We live in an era where stem cell treatments are already being tested in human clinical trials for eye disease, spinal cord injury, and type 1 diabetes. The hope is that transplanting stem cells or their cell derivatives will replace diseased tissue, restore function, and cure patients – all while being safe and without causing negative side effects.

Safety will be the key to the future success of stem cell replacement therapies. We’ve learned our lesson from early failed gene therapy experiments where genetically altered stem cells that were supposed to help patients actually caused them to get cancer. Science has since developed methods of gene therapy that appear safe, but new concerns have cropped up around the safety of the methods used to generate pluripotent stem cells, which are considered a potential starting material for cell replacement therapies.

Stem cell reprogramming can cause problems

Induced pluripotent stem cells, or iPS cells, are a potential source of pluripotent stem cells for cell therapy. These cells are equivalent to embryonic stem cells but can be generated from adult tissue (such as skin or even blood) by reprogramming cells back to a pluripotent state. During cellular reprogramming, one set of genes is turned off and another set is turned on through a process called epigenetic remodeling. We don’t have time to explain epigenetics in this blog, but to be brief, it involves chromatin remodeling (chromatin is the complex of DNA and protein that make up chromosomes) and is essential for controlling gene expression.

To make healthy iPS cells, the intricate steps involved in cellular reprogramming and epigenetic remodeling have to be coordinated perfectly. Scientists worry that these processes aren’t always perfect and that cancer-causing mutations could be introduced that could cause tumors when transplanted into patients.

A CIRM-funded study published Friday in Nature Communications offers some relief to this potential roadblock to using reprogrammed iPS cells for cell therapy. Scientists from The Scripps Research Institute (TSRI) and the J. Craig Venter Institute (JCVI) collaborated on a study that assessed the safety of three common methods for generating iPS cells. Their findings suggest that these reprogramming methods are relatively safe and unlikely to give cancer-causing mutations to patients.

Comparing three reprogramming methods

In case you didn’t know, iPS cells are typically made by turning on expression of four genes – OCT4, SOX2, KLF4, and c-MYC – that maintain stem cells in a pluripotent state. Scientists can force an adult cell to express these genes by delivering extra copies into the cell. In this study, the scientists conducted a comparative genomic analysis of three commonly used iPS cell reprogramming methods (integrating retroviral vectors, non-integrating Sendai virus, and synthetic mRNAs) to search for potential cancer-causing mutations in the DNA of the iPS cells.

Unlike previous studies that focused on finding a single type of genetic mutation in reprogrammed iPS cells, the group looked at multiple types of genetic mutations – from single nucleotide changes in DNA to large structural variations – by comparing whole-genome sequencing data of the starting parental cells (skin cells) to iPS cells.

They concluded that the three reprogramming methods generally do not cause serious problems and hypothesized that cancer-causing mutations likely happen at a later step after the iPS cells are already made, an issue the team is addressing in ongoing work.

They explained in their publication:

“We detected subtle differences in the numbers of [genetic] variants depending on the method, but rarely found mutations in genes that have any known association with increased cancer risk. We conclude that mutations that have been reported in iPS cell cultures are unlikely to be caused by their reprogramming, but instead are probably due to the well-known selective pressures that occur when hPSCs [human pluripotent stem cells] are expanded in culture.”

The safety of patients comes first

Senior authors on the study, Dr. Jeanne Loring from TSRI and Dr. Nicholas Schork from JCVI, explained in a TSRI News Release that the goal of this study was to make sure that the reprogramming methods used to make iPS cells were safe for patients.

Jeanne Loring

“We wanted to know whether reprogramming cells would make the cells prone to mutations,” said Jeanne Loring, “The answer is ‘no.’ The methods we’re using to make pluripotent stem cells are safe.”

 

Nicholas Schork added:

Nicholas Schork

“The safety of patients comes first, and our study is one of the first to address the safety concerns about iPSC-based cell replacement strategies and hopefully will spark further interest.”

 

 

Moving from bench to clinic

It’s good news that reprogramming methods are relatively safe, but the fact that maintaining and expanding iPS cells in culture causes cancerous mutations is still a major issue that scientists need to address.

Jeanne Loring recognizes this important issue and says that the next steps are to use similar genomic analyses to assess the safety of reprogrammed iPS cells before they are used in patients.

“We need to move on to developing these cells for clinical applications,” said Loring. “The quality control we’re recommending is to use genomic methods to thoroughly characterize the cells before you put them into people.”