TSRI and JCVI scientists conclude that the process of reprogramming is unlikely to introduce variants that would make the cells appropriate for therapy. [Source: iStock/© Archeophoto]
TSRI and JCVI scientists conclude that the process of reprogramming is unlikely to introduce variants that would make the cells appropriate for therapy. [Source: iStock/© Archeophoto]

Cell-replacement therapies that depend on induced pluripotent stem cells (iPSCs) inspire hope and fear—hope that cells derived from iPSCs will actualize regenerative medicine; fear that the very same cells will bring cancer-causing mutations to patients. The fear lingers even though several studies have already suggested that iPSCs can be considered safe. These studies were conducted because iPSCs are created only after they have endured the rigors of reprogramming, stresses thought to be capable of introducing deleterious mutations.

A new study, led by scientists at The Scripps Research Institute (TSRI) and the J. Craig Venter Institute (JCVI), has examined the safety of iPSCs more comprehensively, and is thus more reassuring. The results of the new study appeared February 19 in the journal Nature Communications in an article entitled “Whole-genome mutational burden analysis of three pluripotency induction methods.”

The article describes how the scientists assessed genome-wide mutation rates from replicate isogenic cell lines generated by three distinct methods. Previous studies considered the genomic integrity of iPSCs using methods such as single-nucleotide polymorphism (SNP) genotyping, comparative genomic hybridization, karyotyping, and exome sequencing. In each of the earlier studies, however, the focus was on a single type of genomic alteration rather than the combined effects of single-nucleotide variants, structural variants, and copy-number variations. “Further,” the authors of the Nature Communications study noted, “detailed comparative genomic analyses of iPSC lines that have been generated via distinct reprogramming methodologies” had not been conducted.

In the current study, the researchers looked at three popular methods of iPSC production (integrating retroviral vectors, non-integrating Sendai virus, and synthetic mRNAs), assessing each for the potential to trigger cancer-causing mutations. While the researchers noted some minor alterations in the iPSCs, none of the methods led to significant mutations. The researchers repeated the experiments two more times and again found no significant risk.

“We used whole-genome sequencing and de novo genome mapping to identify single-nucleotide variants, insertions and deletions, and structural variants,” wrote the authors of the study. “Our results show a moderate number of variants in the iPSCs that were not evident in the parental fibroblasts, which may result from reprogramming.” They continued that, “Most importantly, a thorough genomic analysis showed that the variants were generally benign.”

The scientists do warn that even though iPSCs don't gain cancer-causing mutations during reprogramming, potentially harmful mutations can accumulate later on as iPSCs multiply in lab cultures. According to the study’s co-leader, Jeanne Loring, Ph.D., professor of developmental neurobiology at TSRI, scientists must analyze their cells for these mutations before using them in therapies.

“We wanted to know whether reprogramming cells would make the cells prone to mutations,” said Dr. Loring. “The answer is 'no.'”

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

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