br Experimental Procedures br Author Contributions br Acknow

Experimental Procedures
Author Contributions
Acknowledgments
Introduction With the first reports on generating human induced pluripotent stem dna pk (hiPSCs) from human cells (Takahashi et al., 2007; Yu et al., 2007), the controversy regarding the ethics of research involving human embryonic stem cells (hESCs) (Thomson et al., 1998) has arisen once again (Holm, 2008). Opponents of hESC research have been quick to argue that, considering the availability of an alternative source of human PSCs (hPSCs), research in hESCs is no longer needed to realize the promise of hPSCs. However, even before the derivation of hiPSCs was first reported, leading scientists in the field of hPSC research emphasized the need to continue research in ESCs in case hiPSCs became available (Hyun et al., 2007). Several arguments have been put forward to support the continuation or even an extension of hESC research. For example, it has been reasoned that hESCs have advantages over hiPSCs for regenerative therapies because the latter may contain somatic mutations or reprogramming-induced epigenetic defects. Indeed, there are currently 11 clinical trials registered with the FDA in which hESC-derived cells are being used, mainly to establish treatments for different forms of macular degeneration, but also for neurological, cardiac, and pancreatic disorders (NIH, clinicaltrials.gov; https://clinicaltrials.gov/). Although the first results from one of the studies on macular degeneration have been reported (Schwartz et al., 2015), the vast majority of these trials started very recently, at a time when hiPSCs have already been available for years. Currently, hiPSC-derived cells are being used in one clinical trial in Japan (UMIN Clinical Trial Registry, ID UMIN000011929; http://www.umin.ac.jp/ctr/). Another argument in favor of continuing the use of hESCs is their utility for basic research (e.g., to gain a better understanding of human ground-state pluripotency) (Gafni et al., 2013), for studies of early human development (Niakan et al., 2012), or as cells that are unimpeded by epigenetic or environmental disturbances that are likely present in hiPSCs (e.g., to study gene function in a rather naive cell). One of the most widely used arguments to justify hESC research is that these cells are still needed as the “gold standard” for human pluripotency to characterize and qualify hiPSC lines and gain a deeper understanding of the reprogramming process. This argument is frequently used in the political debate among stem cell researchers and proponents of hESC research, and has become a central point in the attempt to justify continued support for this research, for example, by the European Union. Thinking this argument through implies that research into hESCs would mainly lead to a more complete understanding of induced pluripotency and would become more and more dispensable with increasing progress in hiPSC research. Indeed, although novel and less invasive methods for reprogramming somatic cells to pluripotency have been developed in recent years, and some difficulties in the reprogramming procedure have been overcome (Anokye-Danso et al., 2011; Kim et al., 2009; Warren et al., 2010; Yoshioka et al., 2013; Yu et al., 2009), many controversial studies have reported differences between the two types of hPSCs on both genetic and epigenetic levels (Liang and Zhang, 2013; Ma et al., 2014) that may, for example, result in deviant behaviors in specific differentiation settings (Bar-Nur et al., 2011; Hu et al., 2010; Mills et al., 2013). Thus, it is currently unequivocally crucial to use hESCs as a reference material to gain a deeper understanding of hiPSC biology and to improve reprogramming strategies.
Results
Discussion To identify global trends in the application of hESCs and hiPSCs in research, we established a curated database of published primary research conducted with these cells between 2008 and 2013, and performed a thorough analysis of studies involving only hESCs or only hiPSCs, as well as intersecting research. The results show that both the hESC and hiPSC research fields increased (hiPSC) or remained at a high level (hESC) with respect to impact and quantitative paper output. Research in which both hPSC types were applied in similar proportions included the development and optimization of cultivation and differentiation protocols, and research on animal models to develop cell-based therapies. Interestingly, we identified early segregation trends for the preferential research use of hESCs and hiPSCs in the recent past. For example, trends for the use of mostly hESCs include basic research on cell pluripotency and plasticity, and analysis of (early) developmental mechanisms. hiPSCs, on the other hand, clearly dominate the field of disease modeling, frequently in conjunction with the derivation of novel disease-specific hiPSC lines and the correction of genetic defects in vitro. Other topics of hiPSC research included the provision of cell models for drug development and toxicity testing, although rather surprisingly, a slight relative overweight of hESCs was found in this application field. This finding may have been influenced by our strict inclusion criteria, which only considered studies that directly used hPSCs, and excluded about 80 studies in which only commercially available hPSC-derived cardiomyocytes, hepatocytes, or neural cells were used. We also excluded other secondary studies that used hPSC-derived nucleic acids, proteins, or data. However, a more likely explanation is the relatively short time span of the research used in this analysis (years 2011–2013). Follow-up studies will be required to establish a trend in this specific area, especially in light of the recent establishment of large-scale hiPSC banking projects to meet the anticipated demand in this field (McKernan and Watt, 2013). It is intriguing that about 20% of the studies involving hiPSCs were focused on the establishment of disease-specific human cell lines, and frequently provided for the first time relevant human cell models for poorly understood, rare, and fatal human diseases (Cherry and Daley, 2013; Peitz et al., 2013). Notably, a large number of projects that aim to derive novel disease-specific hiPSC lines are currently registered with the NIH (ClinicalTrials.gov). While hESCs are a valuable resource for generating isogenic variants for specific diseases on a naive background, and therefore are also playing an increasing role in disease modeling, banking projects involving hESCs are mostly directed toward the distribution of highly characterized lines for comparable basic research and prospective clinical applications (Stacey et al., 2013). Moreover, in many cases, hESCs are used to provide a reliable source for differentiated or progenitor human cells such as neurons and cardiomyocytes, which are not readily accessible in other ways.