Reprogramming Pluripotent Cells into Totipotent Cells

With the advent of the Nobel Prize-winning research of Shinya Yamanaka, scientists are presently able to reprogram mature, adult cells into pluripotent cells. These “induced pluripotent stem cells” or iPSCs are made by genetically engineering adult cells and culturing them in special conditions. These iPSCs can also be differentiated, potentially, into every cell type in the adult human body. Now Maria-Elena Torres-Padilla‘s research team is trying to push the limits of stem cell science even further.

Torres-Padilla and her coworker successfully made “totipotent” cells, which have the same characteristics as those of the earliest embryonic stages, from pluripotent stem cells. This work was the result of a fruitful collaboration between Juanma Vaquerizas from the Max Planck Institute for Molecular Biomedicine (Münster, Germany), and Maria-Elena Torres-Padilla and her colleagues at the Institute of Genetics and Molecular and Cellular Biology (IGBMC) at Illkirch, France. This work has been published in the journal Nature Structural & Molecular Biology.

Soon after fertilization, the embryo begins it first rounds of cell division, which is known as the “early cleavage” stages. At this early stage of development, when the embryo is composed of only 1 or 2 cells, the “blastomeres” or cells of the embryo are “totipotent.” Totipotent means that these blastomeres can produce an entire embryo, or the placenta and umbilical cord that accompany it.

Early Cleavage Stages

After the 12-16-cell stage, the embryo undergoes a complex process called “compaction,” in which the cells become very tightly bound together and two populations of cells become apparent.

Post-Compaction Embryo
Post-Compaction Embryo

The cells on the inside, which give rise to the cells of the “inner cell mass” (ICM), and outside cells, which give rise to the “trophectoderm” that produce the placenta. Trophectoderm cells express a specific set of genes; Yap1, Tead4, Gata3, Cdx2, Eomes and Elf5. The ICM generates the embryo proper and the ICM cells express a cadre of genes specific to these cells; Oct4, FGF4, Sall4, Sox2 and Nanog. These ICM cells are no longer totipotent, but have become “pluripotent,” can differentiate into any tissue, but they cannot alone produce the placenta or a whole embryo. As development progresses, these pluripotent cells continue to specialize and form the various tissues of the body through the process of cellular differentiation.

While it is possible to make pluripotent cells from mature, adult cells, Torres-Padilla and her coworkers have studied the characteristics of totipotent cells of the embryo and discovered factors capable of inducing a totipotent-like state.

When they cultured pluripotent stem cells in culture, a small percentage of totipotent cells appear spontaneously. Such cells are called “2C-like cells,” after their resemblance to the 2-cell stage embryo. Torres-Padilla and her team compared these 2C-like cells to totipotent cells in early embryos in order to determine their common characteristics and the features that distinguish them from pluripotent cells. In particular, Torres-Padilla and her collaborators found that the chromosomes of totipotent cells were less condensed and that the amount of the protein complex CAF1 was diminished. CAF1 (Chromatin Assembly Factor 1) is a protein complex that helps assemble histone proteins onto DNA.


Histones act as tiny spools around which DNA is wound. Because DNA is negatively charged, and histones are positively charged, the two have a natural affinity for each other. CAF1 binds to histones and regulates the association of histones with DNA in order to ensure that the assembly of histones on DNA is and orderly process. Histones wind DNA into a tight structure called “chromatin.” CAF1, as it turns out, is responsible for maintaining the pluripotent state by ensuring that the DNA remains properly wound around histones.


As an extension of this hypothesis, Torres-Padilla and her crew were able to induce a totipotent state by inactivating the expression of the CAF1 complex. CAF1 inactivation caused the chromatin of pluripotent cells to reform into a less condensed state, and this less condensed state was conducive to totipotency.

These data provide new avenues for understanding the nature of pluripotency, and could increase the efficiency of reprogramming somatic cells to be used for applications in regenerative medicine,

STAP Cells: The Plot Thickens Even More

You might remember that Charles Vacanti and researchers at the RIKEN Institute in Japan reported a protocol for reprogramming mature mouse cells into pluripotent stem cells that could not only integrate into mouse embryos, but could also contribute to the formation of the placenta. To convert mature cells into pluripotent cells, Vacanti and others exposed the cells to slightly acidic conditions or other types of stressful conditions and the cells reverted to a pluripotent state.

Even though Vacanti and others published these results in the prestigious journal Nature, as other scientists tried to replicate the results in these papers, they found themselves growing more and more frustrated. Also, some gaffes with a few of the figures contributed to a kind of pall that has hung over this research in general.

The original makers of these cells, stress-acquired acquisition of pluripotency or STAP cells, have now made a detailed protocol of how they made their STAP cells publicly available at the Nature Protocol Exchange. Already. it is clear that a few things about the original paper are generating many questions.

First of all, Charles Vacanti’s name does not appear on the protocol. He was the corresponding author of the original paper. Therefore the absence of his name raises some eyebrows. Secondly, the authors seem to have backed off a few of their original claims.

For example one of the statements toward the beginning of the protocol says, “Despite its seeming simplicity, this procedure requires special care in cell handling and culture conditions, as well as in the choice of the starting cell population.” Whereas the original paper, on the first reading at least, seemed to convey that making STAP cells was fairly straightforward, this seems to no longer be the case, if the words of this protocol are taken at face value.

Also, the protocol notes that cultured cells do not work with their protocol. The authors write, “Primary cells should be used. We have found that it is difficult to reprogram mouse embryonic fibroblasts (MEF) that have been expanded in vitro, while fresh MEF are competent.”  This would probably explain inability of several well-regarded stem cell laboratories to recapitulate this work, since the majority of them probably used cultured cells. This, however, seems to contradict claims made in the original paper that multiple, distinct cell types could be converted into STAP cells.

Another clarification that the protocol provides that was not made clear in the original paper is that STAP cells and STAP stem cells are not the same thing. According to the authors, the protocol provided at Nature Protocol Exchange produces STAP cells, which have the capacity to contribute to the embryo and the placenta. On the other hand, STAP stem cells, are made from STAP cells by growing them in ACTH-containing medium on feeder cells, after which the cells are switched to ESC media with 20% Fetal Bovine Serum. STAP stem cells have lost the ability to contribute to extra-embryonic tissues.

Of even greater concern is a point raised by Paul Knoepfler at UC Davis. Knoepfler noticed that the original paper argued that some of their STAP cells were made from mature T cells. T cells rearrange the genes that encode the T cell receptor. If these mature T cells were used to make STAP cells, then they should have rearranged T cell receptor genes. The paper by Vacanti and others shows precisely that in a figure labeled 1i. However, in the protocol, the authors state that their STAP cells were NOT made from T-cells. In Knoepfler’s words: “On a simple level to me this new statement seems like a red flag.”

Other comments from Knoepfler’s blog noted that the protocol does not work on mice older than one week old. Indeed, the protocol itself clearly states that “Cells from mice older than one week showed very poor reprogramming efficiency under the current protocol. Cells from male animals showed higher efficiency than those from female.”  Thus the universe of cells that can be converted into STAP cells seems to have contracted by quite a bit.

From all this it seems very likely that the STAP paper will need to go through several corrections. Some think that the paper should be retracted altogether. I think I agree with Knoepfler and we should take a “wait and see” approach. If some scientists can get this protocol to work, then great. But even then, multiple corrections to the original paper will need to be submitted. Also, the usefulness of these procedure for regenerative medicine seems suspect, at least at the moment. The cells types that can be reprogrammed with this protocol are simply too few for practical use. Also, to date, we only have Vacanti’s word that this protocol works on human cells. Forgive me, but given the gaffes associated with this present paper, that’s not terribly reassuring.