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

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 CampsHelene 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^*

^*Corresponding author for this work

Immunology and Immunotherapy

Research output: Contribution to journal › Article › peer-review

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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.

Original language	English
Article number	eabj9247
Number of pages	19
Journal	Science Advances
Volume	7
Issue number	49
DOIs	https://doi.org/10.1126/sciadv.abj9247
Publication status	Published - 3 Dec 2021

Bibliographical note

Acknowledgments:
We thank R. Geha and T. Barthlott for helpful discussions and G. Riddihough (LSE) for editorial assistance. We thank S. Palmer for generating the graph in fig. S7F. Funding: This work was supported by Swiss National Science Foundation (IZLJZ3_171050; 310030_184672) and the Wellcome Trust (105045/Z/14/Z) to G.A.H.; National Institute for Health Research (NIHR) Oxford Biomedical Research Centre (BRC) to G.A.H.; departmental stipend (Department of Paediatrics, University of Oxford) to I.A.R.; NIHR Clinical Lectureship to A.E.H.; Wellcome Trust (109032/Z/15/Z) and an NIHR Clinical Lectureship to F.D.; International postdoc fellowship from the Swedish research council (Vetenskapsrådet) to S.C.; Swiss National Science Foundation–Early Postdoc.Mobility Fellowship–P2BSP3_188183 to F.K.; SciLifeLab Fellowship and Swedish Research Council Starting Grant (2020-02682) to E.S.; Wellcome Trust and Department of Health as part of a Health Innovation Challenge Fund scheme grant (Wellcome Core Award grant number 203141/Z/16/Z) to J.C.T., A.T.P., and C.C. as part of the The OxClinWGS Study Health Innovation Challenge Fund (R6-388/WT 100127), a parallel funding partnership between the Wellcome Trust, the Department of Health to J.C.T.; and the National Institute for Health Research (NIHR) Oxford Biomedical Research Centre (BRC) to J.C.T., A.T.P., and C.C. The views expressed are those of the authors and not necessarily those of the NHS, the NIHR, or the Department of Health or Wellcome Trust. This work was also supported by MRC Programme Grant (MR/T029765/1) to G.A. NIHR (RP-2014-05-007); the Great Ormond Street Hospital Biomedical Research Centre to W.Q., E.G.D., and A.S.G.; and a Wellcome trust grant 106169/ZZ14/Z to O.G. and J.A.N.

Publisher Copyright:
Copyright © 2021 The Authors, some rights reserved;

ASJC Scopus subject areas

General

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10.1126/sciadv.abj9247Licence: Creative Commons: Attribution (CC BY)

RotaI2021FOXN1Final published version, 1.53 MBLicence: Creative Commons: Attribution (CC BY)

Targeting New Mechanisms In The Control Of Thymus Function To Restore Balanced T-cell Production
Anderson, G.
Medical Research Council
1/01/21 → 31/12/25
Project: Research Councils

Cite this

Rota, I. A., Handel, A. E., Maio, S., Klein, F., Dhalla, F., Deadman, M. E., Cheuk, S., Newman, J. A., Michaels, Y. S., Zuklys, S., Prevot, N., Hublitz, P., Charles, P. D., Gkazi, A. S., Adamopoulou, E., Qasim, W., Davies, E. G., Hanson, I., Pagnamenta, A. T., ... Holländer, G. A. (2021). FOXN1 forms higher-order nuclear condensates displaced by mutations causing immunodeficiency. Science Advances, 7(49), Article eabj9247. https://doi.org/10.1126/sciadv.abj9247

@article{28ddb43112004226b496ad23227ef5f4,

title = "FOXN1 forms higher-order nuclear condensates displaced by mutations causing immunodeficiency",

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{\textquoteright}s transcriptional activity. FOXN1{\textquoteright}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.",

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

note = "Acknowledgments: We thank R. Geha and T. Barthlott for helpful discussions and G. Riddihough (LSE) for editorial assistance. We thank S. Palmer for generating the graph in fig. S7F. Funding: This work was supported by Swiss National Science Foundation (IZLJZ3_171050; 310030_184672) and the Wellcome Trust (105045/Z/14/Z) to G.A.H.; National Institute for Health Research (NIHR) Oxford Biomedical Research Centre (BRC) to G.A.H.; departmental stipend (Department of Paediatrics, University of Oxford) to I.A.R.; NIHR Clinical Lectureship to A.E.H.; Wellcome Trust (109032/Z/15/Z) and an NIHR Clinical Lectureship to F.D.; International postdoc fellowship from the Swedish research council (Vetenskapsr{\aa}det) to S.C.; Swiss National Science Foundation–Early Postdoc.Mobility Fellowship–P2BSP3_188183 to F.K.; SciLifeLab Fellowship and Swedish Research Council Starting Grant (2020-02682) to E.S.; Wellcome Trust and Department of Health as part of a Health Innovation Challenge Fund scheme grant (Wellcome Core Award grant number 203141/Z/16/Z) to J.C.T., A.T.P., and C.C. as part of the The OxClinWGS Study Health Innovation Challenge Fund (R6-388/WT 100127), a parallel funding partnership between the Wellcome Trust, the Department of Health to J.C.T.; and the National Institute for Health Research (NIHR) Oxford Biomedical Research Centre (BRC) to J.C.T., A.T.P., and C.C. The views expressed are those of the authors and not necessarily those of the NHS, the NIHR, or the Department of Health or Wellcome Trust. This work was also supported by MRC Programme Grant (MR/T029765/1) to G.A. NIHR (RP-2014-05-007); the Great Ormond Street Hospital Biomedical Research Centre to W.Q., E.G.D., and A.S.G.; and a Wellcome trust grant 106169/ZZ14/Z to O.G. and J.A.N. Publisher Copyright: Copyright {\textcopyright} 2021 The Authors, some rights reserved;",

year = "2021",

month = dec,

day = "3",

doi = "10.1126/sciadv.abj9247",

language = "English",

volume = "7",

journal = "Science Advances",

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Rota, IA, Handel, AE, Maio, S, Klein, F, Dhalla, F, Deadman, ME, Cheuk, S, Newman, JA, Michaels, YS, Zuklys, S, Prevot, N, Hublitz, P, Charles, PD, Gkazi, AS, Adamopoulou, E, Qasim, W, Davies, EG, Hanson, I, Pagnamenta, AT, Camps, C, Dreau, HM, White, A , James, K, Fischer, R, Gileadi, O, Taylor, JC, Fulga, T, Christoffer Lagerholm, B, Anderson, G, Sezgin, E & Holländer, GA 2021, 'FOXN1 forms higher-order nuclear condensates displaced by mutations causing immunodeficiency', Science Advances, vol. 7, no. 49, eabj9247. https://doi.org/10.1126/sciadv.abj9247

TY - JOUR

T1 - FOXN1 forms higher-order nuclear condensates displaced by mutations causing immunodeficiency

AU - Rota, Ioanna A.

AU - Handel, Adam E.

AU - Maio, Stefano

AU - Klein, Fabian

AU - Dhalla, Fatima

AU - Deadman, Mary E.

AU - Cheuk, Stanley

AU - Newman, Joseph A.

AU - Michaels, Yale S.

AU - Zuklys, Saulius

AU - Prevot, Nicolas

AU - Hublitz, Philip

AU - Charles, Philip D.

AU - Gkazi, Athina Soragia

AU - Adamopoulou, Eleni

AU - Qasim, Waseem

AU - Davies, Edward Graham

AU - Hanson, Imelda

AU - Pagnamenta, Alistair T.

AU - Camps, Carme

AU - Dreau, Helene M.

AU - White, Andrea

AU - James, Kieran

AU - Fischer, Roman

AU - Gileadi, Opher

AU - Taylor, Jenny C.

AU - Fulga, Tudor

AU - Christoffer Lagerholm, B.

AU - Anderson, Graham

AU - Sezgin, Erdinc

AU - Holländer, Georg A.

N1 - Acknowledgments: We thank R. Geha and T. Barthlott for helpful discussions and G. Riddihough (LSE) for editorial assistance. We thank S. Palmer for generating the graph in fig. S7F. Funding: This work was supported by Swiss National Science Foundation (IZLJZ3_171050; 310030_184672) and the Wellcome Trust (105045/Z/14/Z) to G.A.H.; National Institute for Health Research (NIHR) Oxford Biomedical Research Centre (BRC) to G.A.H.; departmental stipend (Department of Paediatrics, University of Oxford) to I.A.R.; NIHR Clinical Lectureship to A.E.H.; Wellcome Trust (109032/Z/15/Z) and an NIHR Clinical Lectureship to F.D.; International postdoc fellowship from the Swedish research council (Vetenskapsrådet) to S.C.; Swiss National Science Foundation–Early Postdoc.Mobility Fellowship–P2BSP3_188183 to F.K.; SciLifeLab Fellowship and Swedish Research Council Starting Grant (2020-02682) to E.S.; Wellcome Trust and Department of Health as part of a Health Innovation Challenge Fund scheme grant (Wellcome Core Award grant number 203141/Z/16/Z) to J.C.T., A.T.P., and C.C. as part of the The OxClinWGS Study Health Innovation Challenge Fund (R6-388/WT 100127), a parallel funding partnership between the Wellcome Trust, the Department of Health to J.C.T.; and the National Institute for Health Research (NIHR) Oxford Biomedical Research Centre (BRC) to J.C.T., A.T.P., and C.C. The views expressed are those of the authors and not necessarily those of the NHS, the NIHR, or the Department of Health or Wellcome Trust. This work was also supported by MRC Programme Grant (MR/T029765/1) to G.A. NIHR (RP-2014-05-007); the Great Ormond Street Hospital Biomedical Research Centre to W.Q., E.G.D., and A.S.G.; and a Wellcome trust grant 106169/ZZ14/Z to O.G. and J.A.N. Publisher Copyright: Copyright © 2021 The Authors, some rights reserved;

PY - 2021/12/3

Y1 - 2021/12/3

N2 - 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.

AB - 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.

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U2 - 10.1126/sciadv.abj9247

DO - 10.1126/sciadv.abj9247

M3 - Article

C2 - 34860543

AN - SCOPUS:85120704294

SN - 2375-2548

VL - 7

JO - Science Advances

JF - Science Advances

IS - 49

M1 - eabj9247

ER -

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

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Targeting New Mechanisms In The Control Of Thymus Function To Restore Balanced T-cell Production

Cite this