Base-Edited Hematopoietic Stem/Progenitor Cell X-Linked Severe Combined Immunodeficiency Gene Therapy

Study Description:

This is a phase 1/2, non-randomized study of a single infusion of autologous hematopoietic stem/progenitor cells base-edited to repair interleukin 2 receptor gamma (IL2RG) mutations (BE-HSPC IL2RG) in 18 participants with X-linked severe combined immunodeficiency (X-SCID).

Primary Objective:

Evaluate the safety of treatment with BE-HSPC IL2RG in participants with X-SCID.

Secondary Objectives:

Evaluate efficacy of treatment with BE-HSPC IL2RG in participants with X-SCID.

Exploratory Objectives:

• Evaluate off-target (OT) editing activity.
• Compare outcomes of immune reconstitution with lentivector (LV) gene therapy.

Primary Endpoint:

Safety of treatment with BE-HSPC IL2RG, by quantifying frequency and severity of adverse events (AEs) related to study agent from infusion to 12 months after infusion.

Secondary Endpoints (24 months post-study agent infusion):

• Percentage of participants with >=5% mutation-repaired myeloid cells.
• Editing efficiency in peripheral blood cells (such as T, B, and natural killer [NK] cells).
• Immune reconstitution:

• T, B, and NK cell number improvement from baseline.
• Emergence of naive T cells and CD31+ recent thymic emigrants.
• B-cell function: immunoglobulin (Ig) production.
• Specific responses to vaccines.
• Clinical efficacy: improvement from baseline problems such as recurrent infection, chronic norovirus, protein-losing enteropathy, gastrointestinal complaints, growth failure, malnutrition, or immune dysregulation.
• Frequency and severity of all study agent-related AEs and serious adverse events (SAEs) from time of study product infusion.

Exploratory Endpoints:

• Evaluate for frequency of off-targets (OTs) by high-throughput sequencing (HTS) of the target mutation at 2 years post-infusion.
• Compare rates of immune reconstitution with LV-X-SCID gene therapy.

• INCLUSION CRITERIA:

In order to be eligible to participate in this study, an individual must meet all of the following criteria:

• Aged >= 3 years and weigh >=10 kg
• Patients with X-SCID
• If previously transplanted, must be >=18 months post-HSCT
• Expected survival of at least 120 days.
• Ability to undergo apheresis for stem cell collection.
• Patients with proven mutation in the common gamma chain gene as defined by direct sequencing of patient DNA. At this time, only patients with a IL2RG p.Q144X, IL2RG p.R289X, IL2RG p.Q235X and IL2RG p.R226H mutations can be treated.
• Participants of reproductive potential must agree to consistently use highly effective contraception throughout study participation and for at least 2 years post-treatment.

Acceptable forms of contraception are:

--For males: Condoms or other contraception with partner.

• Documented to be negative for HIV infection by PCR
• The patient must be judged by the primary evaluating physician to have a suitable family and social situation consistent with ability to comply with protocol procedures and the long-term follow-up requirements.
• Medical lab data (historical) of severe B cell dysfunction (low or absent IgG levels, failed immune response to vaccines);

OR

demonstrated requirement for intravenous gamma globulin (IVIG) (significant drop over 3 to 6 weeks between peak and trough IgG levels).

-Must be willing to have blood and tissue samples stored IN ADDITION, patients must satisfy the following Laboratory Criteria AND Clinical Criteria

Laboratory Criteria: (>=1 must be present)

• CD4+ lymphocytes: absolute number <= 50% of the lower limit of normal (LLN)
• CD4+CD45RA+ lymphocytes: absolute number <= 50% of the LLN OR T-cell receptor excision circles (TRECs) <= 5% of normal for age.
• Memory B Cells: absolute number <= 50% of LLN
• Serum IgM<normal for age
• NK cells: absolute number <= 50% of LLN
• Lymphocyte proliferative response to each of 2 mitogens, phytohemagglutinin (PHA) and concanavalin A (ConA), is <= 25% compared with a normal control.
• Molecular spectratype analysis- absent or very oligoclonal (1-3 dominant peaks) in >=6 of the 24 V(Beta) T-cell receptor families.

Clinical Criteria: (>=1 must be present)

I. Infections (not including molluscum, warts or mucocutaneous candidiasis; see VII and VIII below):

Three significant new or chronic active infections during the 2 years preceding evaluation for enrollment, with each infection accounting for one criterion.

Infections are defined as an objective sign of infection

• (fever >=38.3 degrees Celsius (101 degrees Fahrenheit) or
• neutrophilia or
• pain/redness/swelling or
• radiologic/ultrasound imaging evidence or
• typical lesion or histology or
• new severe diarrhea or
• cough with sputum production.

In addition to one or more of these signs/symptoms of possible infection, there also must be at least 1 of the following criteria as evidence of the attending physician s intent to treat a significant infection (a. and b.) or objective evidence for a specific pathogen causing the infection (c.)

• Treatment (not prophylaxis) with systemic antibacterial, antifungal or antiviral antibiotics >=14 days

OR

• Hospitalization of any duration for infection

OR

• Isolation of a bacteria, fungus, or virus from biopsy, skin lesion, blood, nasal washing, bronchoscopy, cerebrospinal fluid or stool likely to be an etiologic agent of infection

II. Chronic pulmonary disease as defined by:

• Bronchiectasis by x-ray computerized tomography

OR

• Pulmonary function test (PFT) evidence for restrictive or obstructive disease that is 60% of Predicted for Age

OR

• Pulse oximetry <=94% in room air (if patient is too young to comply with performance of PFTs).

III. Gastrointestinal enteropathy:

• Diarrhea-watery stools >=3 times per day (of at least 3 months duration that is not a result of infection as defined in criterion I. above)

OR

• Endoscopic evidence (gross and histologic) for enteropathy (endoscopy will only be performed if medically indicated)

OR

• Other evidence of enteropathy or bacterial overgrowth syndrome: including malabsorption of fat soluble vitamin(s), abnormal D-xylose absorption, abnormal hydrogen breath test, evidence of protein losing enteropathy (for example increasingly high or frequent dosing of intravenous gamma globulin supplement required to maintain blood IgG level).

IV. Poor nutrition: Requires G-tube or intravenous feeding supplement to maintain weight or nutrition.

V. Auto- or allo-immunity: Examples must include objective physical findings that include, but are not limited to any one of alopecia, severe rashes at more than one anatomic site and not due to infection, uveitis, joint pain with redness or swelling or limitation of movement that is not a result of infection, lupus-like lesions, and granulomas (Does not include auto- or allo-immune enteropathy which is criterion iii). Where possible and appropriate, diagnosis will be supported by histopathology or other diagnostic modality.

VI. Failure to grow in height: <=3rd percentile for age

VII. Skin molluscum contagiosum OR warts (this criterion is satisfied if molluscum consists of >=10 lesions or there are two or more lesions at each of two or more widely separated anatomic sites; or there are >=3 warts at different anatomic sites at the same time; or the patient has both molluscum and warts)

VIII. Mucocutaneous candidiasis (chronic oral thrush or candida esophagitis or candida intertriginous infection or candida nail infections; must be culture positive to satisfy this criterion)

IX. Hypogammaglobulinemia: requires regular IgG supplementation

Exclusion criteria

An individual who meets any of the following criteria will be excluded from participation in this study:

• Available HLA-matched sibling donors.
• Known hypersensitivity to busulfan or any component of the product.
• Contraindications for administration of busulfan.
• Childhood malignancy (occurring before 18 years of age) in the participant or a first degree relative, or previously diagnosed known genotype of the participant conferring a predisposition to cancer unless approved by the Hematology consult team (no DNA or other testing for cancer predisposition genes will be performed as part of the screen for this protocol).
• Any other condition that, in the opinion of the investigator, may compromise the safety or compliance of the participant, or would preclude the patient from successful study completion.