A new strategy to monitor gene therapy long-term safety and efficacy

To assess long-term safety and efficacy of hematopoietic stem cell-based gene therapy approaches, researchers need to infer the fate of engineered cells re-infused in the blood of patients. Up to now, the easiest way to perform this analysis was by performing clonal tracking techniques on the DNA of blood cells collected overtime from treated patients. This procedure – although very useful – cannot provide any information on those cells that upon transplantation migrate and end up residing in solid organs, such as the liver. These cells remain invisible, if not for invasive testing techniques such as the classic biopsies.

 According to a new research published in Nature Medicine, the analysis of cell-free DNA – released into the bloodstream by many different cells and tissues – can convey more information about the clonal composition and turnover of engineered cells, as well as enable earlier detection of vector-marked clones with aberrant behaviors. The research unit Safety of Gene Therapy and Insertional Mutagenesis lead by Eugenio Montini at the San Raffaele Telethon Institute for Gene Therapy (SR-Tiget) in Milan developed a new technique, called liquid biopsy integration site sequencing (LiBIS-seq), allowing to probe cell free-DNA circulating in the bloodstream to obtain information regarding engineered cells.

Assessing long-term safety and efficacy of new medicinal products is of fundamental importance, even more in the field of advanced medicine – gene and cell therapies – that are adopted for the very first time in clinic. “Given the novelty nature of many of these interventions, we must combine clinical observations with innovative molecular testing to unravel the biological properties and behavior of engineered cells engrafted in tissues ” explains Eugenio Montini. Thanks to the pioneering work of the researchers at SR-Tiget, this important task has been largely improved.

“Cell free-DNA is composed by DNA fragments released in the body fluids by both circulating cells – such as immune cells – and cells residing in different solid tissues and organs,” explains Daniela Cesana first name of the work. “Its complex and diverse origin conveys a better description of the clonal fate of engineered cells in treated patients, making it a complementary tool to those currently available for monitoring the safety and efficacy of the gene therapy approaches.”

Moreover, researchers at SR-Tiget discovered that, in patients affected by Metachromatic Leukodystrophy, the plasma concentration of cell free-DNA reach a physiological level only when gene therapy proves to be clinical effective, making it an effective bio-marker not only for gene therapy safety but also for its efficacy.