A multimorphic variant in ThPOK causes a novel human disease characterized by T cell abnormalities, immunodysregulation, allergy, and fibrosis

The role of the transcription factor ThPOK, encoded by ZBTB7B, has not been formally established in humans since individuals with ThPOK deficiency or dysfunction have not yet been identified. We report the first case of a human with a damaging variant in ThPOK causing a syndrome encompassing CD4 T cell deficiency, allergic disease, severe fibrotic interstitial lung disease, global developmental delay, and growth failure. Trio whole-genome sequencing revealed a de novo variant (NM_001256455.2:c.1080A>C, p.K360N) in ZBTB7B. Despite normal expression, ThPOKK360N exhibited dysfunctional multimorphic activity. It demonstrated dominant-negative effects by hindering the capacity of ThPOKWT to regulate target gene expression (antimorph). Protein-DNA interaction assays showed inability of ThPOKK360N to bind to WT consensus sequences (amorph) and revealed a novel DNA-binding specificity (neomorph). Single-cell sequencing confirmed the patient's CD4 T cell deficiency, revealing that most T cells were less mature compared to healthy controls. Furthermore, naive CD4 and CD8 T cells showed diminished activation after stimulation. The link between ThPOKK360N and the patient’s symptoms was confirmed through lentiviral transduction experiments in healthy T cells and pulmonary fibroblasts. While T cells expressing ThPOKWT upregulated genes involved in activation, proliferation, and interferon responses, those with ThPOKK360N did not. When overexpressed in fibroblasts, ThPOKK360N significantly increased expression of pro-fibrotic genes implicated in pulmonary fibrosis. This description of a novel human disease caused by a multimorphic variant in ThPOK confirms its role in CD4 T cell development in an intact human context, while also revealing an unanticipated role for ThPOK in T cell function and fibrosis.