Remarkable similarity between embryonic and induced pluripotent stem cells - a UW proteomic study
In a new study published in Nature Methods, researchers at the University of Wisconsin-Madison report the first full measurement of the proteins made by human embryonic and induced pluripotent stem cells.
They looked at four embryonic stem cells (ESC) and four induced pluripotent stem cells (IPSC). The proteins turned out to be 99 percent similar, says Joshua Coon, an associate professor of chemistry and biomolecular chemistry who directed the project.
However, their study revealed subtle but reproducible differences in protein expression and protein phosphorylation in these two cell types. With multiple biological replicates they found 293 proteins and 292 phosphoisoforms to be differed significantly between ESCs and IPSCs, though most of them differed only by less than two-fold. Those interested in IPS cells might have been looking forward to find out more about these differences between the cell types rather than similarity.
According to the paper, similarity of human ESCs and iPSCs at the protein level remains completely unexplored.
Ever since human induced pluripotent stem cells were first derived in 2007, scientists have wondered whether they were functionally equivalent to embryonic stem cells, which are sourced in early stage embryos.
Both cell types have the ability to differentiate into any cell in the body, but their origins - in embryonic and adult tissue - suggest that they are not identical.
Although both cell types have great potential in basic biological research and in cell- and tissue-replacement therapy, the newer form, called IPS cells, have two advantages. They face less ethical constraint, as they do not require embryos. And they could be more useful in cell-replacement therapies: growing them from the patient's own cells would avoid immune rejection.
But until IPS cells are proven to have the same traits as embryonic stem cells, they cannot be considered to be identical.
"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," Dr Coon says.
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.
The study in Nature Methods, published online, is the first comprehensive comparison of proteins in the two stem cell types, says Doug Phanstiel, who is now at Stanford University and who worked with Justin Brumbaugh on the project as graduate students at UW-Madison.
"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.
The new study measured each of these activities, Phanstiel says.
"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 says, 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.
The ability to measure proteins in such detail emerged from improved ways to measure mass, Coon says.
"New technical developments in both our ability to measure a protein's mass - accurate to the third or fourth decimal place - and to compare the proteins from up to eight different cell lines at a time - permitted this important comparison for the first time," says Coon.
The study is not the last word in determining the similarity of the two types of pluripotent stem cells, says Coon, who worked with UW-Madison stem-cell pioneer James Thomson on the project.
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."
Source article: Proteomic and phosphoproteomic comparison of human ES and iPS cells. Douglas H Phanstiel, Justin Brumbaugh, Craig D Wenger, Shulan Tian, Mitchell D Probasco, Derek J Bailey, Danielle L Swaney, Mark A Tervo, Jennifer M Bolin, Victor Ruotti, Ron Stewart, James A Thomson & Joshua J Coon. Nature Methods. Published online: 11 September 2011 doi:10.1038/nmeth.1699.
Additional source: University of Wisconsin Madison.