Shedding new light on DNA repair in early human embryos, with implications for gene editing

by Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences (IOCB Prague)

edited by Robert Egan

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Treating inherited diseases is one of the greatest challenges in modern medicine. In the future, targeted gene corrections at the earliest stages of embryonic development could help prevent certain inherited diseases from developing and being passed on to future generations. However, the safety of such approaches depends on how human embryos repair the DNA damage caused during gene editing and on the limitations of available technologies. These questions are addressed in a study published in the journal Nature, led by first author Štěpán Jeřábek, who is affiliated with both Columbia University and IOCB Prague. The research also involved two other IOCB Prague scientists, Iva Pichová and Michal Doležal.

How embryos handle DNA damage

Although DNA repair is one of the fundamental processes required for normal human embryonic development, little has been known about how it operates during the earliest stages of development. The new study is the first to provide a detailed comparison of how human embryos respond to two different types of DNA damage. "The study shows that early human embryos are able to effectively repair single-strand DNA damage, whereas the repair of double-strand breaks is significantly less reliable at this stage of development," says the study's first author, Jeřábek.

To examine these repair mechanisms in detail, the researchers introduced targeted changes into two well-studied genes using two different genome-editing tools. Using CRISPR–Cas9, the researchers introduced double-strand breaks into embryonic DNA, while base editing produced only a single-strand nick. They then analyzed how the embryos' DNA repair mechanisms responded to each type of DNA damage.

Doležal and Pichová from IOCB Prague contributed to the purification of the protein-based editors used in the study to introduce precisely defined single-strand DNA changes. "Collaboration on the study began as early as 2021, and over the following years we prepared several editor variants for experiments carried out by our colleagues at Columbia University. Some of these were ultimately used in the study. We found that delivering the editors directly into embryonic cells as proteins, rather than as mRNA, was compatible with normal embryonic development," says Doležal.

Stem cells open a closer look

One of the study's key findings is that the researchers successfully isolated stem cells from the edited six-day-old embryos. The stem cells provide sufficient genetic material for detailed analyses, allowing the researchers to investigate the effects of gene editing in greater depth. In addition, they make it possible to study the consequences of introduced genetic changes in subsequent generations of cells.

Safety questions remain unresolved

In addition to providing new insights into DNA repair, the study also highlights the limitations of current genome-editing technologies and the need for continuous research. "Our goal was not to develop a method for genetically modifying human embryos but rather to better understand, through basic research, how DNA repair mechanisms function in the early stages of human development. Although base editing represents a significant improvement over CRISPR–Cas9 in terms of DNA repair precision, our findings also show that many important questions regarding safety must be answered before these methods can be considered for clinical use in human embryos," says Jeřábek.

The research was conducted in Dieter Egli's laboratory under the oversight of Columbia University's ethics committee. Even before publication, the study attracted international attention and was covered by international media, including The New York Times.

Jan Konvalinka, IOCB Prague director, emphasizes that this type of basic research is important not only scientifically but also from a broader societal perspective. "I consider the ethical debate surrounding studies like this to be both legitimate and necessary. The purpose of basic research is to expand the boundaries of knowledge while helping us better understand the possibilities and limitations of current technologies. That is precisely why this work represents an important contribution to both scientific and public debate."

Publication details

Stepan Jerabek et al, Highly efficient base editing at PCSK9 and normal human embryo development, Nature (2026). DOI: 10.1038/s41586-026-11118-x

Journal information: Nature

Key medical concepts

Editing, BaseStem Cells

Clinical categories

Clinical genetics Provided by Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences (IOCB Prague) Who's behind this story?

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