Chronic Granulomatous Disease

Overview

Chronic Granulomatous Disease (CGD) is a rare inherited immune disorder in which certain white blood cells—especially neutrophils—cannot generate the reactive oxygen species needed to kill some bacteria and fungi. It is caused by disease-causing variants in genes encoding the NADPH oxidase complex, most often the X-linked CYBB gene and, less commonly, autosomal genes including NCF1, CYBA, NCF2, and CYBC1. CGD usually begins in childhood, although severity varies; recurrent or invasive infections and damaging inflammation can affect the lungs, lymph nodes, liver, bowel, skin, and other organs. Clinical presentation and treatment

Current standard care aims to prevent and rapidly treat infections, commonly with antibacterial and antifungal prophylaxis, while anti-inflammatory medicines may be needed for complications such as CGD-associated colitis. Allogeneic hematopoietic stem-cell transplantation (HSCT), which replaces a person’s blood-forming system with donor cells, is an established curative option for selected patients, but carries risks including graft rejection and graft-versus-host disease. Clinical presentation and treatment

Scope of Recent Research (2020–present)

Since 2020, CGD cure research has moved from proof-of-concept viral gene addition toward more precise repair of a patient’s own blood-forming stem cells. The major questions are whether corrected stem cells will engraft durably, restore enough NADPH oxidase activity to prevent infection and inflammation, and do so without insertional mutagenesis, unintended genome edits, or excessive chemotherapy toxicity. The field now has human evidence for lentiviral gene therapy and first-in-human evidence for prime editing, but no gene-based CGD cure is yet an approved standard treatment. Lentiviral gene therapy Prime editing for p47phox CGD

Major Breakthroughs and Emerging Therapies

Lentiviral gene therapy has provided the strongest longer-term clinical evidence that autologous gene therapy can correct CGD. In a 2020 report involving nine people with severe X-linked CGD, patients received their own CD34-positive blood-forming stem and progenitor cells after those cells were modified outside the body with a self-inactivating lentiviral vector carrying a functional CYBB gene. At 12 months, six of seven surviving participants had stable gene-marked blood cells and 16–46% oxidase-positive neutrophils; six survivors stopped CGD-related antibiotic prophylaxis. Two participants died from serious pre-existing complications shortly after treatment, emphasizing that advanced disease and transplantation conditioning remain major hazards. Lentiviral gene therapy

Subsequent work has clarified both the promise and the limitations of lentiviral approaches. A French Phase 1/2 study found durable engraftment and clinical benefit in two of four treated patients, while two progressively lost corrected cells. Single-cell analyses linked poor engraftment to severe inflammation, interferon-pathway activation, abnormal stem-cell states, and stem-cell exhaustion before treatment. Stem-cell inflammation and gene therapy Researchers are also improving vector design: one 2022 study developed a lentiviral vector using native CYBB regulatory elements to more closely reproduce the normal timing and cell-type specificity of gp91phox production. Physiologically regulated lentiviral vector

Precise genome editing seeks to repair the disease-causing DNA sequence rather than add a separate copy of a gene. For X-linked CGD, NIH investigators developed a high-fidelity, PAM-flexible adenine base editor that corrected a specific CYBB missense variant in patient-derived blood-forming cells while reporting minimal measured off-target DNA, RNA, and chromosomal effects in preclinical testing. PAMless base editing In parallel, researchers in Denmark reported correction strategies for both CYBA- and CYBB-related CGD, including targeted insertion of a shortened CYBB complementary DNA sequence that could theoretically cover most X-linked CGD variants; a paired Cas9 nickase approach reduced detectable off-target editing and chromosomal translocations in their experimental systems. Targeted editing and CYBB insertion

Prime editing has reached the clinic for the autosomal-recessive p47phox form of CGD caused by the common NCF1 “delGT” mutation. Prime editing is a targeted “search-and-replace” approach designed to make a specified DNA change without creating the double-strand DNA break used in conventional CRISPR-Cas9 editing. In the first two participants treated with PM359, edited autologous CD34-positive cells engrafted after busulfan conditioning, NADPH oxidase activity appeared within one month, and corrected neutrophil function was maintained through six months in one participant and four months in the other at the report’s cutoff. Prime editing for p47phox CGD This is an important clinical proof of concept, but it is not yet evidence of a durable cure because only two people were treated and follow-up was under one year. Prime editing for p47phox CGD

Clinical Trials and Experimental Approaches

The 2020 multicenter lentiviral studies of X-linked CGD were early first-in-human studies rather than conventional large trials, involving centers associated with the Net4CGD consortium. Their results showed that gene-corrected neutrophils can persist and function after infusion of autologous modified stem cells, but outcomes were strongly affected by participants’ pre-existing infections and inflammatory disease. Lentiviral gene therapy Genethon’s later G1XCGD Phase 1/2 study, NCT02757911, is listed as terminated; its registry record identifies Genethon as sponsor and reports three enrolled participants, while the related published investigation analyzed four infused patients from the clinical program. G1XCGD trial record Stem-cell inflammation and gene therapy

The NIH/NIAID-sponsored NCT06325709 is a recruiting Phase 1/2 trial of autologous base-edited hematopoietic stem and progenitor cells for adult men with X-linked CGD caused by selected CYBB mutations, initially including c.676C>T. The study’s primary efficacy benchmark is at least 10% oxidase-positive granulocytes 12 months after infusion, with long-term monitoring planned for gene correction, NADPH oxidase function, infections, and unintended edits. NIAID base-editing trial PM359, developed by Prime Medicine, was also a Phase 1/2 study for NCF1-related p47phox CGD; although the two-person report showed early biological and clinical benefit, the publication states that the sponsor terminated the clinical study, limiting near-term enrollment and the amount of follow-up data expected from that protocol. PM359 trial record Prime editing for p47phox CGD

Methodologies and Scientific Approaches

Most curative programs collect CD34-positive hematopoietic stem and progenitor cells from the patient, modify them outside the body, use chemotherapy conditioning to create bone-marrow space, and reinfuse the corrected cells. Researchers then measure engraftment, the proportion of corrected cells, gp91phox or p47phox protein expression, and the neutrophil oxidative burst using the dihydrorhodamine (DHR) assay. NIAID base-editing trial Preclinical studies also test whether edited human cells can produce functional myeloid cells and engraft in immunodeficient mouse models. Targeted editing and CYBB insertion

Safety assessment is unusually central in CGD because the disease genes and the editing strategies can present distinct genomic risks. Programs use sequencing to look for unintended edits, insertions, chromosomal deletions, translocations, and abnormal clonal expansion. The repeated, highly similar NCF1 gene and pseudogene region is particularly challenging: conventional CRISPR-Cas9 correction can create harmful large deletions when multiple nearby sites are cut. NCF1 editing and chromosomal deletions Researchers are also using single-cell RNA sequencing and inflammatory biomarkers to identify patients whose chronically inflamed stem cells may be less likely to engraft successfully. Stem-cell inflammation and gene therapy

Leading Institutions and Funding

The major clinical and translational network has included the U.S. National Institute of Allergy and Infectious Diseases and NIH Clinical Center, UCLA, Boston Children’s Hospital, University College London and Great Ormond Street Hospital, Genethon in France, and other Net4CGD collaborators. The landmark lentiviral program reported support from the California Institute for Regenerative Medicine, NIH programs, the European Union’s FP7 NET4CGD grant, the Wellcome Trust, AFM-Téléthon, and institutional programs at Boston Children’s Hospital and UCL/Great Ormond Street Hospital. Lentiviral gene therapy

NIH/NIAID is sponsoring the ongoing X-linked CGD base-editing trial, while the related preclinical base-editing work was led by NIAID investigators. NIAID base-editing trial PAMless base editing Prime Medicine funded PM359, with additional support from NIH/NIAID intramural projects ZIA AI000644 and ZIA AI000645. Prime editing for p47phox CGD The Danish gene-editing work was conducted through the PASCAL-MID research effort, supported by Innovation Fund Denmark grant 8056-00010 A. Targeted editing and CYBB insertion

Strengths, Limitations, and Challenges

The central strength of autologous gene therapy is that it can restore the missing antimicrobial function while avoiding donor-cell immune complications such as graft-versus-host disease. Lentiviral therapy has already shown multi-year persistence of corrected cells in some patients, and prime editing has shown that precise repair of an endogenous disease gene can restore near-normal neutrophil oxidative-burst activity in early clinical use. Lentiviral gene therapy Prime editing for p47phox CGD

However, the treatment burden and uncertainty remain substantial. Myeloablative busulfan conditioning can cause serious short-term toxicities, and severe active infection or inflammation may impair stem-cell collection, fitness, and engraftment. Stem-cell inflammation and gene therapy Lentiviral vectors integrate into the genome, requiring long-term surveillance for clonal abnormalities, while nuclease-based editing must avoid off-target changes and large chromosome rearrangements. Lentiviral gene therapy NCF1 editing and chromosomal deletions Finally, early-stage programs are mutation-specific, involve very few participants, require specialized transplant centers, and may be vulnerable to commercial reprioritization, as illustrated by termination of the initial PM359 study. Prime editing for p47phox CGD

Outlook and Future Directions

CGD is closer to a gene-based cure than it was in 2020: durable lentiviral correction has been demonstrated in some people, and both base editing and prime editing have entered human testing. Still, the evidence is not yet sufficient to call any investigational approach a reliable cure for the broader CGD population. The milestones to watch are durable correction beyond several years, prevention or resolution of serious infections and inflammatory disease, reproducible engraftment in patients with severe inflammation, absence of late genomic toxicity, safer conditioning approaches, and extension of treatment beyond a small number of CYBB or NCF1 variants. NIAID base-editing trial Prime editing for p47phox CGD Targeted editing and CYBB insertion

References

• Clinical presentation and treatment — Staudacher and von Bernuth, 2024.
• Lentiviral gene therapy — Kohn et al., 2020.
• Stem-cell inflammation and gene therapy — Sobrino et al., 2023.
• Physiologically regulated lentiviral vector — Wong et al., 2022.
• PAMless base editing — Bzhilyanskaya et al., 2024.
• Targeted editing and CYBB insertion — Wolff et al., 2025.
• Prime editing for p47phox CGD — Gori et al., 2026.
• NIAID base-editing trial — ClinicalTrials.gov, 2026.
• PM359 trial record — ClinicalTrials.gov, 2026.
• G1XCGD trial record — ClinicalTrials.gov, 2026.
• NCF1 editing and chromosomal deletions — Wrona et al., 2020.