High-resolution analysis with novel cell-surface markers identifies routes to iPS cells

Nature

Volumn 499, Issue 7456, 2013, Pages 88-91

  O'Malley, James ^a   Skylaki, Stavroula ^b   Iwabuchi, Kumiko A ^a   Chantzoura, Eleni ^a   Ruetz, Tyson ^a   Johnsson, Anna ^c   Tomlinson, Simon R ^a   Linnarsson, Sten ^c   Kaji, Keisuke ^a  

^a UNIVERSITY OF EDINBURGH   (United Kingdom)

^b INSTITUTE OF EPIDEMIOLOGY   (Germany)

^c KAROLINSKA INSTITUTE   (Sweden)

Author keywords

[No Author keywords available]

Indexed keywords

CD44V ANTIGEN; ENHANCED GREEN FLUORESCENT PROTEIN; INTERCELLULAR ADHESION MOLECULE 1; TRANSCRIPTION FACTOR NANOG;

CELL ORGANELLE; GENETIC ANALYSIS; GENETIC MARKER; HETEROGENEITY; IDENTIFICATION METHOD; MOLECULAR ANALYSIS; POPULATION STRUCTURE; PROTEIN; RESOLUTION;

ANIMAL CELL; ARTICLE; CONTROLLED STUDY; EMBRYO; FIBROBLAST; MOUSE; NONHUMAN; NUCLEAR REPROGRAMMING; PLURIPOTENT STEM CELL; PRIORITY JOURNAL; RNA SEQUENCE; UPREGULATION;

ANIMALS; ANTIGENS, CD44; BIOLOGICAL MARKERS; EPIDERMIS; FIBROBLASTS; FLOW CYTOMETRY; GENE EXPRESSION PROFILING; GENES, REPORTER; INDUCED PLURIPOTENT STEM CELLS; INTERCELLULAR ADHESION MOLECULE-1; MICE; NUCLEAR REPROGRAMMING; SEQUENCE ANALYSIS, RNA; SINGLE-CELL ANALYSIS; UP-REGULATION;

IPS;

EID: 84879879314     PISSN: 00280836     EISSN: 14764687     Source Type: Journal    
DOI: 10.1038/nature12243     Document Type: Article

References (38)

1. Sridharan, R. et al. Role of the murine reprogramming factors in the induction of pluripotency. Cell 136, 364-377 (2009).
2. Golipour, A. et al. A late transition in somatic cell reprogramming requires regulators distinct from the pluripotency network. Cell Stem Cell 11, 769-782 (2012).
3. Samavarchi-Tehrani, P. et al. Functional genomics reveals a BMP-driven mesenchymal-to-epithelial transition in the initiation of somatic cell reprogramming. Cell Stem Cell 7, 64-77 (2010).
4. Mikkelsen, T. S. et al. Dissecting direct reprogramming through integrative genomic analysis. Nature 454, 49-55 (2008).
5. Buganim, Y. et al. Single-cell expression analyses during cellular reprogramming revealanearly stochasticanda late hierarchic phase. Cell 150, 1209-1222 (2012).
6. Polo, J. M. et al. A molecular roadmap of reprogramming somatic cells into iPS cells. Cell 151, 1617-1632 (2012).
7. Chen, J. et al. H3K9 methylation is a barrier during somatic cell reprogramming into iPSCs. Nature Genet. 45, 34-42 (2013).
8. Stadtfeld, M. , Maherali, N. , Breault, D. T. & Hochedlinger, K. Defining molecular cornerstones during fibroblast to iPS cell reprogramming in mouse. Cell Stem Cell 2, 230-240 (2008).
9. Brambrink, T. et al. Sequential expression of pluripotency markers during direct reprogramming of mouse somatic cells. Cell Stem Cell 2, 151-159 (2008).
10. Li, R. et al. A mesenchymal-to-epithelial transition initiates and is required for the nuclear reprogramming of mouse fibroblasts. Cell Stem Cell 7, 51-63 (2010).
11. Woltjen, K. et al. piggyBac transposition reprograms fibroblasts to induced pluripotent stem cells. Nature 458, 766-770 (2009).
12. Kaji, K. et al. Virus-free induction of pluripotency and subsequent excision of reprogramming factors. Nature 458, 771-775 (2009).
13. Chambers, I. et al. Nanog safeguards pluripotency and mediates germline development. Nature 450, 1230-1234 (2007).
14. Esteban, M. A. et al. Vitamin C enhances the generation of mouse and human induced pluripotent stem cells. Cell Stem Cell 6, 71-79 (2010).
15. Maherali, N. & Hochedlinger, K. Tgfb signal inhibition cooperates in the induction of iPSCs and replaces Sox2 and cMyc. Curr. Biol. 19, 1718-1723 (2009).
16. Chan, E. M. et al. Live cell imaging distinguishes bona fide human iPS cells from partially reprogrammed cells. Nature Biotechnol. 27, 1033-1037 (2009).
17. Carey, B. W. et al. Reprogramming of murine and human somatic cells using a single polycistronic vector. Proc. Natl Acad. Sci. USA 106, 157-162 (2009).
18. Hanna, J. et al. Direct cell reprogramming is a stochastic process amenable to acceleration. Nature 462, 595-601 (2009).
19. Silva, J. et al. Nanog is the gateway to the pluripotent ground state. Cell 138, 722-737 (2009).
20. Islam, S. et al. Characterization of the single-cell transcriptional landscape by highly multiplex RNA-seq. Genome Res. 21, 1160-1167 (2011).
21. Islam, S. et al. Highly multiplexed and strand-specific single-cell RNA 59 end sequencing. Nature Protocols 7, 813-828 (2012).
22. Halbritter, F. , Vaidya, H. J. &Tomlinson, S. R. GeneProf: analysis of high-throughput sequencing experiments. Nature Methods 9, 7-8 (2012).
23. Anders, S. & Huber, W. Differential expression analysis for sequence count data. Genome Biol. 11, R106 (2010).
24. Robinson, M. D. , McCarthy, D. J. & Smyth, G. K. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 26, 139-140 (2010).
25. Gentleman, R. C. et al. Bioconductor: open software development for computational biology and bioinformatics. Genome Biol. 5, R80 (2004).
26. Huang, d. W. , Sherman, B. T. & Lempicki, R. A. Systematic and integrative analysis of large genelists usingDAVIDbioinformatics resources. Nature Protocols 4,44-57 (2009).
27. Kim, J. , Chu, J. , Shen, X. ,Wang, J. &Orkin, S. H. An extended transcriptional network for pluripotency of embryonic stem cells. Cell 132, 1049-1061 (2008).
28. Xu, H. , Lemischka, I. R. & Ma'ayan, A. SVMclassifier to predict genes important for self-renewal and pluripotency of mouse embryonic stem cells. BMC Syst. Biol. 4, 173 (2010).
29. Nemajerova, A. , Kim, S. Y. , Petrenko, O. & Moll, U. M. Two-factor reprogramming of somatic cells to pluripotent stem cells reveals partial functional redundancy of Sox2 and Klf4. Cell Death Differ. 19, 1268-1276 (2012).
30. Soufi, A. , Donahue, G. & Zaret, K. S. Facilitators and impediments of the pluripotency reprogramming factors' initial engagement with the genome. Cell 151, 994-1004 (2012).
31. Gaszner, M. & Felsenfeld, G. Insulators: exploiting transcriptional and epigenetic mechanisms. Nature Rev. Genet. 7, 703-713 (2006).
32. Fu, H. et al. Preventing gene silencing with human replicators. Nature Biotechnol. 24, 572-576 (2006).
33. Wang, W. et al. Chromosomal transposition of PiggyBac in mouse embryonic stem cells. Proc. Natl Acad. Sci. USA 105, 9290-9295 (2008).
34. Saldanha, A. J. Java Treeview-extensible visualization of microarray data. Bioinformatics 20, 3246-3248 (2004).
35. de Hoon, M. J. , Imoto, S. , Nolan, J. & Miyano, S. Open source clustering software. Bioinformatics 20, 1453-1454 (2004).
36. Ligges, U. & Maechler, M. scatterplot3d-an R package for visualizing multivariate data. J. Stat. Softw. 8, 1-20 (2003).
37. Irizarry, R. A. et al. Summaries of Affymetrix GeneChip probe level data. Nucleic Acids Res. 31, e15 (2003).
38. Gautier, L. , Cope, L. , Bolstad, B. M. & Irizarry, R. A. affy-analysis of Affymetrix GeneChip data at the probe level. Bioinformatics 20, 307-315 (2004).