World news – The researchers call for greater awareness of the unintended consequences of CRISPR gene editing

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April 12, 2021

from the Francis Crick Institute

Researchers at the Francis Crick Institute have found that editing the CRISPR-Cas9 genome can lead to inadvertent mutations at the target portion of DNA in early human embryos. The work underscores the need for greater awareness and further exploration of the effects of CRISPR-Cas9 genome editing, particularly in human DNA editing in laboratory research.

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CRISPR-Cas9 genome editing is a widely used research tool that allows scientists to remove and replace sections of DNA in cells, for example to study the function of a particular gene or to repair mutations. Last year, the researchers who developed CRISPR-Cas9 received the Nobel Prize in Chemistry.

In their study published in PNAS, Crick scientists retrospectively analyzed data from previous research investigating the role of the OCT4 protein in human embryos in the early days of development.

The team found that the majority of CRISPR-Cas9-induced mutations were small insertions or deletions, but in approximately 16% of samples were large unintentional mutations that were detected by conventional methods of assessing DNA changes would have been overlooked.

Research is underway to understand the exact nature of the changes in the destinations. However, this could include deletions of DNA segments or more complex genomic rearrangements.

The discovery underscores the need for researchers using CRISPR-Cas9-mediated genomic editing to manipulate human cells, whether somatic or germline, to identify and test these potential unintended consequences. This is even more important if they hope their work will be used clinically, as unintended genetic changes like this can lead to diseases like cancer.

« Other research teams have reported these types of unintended mutations in human stem cells, cancer cells and other cellular contexts, and now we have detected them in human embryos, » says Professor Kathy Niakan, group leader at the Human Embryo and Stem Cell Laboratory at Francis Crick Institute and Professor of Reproductive Physiology at the University of Cambridge and lead author of the study.

« This work underscores the importance of testing for these unintended mutations in order to understand exactly what changes occur in a human cell type appeared. »

The Crick researchers developed an open source computation pipeline to identify whether CRISPR-Cas9 caused unintended target mutations based on different types of next generation sequencing data.

« We and others are trying to to develop and refine the tools to evaluate these complex mutations, « added Niakan.

« It is important to understand these events, how they arise, and how often they occur so that we can assess the current limitations of the technology and determine strategies for future improvements in these technologies to minimize these mutations. »

Gregorio Alanis-Lobato, lead author and former postdoctoral fellow in the Human Embryo and Stem Cell Laboratory at Crick, says, « Traditional tests to check the accuracy of CRISPR-Cas9 can miss the types of unintended target mutations we have in this study There is still so much to learn about the implications of CRISPR-Cas9 technology, and while this valuable tool is being refined we must thoroughly examine any changes. « There are important ongoing debates about the safety and ethics of the Using CRISPR-Cas9 genome editing on human embryos for reproductive purposes. And in 2019, the work of a researcher in China who edited embryos that led to the birth of twins was internationally condemned. In the UK, use on human embryos is strictly regulated and only allowed for research purposes. Research is limited to the first 14 days of development and embryos must not be implanted in a uterus.

The data for this work referred to embryos previously examined by Crick’s Human Embryo and Stem Cell Laboratory. The embryos were in the blastocyst stage of early development and consisted of approximately 200 cells. They were donated for research purposes by people undergoing in vitro fertilization (IVF) and were not needed during the course of their treatment.

The research was led by scientists from the Francis Crick Institute in collaboration with colleague Professor Dagan Wells from the University of Oxford. Kathy Niakan is Incoming Director of the Center for Trophoblast Research at the University of Cambridge and Chair of the Cambridge Strategic Research Initiative in Reproduction.

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