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

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+ but lower than normal CD8+ 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 Foxn1nu/+ (nu/+) mice and age-matched wild-type (+/+) littermate controls. Both the frequency and the absolute count of ETP were significantly reduced in nu/+ 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/+ 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

A reference map of the human binary protein interactome.

Global insights into cellular organization and genome function require comprehensive understanding of the interactome networks that mediate genotype-phenotype relationships(1,2). Here we present a human 'all-by-all' reference interactome map of human binary protein interactions, or 'HuRI'. With approximately 53,000 protein-protein interactions, HuRI has approximately four times as many such interactions as there are high-quality curated interactions from small-scale studies. The integration of HuRI with genome(3), transcriptome(4) and proteome(5) data enables cellular function to be studied within most physiological or pathological cellular contexts. We demonstrate the utility of HuRI in identifying the specific subcellular roles of protein-protein interactions. Inferred tissue-specific networks reveal general principles for the formation of cellular context-specific functions and elucidate potential molecular mechanisms that might underlie tissue-specific phenotypes of Mendelian diseases. HuRI is a systematic proteome-wide reference that links genomic variation to phenotypic outcomes

Post-SARS-CoV-2 Atypical Inflammatory Syndrome in a Toddler with X-Linked Inhibitor of Apoptosis Deficiency After Stem Cell Transplant

A 10-month-old boy was diagnosed with X-linked lymphoproliferative syndrome type 2 due to X-linked inhibitor of apoptosis deficiency after presenting with failure to thrive and refractory inflammatory bowel disease. He underwent a matched unrelated donor stem cell transplant with reduced intensity conditioning at 16 months. At 27 months, he presented with an atypical inflammatory syndrome in the setting of recent COVID-19 infection, Epstein-Barr viremia, and low chimerism (7.3%). He recovered after treatment with intravenous immunoglobulin and steroids

Refractory Pediatric Autoimmune Enteropathy Successfully Treated with Hematopoietic Stem Cell Transplant

Both allogeneic and autologous hematopoietic stem cell transplant (HSCT) have utility in refractory autoimmune diseases. We report a pediatric case of autoimmune enteropathy (AIE) that was successfully treated with haploidentical SCT and post-transplant cyclophosphamide. A 4 year old male with chronic diarrhea, multiple food allergies, eczema, recurrent infections, failure to thrive and TPN dependence was diagnosed as AIE with biopsy proven anti-enterocyte antibodies. Immune evaluation revealed no mutation for immunodysregulation polyendocrinopathy enteropathy X-linked and cytotoxic T-lymphocyte-associated protein 4 sequencing. T cell function and primary immunodeficiency panel were normal. He failed conventional treatments with TNF blockade, calcineurin inhibitors, mTOR inhibitors, and costimulatory blockade (abatacept). A haplo-HSCT was performed with rituximab 375 mg/m2 day (D) -14, fludarabine 150 mg/m2 D -11 to D -7, thiotepa 10 mg/kg D -7, melphalan 140 mg/m2 D -6, Thymoglobulin 10 mg/kg D -5 to D -2, along with post-transplant cyclophosphamide 100 mg/kg D +3 to D +4. The patient engrafted on D +16 with neutrophils above 500 mcL on three consecutive CBCs, and he was platelet transfusion independent after D+19 to maintain platelets above 50,000 mcL. He resumed regular diet on day + 46 post haplo-HSCT without any gastrointestinal symptoms and is gaining weight at the time of this report. Post-transplant course was complicated by grade II acute skin graft versus host disease that responded to prednisolone and tacrolimus, and HHV6 reactivation which resolved after starting ganciclovir. This is a case of a pediatric patient with refractory AIE who is now asymptomatic post haplo-HSCT after failing treatment with extensive immune modulators. This treatment may prove to be helpful for similar challenging patients with AIE

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

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+ but lower than normal CD8+ 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 Foxn1nu/+ (nu/+) mice and age-matched wild-type (+/+) littermate controls. Both the frequency and the absolute count of ETP were significantly reduced in nu/+ 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/+ 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