Conditioning SCID Infants Diagnosed Early

This is a prospective, multicenter, phase II, open-label study of two reduced busulfan dose
levels in newborns identified at birth with SCID of appropriate genotype/phenotype and
clinical status, undergoing either haploidentical related or well-matched unrelated donor
TCRαβ+/CD19+ depleted HCT. Subjects will be enrolled on either of 2 strata according to
genotype (defects of cytokine receptor function i.e. IL2RG or JAK3 and defects of receptor
recombination i.e. RAG1 or RAG2). Thus up to 32 subjects on each of 2 strata or 64 subjects
total would be enrolled over 4 years with 3 years follow-up.

Patients with IL2RG/JAK3 would be randomized to receive busulfan targeted either to
cumulative exposure of 25-35 mg*h/L or 55-65 mg*h/L with Thymoglobulin. Patients with RAG1/2
would be randomized to receive busulfan targeted to cumulative exposure of 25-35 mg*h/L or
55-65 mg*h/L, in conjunction with fludarabine, thiotepa and Thymoglobulin. Safety/feasibility
of the novel TCR αβ+/CD19+ depleted allogeneic HCT strategy will be monitored on an ongoing
basis using stopping rules for lack of neutrophil engraftment and other important short-term
toxicities.

Donor selection would be determined clinically at the discretion of the treating clinicians
at each site. Pharmacokinetic monitoring of busulfan exposure will be performed per local
practices at CLIA-certified laboratories. Patients will receive busulfan and pharmacokinetic
measurement to individualize dosing. Time-concentration data of the initial dose and
subsequent doses will be reviewed centrally (Dr. Janel Long-Boyle) using a cloud-based
application (InsightRx) to guide dose adjustment in real-time (Long-Boyle, Chan, Keizer,
2017, ASBMT Tandem abstract accepted). Clinical and laboratory data will be collected at
defined time points over 3 years and entered in an electronic data capture system using
study-specific case report forms. These data will be used to measure the outcomes including
the primary outcome (cAUC of busulfan that promotes humoral immune reconstitution at 2 years
post HCT with acceptable regimen-related toxicity at 42 days post HCT) and secondary outcomes
(the quality of donor cell engraftment and immune function achieved in B and T cell
compartments and survival). Mechanistic studies supporting the exploratory endpoints will be
conducted centrally in designated laboratories.

Inclusion Criteria:

1. Infants with SCID, either typical or leaky or Omenn syndrome.

1. Typical SCID is defined as either of the following

- Absence or very low number of T cells (CD3+ T cells <300/microliter AND no or
very low T cell function (<10% of lower limit of normal) as measured by response
to phytohemagglutinin OR

- Presence of maternally derived T cells

2. Leaky SCID is defined as the following

• Absence of maternally derived T cells

• AND either one or both of the following (i, ii): i) <50% of lower limit of normal T
cell function as measured by response to PHA OR <30% of lower limit of normal T cell
function as measured by response to CD3 ii) Absent or <10% of lower limit of normal
proliferative responses to candida and tetanus toxoid antigens (must document post
vaccination or exposure for this criterion to apply)

• AND at least two of the following (i through iii): i) CD3 T cells < 1500/microliter
ii) >80% of CD3+ or CD4+ T cells are CD45RO+ AND/OR >80% of CD3+ or CD4+ T cells are
CD62L negative AND/OR >50% of CD3+ or CD4+ T cells express HLA-DR (at < 4 years of
age) AND/OR are oligoclonal T iii) Low TRECs and/or the percentage of CD4+/45RA+/CD31+
or CD4+/45RA+/CD62L+ cells is below the lower level of normal.

3. Omenn syndrome • Generalized skin rash

- Maternal lymphocytes tested for and not detected.

- >80% of CD3+ or CD4+ T cells are CD45RO+ AND/OR >80% of CD3+ or CD4+ T cells are
CD62L negative AND/OR >50% of CD3+ or CD4+ T cells express HLA-DR (<2 years of
age)

- Absent or low (up to 30% lower limit of normal (LLN)) T cell proliferation to
antigens (Candida, tetanus) to which the patient has been exposed IF:
Proliferation to antigen was not performed, but at least 4 of the following 8
supportive criteria, at least one of which must be among those marked with an
asterisk (*) below are present, the patient is eligible as Omenn Syndrome.

1. Hepatomegaly

2. Splenomegaly

3. Lymphadenopathy

4. Elevated IgE

5. Elevated absolute eosinophil count

6. *Oligoclonal T cells measured by CDR3 length or flow cytometry (upload
report)

7. *Proliferation to PHA is reduced to < 50% of lower limit of normal (LLN) or
SI < 30

8. *Low TRECs and/or percentage of CD4+/RA+ CD31+ or CD4+/RA+ CD62L+ cells
below the lower level of normal

2. Documented mutation in one of the following SCID-related genes

a. Cytokine receptor defects (IL2RG, JAK3) b. T cell receptor rearrangement defects (RAG1,
RAG2) 3. No available genotypically matched related donor (sibling) 4. Availability of a
suitable donor and graft source

1. Haploidentical related mobilized peripheral blood cells

2. 9/10 or 10/10 allele matched (HLA-A, -B, -C, -DRB1, -DQB1) volunteer unrelated donor
mobilized peripheral blood cells 5. Age 0 to 2 years at enrollment

Note: to ensure appropriate hepatic metabolism, age at time of busulfan start:

For IL2RG/JAK3: 8 weeks For RAG1/RAG2: 12 weeks

6. Adequate organ function defined as:

1. Cardiac:

Left ventricular ejection fraction (LVEF) at rest ≥ 40% or, shortening fraction (SF) ≥
26% by echocardiogram.

2. Hepatic:

Total bilirubin < 3.0 x the upper limit of normal (ULN) for age (patients who have
been diagnosed with Gilbert's Disease are allowed to exceed this limit) and AST and
ALT < 5.0 x ULN for age.

3. Renal:

GFR estimated by the updated Schwartz formula ≥ 90 mL/min/1.73 m2. If the estimated
GFR is < 90 mL/min/1.73 m2, then renal function must be measured by 24-hour creatinine
clearance or nuclear GFR, and must be > 50 mL/min/1.73 m2.

4. Pulmonary No need for supplemental oxygen and O2 saturation > 92% on room air at sea
level (with lower levels allowed at higher elevations per established center standard
of care).

Exclusion Criteria:

1. Presence of any serious life-threatening or opportunistic infection at time of
enrollment and prior to the initiation of the preparative regimen. Serious infections
as defined below that occur after enrollment must be reported immediately to the Study
Coordinating Center, and enrollment will be put on hold until the infection resolves.
Ideally enrolled subjects will not have had any infection. If patients have
experienced infections, these must have resolved by the following definitions:

a. Bacterial i. Positive culture from a sterile site (e.g. blood, CSF, etc.): Repeat
culture(s) from same site must be negative and patient has completed appropriate
course of antibacterial therapy (typically at least 10 days).

ii. Tissue-based clinical infection (e.g. cellulitis): Complete resolution of clinical
signs (e.g. erythema, tenderness, etc.) and patient has completed appropriate course
of antibacterial therapy (typically at least 10 days).

iii. Pneumonia, organism not identified by bronchoalveolar lavage: Complete resolution
of clinical signs (e.g. tachypnea, oxygen requirement, etc.) and patient has completed
appropriate course of antibacterial therapy (typically at least 10 days). If possible,
radiographic resolution should also be demonstrated.

b. Fungal i. Positive culture from a sterile site (e.g. blood, CSF, etc.): Repeat
culture(s) from same site is negative and patient has completed appropriate course of
antifungal therapy (typically at least 14 days). The patient may be continued on
antifungal prophylaxis following completion of the treatment course.

c. Pneumocystis i. Complete resolution of clinical signs (e.g. tachypnea, oxygen
requirement, etc.) and patient has completed appropriate course of therapy (typically
at least 21 days). If possible, radiographic resolution should also be demonstrated.
The patient may be continued on prophylaxis following completion of the treatment
course.

d. Viral i. Viral PCRs from previously documented sites (blood, nasopharynx, CSF) must
be re-tested and are negative.

ii. If re-sampling a site is not clinically feasible (i.e. BAL fluid): Complete
resolution of clinical signs (e.g. tachypnea, oxygen requirement, etc.). If possible,
radiographic resolution should also be demonstrated.

2. Patients with HIV or HTLV I/II infection will be excluded.