Molecular control of induced pluripotency

Abstract

Deciphering the mechanisms of epigenetic reprogramming provides fundamental insights into cell fate decisions, which in turn reveal strategies to make the reprogramming process increasingly efficient. Here we review recent advances in epigenetic reprogramming to pluripotency with a focus on the principal molecular regulators. We examine the trajectories connecting somatic and pluripotent cells, genetic and chemical methodologies for inducing pluripotency, the role of endogenous master transcription factors in establishing the pluripotent state, and functional interactions between reprogramming factors and epigenetic regulators. Defining the crosstalk among the diverse molecular actors implicated in cellular reprogramming presents a major challenge for future inquiry.

Figure 1. Roadmaps of epigenetic reprogramming

(A) Trajectory of reprogramming intermediates defined by Thy1, SSEA1 and Oct4-GFP (OGFP) expression (Polo et al., 2012); (B) Trajectories of reprogramming intermediates defined by CD44, ICAM1 and Nanog-GFP (NGFP) expression (O’Malley et al., 2013). Double lanes indicate transitions that occur at a higher frequency. iPS cell: induced pluripotent stem cell; MEF: mouse embryonic fibroblast; MET: mesenchymal-epithelial transition; OSKM: Oct4, Sox2, Klf4 and c-Myc.

Figure 2. Models of epigenetic reprogramming

Kinetics of reprogramming are graphically represented as a function of latency and the cumulative proportion of donor cells that gives rise to iPS cells. Latency indicates absolute time or the number of cell divisions. (A) Numerical modeling during OSKM-mediated reprogramming of secondary B cells demonstrated that induced pluripotency is essentially stochastic, but amenable to acceleration by cell-division-rate-dependent modifications such as overexpression of Lin28 or disruption of the p53/p21 pathway or a cell-division-rate-independent modification such as overexpression of Nanog (Hanna et al., 2009); (B) Deterministic model of reprogramming whereby somatic cells transit to pluripotency with a fixed latency. This type of reprogramming has only been observed by overexpression of C/EBPα (Di Stefano et al., 2013) or with the use of highly cycling donor cells (Guo et al., 2014). Deterministic reprogramming was also observed upon elimination of Mbd3 (Rais et al., 2013), but a recent study concluded that Mbd3 has a beneficial effect during the reprogramming process (Dos Santos et al., 2014); (C) Model of reprogramming inferred from single cell expression profiling (Buganim et al., 2012); (D) Biphasic model of reprogramming inferred from gene expression profiling along the Thy1/SSEA1/Oct4-GFP roadmap (Polo et al., 2012).

Figure 3. Methodologies for inducing pluripotency

(A) Transgene-mediated reprogramming strategies: ¹(Takahashi and Yamanaka, 2006), ²(Yu et al., 2007), ³(Nakagawa et al., 2008), ⁴(Feng et al., 2009), ⁵(Heng et al., 2010), ⁶(Maekawa et al., 2011), ⁷(Buganim et al., 2012), ⁸(Mansour et al., 2012), ⁹(Redmer et al., 2011), ¹⁰(Yang et al., 2011), ¹¹(Shinagawa et al., 2014), ¹²(Gao et al., 2013), ¹³(Onder et al., 2012), ¹⁴(Kawamura et al., 2009), ¹⁵(Tahmasebi et al., 2014), ¹⁶(Judson et al., 2009), ¹⁷(Worringer et al., 2014), ¹⁸(Anokye-Danso et al., 2011), ¹⁹(Miyoshi et al., 2011), ²⁰(Shu et al., 2013), ²¹(Montserrat et al., 2013). (B) Chemical reprogramming strategies: ²²(Huangfu et al., 2008a), ²³⁽Huangfu et al., 2008b), ²⁴(Lyssiotis et al., 2009), ²⁵(Esteban et al., 2010), ²⁶(Wang et al., 2011), ²⁷(Chen et al., 2011), ²⁸(Maherali and Hochedlinger, 2009), ²⁹(Ichida et al., 2009), ³⁰(Hou et al., 2013), ³¹(Zhu et al., 2010). Original Yamanaka factors are colored light gray. This is not an exhaustive list of factor and chemical combinations, but only includes those methods highlighted in the text. Note that these studies were mainly performed in fibroblasts and transgene requirements may be different for other types of somatic donor cells, such as neural stem cells.

Figure 4. Gatekeepers of pluripotency

Requirements of the master transcription factors Oct4 and Nanog during epigenetic reprogramming events in the mouse system in vitro and in vivo. Broken lines indicate cell fate transitions where the role of Oct4 or Nanog is contested (see text for details). ESCs: embryonic stem cells; EpiSCs: epiblast stem cells; SCNT: somatic cell nuclear transfer; 2i: cocktail of MEK and GSK3 inhibitors.

Figure 5. An interactome of reprogramming factors

Protein-protein interactions between reprogramming factors (blue) and epigenetic modifiers (red) implicated in the induction of pluripotency. Red borders indicate the original Yamanaka factors. Interaction data was curated from interactome studies in mouse ESCs (Costa et al., 2013; Ding et al., 2012; Gagliardi et al., 2013; Gao et al., 2012; Wang et al., 2006) and additional studies described in the text. Superimposed on the interactome are regulatory relationships inferred from single cell analysis during reprogramming (yellow arrows) (Buganim et al., 2012).