According to a recent press report from Applied Biosystems, researchers with the International Stem Cell Initiative (ISCI) have identified a set of common gene expression markers that may be used to reliably characterize diverse human embryonic stem cell (hESC) lines. The initiative represents the first internationally coordinated effort to provide a systematic and comparative survey of the hESC lines available from various research groups around the world. The research findings were published in the July issue of Nature Biotechnology.

Well-characterized, stable cell lines that can be predictably reproduced are essential for successful stem cell research, yet scientists previously have not had a reliable means to understand similarities and differences among the cell lines available for study.

To address this challenge, the ISCI employed technology from Applied Biosystems to carry out the first comparative study of a large and diverse collection of hESC lines from 17 laboratories in the U.S., Europe, Israel, Japan, and Australia. The team used several approaches to identify a reliable set of genetic markers to characterize hESCs, which included profiling 93 genes in 59 different cell lines.

A major finding from this first phase of the ICSI project was that all of the cell lines studied shared a number of key molecular signatures, despite different genetic constitutions and the various culture techniques to which they have been subjected. It is expected that these newly identified molecular markers may be used to validate the potential of individual hESC lines to differentiate into other types of cells, also referred to as their pluripotency status, the report outlined.

The ISCI scientists used the Applied Biosystems 7900HT Fast Real-Time PCR System and custom Applied Biosystems TaqMan Arrays to identify six key genetic markers and 14 additional genes highly correlated with a key pluripotency marker in all the cell lines tested. Applied Biosystems worked with the ISCI researchers at the centralized analytical laboratory at the University of Sheffield in the U.K., to select the assays, process the arrays and analyze the results.

“These findings are a crucial first step in ensuring that future advances in the field of stem cell research involve internationally coordinated quality standards,” said Paul Gokhale, of the Centre for Stem Cell Research at the University of Sheffield. “Our collective aim is to provide openness, reliability, and the ability for scientists to confidently reproduce and extend each other’s work.”

As a result of this ISCI study, Applied Biosystems has developed the TaqMan Array Human Stem Cell Pluripotency Panel, which targets 96 genes for independent monitoring of hESC lines to help investigators compare cell lines derived from diverse sources. The company said it has also created a TaqMan Array Mouse Stem Cell Pluripotency Panel comprised of mouse orthologs to the genes on the human panel.

 The new TaqMan arrays, along with a complete line of TaqMan Array gene signature panels and more than 700,000 individual TaqMan Gene Expression Assays are available on the Applied Biosystems website.

The TaqMan Arrays used in this study are microfluidic cards that enable parallel analysis of up to eight biological samples across 12 to 384 pre-loaded TaqMan Gene Expression Assays, without requiring liquid-handling robots or multi-channel pipettes. To perform gene expression analysis, researchers simply add cDNA to the TaqMan Arrays. The arrays were then analyzed on the Applied Biosystems 7900HT Fast Real-Time PCR System.

The next phase of the ISCI work will expand on the current findings by adding additional hESCs to the study in order to further verify the team’s initial results, as well as to test the effects of different culture media on hESC growth and differentiation, and on genetic changes in these cells. A comprehensive registry of the ISCI cell lines and their molecular characteristics is now publicly available at http://www.stemcellforum.org/