Addressing the safety of vector integration

Gene therapy (GT) uses different vectors to deliver genes or edit genetic sequences into cells at high efficiency and is used as cure of several genetic and acquired diseases, and the accomplishments achieved are greatly expanding the number of potential therapeutic applications. Nevertheless, vector related risks caused by the deregulation of cancer-related genes still exists, potentially driving towards cancer, and even rare genotoxic events could trigger the development of severe adverse - side effects. Moreover, no predictive biomarkers for safety, efficacy and disease burden have been validated yet. We will unveil the rules governing vector/genome interaction by multi-omics analysis and use the acquired knowledge to design novel vectors with improved safety and potency. We will also refine the methods for the identification and possibly the elimination of cells harboring oncogene-activating insertions before malignant transformation occurs. For this approach we will take advantage of our recently identified dataset of genes which are strongly induced in human HSCPs specifically upon oncogene induced senescence and well before cell transformation. Moreover, we will study the impact of the disease background and other clinical variables by studying the clonal composition and fate of genetically modified cells in circulating blood cells as well as in cfDNA in GT patients affected by diverse genetic diseases. Finally, we will study the methylome and nucleosomal footprint -based epigenetic cell specific signatures in cfDNA of GT patients overtime after treatment. Thus, we will determine which cells contribute to cfDNA in specific disease condition phases of therapy or disease unravel the basic biological properties of tissue turnover during regeneration and homeostasis after GT and possibly identify novel prognostic biomarkers of disease progression and severity and eventually early treatment indicators.