title: Mechanistic elements and critical factors of cellular reprogramming revealed by stepwise global gene expression analyses.
abstract: A better understanding of the cellular and molecular mechanisms involved in the reprogramming of somatic cells is essential for further improvement of induced pluripotent stem (iPS) cell technology. In this study, we enriched for cells actively undergoing reprogramming at different time points by sorting the cells stained with a stem cell-selective fluorescent chemical probe CDy1 for their global gene expression analysis. Day-to-day comparison of differentially expressed genes showed highly dynamic and transient gene expressions during reprogramming, which were largely distinct from those of fully-reprogrammed cells. An unbiased analysis of functional regulation indicated robust modulation of concurrent programs at critical junctures. Globally, transcriptional programs involved in cell proliferation, morphology and signal transduction were instantly triggered as early as 3 days-post-infection to prepare the cell for reprogramming but became somewhat muted in the final iPS cells. On the other hand, the highly coordinated metabolic reprogramming process was more gradually activated. Subsequent network analysis of differentially expressed genes indicated PDGF-BB as a core player in reprogramming which was verified by our gain- and loss-of-function experiments. As such, our study has revealed previously-unknown insights into the mechanisms of cellular reprogramming.
authors.affiliation: Laboratory of Bioimaging Probe Development, Singapore Bioimaging Consortium, Agency for Science, Technology and Research, Singapore 138667, Republic of Singapore.
authors.forename: Sung-Jin
authors.initials: SJ
authors.lastname: Park
authors.affiliation: Bioinformatics Group, Bioprocessing Technology Institute, Agency for Science, Technology and Research, Singapore 138668, Republic of Singapore.
authors.forename: Hock Chuan
authors.initials: HC
authors.lastname: Yeo
authors.affiliation: Laboratory of Bioimaging Probe Development, Singapore Bioimaging Consortium, Agency for Science, Technology and Research, Singapore 138667, Republic of Singapore.
authors.forename: Nam-Young
authors.initials: NY
authors.lastname: Kang
authors.affiliation: Department of Chemistry & NUS MedChem Program of Life Sciences Institute, National University of Singapore, Singapore 117543, Republic of Singapore.
authors.forename: Hanjo
authors.initials: H
authors.lastname: Kim
authors.affiliation: Bioinformatics Group, Bioprocessing Technology Institute, Agency for Science, Technology and Research, Singapore 138668, Republic of Singapore.
authors.forename: Joyce
authors.initials: J
authors.lastname: Lin
authors.affiliation: Department of Chemistry & NUS MedChem Program of Life Sciences Institute, National University of Singapore, Singapore 117543, Republic of Singapore.
authors.forename: Hyung-Ho
authors.initials: HH
authors.lastname: Ha
authors.affiliation: Laboratory of Bioimaging Probe Development, Singapore Bioimaging Consortium, Agency for Science, Technology and Research, Singapore 138667, Republic of Singapore.
authors.forename: Marc
authors.initials: M
authors.lastname: Vendrell
authors.affiliation: Department of Chemistry & NUS MedChem Program of Life Sciences Institute, National University of Singapore, Singapore 117543, Republic of Singapore.
authors.forename: Jun-Seok
authors.initials: JS
authors.lastname: Lee
authors.affiliation: Laboratory of Bioimaging Probe Development, Singapore Bioimaging Consortium, Agency for Science, Technology and Research, Singapore 138667, Republic of Singapore.
authors.forename: Yogeswari
authors.initials: Y
authors.lastname: Chandran
authors.affiliation: Bioinformatics Group, Bioprocessing Technology Institute, Agency for Science, Technology and Research, Singapore 138668, Republic of Singapore; Department of Chemical and Biomolecular Engineering, National University of Singapore, Singapore 117576, Republic of Singapore. Electronic address: cheld@nus.edu.sg.
authors.forename: Dong-Yup
authors.initials: DY
authors.lastname: Lee
authors.affiliation: Laboratory of Bioimaging Probe Development, Singapore Bioimaging Consortium, Agency for Science, Technology and Research, Singapore 138667, Republic of Singapore. Electronic address: yun_seong_wook@sbic.a-star.edu.sg.
authors.forename: Seong-Wook
authors.initials: SW
authors.lastname: Yun
authors.affiliation: Laboratory of Bioimaging Probe Development, Singapore Bioimaging Consortium, Agency for Science, Technology and Research, Singapore 138667, Republic of Singapore; Department of Chemistry & NUS MedChem Program of Life Sciences Institute, National University of Singapore, Singapore 117543, Republic of Singapore. Electronic address: chmcyt@nus.edu.sg.
authors.forename: Young-Tae
authors.initials: YT
authors.lastname: Chang
mesh_terms: D000818:Animals; D000077214:Becaplermin; D002454:Cell Differentiation; D049109:Cell Proliferation; D065150:Cellular Reprogramming; D005347:Fibroblasts / Q000166:cytology / Q000378:metabolism; D020869:Gene Expression Profiling; D053263:Gene Regulatory Networks; D057026:Induced Pluripotent Stem Cells / Q000166:cytology / Q000378:metabolism*; D051379:Mice; D020574:Proto-Oncogene Proteins c-sis / Q000378:metabolism
chemical_list: D020574:Proto-Oncogene Proteins c-sis; D000077214:Becaplermin