Severe hematopoietic stem cell inflammation compromises chronic granulomatous disease gene therapy (Single Cell)

X-linked chronic granulomatous disease (CGD, caused by CYBB gene mutations) is associated with defective phagocytosis, life-threatening infections, and inflammatory complications. We performed a clinical trial of lentivirus-based gene therapy in four patients (NCT02757911). Two patients showed stable engraftment and clinical benefits, whereas the other two progressively lost gene-corrected cells. Single-cell transcriptomic analysis revealed a significantly lower frequency of the most immature hematopoietic stem cells (HSCs) in CGD patients, especially in the two patients with defective engraftment. The latter presented a profound change in HSCs status, a high interferon score, and elevated myeloid progenitor frequency. We used elastic-net logistic regression to identify a set of 51 interferon genes and transcription factors that predicted the failure of HSCs engraftment. In one patient, an aberrant HSCs state with elevated CEBPb expression drove HSCs exhaustion, as demonstrated by low repopulation in a xenotransplantation model. Targeted treatments that protect HSCs, coupled to targeted gene expression screening, might improve clinical outcomes in CGD.