Inborn errors of immunity (IEIs) affecting thymic cell development or function can result in thymic aplasia or hypoplasia, autoimmunity, and the generation of neutralizing autoantibodies (Auto-Abs) targeting type I interferons (IFNs) (AAN-I-IFNs). FOXN1 is a master transcriptional regulator of thymic epithelial cells and the impact of the FOXN1 variants spans a spectrum from pathogenic to benign. In pediatric patients with heterozygous FOXN1 variants the full spectrum of clinical and immunological determinants remains to be defined. Using a luminex multiplex immunoassay, we assessed the presence of auto-Abs against 14 cytokines. We then employed two complementary in vitro cellular assays to test the neutralizing capacity of circulating auto-Abs against type I IFNs. Here, we present the case of an 11-year-old child who presented at 20 days of age with multiple severe infections. Genetic analysis revealed a heterozygous FOXN1 variant: c.1448_1451del. The patient tested positive for auto-Abs against type I IFNs. Functional assays confirmed the presence of auto-Abs with neutralizing activity against IFN-α2 (at both low [10 ng/mL] and high [50 ng/mL] concentrations) and against IFN-ω (only at 0.1 ng/mL and 10 ng/mL), but not against IFN-β. Five months later, following four doses of rituximab, circulating autoantibodies levels decreased by about 60%. These findings suggest that heterozygous FOXN1 variants can impair thymic development in a manner that promotes the selective emergence of neutralizing auto-Abs against type I IFNs, thereby predisposing affected individuals to severe viral infections. Monitoring these auto-Abs may support personalized therapeutic strategies for affected patients.

Spondylocostal dysostosis (SCDO) is a rare genetic disorder characterized by abnormal development of the axial skeleton, resulting in malformations of the vertebrae and ribs that often impair lung development and lead to significant respiratory morbidity. SCDO is thought to arise from defects in the paraxial presomitic mesoderm, an embryonic tissue that forms the vertebral column and ribs. Pathogenic variants in DLL3, MESP2, LFNG, HES7, TBX6, and RIPPLY2 have been identified in various SCDO subtypes. In addition, a single case of a lethal SCDO-like phenotype caused by a homozygous start-loss variant in DMRT2 has been reported. DMRT2 encodes a transcription factor expressed in the dermomyotome during early somite formation in mice. Here, we describe a newborn with severe costovertebral malformations and dysmorphic features, in whom exome sequencing identified a homozygous loss-of-function variant in DMRT2. The phenotype strikingly overlaps the previous report, further supporting the role of biallelic pathogenic DMRT2 variants in a severe SCDO-like disorder. Notably, our patient also exhibited thymic aplasia and immunodeficiency. A review of the exome sequencing data did not reveal any variant that could account for the immunodeficiency. These features have not been previously associated with SCDO, suggesting a potential phenotypic expansion.

Thymic T-cell development is orchestrated by thymic epithelial cells. The master transcriptional regulator of these cells is forkhead box N1 (FOXN1), which controls their differentiation, expansion, and function. Biallelic founder mutations in FOXN1 caused a nude/severe combined immunodeficiency phenotype due to congenital thymic aplasia and alopecia universalis. This established the critical role of FOXN1 in thymic epithelial cells and epithelial cells in the skin and nails. The emergence of newborn screening for severe T-cell deficiency via the T-cell receptor excision circle assay, along with exome and genome sequencing, has led to dramatic increases in the number of FOXN1 variants identified. The consequent impact of the FOXN1 variants ranges from pathogenic to benign, yet most FOXN1 mutations are listed as variants of unknown significance. Among monoallelic FOXN1 variants are some that act as dominant negative, resulting in a transient T-cell lymphopenia. In this review, the clinical impacts of diverse FOXN1 variants are categorized by mutation type and location. Knowing how these FOXN1 mutations affect protein function informs clinical care as well as laboratory monitoring, prophylactic measures, and allogeneic thymic implant decisions. This review provides key functional insights into FOXN1, enabling better clinical care.

Thymus organogenesis is critical for proper maturation of developing T cells. In this study, we identified Topoisomerase 1 (Top1) as a novel gene involved in thymus development and function. We created a mouse line with deletion of Top1 in thymic epithelial cells (TECs) and our results demonstrate that biallelic loss of Top1 in TECs causes congenital thymic aplasia, precipitating T cell immunodeficiency. Transcriptomic analysis provides insights into the molecular mechanism of Top1 in thymus development as we identify key genes involved in thymus organogenesis as the transcriptional targets of Top1 in TECs. Analysis of peripheral immunological compartments revealed severe loss of αβ T cells complemented with a disproportionate accumulation of γδ T cells and myeloid cells upon deletion of Top1 in TECs. The residual αβ T cells in Top1 knock-out mice were effector and oligoclonal in nature highlighting their self-reactivity. These results reveal a previously unknown role of Top1 in thymus development and T cell homeostasis. We propose Top1 as a genetic target for altered thymic development and T cell lymphopenia.

CHARGE syndrome is a congenital malformation syndrome caused by heterozygous mutations in the CHD7 gene. Severe combined immunodeficiency (SCID) arises from congenital athymia called CHARGE/complete DiGeorge syndrome. While cultured thymus tissue implantation (CTTI) provides an immunological cure, hematopoietic cell transplantation (HCT) is an alternative option for immuno-reconstitution of affected infants. We aimed to clarify the clinical outcomes of patients with athymic CHARGE syndrome after HCT. We studied the immunological reconstitution and outcomes of four patients who received non-conditioned unrelated donor cord blood transplantation (CBT) at Kyushu University Hospital from 2007 to 2022. The posttransplant outcomes were compared with the outcomes of eight reported patients. Four index cases received CBT 70-144 days after birth and had no higher than grade II acute graft-versus-host disease. One infant was the first newborn-screened athymic case in Japan. They achieved more than 500/μL naïve T cells with balanced repertoire 1 month post transplant, and survived more than 12 months with home care. Twelve patients including the index cases received HCT at a median 106 days after birth (range: 70-195 days). One-year overall survival rate was significantly higher in patients who underwent non-conditioned HCT than in those who received conditioned HCT (100% vs. 37.5%, p = .02). Nine patients died, and the major cause of death was cardiopulmonary failure. Athymic infants achieved a prompt reconstitution of non-skewing naïve T cells after non-conditioned CBT that led to home care in infancy without significant infections. Non-conditioned CBT is a useful bridging therapy for newborn-screened cases toward an immunological cure by CTTI.