Base Editing for Mutation Repair in Hematopoietic Stem & Progenitor Cells for X-Linked Chronic Granulomatous Disease

Overview

Background: Chronic granulomatous disease (CGD) is a rare immune disorder caused by a mutation in the CYBB gene. People with CGD have white blood cells that do not work properly and are at greater risk of getting infections. Gene therapy using lentivector has helped people with CGD. Researchers want to know if the base-edited stem cells can improve the white cells' functioning and result in fewer CGD-related infections. Objective: To learn if base-edited stem cells will correct the white blood cells in people with CGD. Eligibility: Males aged 18 years and older with X-linked CGD. Design: This is a non-randomized study. Participants with the specific mutation under study will be screened during the initial phase. During the development phase, participants will undergo apheresis to collect stem cells for base-editing correction of the mutation. During the treatment phase, participants will receive the base-edited cells after chemotherapy with busulfan. Participants will remain in the hospital until their immunity recovers. Participants will be maintained on sirolimus to prevent an immune response to the new protein expressed by the base-edited cells. Follow-up visits will continue for 15 years.

Study Description: Open-label, phase 1/2 trial to determine the safety, and efficacy of a single infusion of base-edited (BE) autologous hematopoietic stem and progenitor cells (HSPCs) for treatment of X-linked chronic granulomatous disease (X-CGD). Base editing is performed to repair CYBB missense gene mutations (eg, CYBB c.676C\>T). The study hypotheses are that 1) base editing can efficiently repair gene mutations in HSPCs; and 2) BE HSPCs can engraft and differentiate into functional phagocytes with restored nicotinamide adenine dinucleotide phosphate (NADPH) oxidase activity. During the initial development phase each study participant will undergo apheresis for CD34+ HSPC collection for the development and validation of a mutation-specific BE system. During the treatment phase, participants will receive a one-time infusion of the BE autologous HSPC (study product) after the administration of busulfan conditioning (total 12 mg/kg with a targeted total AUC of 65,000 ng/mL x hr). Sirolimus will be initiated at Day -1 and will be given for approximately 3-6 months. Participants will have follow-up evaluations at months 3, 6, 12, 18, and 24, and yearly thereafter until 5 years after treatment. Key study assessments include adverse event (AE) assessment, blood laboratory evaluations of functional protein made from the target gene (CYBB, encodes for gp91\^phox), and deoxyribonucleic acid (DNA) sequencing to identify rates of gene repair and off-target mutation. The final study follow-up under this protocol will be at 5 years, but long-term follow-up under a separate NIH protocol will continue annually to 15 years after treatment. Objectives: Primary Objectives: * To evaluate the safety of BE autologous CD34+ cells. * To evaluate the efficacy of BE autologous CD34+ cells. Secondary Objectives: -To evaluate: * Efficiency of base editing (percentages of target nucleotide conversion). * Engraftment capability of BE HSPCs. * Efficiency in restoring gp91\^phox expression * Efficiency in restoring NADPH oxidase function. * Clinical efficacy. * Stability of gene correction. Exploratory Objectives: -To evaluate: * Specificity of base editing by assessing rates of off-target edits at top predicted sites. * Random off-target edits by whole genome sequencing (WGS). Endpoints: Primary Endpoints: * Safety of gene therapy using BE autologous HSPCs as measured by study product-related AEs and serious AEs (SAEs) through 2 years after treatment. * Efficacy of gene therapy determined as percentages of subjects who have \>= 10% oxidase-positive granulocytes at 12 months after infusion. Secondary Endpoints: * Determine frequency of converted target nucleotide alleles. * Assess the frequency of gene-modified alleles compared to infusion product in peripheral blood at 12 months. * Evaluate efficacy of restoring gp91\^phox expression. * Evaluate efficacy of NADPH oxidase functional restoration as measured by the dihydrorhodamine (DHR) flow cytometry oxidase assay at 12 months after treatment (\>=10% oxidase-positive neutrophils), or by quantitative measurement of reactive oxygen species (ROS) using the ferricytochrome C assay on peripheral blood granulocytes. * Evaluate clinical benefit by improvement of baseline clinical problems such as recurrent infections, growth failure, malnutrition, inflammatory bowel disease, or antibiotic usage. * Assess stability of gene correction by serial measurement of percent of nucleotide-converted alleles. Exploratory Endpoints: * Evaluate specificity by assessing for off-target edits at predicted sites with high-throughput sequencing of the 5 most common candidate off-target loci identified by a comprehensive in vitro screen, Circularization for High-throughput Analysis of Nuclease Genome-wide Effects by sequencing (CHANGE-seq-BE), in peripheral blood cells. * Determine rate of random off-target edits WGS.