A bioinformatic assay for pluripotency in human cells

Abstract

Pluripotent stem cells (PSCs) are defined by their potential to generate all cell types of an organism. The standard assay for pluripotency of mouse PSCs is cell transmission through the germline, but for human PSCs researchers depend on indirect methods such as differentiation into teratomas in immunodeficient mice. Here we report PluriTest, a robust open-access bioinformatic assay of pluripotency in human cells based on their gene expression profiles.

Figure 1. A multidimensional data model for assessing pluripotent stem cells

A Schematic for PluriTest. (b–c) We constructed and optimized a multi-class classifier (Pluripotency Score, b, c) and a one-class classifier (Novelty Score, c) to distinguish pluripotent stem cells (PSC) from other cell types and tissues. In (b), we show pluripotent (red) and somatic samples (blue) in the training dataset as assessed with the Pluripotency Score and in (c) with both PluriTest scores. In (d–g), we plot Pluripotency Scores against Novelty Scores for test data set samples. The classifiers were tested against datasets generated on four different microarray platforms: Illumina WG6v1 (c, 177 samples), HT12v3 (d, 498 samples), HT12v4 (e, 38 samples) and Affymetrix U133A (f, 5372 samples)10). Samples for these datasets were independently generated (c and d) or curated from published studies (c, d, f). In d, the lines in the plot indicate empirically determined thresholds for defining normal pluripotent lines (see also Supplementary Fig. 2).

Figure 2. Application of PluriTest

The graphs show the actual output of PluriTest. Pluripotency score is plotted against novelty score for the indicated samples. The background encodes an empirical density map indicating pluripotency (red) and novelty (blue). (a–c) PluriTest results for known pluripotent cells and somatic cells and tissues (a), for fully and partially reprogrammed iPSC lines (b), and for an hESC line (WA09) being differentiated into neural precursors, at the indicated time points. In (d) PluriTest was run on mixed samples of hESC and hESC-derived neural precursor RNA (day 0 and day 14 from c) at the indicated ratios. hESC, human embryonic stem cell, hiPSC, human induced pluripotent stem cell.