Computational Approach Identifies “Safe Harbors” for Therapeutic Genes

Researchers from the Wyss Institute for Biologically Inspired Engineering, Harvard Medical School (HMS), and ETH Zurich have used a computational approach to identify and validate 2,000 sites on the human genome with the potential to accommodate insertion of therapeutic genes without causing unintended genomic changes.

Dubbed genomic safe harbors (GSHs), such sites have a long list of criteria. They need to be accessible by genome-editing technologies, free of physical obstacles like genes and other functional sequences, and allow high, stable, and safe expression of a “landed” therapeutic gene.

“While GSHs could be utilized as universal landing platforms for gene targeting, and thus expedite the clinical development of gene and cell therapies, so far no site of the human genome has been fully validated and all of them are only acceptable for research applications,” says George Church, Ph.D., a senior author on the study, leader of the Wyss Institute’s Synthetic Biology Platform, Robert Winthrop Professor of Genetics at HMS, and Professor of Health Sciences and Technology at Harvard University and the Massachusetts Institute of Technology (MIT).

The new work, published recently by Cell Reports Methods, describes a computational pipeline to find potential GSH regions by harnessing sequencing data from human cell lines and tissues. The team was then able to “computationally exclude” regions encoding proteins, including those involved in the formation of tumors, as well as regions encoding certain types of RNAs with functions in gene expression and other cellular processes. “We also eliminated regions that contain so-called enhancer elements, which activate the expression of genes, often from afar, and regions that comprise the centers and ends of chromosomes to avoid mistakes in the replication and segregation of chromosomes during cell division,” says lead author Erik Aznauryan, Ph.D. “This left us with around 2,000 candidate loci all to be further investigated for clinical and biotechnological purposes.”

The team was then able to validate 2 of those 2,000 GSH sites for adoptive T cell therapies and in vivo gene therapies for skin diseases and demonstrated safe and long-lasting expression of the newly introduced genes.  “An extensive sequencing analysis that we undertook in GSH-engineered primary human T cells clearly demonstrated that the insertion has minimal potential for causing tumor-promoting effects, which always is a main concern when genetically modifying cells for therapeutic use,” adds Sai Reddy, coauthor with ETH Zurich’s Department of Biosystems Science and Engineering.