Evolution of iPSC disease models

Abstract

Human induced pluripotent stem cells (iPSCs) hold unprecedented potential to model human development and genetic disorders due to their capability to self-renew and differentiate into any somatic cell type. In the year of 2011, a number of iPSC disease models have been successfully developed for studying the mechanism of human diseases as well as establishing platforms for drug screening and testing (Batista et al., 2011; Brennand et al., 2011; Devine et al., 2011; Itzhaki et al., 2011; Koch et al., 2011; Liu et al., 2011a; Mazzulli et al., 2011; Nguyen et al., 2011; Pasca et al., 2011; Quarto et al., 2011; Tiscornia et al., 2011; Wu and Hochedlinger, 2011; Yazawa et al., 2011; Zhang et al., 2011; Zhu et al., 2011). One key hypothesis of current iPSC disease models is based on the presumption that wild type and diseased iPSCs are equal to their embryonic stem cell (ESC) counterparts. However, this hypothesis seems to be challenged by several recent findings on the striking differences between ESCs and iPSCs. At the genomic level, the reprogramming process tends to cause the accumulation of DNA mutations as well as other chromosomal abnormalities related to cancer pathways (Panopoulos et al., 2011). Whereas there is no relevant in vivo data indicating that these mutations are indeed linked to tumorigenesis, the genetic aberrances accumulated during reprogramming probably interfere with the cellular parameters in either iPSCs or their differentiated derivatives. If specific diseases, especially those associated with genomic instability, facilitate the accumulation of more genetic mutations during reprogramming, this could result in wrong explanation of the phenotypes of iPSC disease models. In fact, the evaluation on how aspects of specific diseases affect reprogramming-associated mutations has not been reported. Additionally, at the epigenomic level, the residual epigenetic memories of iPSCs from their original cellular environment likely represent another barrier to being a true phenocopy of their ESC counterparts. In support of this, mouse iPSCs, but not ESCs, show immune rejection upon transplantation (Zhao et al., 2011), suggesting that subtle epigenetic differences might cause substantially different cell identities. To date, it is not clear whether disease-associated epigenetic memories exist in patient-specific iPSCs. Only a few groups examined the successful resetting of abnormal epigenetic marks during reprogramming, such as histone and DNA methylation, in their iPSC disease models (Marchetto et al., 2010; Liu et al., 2011a). At the differentiation level, a number of reports have shown that iPSCs behave differently from their ESC counterparts (Buchholz et al., 2009; Bock et al., 2011; Kim et al., 2011), although researchers still don’t know how this difference affects recapitulation of disease phenotypes in vitro. It should also be noted that certain diseased somatic cellular environments might contribute to the defective reprogramming with a higher possibility. For example, cellular defects in Fanconi anemia patient fibroblasts resulted in a complete blockage of iPSC generation (Raya et al., 2009). Hence, to avoid misinterpretation of results, it seems essential to first evaluate whether generated patient iPSCs are completely reset to a patient ESC-like status. Along this line, thorough examination of various cellular parameters in patient-specific iPSCs could be a critical step before employment of any iPSC disease model in mechanistic studies or drug testing. As complementary approaches, the relevant assays with overexpression of a mutant (e.g. for dominant mutation) or knock-down of an endogenous protein (e.g. for recessive mutation) in disease-related cell types should be included to verify the specific aspects of disease phenotypes. Furthermore, the lack of appropriate control iPSC lines constructs another important experimental limitation for the use of patient-derived iPSCs. In fact, the “wild type” or “healthy” iPSC lines currently used as controls are derived from “phenotypically normal” populations, which nevertheless carry various genetic and epigenetic polymorphisms. The major concern with respect to these epigenetic and genetic variations is that they may cause inconsistent phenotypic