case_images: PMC11448704_01
case_images: (A) Gene map of previously described TP63 pathogenic variants and associated syndromes as indicated by color key. Given that there is overlap and variability in the features of AEC and EEC, variants have been categorized based on the most prevalent disease features that were reported. Numbering of pathogenic variants in TA*-p63 isoform is based on reference sequence NP_003713.3. Start codons for TA*-p63, TA-p63 and DeltaN-p63 isoforms are indicated by arrows. TA Transactivation domain; DBD DNA binding domain; OD oligomerization domain; SAM sterile-alpha-motif domain; TID transcriptional inhibitory domain. Figure adapted from Osterburg et al.. The TP63 variant identified in our patient is highlighted with a star. (B) Uniform manifold approximation and projection (UMAP) visualization showing the cellular composition of the human thymus obtained from the collection of single-cell datasets available on the UCSC Cell Browser [https://fetal-thymus.cells.ucsc.edu]. (C) Expression level of TP63 gene in the human thymus atlas is restricted to cTEC and mTEC subsets. DN, CD4/CD8 double negative T cells; DP, CD4/CD8 double positive T cells; SP, CD4/CD8 single positive T cells; Treg, regulatory T cells; NK, natural killer cells; Endo, endothelial cells; VSMC, vascular smooth muscle cells; Fb, fetal bone; mTEC, medullary thymic epithelial cells; cTEC, cortical thymic epithelial cells; DC, dendritic cells; B, B cells; NMP, neutrophil myeloid progenitors; Mac/Mono, macrophages/monocytes; Mast, mast cells; MGK, megakaryocytes; ETP, early thymic progenitor; Ery, erythrocytes.
case_images: fimmu-15-1438383-g001.jpg
case_images: PMC11448704_01_fimmu-15-1438383-g001.jpg
case_images: f1
case_images: TP63 corresponding to c.1040 G>A with predicted protein change C347Y in the DBD of p63 ( Figure 1 ). This variant has been previously reported in patients with syndromic features consistent with CD3+TCRalphabeta+ cells in the patient as compared to an unaffected control. These data suggested that the patient's TCL was extrinsic to the hematopoietic cell lineage and most likely due to a thymic stromal cell defect in the setting of her TP63 variant. Consistent with this, interrogation of a publicly available database of gene expression profile in the human thymus demonstrated that TP63 expression is restricted to cortical and medullary thymic epithelial cells, and is not observed in thymic hematopoietic cell types ( Figures 1B, C ). Supplementary Figure 1 ) was characterized by extubation to high flow nasal cannula by 1 month of age and subsequent weaning to room air. She had severe obstructive sleep apnea resulting in the need for supplemental oxygen during sleep.
case_images: Clinical findings in a patient with TP63 variant and T cell lymphopenia. (A) Right foot with widely spaced toes, polysyndactyly and severe skin erosion at the heel at 1 week of age (B) left foot with skin erosions at the heel at 1 week of age. (C) Severe skin erosions on scalp at 4 months of age (D) skin erosions on the right cheek at 4 months of age. (E) Right foot with improved skin erosions at 1 month of age (F) left foot with widely spaced toes, polysyndactyly and improved skin erosions at 1 month of age. (G) Scalp with improved skin erosions at 13 months of age (H) Left eye with central thinning at 13 months of age. (I, J) T cell differentiation induced by artificial thymic organoids culturing CD34+ cells from individual with TP63 pathogenic variant (case) and unaffected age-matched control in the Artificial Thymic Organoid (ATO) system. Representative analysis of T cell differentiation in case and control at 4 months of age (I) and 26 months of age (J) after 6 weeks in culture in the ATO system. Cells were gated on LIVE/DEAD-CD45+CD14-CD56- cells and the expression of early and late T cell commitment markers (CD5, CD7, CD1alpha, CD4, CD8beta, CD3, TCRalphabeta. Absolute cell counts per artificial thymic organoid and indicated early and late T cell commitment markers in TP63 variant (purple) and control (green) at 4 months (I) and 26 months of age (J).
case_images: fimmu-15-1438383-g002.jpg
case_images: PMC11448704_01_fimmu-15-1438383-g002.jpg
case_images: f2
case_images: In addition to her cleft palate, features consistent with EEC included complex hand anomalies (i.e. anterior polydactyly; 3, 4 syndactyly; unilateral ectrodactyly), hypoplastic nails and foot anomalies (i.e. bilateral ectrodactyly, posterior polydactyly, hypoplastic nails) ( Figures 2A-H ). T cell maturation was analyzed after 6 weeks in culture in the ATO system both at 4 and at 26 months of age.  Figures 2I, J  show the flow cytometry gating strategy and absolute T cell counts of cells at different stages of intrathymic development. Eye exams demonstrated neovascularization and thinning of bilateral corneas ( Figure 2H ), which led to corneal perforation of both eyes requiring Gundersen conjunctival flap repair and corneal transplant.