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

Ioanna A Rota; Adam E Handel; Stefano Maio; Fabian Klein; Fatima Dhalla; Mary E Deadman; Stanley Cheuk; Joseph A Newman; Yale S Michaels; Saulius Zuklys; Nicolas Prevot; Philip Hublitz; Philip D Charles; Athina Soragia Gkazi; Eleni Adamopoulou; Waseem Qasim; Edward Graham Davies; Imelda Hanson; Alistair T Pagnamenta; Carme Camps; Helene M Dreau; Andrea White; Kieran James; Roman Fischer; Opher Gileadi; Jenny C Taylor; Tudor Fulga; B Christoffer Lagerholm; Graham Anderson; Erdinc Sezgin; Georg A Holländer

doi:10.1126/sciadv.abj9247

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

Sci Adv. 2021 Dec 3;7(49):eabj9247. doi: 10.1126/sciadv.abj9247. Epub 2021 Dec 3.

Authors

Ioanna A Rota¹, Adam E Handel^{1

2}, Stefano Maio¹, Fabian Klein¹, Fatima Dhalla¹, Mary E Deadman¹, Stanley Cheuk¹, Joseph A Newman³, Yale S Michaels⁴, Saulius Zuklys⁵, Nicolas Prevot¹, Philip Hublitz⁶, Philip D Charles⁷, Athina Soragia Gkazi⁸, Eleni Adamopoulou¹, Waseem Qasim⁸, Edward Graham Davies⁸, Imelda Hanson⁹, Alistair T Pagnamenta^{10

11}, Carme Camps^{10

11}, Helene M Dreau¹², Andrea White¹³, Kieran James¹³, Roman Fischer⁷, Opher Gileadi³, Jenny C Taylor^{10

11}, Tudor Fulga⁴, B Christoffer Lagerholm¹⁴, Graham Anderson¹³, Erdinc Sezgin^{5

15}, Georg A Holländer^{1

5

16}

Affiliations

¹ Department of Paediatrics and the MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK.
² Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK.
³ Structural Genomics Consortium, University of Oxford, ORCRB, Roosevelt Drive, Oxford, UK.
⁴ Genome Engineering and Synthetic Biology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK.
⁵ Paediatric Immunology, Department of Biomedicine, University of Basel and University Children's Hospital Basel, Basel, Switzerland.
⁶ MRC Weatherall Institute of Molecular Medicine, Genome engineering services, Radcliffe Department of Medicine, University of Oxford, Oxford, UK.
⁷ Target Discovery Institute, University of Oxford, Oxford OX3 7FZ, UK.
⁸ Great Ormond Street Hospital and Great Ormond Street Institute of Child Health, University College London, London WC1N 1EH, UK.
⁹ Department of Pediatrics, Section of Pediatric Immunology, Allergy, and Retrovirology, Baylor College of Medicine, Houston, TX, USA.
¹⁰ National Institute for Health Research Biomedical Research Centre, Oxford, UK.
¹¹ Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK.
¹² Department of Oncology, University of Oxford, Oxford OX3 7DQ, UK.
¹³ Institute for Immunology and Immunotherapy, Medical School, University of Birmingham, Birmingham B15 2TT, UK.
¹⁴ Wolfson Imaging Centre Oxford, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Headley Way, Oxford OX3 9DS, UK.
¹⁵ MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK.
¹⁶ Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland.

Abstract

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.

Abstract

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