First Full Measurement and Comparison of Proteins Made By Embryonic and Induced Pluripotent Stem Cells

In a study of four embryonic stem cells and four IPS cells, proteins turned out to be 99 percent similar according to  Joshua Coon, associate professor of chemistry and biomolecular chemistry at the University of Wisconsin Madison.

Proteins are complex molecules made by cells for innumerable structural and chemical purposes, and the new study measured more than 6,000 individual proteins using highly accurate mass spectrometry, a technique that measures mass as the first step of identifying proteins.

"This study is the first comprehensive comparison of proteins in the two stem cell types," said Doug Phanstiel, who is now at Stanford University.

"From a biological standpoint, what is novel is that this is the first proteomic comparison of embryonic stem cells and IPS cells," says Phanstiel, referring to the study of which proteins a cell produces.

In essence, every cell in the body has the genes to make any protein the body might need, but cells make only the proteins that further their own biological role. Cells regulate the formation and activity of proteins in three ways: First, by controlling the production of RNA, a molecule that transfers the DNA code to protein-making structures; second, by controlling the quantity of each protein made; and third, by adding structures to the protein that regulate when it will be active.

"And because we compared four lines of each type of stem cell and the comparisons were run three times, the statistics are extremely robust," he adds.

The new report, Coon said, suggests that embryonic stem cells and IPS cells are quite similar. According to some measurements, the protein production of an embryonic stem cell was closer to that of an IPS cell than to a second embryonic stem cell.

"We looked at RNA, at proteins and at structures on the proteins that help regulate their activity and saw substantial similarity between the two stem-cell types," he added.

Because clinical uses of either type of stem cells will require that they be transformed into more specialized cells, researchers still need to know more about protein production after a stem cell is differentiated into, for example, a neuron or heart muscle cell.

This technology, Coon says, "is now well-positioned to study how closely molecules contained in these promising cells change after they are differentiated into the cells that do the work in our bodies — a critical next step in regenerative medicine."

Adapted from the University of Wisconsin Madison announcement.