Assessment of human pluripotent stem cells with PluriTest

Abstract

Assessing pluripotency in human cells is inherently an intractable problem. In animal systems, pluripotency can be verified through direct means: pluripotent stem cells can be introduced into an developing embryo and thus the cellular developmental potential of any given in vitro preparation can be directly determined by observing the amount of chimaerism or viability of organisms partially or fully derived from in vitro stem cells (Nagy, Rossant et al., 1993).

     For obvious ethical reasons such stringent experimentation is impossible in the human system; thus indirect evidence through biomarkers and correlative measures of differentiation potential are the next best level of evidence for human stem cell pluripotency.

Many if not most stem cell markers that are widely used for predicting pluripotency in human cells are chosen because of evidence from other species. Yet there are hard limitations to this approach because of two main obstacles: first, using only few markers will erroneously validate potentially abnormal stem cells when these irregular preparations express the limited set of markers similar to normal stem cells. Second, in spite of some striking orthologous similarities, the transfer of mechanistic insight from animals to the human systems for fine-grained determination of pluripotent features is problematic. There are species-specific differences in the cultured pluripotent phenotypes and significant evolutionary structural variations in the transcription network wiring of human and animal cells.

     We have developed a pragmatic, purely data-driven approach toward empirically defining the “normal” human pluripotent state via interrogation of large scale datasets of genome-wide somatic and pluripotent expression profiles (Müller, Schuldt et al., 2011). Models derived from this dataset can be used to rapidly, confidently and inexpensively assess the pluripotency of human cells through web-based analysis of microarray data from new stem cell preparations. In this article, we will introduce the reader into some of the underlying concepts of the tool we call “PluriTest”, demonstrate a real world use case, and discuss the potential as well as the limitations of our approach.