Targeting Inflammation to Improve Gene Therapy Outcomes in Sickle Cell Disease

A recent Phase I/II clinical trial has shed new light on the promise and limitations of autologous gene therapy in sickle cell disease (SCD). Conducted at Necker Hospital in Paris, the study used a potent lentiviral vector (DREPAGLOBE) to deliver an anti-sickling β-globin gene variant (βAS3) into patients’ hematopoietic stem and progenitor cells (HSPCs). While the treatment proved safe across all four treated patients, its efficacy varied considerably—offering key insights into the biological barriers to successful engraftment in SCD.

The trial enrolled six patients with severe SCD, but only four received the gene therapy. Eligibility required absence of clonal hematopoiesis, confirmed via next-generation sequencing. Patients were conditioned with busulfan and infused with autologous, DREPAGLOBE-transduced HSPCs mobilized using plerixafor. The study evaluated safety, efficacy, and biological responses over an 18- to 36-month follow-up period.

Reassuringly, no drug-related adverse events or clonal hematopoiesis were reported. The therapy was well tolerated, and engraftment occurred within a reasonable timeframe. Yet clinical outcomes diverged:

• Patient (P) 1 and P2 achieved transfusion independence, improved RBC deformability, and sustained high levels of therapeutic HbAS3 (25–33 g/L).
• P3 and P4 remained transfusion-dependent with limited clinical improvement and lower HbAS3 levels (<10 g/L).

Despite similar initial vector copy numbers (VCN) in the infused product, P3 and P4 experienced marked drops in gene marking post-infusion (3.6- and 5.5-fold respectively), suggesting poor long-term engraftment of genetically modified cells.

The trial’s exploratory analyses brought a fresh, mechanistic lens to SCD gene therapy. Bulk and single-cell transcriptomics uncovered high inflammatory signatures and lineage biases in patients with poor engraftment.

Key findings include:

• P3 showed a dramatic increase in megakaryocyte progenitors (MkPs) and HSCs with a dual HSC/MkP identity, expressing IL-1β and von Willebrand factor—both markers of platelet-biased HSCs linked to poor self-renewal.
• P4 exhibited elevated TNF-α and interferon (IFN) signaling in HSCs, alongside a myeloid lineage bias. These inflammatory profiles mirrored patterns seen in hematopoietic aging.

The authors connected these biases to impaired HSC quality, suggesting that chronic inflammation and oxidative stress in SCD may compromise HSC regenerative potential, even before gene therapy begins.

Encouragingly, ex vivo treatments of P3 and P4’s HSPCs with JAK and TNF-α inhibitors (ruxolitinib, baricitinib, infliximab, and etanercept) reduced inflammatory gene expression. This opens the door to pre-conditioning regimens aimed at improving HSPC quality prior to gene therapy.

Additionally, the study advocates for a “pre-GT HSC score” based on flow cytometry and transcriptomic profiling to guide therapeutic decisions. Patients with high inflammation scores may benefit from pretreatment with anti-inflammatory drugs or from haploidentical HSC transplants rather than autologous gene therapy.

Though small, this study furthers our understanding of gene therapy in SCD. It highlights that inflammatory HSC programming, not just vector potency or transduction efficiency, can be a decisive factor in clinical success. A paradigm shift—from focusing solely on the gene to optimizing the cell—may be necessary to unlock consistent, long-term success.

Reference
Sobrino S, Joseph L, Magrin E, et al. Severe inflammation and lineage skewing are associated with poor engraftment of engineered hematopoietic stem cells in patients with sickle cell disease. Nat Commun. 2025;16(1):3137. doi:10.1038/s41467-025-58321-4