Autologous Gene Therapy for Artemis-Deficient SCID

Children with SCID generally do not survive beyond the first year of life without definitive treatment. The most effective current cure is hematopoietic stem cell transplant (HCT) with a human leukocyte antigen (HLA) matched sibling. While a matched sibling HCT can successfully treat ART-SCID, fewer than 20% of affected children have such a donor, and even when a matched sibling donor is available there is often incomplete T and B cell immune reconstitution. ART-SCID is the most difficult type of SCID to cure by hematopoietic stem cell transplant using alternative donors. Engraftment typically requires intensive conditioning with high dose alkylating agents to prevent rejection and to open marrow niches. These patients also have a high risk of developing graft versus host disease (GVHD) when alternative donors are used. The great majority of patients have absent B cell reconstitution and require lifelong administration of immunoglobulin infusions. Patients with ART-SCID who do receive high doses of alkylators, especially when 2 agents are used, have poorer survival, abnormal dental development, endocrinopathies, and short stature in comparison with children exposed to no or limited alkylators or children with SCID types that are not associated with a DNA repair defect. For these reasons, a safer, more effective approach to curing ART-SCID is needed. Autologous gene-corrected hematopoeitic stem cell transplant may eliminate both the risk of GVHD and the need for alkylators to prevent rejection.

The study design is a single-cohort, longitudinal experiment using non-randomized patients treated once with a lentiviral vector for gene-correction of Artemis-deficient SCID after conditioning with low-dose busulfan. No formal control group is planned for gauging safety; rather, intensive monitoring of the initial 6 enrollees was undertaken to preclude continued accrual in the presence of safety signals. This enrollment stage was completed in 2019 with no safety signals identified, and long-term safety will be monitored for 15 years. Bone marrow stem cells will be harvested from participants, and CD34 cells will be isolated using the CliniMACS® CD34 Reagent System cell sorter device. The CD34 cells will be transduced with the AProArt lentiviral vector, and cryopreserved. Aliquots of the cells will undergo safety testing and be reserved for potency evaluation. All patients will receive busulfan conditioning targeted over 2 days to achieve a cumulative area under the curve (AUC) of 20 mg*hr/L (an ablative cumulative AUC is 60-90mg*hr/L).

Following the infusion of AProArt-transduced cells, patients will be assessed weekly through 12 weeks post-transplant and at week 16, monthly through month 6 post-transplant, every 3 months through month 24, every 6 months during years 2-5, and then annually through year 15. Assessments will include physical examination, clinical laboratory tests, collection of specimens for research studies, and completion of Quality of Life questionnaires. Neurodevelopmental testing will be performed at age-appropriate time points.

At weeks 4, 6, 8, 12, 16, and 24, research specimens will be evaluated for evidence of gene transduced peripheral blood mononuclear cells and when possible, cell lineages including T, B, NK and granulocyte/myeloid cells. If there is no evidence of gene transduced cells at 6 weeks (42 days) post infusion, planning for an alternative treatment will begin, with the final decision regarding further therapy to be based on gene-marking results at 10 weeks.

If the absolute neutrophil count is < 200/µl or platelets < 20,000/µl on 3 independent determinations after day 42 post infusion of transduced cells, the patient may receive an allogeneic hematopoeitic stem cell transplant. Patients who were neutropenic prior to conditioning (SCID-related neutropenia) but responsive to granulocyte-colony stimulating factor (GCSF) will not be considered to have failed, provided the absolute neutrophil count can be maintained above >300/µl with GCSF.

Recipients will be followed for toxicity and durable reconstitution of T and B cell immunity. Immune reconstitution of T cells will be monitored on a regular basis. Patients with evidence of clinically inadequate immune reconstitution, low vector copy number (VCN), or any other features suggesting clinically inadequate response to the initial gene therapy procedure will be offered a repeat infusion of gene-transduced cells. Conditioning regimens given prior to a repeat gene therapy procedure may include low-dose busulfan, other conditioning, or no conditioning.

Historical controls who received alternative donor allogeneic transplants as treatment for ART-SCID will serve as the comparator arm for secondary endpoints.

An independent Data Safety Monitoring Board (DSMB) has been appointed for safety monitoring of this trial. The DSMB reviews all data for safety on a regular schedule, based on numbers of enrolled subjects and conducts special urgent review of any protocol related Serious Adverse Events (SAE). In the early stage of the trial, the DSMB reviewed results of each of the first 3 cases prior to proceeding with subsequent patients.

The investigational product (IND17711) for the ART-SCID gene transfer study is not available for expanded access use. As per 21 CFR Part 312.305(3), the study management team has determined that providing the investigational product for expanded access use at this time would interfere with the conduct and completion of the clinical trial and potential development of future expanded access use. The investigational product is available to eligible patients through participation in this clinical trial.

Inclusion criteria

• ≥2.0 months of age at initiation of busulfan conditioning
• New diagnosis of typical or minimally leaky ART-SCID, as defined by the criteria below:
• Artemis deficiency with bi-allelic pathogenic or likely pathogenic mutations in DCLRE1C; AND
• CD3 count < 50 autologous cells/µL (typical ART-SCID) OR spontaneous maternal chimerism, OR CD3 count >50/µL and <300/uL and with restricted T cell receptor Vb diversity; AND
• CD45 cell response to mitogens (PHA) < 50% of the lower limit of normal range for the lab (leaky ART-SCID).
• No medically eligible HLA-identical sibling with a normal immune system who could serve as an allogeneic bone marrow donor (applies to newly diagnosed patients only).

Exclusion criteria

• Presence of a medically eligible HLA-matched sibling
• Evidence of HIV infection by polymerase chain reaction or p24 antigen testing.
• Unable to tolerate general anesthesia and/or marrow harvest or insertion of central venous catheter.
• Any one of liver function tests AST, ALT, gamma-glutamyl transpeptidase (GGT) >5X the upper limit of normal for lab and/or total bilirubin >2.0 mg/dl (not due to Gilbert's) at the time of planned initiation of busulfan conditioning unless the elevated LFTs are considered to be due to medication, a viral infection for which there is no treatment other than reconstituting T cell immunity, or maternal GVHD.
• Presence of any severe medical conditions making a patient unsuitable for busulfan administration
• Presence of a recognized second gene mutation that results in an autosomal dominant or recessive disorder intrinsic to hematopoietic cells and that could be treated by an allogeneic HCT.
• Presence of a medical condition indicating that survival is predicted to be less than 4 months, such as the requirement for mechanical ventilation, severe failure of a major organ system, or evidence of a serious, progressive infection that is refractory to medical therapy.
• A social situation indicating that the family may not be able to comply with protocol procedures and recommended medical care and follow-up.
• Other conditions which in the opinion of the Principal Investigator and/or co-investigators, contra-indicate the infusion of transduced cells or study participation.