Autologous Gene Therapy for Artemis-Deficient SCID

A Phase I/II Feasibility Study of Gene Transfer for Artemis-Deficient Severe Combined Immunodeficiency (ART-SCID) Using a Self-Inactivating Lentiviral Vector (AProArt) to Transduce Autologous CD34 Hematopoietic Cells

This study aims to determine if a new method can be used to treat Artemis-deficient Severe Combined Immunodeficiency (ART-SCID), a severe form of primary immunodeficiency caused by mutations in the DCLRE1C gene. This method involves transferring a normal copy of the DCLRE1C gene into stem cells of an affected patient. Participants will receive an infusion of stem cells transduced with a self-inactivating lentiviral vector that contains a normal copy of the DCLRE1C gene. Prior to the infusion they will receive sub-ablative, dose-targeted busulfan conditioning. The study will investigate if the procedure is safe, whether it can be done according to the methods described in the protocol, and whether the procedure will provide a normal immune system for the patient. A total of 25 patients will be enrolled at the University of California San Francisco in this single-site trial, and will be followed for 15 years post-infusion. It is hoped that this type of gene transfer may offer improved outcomes for ART-SCID patients who lack a brother or sister who can be used as a donor for stem cell transplantation or who have failed to develop a functioning immune system after a previous stem cell transplant.

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 will preclude continued accrual in the presence of safety signals, and long-term safety will be monitored for 15 years. Bone marrow stem cells will be harvested from participants who weigh ≤7.5 kilograms or have failed cytokine mobilization previously, and cytokine-mobilized peripheral blood stem cells will be harvested from participants weighing >7.5 kilograms. CD34 cells will be isolated using the CliniMACS® CD34 Reagent System cell sorter device. The cells will be transduced with the AProArt lentiviral vector. Transduction enhancers will be used to increase the transduction efficiency in peripheral blood CD34+ cells from patients who undergo a peripheral blood stem cell collection. These transduced cells will then be cryopreserved, and 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 evaluated at 4, 6, 8, 16, and 24 weeks 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, a decision will be made regarding further therapy. After day 42 post-transplant, 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. 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 infusion of the back-up cells or 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 >500/µl with GCSF. After day 42, patients will be assessed weekly through 12 weeks post-transplant and at week 16, monthly through month 6 post-transplant, and then 3 monthly through month 24. They will then be assessed at 6 monthly intervals during years 2-5 and annually through year 15. Study follow-up will include completion of Quality of Life questionnaires and administration of neurodevelopmental testing. Patients with evidence of clinically inadequate reconstitution, low 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. An independent Data Safety Monitoring Board (DSMB) will be appointed for safety monitoring of this trial. The DSMB will review all data for safety on a regular schedule, based on numbers of enrolled subjects and will also conduct special urgent review of any protocol related Serious Adverse Events (SAE). As the trial is initiated, the DSMB will review results of each of the first 3 cases prior to proceeding with subsequent patients. The investigational product (IND1711) 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.

Longitudinal study of autologous stem cell transplant of cells transduced with corrected DCLRE1C gene using a self-inactivating lentiviral vector (AProArt). The CliniMACS® CD34 Reagent System cell sorter device will be used to select CD 34 cells. Sub-ablative busulfan will be used for pre-transplant conditioning.

Gene Transfer for Artemis-Deficient Severe Combined Immunodeficiency (ART-SCID) Using a Self-Inactivating Lentiviral Vector (AProArt) to Transduce Autologous CD34 Hematopoietic Cells. The CliniMACS® CD34 Reagent System sorter device will be used to select CD34 cells. Patients will be conditioned with low dose busulfan prior to transplant.

Participants will undergo infusion with autologous hematopoietic cells transduced with a lentiviral vector, AProArt, which contains the correct form of DCLRE1C complementary deoxyribonucleic acid DNA, after receiving sub-ablative, exposure-targeted busulfan conditioning.

Processing of hematopoietic progenitor cells to select CD34 cells, using the CliniMACS® CD34 Reagent System, prior to infusion.

Busulfan is a cell cycle non-specific alkylating antineoplastic agent, in the class of alkyl sulfonates. Patients will receive low-dose busulfan conditioning targeted over 2 days to achieve a cumulative area under the curve (AUC) of 20 mg*hr/L.

Survival of patients with ART-SCID who receive self-inactivating (SIN) lentiviral vector (AProArt)-transduced CD34 cells through autologous stem cell transplant

Patient survival status and (if applicable) cause of death will be recorded to assess overall survival.

Number of AProArt-transduced CD34 cells infused per kg of body weight will be calculated, with a target of at least 2x10e6 transduced cells and up to 15x10e6 transduced cells per kilogram.

Hematopoietic recovery in patients with ART-SCID who receive self-inactivating (SIN) lentiviral vector (AProArt)-transduced CD34 cells through autologous stem cell transplant.

Lymphocyte studies to measure immune system reconstitution in patients who have received AProArt lentiviral vector-transduced autologous CD34 hematopoietic stem cell transplant after low dose busulfan conditioning

Specific antibody titers to measure establishment of immune function in patients who have received AProArt lentiviral vector-transduced autologous CD34 hematopoietic stem cell transplant after low dose busulfan conditioning

Patients will undergo blood tests to measure antibody production to tetanus toxoid as documented by achieving protective levels following immunization.

Immunoglobulin levels to measure establishment of B cell immune function in patients who have received AProArt lentiviral vector-transduced autologous CD34 hematopoietic stem cell transplant after low dose busulfan conditioning

Engraftment will be measured by performing quantitative PCR assays to detect transduced cells in at least two of the following lineages: T, B, NK and granulocyte/myeloid.

Incidence of Adverse Events related to autologous stem cell transplant of self-inactivating (SIN) lentiviral vector (AProArt)-transduced CD34 cells

Vector copy number sustained over time after infusion of transduced hematopoeitic stem cell transplant.

Laboratory studies will measure the number of vector copies found in blood leukocyte populations, including granulocytes, T-cells, B-cells and NK cells. The cell populations will be isolated by gradient centrifugation followed by staining with monoclonal antibodies and flow sorting.

From a mixed population of blood leukocytes, gradient isolated and flow-sorted components (T, B, myeloid, and NK cells), will have genomic DNA fragments amplified by linker-mediated PCR. Massively parallel sequencing will be performed and the junction host DNA sequences between the integrated vector and linkers will be mapped to the human genome using BLAST software. The genomic location of each insertion site will be determined, and number of cells with the same insertion site will be monitored.

Incidence of long-term Adverse Events related to autologous stem cell transplant of self-inactivating (SIN) lentiviral vector (AProArt)-transduced CD34 cells.

Long term survival in ART-SCID patients who undergo autologous stem cell transplant of self-inactivating (SIN) lentiviral vector (AProArt)-transduced CD34 cells.

Efficacy of transduction enhancers (dmPGE2 and LentiBOOST™) to impact immune reconstitution in ART-SCID patients.

Efficacy of transduction enhancers (dmPGE2 and LentiBOOST™) to impact T and B cell immune reconstitution in ART-SCID patients.

Effect of prophylactic sirolimus to reduce the occurrence of autoimmune hemolytic anemia following infusion of gene-corrected cells.

Regular monitoring of reticulocytes, direct Coombs, indirect Coombs, and LDH, starting at week 12 post-infusion.

Effects of treatment with a repeat infusion of gene-corrected cells on survival for patients who do not develop adequate immunity

Patient survival status and (if applicable) cause of death will be recorded to assess overall survival.

Number of AProArt-transduced CD34 cells infused per kg of body weight will be calculated for the repeat infusion, with a target of at least 2x10e6 transduced cells and up to 15x10e6 transduced cells per kilogram.

Hematopoietic recovery in patients with ART-SCID who receive self-inactivating (SIN) lentiviral vector (AProArt)-transduced CD34 cells through a repeat infusion autologous stem cell transplant.

Patients will undergo blood tests to measure complete blood count and differential following a repeat infusion of gene corrected cells.

Specific antibody titers to measure establishment of immune function in patients who have received a repeat infusion AProArt lentiviral vector-transduced autologous CD34 hematopoietic stem cell transplant

Patients will undergo blood tests following a repeat infusion of gene-corrected cells to measure antibody production to tetanus toxoid as documented by achieving protective levels following immunization.

Incidence of Adverse Events related to a repeat infusion autologous stem cell transplant of self-inactivating (SIN) lentiviral vector (AProArt)-transduced CD34 cells

Adverse events will be measured following a repeat infusion of gene-corrected cells using CTCAE version 4.0, including any oncogenic events.

Repertoire diversity in ART-SCID recipients gene therapy post-repeat infusion of gene-corrected cells.

Measurement via spectratyping of the T cell receptor Vb rearranged receptors following a repeat infusion of gene-corrected cells.

Incidence of long-term Adverse Events related to a repeat autologous stem cell transplant of self-inactivating (SIN) lentiviral vector (AProArt)-transduced CD34 cells.

Vector copy number sustained over time after a repeat infusion of transduced hematopoeitic stem cell transplant.

Laboratory studies will measure the number of vector copies found in blood leukocyte populations following a repeat infusion of gene-corrected cells, including granulocytes, T-cells, B-cells and NK cells. The cell populations will be isolated by gradient centrifugation followed by staining with monoclonal antibodies and flow sorting.

Patient reported outcome of undergoing treatment with gene-corrected cells as assessed by the PedsQL questionnaires.

Age-appropriate PedsQL questionnaires will be administered at baseline and years 1, 2, 4, 8, 10, 12, and 15.

The PedsQL Family Impact module will be administered at baseline and years 1, 2, 4, 8, 10, 12, and 15.

Inclusion Criteria: ≥2.0 months of age at initiation of busulfan conditioning Diagnosis of typical or leaky ART-SCID: Newly diagnosed ART-SCID patients must have: Artemis deficiency; AND CD3 count < 300 autologous cells/µL (typical ART-SCID) OR spontaneous maternal chimerism, OR CD3 count >300/µL but with restricted T cell receptor Vb diversity, defined as 18/24 or fewer polyclonal families. AND - CD45 cell response to mitogens (PHA) < 50% of the lower limit of normal range for the lab (leaky ART-SCID). Patients diagnosed with ART-SCID per the criteria above who have failed an allogeneic transplant (including an HLA matched sibling transplant) may participate if they meet the criteria below: - Are at least 3 months post allogeneic hematopoeitic stem cell transplant without evidence of engraftment of allogeneic donor cells (excluding maternal cells) OR are engrafted but have at least 2 of the following 4 conditions: Declining CD3 donor chimerism with at least 3 evaluations separated by at least 1 month prior to time of enrollment OR < 5% overall donor chimerism in blood and marrow at ≥3 months post transplant. Incompletely reconstituted T cell immunity at ≥6 months (1 of the following 2): CD4 < 200/μL AND CD45 cell PHA < 50% of the lower limit of normal for lab; CD4 CD45RA < 20% of total CD4 cells OR T cell receptor Vb diversity is restricted, defined as 18/24 or fewer polyclonal families. No donor B cells OR lack of B cell function (immunoglobulin M isohemagglutinins < 1:8 (not blood type AB) AND immunoglobulin A (IgA) or IgM values below reference range for age AND if not receiving intravenous immunoglobulin (IVIG), no protective level of antibody to tetanus immunization x2). Clinical manifestations consistent with persistent T and B cell immunodeficiency e.g., chronic infection including norovirus, cytomegalovirus, human herpes virus 6; OR acute or recurrent infection (e.g., PJP), bronchiectasis, chronic sinusitis. AND Have no prior exposure to high dose busulfan (≥10 mg/kg total dose or average cumulative exposure of ≥40 mg*hr/L). If the total cumulative AUC including previous busulfan exposure plus the dose to be administered in this protocol is predicted to be ≤60 mg*hr/L, then patient would be eligible providing other criteria are satisfied. 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). Written informed consent according to guidelines of the Institutional Review Board (IRB). Exclusion Criteria: Liver function tests (aspartate aminotransferase, alanine transaminase, gamma-glutamyl transferase) > three times the upper limit of normal for lab and/or total bilirubin >1.50 mg/dl at the time of planned initiation of busulfan conditioning. Prior history of veno-occlusive disease (Sinusoidal obstruction syndrome) of the liver. Medically eligible HLA-matched sibling (applies to newly diagnosed patients only). Evidence of HIV infection by polymerase chain reaction or p24 antigen testing. Unable to tolerate general anesthesia and/or marrow harvest or peripheral blood stem cell collection (apheresis) or insertion of central venous catheter. 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. Pregnancy 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.

Individual participant data that underlie the results reported in scientific journals (text, tables, figures, and appendices) after de-identification.

Researchers can submit a request for access to the study Steering Committee. If the proposal is determined to be methodologically sound, data requestors will need to sign a data access agreement prior to gaining access.

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