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SUMMARY PARAGRAPH Fanconi anemia (FA) is a monogenic inherited disease associated with mutations in genes that encode for proteins participating in the FA/BRCA DNA repair pathway. Mutations in FA genes result in chromosomal instability and cell death, leading to cancer risks and progressive cell mortality, most notably in hematopoietic stem and progenitor cells (HSPC). Recently, we showed the first clinical evidence that gene therapy confers engraftment and proliferative advantage of gene-corrected HSPCs in FA patients1. Despite this and many other gene therapy advances, the question of whether the molecular pathways affected in monogenic diseases can be reverted by lentiviral-mediated gene therapy has never been addressed. This is even more challenging in DNA repair syndromes such as FA since in these cases, transcriptional defects in affected cells might not be restored due to DNA damage accumulated prior to gene therapy. Using single-cell RNA sequencing in HSPCs from FA-A patients previously treated by ex vivo gene therapy, we demonstrate that lentiviral-mediated gene therapy prior to severe bone marrow failure not only restores the expression of the defective gene, but also induces a long-term correction of the transcriptional program in FA HSPCs, which then acquire a signature characteristic of healthy HSPCs. Our results reveal new molecular evidence showing the potential of gene therapy to fully rescue phenotypic defects in FA, a devastating HSPC disease characterized by defective DNA repair.