An integrated systems biology approach identifies positive cofactor 4 as a factor that increases reprogramming efficiency

Spermatogonial stem cells (SSCs) can spontaneously dedifferentiate into embryonic stem cell (ESC)-like cells, which are designated as multipotent SSCs (mSSCs), without ectopic expression of reprogramming factors. Interestingly, SSCs express key pluripotency genes such as Oct4, Sox2, Klf4 and Myc. Therefore, molecular dissection of mSSC reprogramming may provide clues about novel endogenous reprogramming or pluripotency regulatory factors. Our comparative transcriptome analysis of mSSCs and induced pluripotent stem cells (iPSCs) suggests that they have similar pluripotency states but are reprogrammed via different transcriptional pathways. We identified 53 genes as putative pluripotency regulatory factors using an integrated systems biology approach. We demonstrated a selected candidate, Positive cofactor 4 (Pc4), can enhance the efficiency of somatic cell reprogramming by promoting and maintaining transcriptional activity of the key reprograming factors. These results suggest that Pc4 has an important role in inducing spontaneous somatic cell reprogramming via up-regulation of key pluripotency genes.

[1]  S. Mitalipov,et al.  Human Embryonic Stem Cells Derived by Somatic Cell Nuclear Transfer , 2013, Cell.

[2]  Fei Yi,et al.  Tcf3 Functions as a Steady‐State Limiter of Transcriptional Programs of Mouse Embryonic Stem Cell Self‐Renewal , 2008, Stem cells.

[3]  Jose M Polo,et al.  Phases of reprogramming. , 2014, Stem cell research.

[4]  Jialiang Liang,et al.  A mesenchymal-to-epithelial transition initiates and is required for the nuclear reprogramming of mouse fibroblasts. , 2010, Cell stem cell.

[5]  Rafael A. Irizarry,et al.  A framework for oligonucleotide microarray preprocessing , 2010, Bioinform..

[6]  I. Lemischka,et al.  Delayed differentiation in embryonic stem cells and mesodermal progenitors in the absence of CtBP2 , 2010, Mechanisms of Development.

[7]  Rudolf Jaenisch,et al.  Mechanisms and models of somatic cell reprogramming , 2013, Nature Reviews Genetics.

[8]  Thomas Lufkin,et al.  Zfp206 Is a Transcription Factor That Controls Pluripotency of Embryonic Stem Cells , 2007, Stem cells.

[9]  Rafael A. Irizarry,et al.  Bioinformatics and Computational Biology Solutions using R and Bioconductor , 2005 .

[10]  Benjamin M. Bolstad,et al.  affy - analysis of Affymetrix GeneChip data at the probe level , 2004, Bioinform..

[11]  Jonghwan Kim,et al.  Transcription Elongation Factor Tcea3 Regulates the Pluripotent Differentiation Potential of Mouse Embryonic Stem Cells Via the Lefty1‐Nodal‐Smad2 Pathway , 2013, Stem cells.

[12]  T. Mikkelsen,et al.  Dissecting direct reprogramming through integrative genomic analysis , 2008, Nature.

[13]  Thomas Vierbuchen,et al.  Direct Lineage Conversions: Unnatural but useful? , 2011, Nature Biotechnology.

[14]  Qikai Xu,et al.  A genome-wide RNAi screen identifies a new transcriptional module required for self-renewal. , 2009, Genes & development.

[15]  E. Morrisey,et al.  How microRNAs facilitate reprogramming to pluripotency , 2012, Journal of Cell Science.

[16]  Erik L. L. Sonnhammer,et al.  Inparanoid: a comprehensive database of eukaryotic orthologs , 2004, Nucleic Acids Res..

[17]  David L. A. Wood,et al.  Divergent reprogramming routes lead to alternative stem-cell states , 2014, Nature.

[18]  X. Tian,et al.  JAK-STAT3 and somatic cell reprogramming , 2013, JAK-STAT.

[19]  Sandy L. Klemm,et al.  Single-Cell Expression Analyses during Cellular Reprogramming Reveal an Early Stochastic and a Late Hierarchic Phase , 2012, Cell.

[20]  Qi-Long Ying,et al.  Gbx2, a LIF/Stat3 target, promotes reprogramming to and retention of the pluripotent ground state , 2013, Journal of Cell Science.

[21]  J. Wrana,et al.  A late transition in somatic cell reprogramming requires regulators distinct from the pluripotency network. , 2012, Cell stem cell.

[22]  G. Daley,et al.  Selective Blockade of MicroRNA Processing by Lin28 , 2008, Science.

[23]  J. Wrana,et al.  Functional genomics reveals a BMP-driven mesenchymal-to-epithelial transition in the initiation of somatic cell reprogramming. , 2010, Cell stem cell.

[24]  E. Marcotte,et al.  Systematic prediction of gene function in Arabidopsis thaliana using a probabilistic functional gene network , 2011, Nature Protocols.

[25]  Giselle Lee "The Developmental Capacity of Nuclei Taken from Intestinal Epithelium Cells of Feeding Tadpoles" (1962), by John B. Gurdon , 2017 .

[26]  Dong Ryul Lee,et al.  Human somatic cell nuclear transfer using adult cells. , 2014, Cell stem cell.

[27]  S. Yamanaka,et al.  Induction of Pluripotent Stem Cells from Mouse Embryonic and Adult Fibroblast Cultures by Defined Factors , 2006, Cell.

[28]  P. Labosky,et al.  Regulation of Embryonic Stem Cell Self‐Renewal and Pluripotency by Foxd3 , 2008, Stem cells.

[29]  Dong Ryul Lee,et al.  Identification of an intermediate state as spermatogonial stem cells reprogram to multipotent cells , 2010, Molecules and cells.

[30]  J. Dadoune Pluripotency of a single spermatogonial stem cell in mice. , 2008 .

[31]  Takashi Aoi,et al.  Generation of induced pluripotent stem cells without Myc from mouse and human fibroblasts , 2008, Nature Biotechnology.

[32]  N. Geijsen,et al.  Uncovering the true identity of naïve pluripotent stem cells. , 2013, Trends in cell biology.

[33]  Herbert Schulz,et al.  A genome-scale RNAi screen for Oct4 modulators defines a role of the Paf1 complex for embryonic stem cell identity. , 2009, Cell stem cell.

[34]  H. Schöler,et al.  Zfp296 Is a Novel, Pluripotent-Specific Reprogramming Factor , 2012, PloS one.

[35]  Terence P. Speed,et al.  A single-sample method for normalizing and combining full-resolution copy numbers from multiple platforms, labs and analysis methods , 2009, Bioinform..

[36]  Marius Wernig,et al.  c-Myc is dispensable for direct reprogramming of mouse fibroblasts. , 2008, Cell stem cell.

[37]  Juan M. Vaquerizas,et al.  A census of human transcription factors: function, expression and evolution , 2009, Nature Reviews Genetics.

[38]  N. D. Clarke,et al.  A genome-wide RNAi screen reveals determinants of human embryonic stem cell identity , 2010, Nature.

[39]  K. Hochedlinger,et al.  Induced pluripotency: history, mechanisms, and applications. , 2010, Genes & development.

[40]  S. Ramaswamy,et al.  A Molecular Roadmap of Reprogramming Somatic Cells into iPS Cells , 2012, Cell.

[41]  Stuart H. Orkin,et al.  A protein interaction network for pluripotency of embryonic stem cells , 2006, Nature.

[42]  Chun Xing Li,et al.  Tgif1 Regulates Quiescence and Self-Renewal of Hematopoietic Stem Cells , 2013, Molecular and Cellular Biology.

[43]  T. Rana,et al.  Discovery of Nonsteroidal Anti‐Inflammatory Drug and Anticancer Drug Enhancing Reprogramming and Induced Pluripotent Stem Cell Generation , 2011, Stem cells.

[44]  A. Simeone,et al.  Otx2 is an intrinsic determinant of the embryonic stem cell state and is required for transition to a stable epiblast stem cell condition , 2013, Development.

[45]  Matko Bosnjak,et al.  REVIGO Summarizes and Visualizes Long Lists of Gene Ontology Terms , 2011, PloS one.

[46]  M. Oshimura,et al.  Generation of Pluripotent Stem Cells from Neonatal Mouse Testis , 2004, Cell.

[47]  N. Benvenisty,et al.  Human oocytes reprogram adult somatic nuclei of a type 1 diabetic to diploid pluripotent stem cells , 2014, Nature.

[48]  John D. Storey A direct approach to false discovery rates , 2002 .

[49]  G. Pan,et al.  MicroRNA-145 Regulates OCT4, SOX2, and KLF4 and Represses Pluripotency in Human Embryonic Stem Cells , 2009, Cell.

[50]  F. van Roy,et al.  Role of cell–cell adhesion complexes in embryonic stem cell biology , 2014, Journal of Cell Science.

[51]  Debbie L C van den Berg,et al.  An Oct4-Centered Protein Interaction Network in Embryonic Stem Cells , 2010, Cell stem cell.

[52]  Wei Wu,et al.  Dax1 and Nanog act in parallel to stabilize mouse embryonic stem cells and induced pluripotency , 2014, Nature Communications.

[53]  E. Marcotte,et al.  Prioritizing candidate disease genes by network-based boosting of genome-wide association data. , 2011, Genome research.

[54]  Jeroen S. van Zon,et al.  Direct cell reprogramming is a stochastic process amenable to acceleration , 2009, Nature.

[55]  P. Geurts,et al.  Inferring Regulatory Networks from Expression Data Using Tree-Based Methods , 2010, PloS one.

[56]  Austin G Smith,et al.  Conversion of embryonic stem cells into neuroectodermal precursors in adherent monoculture , 2003, Nature Biotechnology.

[57]  G. Hong,et al.  Nucleic Acids Research , 2015, Nucleic Acids Research.

[58]  Marcos J. Araúzo-Bravo,et al.  Chromatin-Remodeling Components of the BAF Complex Facilitate Reprogramming , 2010, Cell.

[59]  M. Babu,et al.  An Expanded Oct4 Interaction Network: Implications for Stem Cell Biology, Development, and Disease , 2010, Cell stem cell.

[60]  Janet Rossant,et al.  Krüppel-like factor 5 is essential for blastocyst development and the normal self-renewal of mouse ESCs. , 2008, Cell stem cell.

[61]  K. Hochedlinger,et al.  Tgfβ Signal Inhibition Cooperates in the Induction of iPSCs and Replaces Sox2 and cMyc , 2009, Current Biology.

[62]  J. Davis Bioinformatics and Computational Biology Solutions Using R and Bioconductor , 2007 .

[63]  J. Kawai,et al.  A genome-wide and nonredundant mouse transcription factor database. , 2004, Biochemical and biophysical research communications.

[64]  J. Nichols,et al.  Naive and primed pluripotent states. , 2009, Cell stem cell.