Cattoglio et al 2010
High-Definition Mapping of Retroviral Integration Sites Defines the Fate of Allogeneic T Cells After Donor Lymphocyte Infusion
The infusion of donor lymphocytes transduced with a retroviral vector expressing the HSVTK  suicide gene in patients undergoing hematopoietic stem cell transplantation for  leukemia/lymphoma promotes immune reconstitution and prevents infections and graft-versus-host  disease. Analysis of the clonal dynamics of genetically modified lymphocytes in vivo is of crucial  importance to understand the potential genotoxic risk of this therapeutic approach. We used linear  amplification-mediated PCR and pyrosequencing to build a genome-wide, high-definition map of  retroviral integration sites in the genome of peripheral blood T cells from two different donors and  used gene expression profiling and bioinformatics to associate integration clusters to transcriptional  activity and to genetic and epigenetic features of the T cell genome. Comparison with matched random  controls and with integrations obtained from CD34+ hematopoietic stem/progenitor cells showed that  integration clusters occur within chromatin regions bearing epigenetic marks associated with active  promoters and regulatory elements in a cell-specific fashion. Analysis of integration sites in T cells  obtained ex vivo two months after infusion showed no evidence of integration-related clonal expansion  or dominance, but rather loss of cells harboring integration events interfering with RNA posttranscriptional  processing. The study shows that high-definition maps of retroviral integration sites  are a powerful tool to analyze the fate of genetically modified T cells in patients and the biological  consequences of retroviral transduction.