New Tool Identifies Safe Places To Introduce Genes Into Human DNA

Scientists at St. Jude Children’s Research Hospital have developed a tool that can locate safe places to introduce genes into human DNA. The tool is an early step in the process of improving the safety and effectiveness of gene and cell therapies. The research was recently published in the journal Genome Biology. 

“We’ve created the Google Maps of editing the genome,” said co-corresponding author Yong Cheng, Ph.D., St. Jude Department of Hematology. “With this tool, we provide a new approach to identify places to safely integrate a gene cassette. We created step-by-step directions, so you can follow the steps and easily find safe harbor sites in specific tissues.”

Advertisement

Gene therapy, in which a patient is given a functioning copy of a dysfunctional gene, has demonstrated success in treating some genetic disorders. However, there have been safety concerns in the field, such as the unintentional activation of an oncogene that caused cancer in some patients.

As a result, scientists have looked for “safe harbor sites” in the genome, or locations where a gene may be introduced without causing cancer or other issues. The researchers developed a pipeline that searches for safe harbor sites using genomic and epigenetic information from specific tissues, such as blood cells.

Co-first author Dewan Shrestha (left), corresponding author Yong Cheng, Ph.D. (center), and co-author Ruiqiong Wu (right). Credit: St. Jude Children’s Research Hospital

A novel way to find safe harbor sites

The tool compares the DNA sequences that are highly variable between healthy people, using data from the 1000 Genomes Project. The researchers reasoned that if a DNA region is often deleted or inserted in healthy individuals, it could probably also be safely modified by gene therapy.

“Our method is a new way to identify genomic safe harbor sites in a tissue-specific manner,” Cheng said. “Nobody has tried it from this angle. Our first step was to find the genomic loci that show a high frequency of insertion or deletion among healthy individuals.”

If DNA in a single cell was a string, it would be two meters long. But in addition to the linear sequence, DNA can loop into complex 3D structures using chromatin, the proteins associated with DNA, to fit within a cell. Just like a string, DNA can have loops that affect its function. The St. Jude tool considers the presence of these loops and other structures when searching for accessible safe harbor sites.

“Our tool assesses the 3D structure of DNA because human DNA is not a one-dimensional linear structure, it’s actually 3D,” Chen said. “So, parts of DNA may be far away in the linear sequence of DNA but may physically be next to each other because of the looping of the 3D structure. In that case, the 3D proximity is more important than the linear distance.”

Balancing safety and therapeutic gene expression

“Safe gene therapy requires two things,” said Cheng. “Number one, maintaining high expression of the new gene. And number two, the integration needs to have minimal effects on the normal human genome, which is a major concern for people performing gene therapy.”

The scientists found that the genes placed in safe harbor sites identified by their tool maintained their expression over time. The researchers also showed that if they put a gene into one of the safe harbor sites identified by their tool, it affected nearby genes less than a classic safe harbor site.

The tool called the Genomics and Epigenetic Guided Safe Harbor mapper (GEG-SH mapper) is freely available.

Reference: “Genomics and epigenetics guided identification of tissue-specific genomic safe harbors” by Dewan Shrestha, Aishee Bag, Ruiqiong Wu, Yeting Zhang, Xing Tang, Qian Qi, Jinchuan Xing and Yong Cheng, 21 September 2022, Genome Biology.
DOI: 10.1186/s13059-022-02770-3k

The study was funded by the National Institutes of Health and the National Cancer Institute.