Induced Pluripotent Stem Cell Mutations Do Not Cluster in Protein-Coding Genes

Induced pluripotent stem cells (iPSCs) are made by introducing genes into adult cells that push the adult cell into an embryonic-like state. The earliest iPSCs were made with engineered retroviruses that actually inserted their genomes into the chromosomes of the host cell. The use of such tools to form iPSCs produces cells with large segments of DNA inserted into their chromosomes, which can cause mutations. This is not a desirable trait if such are to be used in a clinical setting. Additionally, detailed genetic examinations of iPSCs have shown that the very process of reprogramming adult cells to form cells with embryonic characteristics causes mutations (Gore, et al., Nature 471 (2011): 63–67).

Thus, iPSCs tend to harbor a variety of mutations that range from base sequence changes in their DNA to changes in the number of copies of various genes. These types of mutations can make iPSCs rather dangerous to use clinically. In fact one study suggest that the mutations generated by making iPSCs can potentially illicitly activate the expression of particular genes.  These inappropriately activated genes can induce the immune system of the person who donated the adult cells from which the iPSCs ere made to attack and reject the iPSCs (Zhao, et al., Nature 474, (2011): 212–215).

One issue that has not been properly addressed to date is the status of iPSCs made by alternative methods.  The Gore paper examined 22 iPSC lines and three of them were derived by methods that do not use viruses that insert themselves into the genome of the host cell.  Their data suggested that these iPSC lines also had higher numbers of mutations than the cells from which they were derived, but the tables in the Gore paper tend to show that the mRNA-derived iPSCs had lower numbers of mutations than those derived from more traditional means. Another issue is that the human genome has a tremendous amount of empty space.  Mutations that do not occur within the coding region of a gene is likely to not cause a problem.

Into the fray comes a paper from the laboratory of Linzhao Cheng at the Johns Hopkins Institute for Cell Engineering.  Cheng and his co-workers made iPSCs from bone marrow stem cells and discovered that while they possessed more mutations than the cells from which they were made, those mutations were typically not in genes that will affect the function of the cells. Cheng and his colleagues also used techniques to make iPSCs that did not utilize viruses that insert into the genomes of the host cell.

Cheng’s group took the bone marrow-derived iPSCs and differentiated them into mesenchymal stem cells, and then sequenced their genomes to determine the new mutations that were caused by the reprogramming.  They discovered that there were 1,000 to 1,800 new mutations in each cell line, but the mutations rarely occurred in protein coding regions.

On the average, each iPSC had six mutations that occurred in coding regions, but each mesenchymal stem cell made from the iPSC lines had about 12 mutations per cell in coding regions.  While this sounds awful, we must remember that some mutations are very consequential for the proteins that are encoded by genes, but many are not.  For example, the sickle-cell disease is due to one mutation in the hemoglobin gene that causes the hemoglobin protein to form chains that deform the red blood cell.  However, there are many other mutations in the hemoglobin gene that do not affect its function in the least.

When Cheng and his colleagues examined where the mutations occurred, they found that none of the mutations in protein coding regions that they had detected were in genes that would cause the iPSCs to grow uncontrollably or predispose the cells to form cancerous tumors.

Based on his findings, Cheng thinks that iPSCs form a smaller risk than was previously thought.  His results are published in Cell Stem Cell.