Co-expression networks in generation of induced pluripotent stem cells

Sharan Paul; Lance Pflieger; Warunee Dansithong; Karla P Figueroa; Fuying Gao; Giovanni Coppola; Stefan M Pulst

doi:10.1242/bio.016402

Co-expression networks in generation of induced pluripotent stem cells

Biol Open. 2016 Feb 18;5(3):300-10. doi: 10.1242/bio.016402.

Authors

Sharan Paul¹, Lance Pflieger², Warunee Dansithong¹, Karla P Figueroa¹, Fuying Gao³, Giovanni Coppola³, Stefan M Pulst⁴

Affiliations

¹ Department of Neurology, University of Utah, Salt Lake City, UT 84132, USA.
² Department of Neurology, University of Utah, Salt Lake City, UT 84132, USA Department of Biomedical Informatics, University of Utah, Salt Lake City, UT 84108, USA.
³ Departments of Psychiatry and Neurology, Semel Institute for Neuroscience and Human Behavior, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA.
⁴ Department of Neurology, University of Utah, Salt Lake City, UT 84132, USA stefan.pulst@hsc.utah.edu.

Abstract

We developed an adenoviral vector, in which Yamanaka's four reprogramming factors (RFs) were controlled by individual CMV promoters in a single cassette (Ad-SOcMK). This permitted coordinated expression of RFs (SOX2, OCT3/4, c-MYC and KLF4) in a cell for a transient period of time, synchronizing the reprogramming process with the majority of transduced cells assuming induced pluripotent stem cell (iPSC)-like characteristics as early as three days post-transduction. These reprogrammed cells resembled human embryonic stem cells (ESCs) with regard to morphology, biomarker expression, and could be differentiated into cells of the germ layers in vitro and in vivo. These iPSC-like cells, however, failed to expand into larger iPSC colonies. The short and synchronized reprogramming process allowed us to study global transcription changes within short time intervals. Weighted gene co-expression network analysis (WGCNA) identified sixteen large gene co-expression modules, each including members of gene ontology categories involved in cell differentiation and development. In particular, the brown module contained a significant number of ESC marker genes, whereas the turquoise module contained cell-cycle-related genes that were downregulated in contrast to upregulation in human ESCs. Strong coordinated expression of all four RFs via adenoviral transduction may constrain stochastic processes and lead to silencing of genes important for cellular proliferation.

Keywords: Adenoviral delivery; Gene expression; Reprogramming; iPSC.

Abstract

Grants and funding