Heterozygous FOXN1 Variants Cause Low TRECs and Severe T Cell Lymphopenia, Revealing a Crucial Role of FOXN1 in Supporting Early Thymopoiesis

Abstract

FOXN1 is the master regulatory gene of thymic epithelium development. FOXN1 deficiency leads to thymic aplasia, alopecia, and nail dystrophy, accounting for the nude/severe combined immunodeficiency (nu/SCID) phenotype in humans and mice. We identified several newborns with low levels of T cell receptor excision circles (TRECs) and T cell lymphopenia at birth, who carried heterozygous loss-of-function FOXN1 variants. Longitudinal analysis showed persistent T cell lymphopenia during infancy, often associated with nail dystrophy. Adult individuals with heterozygous FOXN1 variants had in most cases normal CD4 þ but lower than normal CD8 þ cell counts. We hypothesized a FOXN1 gene dosage effect on the function of thymic epithelial cells (TECs) and thymopoiesis and postulated that these effects would be more prominent early in life. To test this hypothesis, we analyzed TEC subset frequency and phenotype, early thymic progenitor (ETP) cell count, and expression of FOXN1 target genes (Ccl25, Cxcl12, Dll4, Scf, Psmb11, Prss16, and Cd83) in Foxn1 nu/þ (nu/þ) mice and age-matched wild-type (þ/þ) littermate controls. Both the frequency and the absolute count of ETP were significantly reduced in nu/þ mice up to 3 weeks of age. Analysis of the TEC compartment showed reduced expression of FOXN1 target genes and delayed maturation of the medullary TEC compartment in nu/þ mice. These observations establish a FOXN1 gene dosage effect on thymic function and identify FOXN1 haploinsufficiency as an important genetic determinant of T cell lymphopenia at birth.

T-Cell Immunodeficiencies With Congenital Alterations of Thymic Development: Genes Implicated and Differential Immunological and Clinical Features

“…Homozyous FOXN1 mutations cause Nude SCID syndrome, first observed in two Italian sisters presenting with congenital universal alopecia, nail dystrophy, and severe T-cell immunodeficiency with rudimentary thymus ( 59 ). In the last few years, neonatal screening and next generation sequencing techniques have led to the identification of subjects with novel homozygous, compound heterozygous, and heterozygous mutations ( 60 ). Homozygous patients suffer from immunodeficiency with susceptibility to pneumonia, chronic diarrhea, candidiasis or mycobacterial infections, and Omenn syndrome ( 59 , 61 – 64 ).…”

“…Homozygous patients suffer from immunodeficiency with susceptibility to pneumonia, chronic diarrhea, candidiasis or mycobacterial infections, and Omenn syndrome ( 59 , 61 – 64 ). Most of the heterozygous patients show nail dystrophy, usually presenting as leukonychia and minor immunological changes ( 60 , 65 , 66 ). Recurrent infections and atopic dermatitis are observed only in a minority of the patients ( 60 ).…”

“…Most of the heterozygous patients show nail dystrophy, usually presenting as leukonychia and minor immunological changes ( 60 , 65 , 66 ). Recurrent infections and atopic dermatitis are observed only in a minority of the patients ( 60 ).…”

Recurrent microdeletions at chromosome 2p11.2 are associated with thymic hypoplasia and features resembling DiGeorge syndrome

“…However, in a recently published study the authors demonstrate that TBX1 and FOXI3 are both important in segmentation of the pharyngeal apparatus and that LOF, either individually or in combination, gives rise to anatomic defects seen in patients with DiGeorge syndrome, including thymic hypoplasia/aplasia. 29 In another very recent publication, Bosticardo et al 30 demonstrate that heterozygous LOF variants in FOXN1 cause thymic hypoplasia and T-cell lymphopenia, most likely as a result a gene dosage effect on thymic epithelial development. Given the number of genes observed to be dysregulated in FOXI3 mutant mice and that the top 2 enriched pathways identified for these genes are adherens junction related, further exploration of the role of FOXI3 in development of the epithelium and its effect on the architecture of the thymus during development would seem warranted.…”

Follow-Up for an Abnormal Newborn Screen for Severe Combined Immunodeficiencies (NBS SCID): A Clinical Immunology Society (CIS) Survey of Current Practices

“…Infants with Omenn syndrome or leaky SCID typically demonstrate oligoclonal expansion of autologous T cells, which can be confirmed by TCR V-β repertoire analysis. In infants with a T low B normal NK normal phenotype it is also important to ensure that the TCL is not due to a primary thymic defect (e.g., complete DiGeorge syndrome [ 21 ], FOXN1 deficiency [ 40 ], PAX1 defect [ 41 ] and Yamazaki Y et al, (manuscript submitted, 2019) which requires thymus transplantation as opposed to HCT.…”