Long-term and real-world safety and efficacy of retroviral gene therapy for adenosine deaminase deficiency

Abstract

Adenosine deaminase (ADA) deficiency leads to severe combined immunodeficiency (SCID). Previous clinical trials showed that autologous CD34⁺ cell gene therapy (GT) following busulfan reduced-intensity conditioning is a promising therapeutic approach for ADA-SCID, but long-term data are warranted. Here we report an analysis on long-term safety and efficacy data of 43 patients with ADA-SCID who received retroviral ex vivo bone marrow-derived hematopoietic stem cell GT. Twenty-two individuals (median follow-up 15.4 years) were treated in the context of clinical development or named patient program. Nineteen patients were treated post-marketing authorization (median follow-up 3.2 years), and two additional patients received mobilized peripheral blood CD34⁺ cell GT. At data cutoff, all 43 patients were alive, with a median follow-up of 5.0 years (interquartile range 2.4-15.4) and 2 years intervention-free survival (no need for long-term enzyme replacement therapy or allogeneic hematopoietic stem cell transplantation) of 88% (95% confidence interval 78.7-98.4%). Most adverse events/reactions were related to disease background, busulfan conditioning or immune reconstitution; the safety profile of the real world experience was in line with premarketing cohort. One patient from the named patient program developed a T cell leukemia related to treatment 4.7 years after GT and is currently in remission. Long-term persistence of multilineage gene-corrected cells, metabolic detoxification, immune reconstitution and decreased infection rates were observed. Estimated mixed-effects models showed that higher dose of CD34⁺ cells infused and younger age at GT affected positively the plateau of CD3⁺ transduced cells, lymphocytes and CD4⁺ CD45RA⁺ naive T cells, whereas the cell dose positively influenced the final plateau of CD15⁺ transduced cells. These long-term data suggest that the risk-benefit of GT in ADA remains favorable and warrant for continuing long-term safety monitoring. Clinical trial registration: NCT00598481 , NCT03478670 .

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Figure 1. Flow diagram of patients treated γ-retroviral vector gene therapy included in the analyses

Data are from all patients treated with Strimvelis (experimental or approved) from 2000 to 09/2022, with a data cut off for analyses at 12/2022. Data were censored after secondary intervention (>3 months on PEG-ADA or allogeneic transplantation). Study AD1115611 is entitled “ADA gene transfer into hematopoietic stem/progenitor cells for the treatment of ADA SCID (NCT00598481)” and amended to include all subjects in long term follow up treated with the experimental drug product (STRIM-004). STRIM-003 is entitled “Adenosine Deaminase Severe Combined Immunodeficiency (ADA-SCID) Registry for Patients Treated With Strimvelis (Previously GSK2696273) Gene Therapy: Long-Term Prospective, Non-Interventional Follow-up of Safety and Effectiveness (NCT03478670). For patients not enrolled in the STRIM003 registry, data were retrieved from long-term follow up study or initial studies/program before intervention. One patient is described only in aggregated analyses due to data block requested by family. ^*An additional patient had a secondary intervention (see Extended Data Table 2); PEG-ADA was started, but continued to be followed due to the persistence of gene corrected cells; data were censored for the analyses 3 months after PEG-ADA start.

Figure 2. Patients’ and γ-retroviral vector gene therapy drug product’s characteristics, overall survival and intervention free survival after treatment.

(A) Age at diagnosis and GT (months). (B) Cell dose of CD34+ cells (×10⁶ per kg). (C) Vector copy number (VCN) per genome in the drug product. CDP+NPP data are shown for patients (n=9) in whom the VCN analytical test was the same as the one currently employed for the STRIM cohort. In the plots, box and whiskers display the median, the first and the third quartile and the minimum and the maximum of the data. Comparison of numerical variables between groups in panels A, B and C was performed with Mann Whitney test (see Statistical Methods). (D) Kaplan–Meier curves showing OS for the entire cohort (n=36) of ADA SCID patients treated pre- (CDP+NPP) and post-approval (Strimvelis), and IFS for CDP+NPP (in blue, n=22) and Strimvelis (in red, n=19). OS: Overall Survival; IFS: Intervention Free Survival, as no need of PEG-ADA >3 months or rescue allogeneic hematopoietic stem cell transplantation.

Figure 3. Immune reconstitution after gene therapy.

Absolute cell counts (cells/uL) of lymphocytes, CD3+, CD3+CD8+, CD3+CD4+, CD4+CD45RA+, CD19+, CD16+CD56+ in peripheral blood in STRIM (A, C, E, G, I, K, M) and CDP+NPP (B, D, F, H, J, L, N) patients are shown in the graphs. In the plots, box and whiskers display the median, the first and the third quartile and the minimum and the maximum of the data. For CDP+NPP population, the last available F-U after year 8 is reported The shaded dark and light grey regions represent median and fifth percentile values, respectively, in normal children. The top edges correspond to levels in children ages 2 to 5 years; bottom edges correspond to levels in children ages 10 to 16 years. Values for children ages 5 to 10 typically fall within the shaded areas.

Figure 4. Humoral compartment restoration, incidence of infections and metabolic detoxification after gene therapy.

Patients off-Ig supplementation in the dark bars and still on-Ig in the light bars are reported at baseline and at subsequent timepoints after gene therapy in STRIM (A) and CDP+NPP (B) cohort, respectively. In (C) and (D), IgG levels were evaluated at baseline and at various timepoints after gene therapy in the STRIM and CDP+NPP groups. Patients off-Ig/patients evaluated are reported at each timepoint. Serum IgM (E, F) and IgA (G, H) levels. The shaded dark and light grey regions represent the fifth and ninety-fifth percentile values, respectively, in normal children aged 4 to 6 months and 12 to 16 years. Top edges correspond to levels in children ages 12 to 16 years; bottom edges correspond to levels in children ages 4 to 6 months38. Top edges of the light grey region represent the ninety-fifth percentile in normal children aged 14 years and the bottom edges the ninety-fifth percentile in the ones aged 6 months38. Incidence of severe infections in the CDP+NPP (blue bars) and STRIM (red bars) cohorts (K). Severe infections in the 3 months immediately following GT were not included in the analysis. RBC dAXP levels measured in peripheral blood in the STRIM (L) and CDP+NPP (M) cohort. Dashed line indicates the lower reference value of dAXP for patients undergone successful hematopoietic stem cell transplantation (≤100 nmol/mL). In the plots, box and whiskers display the median, the first and the third quartile and the minimum and the maximum of the data. GT: gene therapy; Ig: intravenous immunoglobulins. dAXP: deoxyadenosine nucleotides; RBC: red blood cells.

Figure 5. Longitudinal analysis of gene corrected cells, lymphocytes, CD3+ cells, CD4+CD45RA+ with respect to age at gene therapy and CD34+ cells infused.

The longitudinal trends were estimated by using mixed-effects models with fractional polynomials due to their nonlinear shape. The possible dependencies of the trend on age at gene therapy and CD34+ cells infused (as continuous variables) were tested within the model (see Supplementary Statistical Method and Suppl. Tables S7 A,B,C,D,E). Only data up to 36 months after gene therapy were used and data of both CDP+NPP and STRIM groups were considered together. The plots show the estimated curves for some specific values of the continuous covariates retained in the models (Q1, Q2 and Q3 denote the first, second and third observed quartiles of the variable, which are Q1=6.66, Q2=9.9, Q3=12.8 for CD34+ cells/Kg). Estimated longitudinal trend of CD15+ VCN (A), CD3+ VCN (B), lymphocytes (C) and CD3+ cells (D) and CD4+CD45RA+ naïve T-cells (E). GT: gene therapy; VCN: vector copy number.