Induced Pluripotent Stem Cells Remember their Past Lives

When adult cells are re-programmed into induced pluripotent stem cells (iPS cells), they still have some characteristics of their past identities. This “hanging on their past” might explain why iPSCs have some limits on their ability to function as candidates for cell replacement therapies. These findings, which were published online July 19 in Nature, highlight a major challenge in developing clinical and scientific applications for iPSCs.
George Daley, Howard Hughes Medical Institute investigator and Director of the Stem Cell Transplantation Program at Children’s Hospital said, “iPS cells retain a ‘memory’ of their tissue of origin. iPS cells made from blood are easier to turn back into blood than, say, iPS cells made from skin cells or brain cells.” If we contrast this to another technique known as nuclear transfer, pluripotent stem cells made from cloned embryos apparently have no memory of their cells of origin, and can transform into several tissue types with equal ease. In iPS cells, however, the memory of the original donor tissue can be more fully erased with additional steps or drugs, the researchers found, which made those iPS cells as good as the nuclear-transfer stem cells at generating different types of early tissue cells in lab dishes.
The residual cellular memory comes in part from lingering genome-wide “epigenetic modifications” to the DNA that gives each cell a distinctive identity, such as skin or blood, despite otherwise identical genomes. In the study, the persistent bits of a certain type of epigenetic modification called methylation were so distinctive in iPS cells that their tissues of origin could be identified by their methylation signatures alone.
It turns out that the genomes of iPSCs were not as completely reprogrammed as those from nuclear transfer cells. DNA methylation was completely reset in nuclear transfer cells and incompletely reset in iPSCs. These epigenetic marks help explain the lineage restriction of iPSCs, since they leave an epigenetic memory of the tissue of origin that remains after reprogramming.
Mind you, epigenetic memory can be a very helpful thing when it comes to some clinical applications. For example, generating blood cells from iPS cells originally derived from a person’s own blood, etc. However, this epigenetic memory may interfere with efforts to engineer other tissues for treatment in diseases such as Parkinson’s or diabetes or to use the cells to study the same disease processes in laboratory dishes and test drugs for potential treatments and toxicities.
In the current study, Kitai Kim, PhD, postdoctoral fellow in the Daley lab, tested mice iPS cells head-to-head with pluripotent cells made through somatic cell nuclear transfer. Best known as the cloning method that created the sheep Dolly fourteen years ago, nuclear transfer reprograms an adult cell by transferring its nucleus into an unfertilized egg cell, or oocyte, whose nucleus has been removed. The process of transferring the nucleus immediately reprograms it epigenetically, replicating the same process that happens to sperm upon fertilization. They noted that stem cells generated by somatic cell nuclear transfer were, for the most part, very much like embryonic stem cells. Daley noted that there is still a need to study the mechanisms by which nuclear transfer reprograms cells, since such finding might help us make better iPS cells.”
However, Kim took this study one step further. He used older mice for this study (older mice – ages 1 to 2). His aim was to simulate future human clinical scenario, which is likely to involve older people. Older cells are more difficult to reprogram. Kim originally wanted to compare the transplantation success of blood cells made from three different pluripotent sources: iPS cells, embryonic stem cells (the gold standard), and nuclear transfer stem cells. He did not get as far as transplantation. Since they saw such striking differences in blood-forming potential, Kim and his co-workers examined this phenomenon instead.
They found that iPS cells from blood were best at making blood, and fibroblasts were best at differentiating into bone. However, if they reset the iPS cells more fully by differentiating them first into blood cells and then reprogramming them again, or by treating them with drugs that change their epigenetic profile, then they could differentiate into other cell types more effectively. In contrast, nuclear transfer stem cells from the same sources — blood cells and skin – were equally able to differentiate into blood and bone, Kim and his colleagues found. Like iPS cells, the nuclear transfer technique also creates patient-specific cells, but has not yet proven successful with human cells.
Another study published online simultaneously in the journal Nature Biotechnology reports similar findings. “Our paper comes to a similar conclusion that a retention of memory reflects the cell of origin and affects the capacity of the iPS cell to differentiate into other cell types,” said senior author Konrad Hochedlinger, PhD, a stem cell biologist at the Massachusetts General Hospital Center for Regenerative Medicine and, like Daley, a member of the Harvard Stem Cell Institute. “When we let the cells go through a lot of cell divisions, they lose the memory,” he said.

Synthetic bone graft recruits stem cells for faster bone healing

Scientists have shown that calcium phosphate materials might one day replace natural bone implants. This new study establishes that calcium phosphate ceramics have the ability to stimulate bone regrowth by attracting stem cells and ‘growth factors’ to promote healing and the integration of the grafted tissue. Professor Joost de Bruijn from the School of Engineering and Materials Science at Queen Mary, University of London said, “The rate of bone repair we see with these materials rivals that of traditional grafts using a patients’ own bone, and what sets it apart from other synthetic graft substitutes is its ability to attract stem cells and the body’s natural growth factors, which coincide to form new, strong, natural bone around an artificial graft.”

When this research group compared natural bone grafts against ceramic particles with varied structural and chemical properties, they discovered that micro-porous ceramic particles composed of calcium phosphate, the primary component of bone ash, induced stem cells to develop into bone cells in the test tube and stimulated bone growth in live tissue in several animal model systems (mice, dogs and sheep).
The study also shows how it also matches a commercially available product that contains artificial growth factors and has the undesirable side-effect of causing bone fragments to form in nearby soft tissue, such as muscle. Bone injuries packed with the ceramic particles healed similarly to implants constructed from the animals’ own bone.

Although the researchers have not yet identified the mechanism that drives bone growth in the synthetic implants, they note that variations in the ceramic material’s chemistry, micro-porosity, micro-structure, and degradation influence the graft’s performance.

The study suggests that biomaterials-based bone grafts can manipulate cell behavior in order to repair injury, and one day may be used to repair bone injuries in humans.

Reduction of teratoma formation in embryonic stem cells

Tumor formation is an ongoing problem with embryonic stem cell treatments. The pluipotency of these cells and their ability to replicate themselves indefinitely that makes them so promising also gives them the ability to form tumors. These tumors, called teratomas, are mixtures of different types of tissues, and depending on where they are located, can be benign or rather dangerous. However, a new study performed at the University of California, San Diego (UCSD) shows that researchers have managed to reduce the size and number of them formed after implantation, which is an important first step to eradicating them completely.

Yang Xu, a biology professor at UCSD, said “To eliminate the residue of undifferentiated embryonic stem cells during the differentiation, it is important to elucidate the pathways that are important to maintain the self-renewal of embryonic stem cells.”

Xu and his colleagues identified a new signaling pathway that undifferentiated cells use for propagation. It depends upon the phosphorylation of the transcription factor called Nanog. It turns out that this phosphorylation (attachment of a phosphate group to a protein) is crucial for cell replication. By inhibiting this phosphorylation with small-molecules, they observed a stark decrease in resulting teratomas after transplantation. Apparently, Xu and colleagues observed a 70% reduction in the mass of teratomas, and also, there was a lack of self-renewing stem cells in those teratomas that did form.

Xu hopes to eventually eliminate teratoma altogether, which will make embryonic stem cells safer for use in human applications. See “Phosphorylation stabilizes Nanog by promoting its interaction with Pin1,” which was published on the PNAS website on July 6.