FOXN1 forms higher-order nuclear condensates displaced by mutations causing immunodeficiency

The transcription factor FOXN1 is a master regulator of thymic epithelial cell (TEC) development and function. Here, we demonstrate that FOXN1 expression is differentially regulated during organogenesis and participates in multimolecular nuclear condensates essential for the factor's transcriptional activity. FOXN1's C-terminal sequence regulates the diffusion velocity within these aggregates and modulates the binding to proximal gene regulatory regions. These dynamics are altered in a patient with a mutant FOXN1 that is modified in its C-terminal sequence. This mutant is transcriptionally inactive and acts as a dominant negative factor displacing wild-type FOXN1 from condensates and causing athymia and severe lymphopenia in heterozygotes. Expression of the mutated mouse ortholog selectively impairs mouse TEC differentiation, revealing a gene dose dependency for individual TEC subtypes. We have therefore identified the cause for a primary immunodeficiency disease and determined the mechanism by which this FOXN1 gain-of-function mutant mediates its dominant negative effect.

Automated summary

The transcription factor FOXN1 plays a crucial role in thymic epithelial cell development and function, with its expression being differentially regulated during organogenesis. It forms multimolecular nuclear condensates important for transcriptional activity, where the C-terminal sequence regulates diffusion velocity and binding to gene regulatory regions. Mutant FOXN1 with modified C-terminal sequence is transcriptionally inactive and acts as a dominant negative factor, causing athymia and severe lymphopenia. This gain-of-function mutant disrupts TEC differentiation in mice, showing gene dose dependency for specific TEC subtypes.