Systematic Search for Recipes to Generate Induced Pluripotent Stem Cells

被引：48

作者：

Chang, Rui ^{[1
]}

Shoemaker, Robert ^{[1
]}

Wang, Wei ^{[1
]}

机构：

[1] Univ Calif San Diego, Dept Chem & Biochem, La Jolla, CA 92093 USA

来源：

PLOS COMPUTATIONAL BIOLOGY | 2011年 / 7卷 / 12期

关键词：

POTENTIAL LANDSCAPE; NETWORK; MODEL; FIBROBLASTS; ROBUSTNESS; EXPRESSION; IDENTIFICATION; DISSIPATION; KNOWLEDGE; INFERENCE;

D O I：

10.1371/journal.pcbi.1002300

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

Generation of induced pluripotent stem cells (iPSCs) opens a new avenue in regenerative medicine. One of the major hurdles for therapeutic applications is to improve the efficiency of generating iPSCs and also to avoid the tumorigenicity, which requires searching for new reprogramming recipes. We present a systems biology approach to efficiently evaluate a large number of possible recipes and find those that are most effective at generating iPSCs. We not only recovered several experimentally confirmed recipes but we also suggested new ones that may improve reprogramming efficiency and quality. In addition, our approach allows one to estimate the cell-state landscape, monitor the progress of reprogramming, identify important regulatory transition states, and ultimately understand the mechanisms of iPSC generation.

引用

页数：13

共 52 条

[11] Recipes and mechanisms of cellular reprogramming: a case study on budding yeast Saccharomyces cerevisiae [J].

Ding, Shengchao ;

Wang, Wei .

BMC SYSTEMS BIOLOGY, 2011, 5

[12] Stem Cell States, Fates, and the Rules of Attraction [J].

Enver, Tariq ;

Pera, Martin ;

Peterson, Carsten ;

Andrews, Peter W. .

CELL STEM CELL, 2009, 4 (05) :387-397

[13] Somatic coding mutations in human induced pluripotent stem cells [J].

Gore, Athurva ;

Li, Zhe ;

Fung, Ho-Lim ;

Young, Jessica E. ;

Agarwal, Suneet ;

Antosiewicz-Bourget, Jessica ;

Canto, Isabel ;

Giorgetti, Alessandra ;

Israel, Mason A. ;

Kiskinis, Evangelos ;

Lee, Je-Hyuk ;

Loh, Yuin-Han ;

Manos, Philip D. ;

Montserrat, Nuria ;

Panopoulos, Athanasia D. ;

Ruiz, Sergio ;

Wilbert, Melissa L. ;

Yu, Junying ;

Kirkness, Ewen F. ;

Izpisua Belmonte, Juan Carlos ;

Rossi, Derrick J. ;

Thomson, James A. ;

Eggan, Kevin ;

Daley, George Q. ;

Goldstein, Lawrence S. B. ;

Zhang, Kun .

NATURE, 2011, 471 (7336) :63-U76

[14] Forcing cells to change lineages [J].

Graf, Thomas ;

Enver, Tariq .

NATURE, 2009, 462 (7273) :587-594

[15] Quantifying robustness and dissipation cost of yeast cell cycle network: The funneled energy landscape perspectives [J].

Han, Bo ;

Wang, Jin .

BIOPHYSICAL JOURNAL, 2007, 92 (11) :3755-3763

[16] Inference in belief networks: A procedural guide [J].

Huang, C ;

Darwiche, A .

INTERNATIONAL JOURNAL OF APPROXIMATE REASONING, 1996, 15 (03) :225-263

[17] Copy number variation and selection during reprogramming to pluripotency [J].

Hussein, Samer M. ;

Batada, Nizar N. ;

Vuoristo, Sanna ;

Ching, Reagan W. ;

Autio, Reija ;

Narva, Elisa ;

Ng, Siemon ;

Sourour, Michel ;

Hamalainen, Riikka ;

Olsson, Cia ;

Lundin, Karolina ;

Mikkola, Milla ;

Trokovic, Ras ;

Peitz, Michael ;

Bruestle, Oliver ;

Bazett-Jones, David P. ;

Alitalo, Kari ;

Lahesmaa, Riitta ;

Nagy, Andras ;

Otonkoski, Timo .

NATURE, 2011, 471 (7336) :58-U67

[18] Exploring the human genome with functional maps [J].

Huttenhower, Curtis ;

Haley, Erin M. ;

Hibbs, Matthew A. ;

Dumeaux, Vanessa ;

Barrett, Daniel R. ;

Coller, Hilary A. ;

Troyanskaya, Olga G. .

GENOME RESEARCH, 2009, 19 (06) :1093-1106

[19] Downregulation of NANOG induces differentiation of human embryonic stem cells to extraembryonic lineages [J].

Hyslop, L ;

Stojkovic, M ;

Armstrong, L ;

Walter, T ;

Stojkovic, P ;

Przyborski, S ;

Herbert, M ;

Murdoch, A ;

Strachan, T ;

Lako, M .

STEM CELLS, 2005, 23 (08) :1035-1043

[20] Direct Reprogramming of Fibroblasts into Functional Cardiomyocytes by Defined Factors [J].

Ieda, Masaki ;

Fu, Ji-Dong ;

Delgado-Olguin, Paul ;

Vedantham, Vasanth ;

Hayashi, Yohei ;

Bruneau, Benoit G. ;

Srivastava, Deepak .

CELL, 2010, 142 (03) :375-386

← 1 2 3 4 5 6 →