A Rare Case of TP63-Associated Lymphopenia Revealed by Newborn Screening Using TREC

Abstract

The expanded newborn screening (NBS) program in the Russian Federation was initiated in 2023, among which severe combined immunodeficiency (SCID) is screened using TREC/KREC assays. Here, we report a rare case of a TP63-associated disease identified through this NBS program. Dried blood spots from newborns were initially screened for TREC/KREC levels, and those with values below the cut-off underwent confirmatory testing and further genetic analysis, including whole-exome sequencing (WES). A male newborn was identified with significantly reduced TREC values, indicative of T cell lymphopenia. Genetic analysis revealed a heterozygous NM_003722.5:c.1027C>T variant in TP63, leading to the p.(Arg343Trp) substitution within the DNA binding domain. This mutation has been previously associated with Ectrodactyly-Ectodermal Dysplasia-Cleft lip/palate syndrome (EEC) syndrome and shown to reduce the transactivation activity of TP63 in a dominant-negative manner. This case represents one of the few instances of immune system involvement in a patient with a TP63 mutation, highlighting the need for further investigation into the immunological aspects of TP63-associated disorders. Our findings suggest that comprehensive immunological evaluation should be considered for patients with TP63 mutations to better understand and manage potential immune dysfunctions.

Keywords: KREC; TP63; TREC; cleft-lip/palate; ectodermal dysplasia; ectrodactyly; lymphopenia; newborn screening.

Figure 3

Locations of TP63 variants identified in patients with immune system abnormalities. The domain structure is illustrated based on the TAp63α isoform [34]: TA—transactivation domain, DBD —DNA binding domain, OD—oligomerization domain, SAM—sterile-alpha motif domain, TI—transactivation inhibitory domain. Figures were created and modified by using the MutationMapper (https://www.cbioportal.org/mutation_mapper, accessed on 9 September 2024) [35].

Figure 1

Clinical picture of the patient. (A)—facial view of the patient in the perinatal period demonstrating bilateral cheilognathopalatoschisis. (B)—syndactyly of 3–4 toes on the left foot. (C)—complete syndactyly of 3–4 fingers on the left palm. (D)—syndactyly of rudimentary 2nd finger with full 1st finger of the right palm (split hand). (E)—view of the patient at the age of 1-year-old demonstrating condition after reconstructive surgery of facial structures, split right hand and left foot.

Figure 2

Genetic examination of the patient: (A) Sanger sequencing of the nuclear family revealed NM_003722.5(TP63):c.1027C>T, p.(Arg343Trp), variant occurred de novo (highlighted in blue background). (B) Modeling of the substitution in the paired domain of the TP63 protein. The five Alphafold 3 computed structure models (CSMs) of the R343W variant from the same in silico experiment are superimposed with the previously experimentally determined crystal structure of TP63 (PDB accession number 3qyn). The CSMs are colored pink, and the crystal structure of WT TP63 with DNA is gray and purple. The section enclosed within the square frame is further magnified in (C). (C) Zoomed-in view of the same superposition in the proximity to the mutation showing the disappearance of a salt bridge between the DNAbinding domain of the R343W variant and the sugar–phosphate backbone.