Gene Therapy Restores the Transcriptional Program of Hematopoietic Stem Cells in Fanconi Anemia

Fanconi anemia (FA) is an inherited disease associated with marked hematopoietic stem and progenitor cell (HSPC) defects. Ongoing clinical trials have shown that lentiviral-mediated gene therapy can ameliorate bone marrow failure (BMF) in non-conditioned FA patients thanks to the proliferative advantage of corrected FA HSPCs. Here we investigated whether gene therapy can revert affected molecular pathways in diseased HSPCs, a question not previously addressed in any HSC gene therapy trial. Single-cell RNA sequencing was performed in chimeric populations of corrected and uncorrected HSPCs coexisting in BM of gene therapy treated FA patients. Our study demonstrates that gene therapy reverts the transcriptional signature of FA HSPCs, which then resembles the transcriptional program of healthy donor HSPCs. This includes a downregulated expression of TGF-{beta} and p21, typically upregulated in FA HSPCs, and upregulation of DNA damage response and telomerase maintenance pathways. Our results show for the first time the potential of gene therapy to rescue defects in the HSPC transcriptional program from patients with inherited diseases, in this case in FA characterized by BMF and cancer predisposition.