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Success of Gene Therapy Relies on Integration Location in DNA


The location of integration of a gene therapy has been crucial for the safety and efficacy of the treatment to cure infants with X-linked severe combined immunodeficiency.

Identified integrome signatures could be biomarkers for gene therapies based on lentiviral vectors, which should be applicable for a range of therapies being developed, according to research published in Science Advances.1

The researchers analyzed more than 280,000 vector integration sites (VIS) from 10 patients with X-linked severe combined immunodeficiency (SCID-X1), also known colloquially as “bubble boy disease.” These patients are born with a defective gene that prevents them from producing immune cells.

“While the precise location of a vector integration site (VIS) can serve as a marker for monitoring the corresponding clone and its subsequent evolution in longitudinal analysis, a systematic mapping of the integrome can provide further insights into integration site selection and may have important implications in terms of biosafety and efficacy for gene therapy,” the authors explained.

Baby feet in parent's hands.

Image credit: Simon Dannhauer - stock.adobe.com

Baby feet in parent's hands.

Image credit: Simon Dannhauer - stock.adobe.com

In 2019, gene therapy restored the immune system in multiple infants with SCID-X1 by supplying copies of the corrected gene. Since then, the patients have been monitored for safety, which led to scientists documenting where the gene copies integrate into DNA.

"We now have a robust pipeline to monitor the safety of lentiviral gene therapies," senior co-corresponding author Jiyang Yu, PhD, St. Jude Department of Computational Biology interim chair, said in a statement.2 "This really gives hope to patients with genetic diseases that can be cured by lentiviral gene therapy. It looks like we cured bubble boy disease safely in these patients."

They determined that the therapy was well tolerated and successfully developed a functional immune system without malignant transformation. Only 1 of 25 patients (patient 1) treated needed a second infusion, which resulted in a functional immune system.

The VISs analyzed were from 273 samples taken from the first 10 patients enrolled in the study. After a detailed genomic and epigenomic analysis, they found the existence of “hotpots,” which were genomic regions that had a high density of integration sites. The vector integrations occurred at a greater frequency than expected and overlapped in patients 2 through 10. All of these patients only required 1 infusion.

In addition, 8 or 9 of the patients shared 7 recurrent integration genes (KDM2A, PACS1, LOC101928855, CHD3, CARD8, GRB2, and KLC2).

These genomic hotspots where the copies of the new, corrected gene was inserted existed for a reason: they are the regions the lentiviral vector would first encounter after entering the cell’s nucleus.

“It’s like someone coming into a room and taking the first available seat near the door,” said co-corresponding Stephen Gottschalk, MD, St. Jude Department of Bone Marrow Transplantation and Cellular Therapy chair. “The room is the nucleus. The seats are these DNA elements right near the door of the nuclear pore. That never occurred to me before this study, but it’s a very simple principle in the end.”

The analysis, coupled with prior research, shows the treatment is safe and effective because the therapy integrates into compartments near the nuclear pore, the channel through which the therapy enters the cell’s nucleus. Previous gene therapies that were not successful ultimately caused cancer because they integrated close to or into oncogenes. This new lentiviral vector used avoids this, which is similar to how chimeric antigen receptor T-cell therapy works.

“The integration pattern data could serve as a map of potentially safe integration sites,” Yu and Gottschalk explained. “The single-cell analysis is like deep cartography, a map with a near pixel-perfect resolution. The large number of integration sites could be used as a safety reference for future lentiviral gene therapies.”


1. Yan KK, Condori J, Ma Z, et al. Integrome signatures of lentiviral gene therapy for SCID-X1 patients. Sci Adv. 2023;9(40):eadg9959. doi:10.1126/sciadv.adg9959

2. 3D genome architecture influences SCID-X1 gene therapy success. News release. St Jude Children’s Research Hospital. October 6, 2023. Accessed October 23, 2023. https://bit.ly/46NxSGM

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