Scientists Create New Tool to Identify Genomic Refuge Sites in Specific Tissues

Scientists at St. Jude Children’s Research Hospital have created a tool that can find safe places to insert genes into human DNA. The tool is a first step in the process of improving the safety and efficacy of gene and cell therapies. The book appears today in Genome biology.

We created the Google Maps of genome editing. With this tool, we provide a new approach to identify where to safely embed a gene cassette. We’ve created step-by-step instructions, so you can follow the steps and easily find refuge sites in specific tissues.”

Yong Cheng, Ph.D., co-corresponding author, St. Jude Department of Hematology

Gene therapy, where a patient receives a working copy of a dysfunctional gene, has successfully cured some genetic disorders. However, the field has encountered safety issues, including the inadvertent activation of an oncogene that led to cancer in some patients. In response, the field has been looking for “safe haven sites” – places in the genome where a gene can be inserted without causing cancer or other problems. The scientists created a pipeline that uses genomic and epigenetic information from specific tissues, such as blood cells, to find safe haven sites.

A new way to find safe sites

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

“Our method is a new way to identify genomic refuge sites in a tissue-specific way,” Cheng said. “No one has tried it from that angle. Our first step was to find the genomic loci that show a high frequency of insertion or deletion in healthy individuals.”

If the DNA of a single cell were a string, it would be two meters long. But in addition to linear sequence, DNA can loop into complex 3D structures using chromatin, the proteins associated with DNA, to fit into a cell. Just like a string, DNA can have loops that affect its function. The St. Jude tool accounts for the presence of these loops and other structures when searching for accessible refuge 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. “Thus, parts of DNA may be far apart in the linear DNA sequence but may be physically side by side due to the looping of the 3D structure. In this case, 3D proximity is more important than linear distance. .”

Balancing the Safety and Expression of Therapeutic Genes

“Safe gene therapy requires two things,” Cheng said. “First, to maintain high expression of the new gene. And second, the integration must have minimal effects on the normal human genome, which is a major concern for people doing gene therapy.”

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

The tool, called Genomics and Epigenetic Guided Safe Harbor mapper (GEG-SH mapper) is available for free at

Authors and funding

The study’s first authors are Dewan Shrestha, of St. Jude and the University of Tennessee Health Sciences Center, and Aishee Bag, of Rutgers, State University of New Jersey. The other authors of the study are

Ruiqiong Wu, Xing Tang and Qian Qi, from St. Jude; Yeting Zhang and co-corresponding author Jinchuan Xing, from Rutgers, State University of New Jersey.

The study was supported by grants from the National Cancer Institute (P30 CA021765), the National Institutes of Health (R35GM133614), the St. Jude Collaborative Research Consortium on Novel Gene Therapies for Sickle Cell Disease (SCD), the Institute of New Jersey Human Genetics and ALSAC, St. Jude’s fundraising and awareness organization.


St. Jude Children’s Research Hospital

Journal reference:

Shrestha, D. et al. (2022) Genomics and epigenetics have guided the identification of tissue-specific genomic safe harbors. Genome biology.