling the dosage of beta-catenin signaling. Nat Genet 32 (2002) 594-605
23. Sato N., et al. Molecular signature of human embryonic stem cells and its comparison with the mouse. Dev Biol 260 (2003) 404-413
24. Ginis I., et al. Differences between human and mouse embryonic stem cells. Dev Biol 269 (2004) 360-380
25. Rao M. Conserved and divergent paths that regulate self-renewal in mouse and human embryonic stem cells. Dev Biol 275 (2004) 269-286
26. Uchida N., and Weissman I.L. Searching for hematopoietic stem cells: evidence that Thy-1.1lo Lin-Sca-1+ cells are the only stem cells in C57BL/Ka-Thy-1.1 bone marrow. J Exp Med 175 (1992) 175-184
27. Spangrude G.J., Heimfeld S., and Weissman I.L. Purification and characterization of mouse hematopoietic stem cells. Science 241 (1988) 58-62
28. Baum C.M., Weissman I.L., Tsukamoto A.S., Buckle A.M., and Peault B. Isolation of a candidate human hematopoietic stem-cell population. Proc Natl Acad Sci U S A 89 (1992) 2804-2808
29. Manz M.G., Miyamoto T., Akashi K., and Weissman I.L. Prospective isolation of human clonogenic common myeloid progenitors. Proc Natl Acad Sci U S A 99 (2002) 11872-11877
30. Kondo M., Weissman I.L., and Akashi K. Identification of clonogenic common lymphoid progenitors in mouse bone marrow. Cell 91 (1997) 661-672
31. Akashi K., Traver D., Miyamoto T., and Weissman I.L. A clonogenic common myeloid progenitor that gives rise to all myeloid lineages. Nature 404 (2000) 193-197
32. Phillips R.L., et al. The genetic program of hematopoietic stem cells. Science 288 (2000) 1635-1640
33. Terskikh A.V., et al. From hematopoiesis to neuropoiesis: evidence of overlapping genetic programs. Proc Natl Acad Sci U S A 98 (2001) 7934-7939
34. Reya T., et al. A role for Wnt signalling in self-renewal of haematopoietic stem cells. Nature 423 (2003) 409-414
35. Jamieson C.H., et al. Granulocyte-macrophage progenitors as candidate leukemic stem cells in blast-crisis CML. N Engl J Med 351 (2004) 657-667
36. Park I.K., et al. Bmi-1 is required for maintenance of adult self-renewing haematopoietic stem cells. Nature 423 (2003) 302-305
37. Zhang J., et al. Identification of the haematopoietic stem cell niche and control of the niche size. Nature 425 (2003) 836-841
38. Hackney J.A., et al. A molecular profile of a hematopoietic stem cell niche. Proc Natl Acad Sci U S A 99 (2002) 13061-13066
39. Terskikh A.V., Miyamoto T., Chang C., Diatchenko L., and Weissman I.L. Gene expression analysis of purified hematopoietic stem cells and committed progenitors. Blood 102 (2003) 94-101
40. Zhong J.F., et al. Gene expression profile of murine long-term reconstituting vs. short-term reconstituting hematopoietic stem cells. Proc Natl Acad Sci U S A 102 (2005) 2448-2453
41. Cross M.A., and Enver T. The lineage commitment of haemopoietic progenitor cells. Curr Opin Genet Dev 7 (1997) 609-613
42. Georgantas III R.W., et al. Microarray and serial analysis of gene expression analyses identify known and novel transcripts overexpressed in hematopoietic stem cells. Cancer Res 64 (2004) 4434-4441
43. Wagner W., et al. Molecular evidence for stem cell function of the slow-dividing fraction among human hematopoietic progenitor cells by genome-wide analysis. Blood 104 (2004) 675-686
44. Reynolds B.A., and Weiss S. Clonal and population analyses demonstrate that an EGF-responsive mammalian embryonic CNS precursor is a stem cell. Dev Biol 175 (1996) 1-13
45. Levison S.W., and Goldman J.E. Multipotential and lineage restricted precursors coexist in the mammalian perinatal subventricular zone. J Neurosci Res 48 (1997) 83-94
46. Geschwind D.H., et al. A genetic analysis of neural progenitor differentiation. Neuron 29 (2001) 325-339
47. Karsten S.L., et al. Global analysis of gene expression in neural progenitors reveals specific cell-cycle, signaling, and metabolic networks. Dev Biol 261 (2003) 165-182
48. Luo Y., et al. Microarray analysis of selected genes in neural stem and progenitor cells. J Neurochem 83 (2002) 1481-1497
49. Livesey F.J., Young T.L., and Cepko C.L. An analysis of the gene expression program of mammalian neural progenitor cells. Proc Natl Acad Sci U S A 101 (2004) 1374-1379
50. Hood L. Systems biology: integrating technology, biology, and computation. Mech Ageing Dev 124 (2003) 9-16
51. Brenner S., et al. In vitro cloning of complex mixtures of DNA on microbeads: physical separation of differentially expressed cDNAs. Proc Natl Acad Sci U S A 97 (2000) 1665-1670
52. Fessler M.B., Malcolm K.C., Duncan M.W., and Worthen G.S. A genomic and proteomic analysis of activation of the human neutrophil by lipopolysaccharide and its mediation by p38 mitogen-activated protein kinase. J Biol Chem 277 (2002) 31291-31302
53. Griffin T.J., et al. Complementary profiling of gene expression at the transcriptome and proteome levels in Saccharomyces cerevisiae. Mol Cell Proteomics 1 (2002) 323-333
54. Aebersold R., and Cravatt B.F. Proteomics-advances, applications and the challenges that remain. Trends Biotechnol 20 (2002) S1-S2
55. Aebersold R., and Goodlett D.R. Mass spectrometry in proteomics. Chem Rev 101 (2001) 269-295
56. Yates III J.R. Mass spectral analysis in proteomics. Annu Rev Biophys Biomol Struct 33 (2004) 297-316
57. Gygi S.P., et al. Quantitative analysis of complex protein mixtures using isotope-coded affinity tags. Nat Biotechnol 17 (1999) 994-999
58. Ross P.L., et al. Multiplexed protein quantitation in Saccharomyces cerevisiae using amine-reactive isobaric tagging reagents. Mol Cell Proteomics 3 (2004) 1154-1169
59. Lee Y.H., Han H., Chang S.B., and Lee S.W. Isotope-coded N-terminal sulfonation of peptides allows quantitative proteomic analysis with increased de novo peptide sequencing capability. Rapid Commun Mass Spectrom 18 (2004) 3019-3027
60. Goodlett D.R., et al. Differential stable isotope labeling of peptides for quantitation and de novo sequence derivation. Rapid Commun Mass Spectrom 15 (2001) 1214-1221
61. Conrads T.P., et al. Quantitative analysis of bacterial and mammalian proteomes using a combination of cysteine affinity tags and 15N-metabolic labeling. Anal Chem 73 (2001) 2132-2139
62. Martinovic S., Veenstra T.D., Anderson G.A., Pasa-Tolic L., and Smith R.D. Selective incorporation of isotopically labeled amino acids for identification of intact proteins on a proteome-wide level. J Mass Spectrom 37 (2002) 99-107
63. Oda Y., Huang K., Cross F.R., Cowburn D., and Chait B.T. Accurate quantitation of protein expression and site-specific phosphorylation. Proc Natl Acad Sci U S A 96 (1999) 6591-6596
64. Shi S.D., Hendrickson C.L., and Marshall A.G. Counting individual sulfur atoms in a protein by ultrahigh-resolution Fourier transform ion cyclotron resonance mass spectrometry: experimental resolution of isotopic fine structure in proteins. Proc Natl Acad Sci U S A 95 (1998) 11532-11537
65. Washburn M.P., Ulaszek R., Deciu C., Schieltz D.M., and Yates III J.R. Analysis of quantitative proteomic data generated via multidimensional protein identification technology. Anal Chem 74 (2002) 1650-1657
66. Zhu H., et al. Residue-specific mass signatures for the efficient detection of protein modifications by mass spectrometry. Anal Chem 74 (2002) 1687-1694
67. Zhu H., Pan S., Gu S., Bradbury E.M., and Chen X. Amino acid residue specific stable isotope labeling for quantitative proteomics. Rapid Commun Mass Spectrom 16 (2002) 2115-2123
68. Ong S.E., et al. Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics. Mol Cell Proteomics 1 (2002) 376-386
69. Stewart I.I., Thomson T., and Figeys D. 18O labeling: a tool for proteomics. Rapid Commun Mass Spectrom 15 (2001) 2456-2465
70. Yao X., Freas A., Ramirez J., Demirev P.A., and Fenselau C. Proteolytic 18O labeling for comparative proteomics: model studies with two serotypes of adenovirus. Anal Chem 73 (2001) 2836-2842
71. Lopez-Ferrer D., Ramos-Fernandez A., Martinez-Bartolome S., Garcia-Ruiz P., and Vazquez J. Quantitative proteomics using (16)O/(18)O labeling and linear ion trap mass spectrometry. Proteomics 6 (2006) S4-S11
72. Lu Y., Bottari P., Turecek F., Aebersold R., and Gelb M.H. Absolute quantification of specific proteins in complex mixtures using visible isotope-coded affinity tags. Anal Chem 76 (2004) 4104-4111
73. Barnidge D.R., Goodmanson M.K., Klee G.G., and Muddiman D.C. Absolute quantification of the model biomarker prostate-specific antigen in serum by LC-Ms/MS using protein cleavage and isotope dilution mass spectrometry. J Proteome Res 3 (2004) 644-652
74. Leenheer A.P., and Thienpont L.M. Applications of isotope dilution mass spectrometry in clinical chemistry, pharmacokinetics, and toxicology. Mass Spectrom Rev 11 (1992) 249-307
75. Buchnall M., Fung K.U.C., and Duncan M.W. Practical quantitative biomedical applications of MALDI-TOF mass spectrometry. J Am Soc Mass Spectrom 13 (2002) 1015-1027
76. Higgs R.E., Knierman M.D., Gelfanova V., Butler J.P., and Hale J.E. Comprehensive label-free method for the relative quantification of proteins from biological samples. J Proteome Res 4 (2005) 1442-1450
77. Silva J.C., et al. Quantitative proteomic analysis by accurate mass retention time pairs. Anal Chem 77 (2005) 2187-2200
78. Wang W., et al. Quantification of proteins and metabolites by mass spectrometry without isotopic labeling or spiked standards. Anal Chem 75 (2003) 4818-4826
79. Unwin R.D., Gaskell S.J., Evans C.A., and Whetton A.D. The potential for proteomic definition of stem cell populations. Exp Hematol 31 (2003) 1147-1159
80. Baharvand H., M.H., S.K.A., and G.H.S. Proteomic signature of human embryonic stem cells. Proteomics 6 (2006) 3544-3549
81. Elliott S.T., D.G.C., C.P.G., K.R.B., and J.E.V.E. Two-dimensional gel electrophoresis database of murine R1 embryonic stem cells. Proteomics 4 (2004) 3813-3832
82. Van Hoof D., Mummery C.L., Heck A.J., and Krijgsveld J. Embryonic stem cell proteomics. Expert Rev Proteomics 3 (2006) 427-437
83. Maurer M.H., Feldmann R.E., Bromme J.O., and Kalenka A. Comparison of statistical approaches for the analysis of proteome expression data of differentiating neural stem cells. J Proteome Res 4 (2005) 96-100
84. Nagano K., et al. Large-scale identification of proteins expressed in mouse embryonic stem cells. Proteomics 5 (2005) 1346-1361
85. Van Hoof D., et al. A quest for human and mouse embryonic stem cell-specific proteins. Mol Cell Proteomics (2006)
86. Lee H.K., Lee B.H., Park S.A., and Kim C.W. The proteomic analysis of an adipocyte differentiated from human mesenchymal stem cells using two-dimensional gel electrophoresis. Proteomics 6 (2006) 1223-1229
87. Wang D., and Gao L. Proteomic analysis of neural differentiation of mouse embryonic stem cells. Proteomics 5 (2005) 4414-4426
88. Unwin R.D., Pierce A., Watson R.B., Sternberg D.W., and Whetton A.D. Quantitative proteomic analysis using isobaric protein tags enables rapid comparison of changes in transcript and protein levels in transformed cells. Mol Cell Proteomics 4 (2005) 924-935
89. Salasznyk R.M., et al. Comparing the protein expression profiles of human mesenchymal stem cells and human osteoblasts using gene ontologies. Stem Cells Dev 14 (2005) 354-366
90. Unwin R.D., et al. Quantitative proteomics reveals post-translational control as a regulatory factor in primary hematopoietic stem cells. Blood 107 (2006) 4687-4694
91. Sakaguchi M., et al. A carbohydrate-binding protein, Galectin-1, promotes proliferation of adult neural stem cells. Proc Natl Acad Sci U S A 103 (2006) 7112-7117
92. Tian Q., et al. Proteomic analysis identifies that 14-3-3zeta interacts with beta-catenin and facilitates its activation by Akt. Proc Natl Acad Sci U S A 101 (2004) 15370-15375
93. Ren B., et al. Genome-wide location and function of DNA binding proteins. Science 290 (2000) 2306-2309
94. Boyer L.A., et al. Core transcriptional regulatory circuitry in human embryonic stem cells. Cell 122 (2005) 947-956
95. Loh Y.H., et al. The Oct4 and Nanog transcription network regulates pluripotency in mouse embryonic stem cells. Nat Genet 38 (2006) 431-440
96. Boyer L.A., et al. Polycomb complexes repress developmental regulators in murine embryonic stem cells. Nature 441 (2006) 349-353
97. Lee T.I., et al. Control of developmental regulators by Polycomb in human embryonic stem cells. Cell 125 (2006) 301-313
98. Mitsui K., et al. The homeoprotein Nanog is required for maintenance of pluripotency in mouse epiblast and ES cells. Cell 113 (2003) 631-642