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Voss K, Bartkowiak T, Sewell AE, Chi C, Landis MD, Schaefer S, Pua HH, Connelly JA, Irish JM, Rathmell JC, Kaviany S. Peripheral T Cell Development and Immunophenotyping of Twins with Heterozygous FOXN1 Mutations. Immunohorizons 2024; 8:492-499. [PMID: 39008056 PMCID: PMC11294276 DOI: 10.4049/immunohorizons.2400006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2024] [Accepted: 06/09/2024] [Indexed: 07/16/2024] Open
Abstract
The transcription factor FOXN1 plays an established role in thymic epithelial development to mediate selection of maturing thymocytes. Patients with heterozygous loss-of-function FOXN1 variants are associated with T cell lymphopenia at birth and low TCR excision circles that can ultimately recover. Although CD4+ T cell reconstitution in these patients is not completely understood, a lower proportion of naive T cells in adults has suggested a role for homeostatic proliferation. In this study, we present an immunophenotyping study of fraternal twins with low TCR excision circles at birth. Targeted primary immunodeficiency testing revealed a heterozygous variant of uncertain significance in FOXN1 (c.1205del, p.Pro402Leufs*148). We present the immune phenotypes of these two patients, as well as their father who carries the same FOXN1 variant, to demonstrate an evolving immune environment over time. While FOXN1 haploinsufficiency may contribute to thymic defects and T cell lymphopenia, we characterized the transcriptional activity and DNA binding of the heterozygous FOXN1 variant in 293T cells and found the FOXN1 variant to have different effects across several target genes. These data suggest multiple mechanisms for similar FOXN1 variants pathogenicity that may be mutation specific. Increased understanding of how these variants drive transcriptional regulation to impact immune cell populations will guide the potential need for therapeutics, risk for infection or autoimmunity over time, and help inform clinical decisions for other variants that might arise.
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Affiliation(s)
- Kelsey Voss
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN
| | - Todd Bartkowiak
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN
| | - Allison E. Sewell
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN
| | - Channing Chi
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN
| | - Madelyn D. Landis
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN
| | - Samuel Schaefer
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN
| | - Heather H. Pua
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN
- Vanderbilt Center for Immunobiology, Vanderbilt University Medical Center, Nashville, TN
- Human Immunology Discovery Initiative of the Vanderbilt Center for Immunobiology, Vanderbilt University Medical Center, Nashville, TN
| | - James A. Connelly
- Vanderbilt Center for Immunobiology, Vanderbilt University Medical Center, Nashville, TN
- Human Immunology Discovery Initiative of the Vanderbilt Center for Immunobiology, Vanderbilt University Medical Center, Nashville, TN
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN
| | - Jonathan M. Irish
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN
- Vanderbilt Center for Immunobiology, Vanderbilt University Medical Center, Nashville, TN
- Human Immunology Discovery Initiative of the Vanderbilt Center for Immunobiology, Vanderbilt University Medical Center, Nashville, TN
| | - Jeffrey C. Rathmell
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN
- Vanderbilt Center for Immunobiology, Vanderbilt University Medical Center, Nashville, TN
- Human Immunology Discovery Initiative of the Vanderbilt Center for Immunobiology, Vanderbilt University Medical Center, Nashville, TN
| | - Saara Kaviany
- Human Immunology Discovery Initiative of the Vanderbilt Center for Immunobiology, Vanderbilt University Medical Center, Nashville, TN
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN
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Tamarín S, Galaz-Davison P, Ramírez-Sarmiento CA, Babul J, Medina E. Dissecting the structural and functional consequences of the evolutionary proline-glycine deletion in the wing 1 region of the forkhead domain of human FoxP1. FEBS Lett 2024. [PMID: 38946055 DOI: 10.1002/1873-3468.14972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Revised: 06/06/2024] [Accepted: 06/07/2024] [Indexed: 07/02/2024]
Abstract
The human FoxP transcription factors dimerize via three-dimensional domain swapping, a unique feature among the human Fox family, as result of evolutionary sequence adaptations in the forkhead domain. This is the case for the conserved glycine and proline residues in the wing 1 region, which are absent in FoxP proteins but present in most of the Fox family. In this work, we engineered both glycine (G) and proline-glycine (PG) insertion mutants to evaluate the deletion events in FoxP proteins in their dimerization, stability, flexibility, and DNA-binding ability. We show that the PG insertion only increases protein stability, whereas the single glycine insertion decreases the association rate and protein stability and promotes affinity to the DNA ligand.
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Affiliation(s)
- Stephanie Tamarín
- Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Pablo Galaz-Davison
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile
- Center for Bioinformatics, Simulation and Modeling (CBSM), Faculty of Engineering, Universidad de Talca, Talca, Chile
| | - César A Ramírez-Sarmiento
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile
- ANID - Millennium Science Initiative Program, Millennium Institute for Integrative Biology (iBio), Santiago, Chile
| | - Jorge Babul
- Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Exequiel Medina
- Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Santiago, Chile
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3
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Moses A, Bhalla P, Thompson A, Lai L, Coskun FS, Seroogy CM, de la Morena MT, Wysocki CA, van Oers NSC. Comprehensive phenotypic analysis of diverse FOXN1 variants. J Allergy Clin Immunol 2023; 152:1273-1291.e15. [PMID: 37419334 PMCID: PMC11071152 DOI: 10.1016/j.jaci.2023.06.019] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 05/05/2023] [Accepted: 06/08/2023] [Indexed: 07/09/2023]
Abstract
BACKGROUND Thymus hypoplasia due to stromal cell problems has been linked to mutations in several transcription factors, including Forkhead box N1 (FOXN1). FOXN1 supports T-cell development by regulating the formation and expansion of thymic epithelial cells (TECs). While autosomal recessive FOXN1 mutations result in a nude and severe combined immunodeficiency phenotype, the impact of single-allelic or compound heterozygous FOXN1 mutations is less well-defined. OBJECTIVE With more than 400 FOXN1 mutations reported, their impact on protein function and thymopoiesis remains unclear for most variants. We developed a systematic approach to delineate the functional impact of diverse FOXN1 variants. METHODS Selected FOXN1 variants were tested with transcriptional reporter assays and imaging studies. Thymopoiesis was assessed in mouse lines genocopying several human FOXN1 variants. Reaggregate thymus organ cultures were used to compare the thymopoietic potential of the FOXN1 variants. RESULTS FOXN1 variants were categorized into benign, loss- or gain-of-function, and/or dominant-negatives. Dominant negative activities mapped to frameshift variants impacting the transactivation domain. A nuclear localization signal was mapped within the DNA binding domain. Thymopoiesis analyses with mouse models and reaggregate thymus organ cultures revealed distinct consequences of particular Foxn1 variants on T-cell development. CONCLUSIONS The potential effect of a FOXN1 variant on T-cell output from the thymus may relate to its effects on transcriptional activity, nuclear localization, and/or dominant negative functions. A combination of functional assays and thymopoiesis comparisons enabled a categorization of diverse FOXN1 variants and their potential impact on T-cell output from the thymus.
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Affiliation(s)
- Angela Moses
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, Tex
| | - Pratibha Bhalla
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, Tex
| | - Austin Thompson
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, Tex
| | - Laijun Lai
- Department of Allied Health Sciences, University of Connecticut, Storrs, Conn
| | - Fatma S Coskun
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, Tex
| | - Christine M Seroogy
- the Department of Pediatrics, University of Wisconsin School of Medicine and Public Health, Madison, Wis
| | - Maria Teresa de la Morena
- the Department of Pediatrics, University of Washington and Seattle Children's Hospital, Seattle, Wash
| | - Christian A Wysocki
- Departments of Pediatrics, University of Texas Southwestern Medical Center, Dallas, Tex; Internal Medicine, University of Texas Southwestern Medical Center, Dallas, Tex
| | - Nicolai S C van Oers
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, Tex; Departments of Pediatrics, University of Texas Southwestern Medical Center, Dallas, Tex; Microbiology, University of Texas Southwestern Medical Center, Dallas, Tex.
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4
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Song J, Li L, Fang Y, Lin Y, Wu L, Wan W, Wei G, Hua F, Ying J. FOXN Transcription Factors: Regulation and Significant Role in Cancer. Mol Cancer Ther 2023; 22:1028-1039. [PMID: 37566097 DOI: 10.1158/1535-7163.mct-23-0208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 06/29/2023] [Accepted: 07/19/2023] [Indexed: 08/12/2023]
Abstract
A growing number of studies have demonstrated that cancer development is closely linked to abnormal gene expression, including alterations in the transcriptional activity of transcription factors. The Forkhead box class N (FOXN) proteins FOXN1-6 form a highly conserved class of transcription factors, which have been shown in recent years to be involved in the regulation of malignant progression in a variety of cancers. FOXNs mediate cell proliferation, cell-cycle progression, cell differentiation, metabolic homeostasis, embryonic development, DNA damage repair, tumor angiogenesis, and other critical biological processes. Therefore, transcriptional dysregulation of FOXNs can directly affect cellular physiology and promote cancer development. Numerous studies have demonstrated that the transcriptional activity of FOXNs is regulated by protein-protein interactions, microRNAs (miRNA), and posttranslational modifications (PTM). However, the mechanisms underlying the molecular regulation of FOXNs in cancer development are unclear. Here, we reviewed the molecular regulatory mechanisms of FOXNs expression and activity, their role in the malignant progression of tumors, and their value for clinical applications in cancer therapy. This review may help design experimental studies involving FOXN transcription factors, and enhance their therapeutic potential as antitumor targets.
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Affiliation(s)
- Jiali Song
- Department of Anesthesiology, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, P.R. China
- Key Laboratory of Anesthesiology of Jiangxi Province, Nanchang City, Jiangxi Province, P.R. China
| | - Longshan Li
- Department of Anesthesiology, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, P.R. China
- Key Laboratory of Anesthesiology of Jiangxi Province, Nanchang City, Jiangxi Province, P.R. China
| | - Yang Fang
- Department of Anesthesiology, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, P.R. China
- Key Laboratory of Anesthesiology of Jiangxi Province, Nanchang City, Jiangxi Province, P.R. China
| | - Yue Lin
- Department of Anesthesiology, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, P.R. China
- Key Laboratory of Anesthesiology of Jiangxi Province, Nanchang City, Jiangxi Province, P.R. China
| | - Luojia Wu
- Department of Anesthesiology, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, P.R. China
- Key Laboratory of Anesthesiology of Jiangxi Province, Nanchang City, Jiangxi Province, P.R. China
| | - Wei Wan
- Department of Anesthesiology, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, P.R. China
- Key Laboratory of Anesthesiology of Jiangxi Province, Nanchang City, Jiangxi Province, P.R. China
| | - Gen Wei
- Department of Anesthesiology, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, P.R. China
- Key Laboratory of Anesthesiology of Jiangxi Province, Nanchang City, Jiangxi Province, P.R. China
| | - Fuzhou Hua
- Department of Anesthesiology, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, P.R. China
- Key Laboratory of Anesthesiology of Jiangxi Province, Nanchang City, Jiangxi Province, P.R. China
| | - Jun Ying
- Department of Anesthesiology, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, P.R. China
- Key Laboratory of Anesthesiology of Jiangxi Province, Nanchang City, Jiangxi Province, P.R. China
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5
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Shi D, Huang Y, Bai C. Studies of the Mechanism of Nucleosome Dynamics: A Review on Multifactorial Regulation from Computational and Experimental Cases. Polymers (Basel) 2023; 15:polym15071763. [PMID: 37050377 PMCID: PMC10096840 DOI: 10.3390/polym15071763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 03/28/2023] [Accepted: 03/31/2023] [Indexed: 04/05/2023] Open
Abstract
The nucleosome, which organizes the long coil of genomic DNA in a highly condensed, polymeric way, is thought to be the basic unit of chromosomal structure. As the most important protein–DNA complex, its structural and dynamic features have been successively revealed in recent years. However, its regulatory mechanism, which is modulated by multiple factors, still requires systemic discussion. This study summarizes the regulatory factors of the nucleosome’s dynamic features from the perspective of histone modification, DNA methylation, and the nucleosome-interacting factors (transcription factors and nucleosome-remodeling proteins and cations) and focuses on the research exploring the molecular mechanism through both computational and experimental approaches. The regulatory factors that affect the dynamic features of nucleosomes are also discussed in detail, such as unwrapping, wrapping, sliding, and stacking. Due to the complexity of the high-order topological structures of nucleosomes and the comprehensive effects of regulatory factors, the research on the functional modulation mechanism of nucleosomes has encountered great challenges. The integration of computational and experimental approaches, the construction of physical modes for nucleosomes, and the application of deep learning techniques will provide promising opportunities for further exploration.
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Affiliation(s)
- Danfeng Shi
- Warshel Institute for Computational Biology, School of Life and Health Sciences, School of Medicine, The Chinese University of Hong Kong (Shenzhen), Shenzhen 518172, China
- School of Chemistry and Materials Science, University of Science and Technology of China, Hefei 230026, China
| | - Yuxin Huang
- Warshel Institute for Computational Biology, School of Life and Health Sciences, School of Medicine, The Chinese University of Hong Kong (Shenzhen), Shenzhen 518172, China
| | - Chen Bai
- Warshel Institute for Computational Biology, School of Life and Health Sciences, School of Medicine, The Chinese University of Hong Kong (Shenzhen), Shenzhen 518172, China
- Chenzhu (MoMeD) Biotechnology Co., Ltd., Hangzhou 310005, China
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6
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Leng F, Zhang W, Ramirez RN, Leon J, Zhong Y, Hou L, Yuki K, van der Veeken J, Rudensky AY, Benoist C, Hur S. The transcription factor FoxP3 can fold into two dimerization states with divergent implications for regulatory T cell function and immune homeostasis. Immunity 2022; 55:1354-1369.e8. [PMID: 35926508 PMCID: PMC9907729 DOI: 10.1016/j.immuni.2022.07.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 05/03/2022] [Accepted: 07/06/2022] [Indexed: 11/26/2022]
Abstract
FoxP3 is an essential transcription factor (TF) for immunologic homeostasis, but how it utilizes the common forkhead DNA-binding domain (DBD) to perform its unique function remains poorly understood. We here demonstrated that unlike other known forkhead TFs, FoxP3 formed a head-to-head dimer using a unique linker (Runx1-binding region [RBR]) preceding the forkhead domain. Head-to-head dimerization conferred distinct DNA-binding specificity and created a docking site for the cofactor Runx1. RBR was also important for proper folding of the forkhead domain, as truncation of RBR induced domain-swap dimerization of forkhead, which was previously considered the physiological form of FoxP3. Rather, swap-dimerization impaired FoxP3 function, as demonstrated with the disease-causing mutation R337Q, whereas a swap-suppressive mutation largely rescued R337Q-mediated functional impairment. Altogether, our findings suggest that FoxP3 can fold into two distinct dimerization states: head-to-head dimerization representing functional specialization of an ancient DBD and swap dimerization associated with impaired functions.
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Affiliation(s)
- Fangwei Leng
- Howard Hughes Medical Institute and Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Wenxiang Zhang
- Howard Hughes Medical Institute and Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Ricardo N Ramirez
- Department of Immunology, Harvard Medical School, Boston, MA 02115, USA; Evergrande Center for Immunologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Juliette Leon
- Department of Immunology, Harvard Medical School, Boston, MA 02115, USA; Evergrande Center for Immunologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Yi Zhong
- Howard Hughes Medical Institute and Immunology Program, Sloan Kettering Institute and Ludwig Center at Memorial Sloan Kettering Cancer Center, New York, NY, USA; Shanghai Immune Therapy Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Lifei Hou
- Department of Anesthesiology, Critical Care and Pain Medicine, Boston Children's Hospital, Boston, MA 02115, USA
| | - Koichi Yuki
- Department of Anesthesiology, Critical Care and Pain Medicine, Boston Children's Hospital, Boston, MA 02115, USA
| | | | - Alexander Y Rudensky
- Howard Hughes Medical Institute and Immunology Program, Sloan Kettering Institute and Ludwig Center at Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Christophe Benoist
- Department of Immunology, Harvard Medical School, Boston, MA 02115, USA; Evergrande Center for Immunologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Sun Hur
- Howard Hughes Medical Institute and Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA.
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7
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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, Lagerholm BC, Anderson G, Sezgin E, Holländer GA. FOXN1 forms higher-order nuclear condensates displaced by mutations causing immunodeficiency. SCIENCE ADVANCES 2021; 7:eabj9247. [PMID: 34860543 PMCID: PMC8641933 DOI: 10.1126/sciadv.abj9247] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Accepted: 10/15/2021] [Indexed: 05/04/2023]
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.
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Affiliation(s)
- Ioanna A. Rota
- Department of Paediatrics and the MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Adam E. Handel
- Department of Paediatrics and the MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK
| | - Stefano Maio
- Department of Paediatrics and the MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Fabian Klein
- Department of Paediatrics and the MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Fatima Dhalla
- Department of Paediatrics and the MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Mary E. Deadman
- Department of Paediatrics and the MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Stanley Cheuk
- Department of Paediatrics and the MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Joseph A. Newman
- Structural Genomics Consortium, University of Oxford, ORCRB, Roosevelt Drive, Oxford, UK
| | - Yale S. Michaels
- Genome Engineering and Synthetic Biology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Saulius Zuklys
- Paediatric Immunology, Department of Biomedicine, University of Basel and University Children’s Hospital Basel, Basel, Switzerland
| | - Nicolas Prevot
- Department of Paediatrics and the MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Philip Hublitz
- MRC Weatherall Institute of Molecular Medicine, Genome engineering services, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Philip D. Charles
- Target Discovery Institute, University of Oxford, Oxford OX3 7FZ, UK
| | - Athina Soragia Gkazi
- Great Ormond Street Hospital and Great Ormond Street Institute of Child Health, University College London, London WC1N 1EH, UK
| | - Eleni Adamopoulou
- Department of Paediatrics and the MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Waseem Qasim
- Great Ormond Street Hospital and Great Ormond Street Institute of Child Health, University College London, London WC1N 1EH, UK
| | - Edward Graham Davies
- Great Ormond Street Hospital and Great Ormond Street Institute of Child Health, University College London, London WC1N 1EH, UK
| | - Imelda Hanson
- Department of Pediatrics, Section of Pediatric Immunology, Allergy, and Retrovirology, Baylor College of Medicine, Houston, TX, USA
| | - Alistair T. Pagnamenta
- National Institute for Health Research Biomedical Research Centre, Oxford, UK
- Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Carme Camps
- National Institute for Health Research Biomedical Research Centre, Oxford, UK
- Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Helene M. Dreau
- Department of Oncology, University of Oxford, Oxford OX3 7DQ, UK
| | - Andrea White
- Institute for Immunology and Immunotherapy, Medical School, University of Birmingham, Birmingham B15 2TT, UK
| | - Kieran James
- Institute for Immunology and Immunotherapy, Medical School, University of Birmingham, Birmingham B15 2TT, UK
| | - Roman Fischer
- Target Discovery Institute, University of Oxford, Oxford OX3 7FZ, UK
| | - Opher Gileadi
- Structural Genomics Consortium, University of Oxford, ORCRB, Roosevelt Drive, Oxford, UK
| | - Jenny C. Taylor
- National Institute for Health Research Biomedical Research Centre, Oxford, UK
- Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Tudor Fulga
- Genome Engineering and Synthetic Biology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - B. Christoffer Lagerholm
- Wolfson Imaging Centre Oxford, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Headley Way, Oxford OX3 9DS, UK
| | - Graham Anderson
- Institute for Immunology and Immunotherapy, Medical School, University of Birmingham, Birmingham B15 2TT, UK
| | - Erdinc Sezgin
- Paediatric Immunology, Department of Biomedicine, University of Basel and University Children’s Hospital Basel, Basel, Switzerland
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Georg A. Holländer
- Department of Paediatrics and the MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- Paediatric Immunology, Department of Biomedicine, University of Basel and University Children’s Hospital Basel, Basel, Switzerland
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
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8
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Hu C, Zhang K, Jiang F, Wang H, Shao Q. Epigenetic modifications in thymic epithelial cells: an evolutionary perspective for thymus atrophy. Clin Epigenetics 2021; 13:210. [PMID: 34819170 PMCID: PMC8612001 DOI: 10.1186/s13148-021-01197-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 11/08/2021] [Indexed: 02/06/2023] Open
Abstract
Background The thymic microenvironment is mainly comprised of thymic epithelial cells, the cytokines, exosomes, surface molecules, and hormones from the cells, and plays a vital role in the development, differentiation, maturation and homeostasis of T lymphocytes. However, the thymus begins to degenerate as early as the second year of life and continues through aging in human beings, leading to a decreased output of naïve T cells, the limited TCR diversity and an expansion of monoclonal memory T cells in the periphery organs. These alternations will reduce the adaptive immune response to tumors and emerging infectious diseases, such as COVID-19, also it is easier to suffer from autoimmune diseases in older people. In the context of global aging, it is important to investigate and clarify the causes and mechanisms of thymus involution. Main body Epigenetics include histone modification, DNA methylation, non-coding RNA effects, and chromatin remodeling. In this review, we discuss how senescent thymic epithelial cells determine and control age-related thymic atrophy, how this process is altered by epigenetic modification. How the thymus adipose influences the dysfunctions of the thymic epithelial cells, and the prospects of targeting thymic epithelial cells for the treatment of thymus atrophy. Conclusion Epigenetic modifications are emerging as key regulators in governing the development and senescence of thymic epithelial cells. It is beneficial to re-establish effective thymopoiesis, identify the potential therapeutic strategy and rejuvenate the immune function in the elderly.
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Affiliation(s)
- Cexun Hu
- Department of Immunology, School of Medicine, Jiangsu University, Zhenjiang, 212013, Jiangsu, People's Republic of China.,Department of Immunology, Key Laboratory of Medical Science and Laboratory Medicine of Jiangsu Province, School of Medicine, Jiangsu University, No. 301 Xuefu Road, Zhenjiang, 212013, Jiangsu, People's Republic of China
| | - Keyu Zhang
- Department of Immunology, School of Medicine, Jiangsu University, Zhenjiang, 212013, Jiangsu, People's Republic of China.,Department of Immunology, Key Laboratory of Medical Science and Laboratory Medicine of Jiangsu Province, School of Medicine, Jiangsu University, No. 301 Xuefu Road, Zhenjiang, 212013, Jiangsu, People's Republic of China
| | - Feng Jiang
- Department of Immunology, School of Medicine, Jiangsu University, Zhenjiang, 212013, Jiangsu, People's Republic of China.,Department of Immunology, Key Laboratory of Medical Science and Laboratory Medicine of Jiangsu Province, School of Medicine, Jiangsu University, No. 301 Xuefu Road, Zhenjiang, 212013, Jiangsu, People's Republic of China
| | - Hui Wang
- Department of Immunology, School of Medicine, Jiangsu University, Zhenjiang, 212013, Jiangsu, People's Republic of China. .,Department of Immunology, Key Laboratory of Medical Science and Laboratory Medicine of Jiangsu Province, School of Medicine, Jiangsu University, No. 301 Xuefu Road, Zhenjiang, 212013, Jiangsu, People's Republic of China.
| | - Qixiang Shao
- Department of Immunology, School of Medicine, Jiangsu University, Zhenjiang, 212013, Jiangsu, People's Republic of China. .,Department of Immunology, Key Laboratory of Medical Science and Laboratory Medicine of Jiangsu Province, School of Medicine, Jiangsu University, No. 301 Xuefu Road, Zhenjiang, 212013, Jiangsu, People's Republic of China. .,Jiangsu College of Nursing, School of Medical Science and Laboratory Medicine, Huai'an, 223002, Jiangsu, People's Republic of China.
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Dai S, Qu L, Li J, Chen Y. Toward a mechanistic understanding of DNA binding by forkhead transcription factors and its perturbation by pathogenic mutations. Nucleic Acids Res 2021; 49:10235-10249. [PMID: 34551426 PMCID: PMC8501956 DOI: 10.1093/nar/gkab807] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 09/01/2021] [Accepted: 09/08/2021] [Indexed: 01/12/2023] Open
Abstract
Forkhead box (FOX) proteins are an evolutionarily conserved family of transcription factors that play numerous regulatory roles in eukaryotes during developmental and adult life. Dysfunction of FOX proteins has been implicated in a variety of human diseases, including cancer, neurodevelopment disorders and genetic diseases. The FOX family members share a highly conserved DNA-binding domain (DBD), which is essential for DNA recognition, binding and function. Since the first FOX structure was resolved in 1993, >30 FOX structures have been reported to date. It is clear now that the structure and DNA recognition mechanisms vary among FOX members; however, a systematic review on this aspect is lacking. In this manuscript, we present an overview of the mechanisms by which FOX transcription factors bind DNA, including protein structures, DNA binding properties and disease-causing mutations. This review should enable a better understanding of FOX family transcription factors for basic researchers and clinicians.
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Affiliation(s)
- Shuyan Dai
- Department of Oncology, NHC Key Laboratory of Cancer Proteomics, Laboratory of Structural Biology, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Linzhi Qu
- Department of Oncology, NHC Key Laboratory of Cancer Proteomics, Laboratory of Structural Biology, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Jun Li
- Department of Oncology, NHC Key Laboratory of Cancer Proteomics, Laboratory of Structural Biology, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Yongheng Chen
- Department of Oncology, NHC Key Laboratory of Cancer Proteomics, Laboratory of Structural Biology, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
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10
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Human FoxP Transcription Factors as Tractable Models of the Evolution and Functional Outcomes of Three-Dimensional Domain Swapping. Int J Mol Sci 2021; 22:ijms221910296. [PMID: 34638644 PMCID: PMC8508939 DOI: 10.3390/ijms221910296] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 09/21/2021] [Accepted: 09/22/2021] [Indexed: 01/18/2023] Open
Abstract
The association of two or more proteins to adopt a quaternary complex is one of the most widespread mechanisms by which protein function is modulated. In this scenario, three-dimensional domain swapping (3D-DS) constitutes one plausible pathway for the evolution of protein oligomerization that exploits readily available intramolecular contacts to be established in an intermolecular fashion. However, analysis of the oligomerization kinetics and thermodynamics of most extant 3D-DS proteins shows its dependence on protein unfolding, obscuring the elucidation of the emergence of 3D-DS during evolution, its occurrence under physiological conditions, and its biological relevance. Here, we describe the human FoxP subfamily of transcription factors as a feasible model to study the evolution of 3D-DS, due to their significantly faster dissociation and dimerization kinetics and lower dissociation constants in comparison to most 3D-DS models. Through the biophysical and functional characterization of FoxP proteins, relevant structural aspects highlighting the evolutionary adaptations of these proteins to enable efficient 3D-DS have been ascertained. Most biophysical studies on FoxP suggest that the dynamics of the polypeptide chain are crucial to decrease the energy barrier of 3D-DS, enabling its fast oligomerization under physiological conditions. Moreover, comparison of biophysical parameters between human FoxP proteins in the context of their minute sequence differences suggests differential evolutionary strategies to favor homoassociation and presages the possibility of heteroassociations, with direct impacts in their gene regulation function.
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Expanding the Nude SCID/CID Phenotype Associated with FOXN1 Homozygous, Compound Heterozygous, or Heterozygous Mutations. J Clin Immunol 2021; 41:756-768. [PMID: 33464451 PMCID: PMC8068652 DOI: 10.1007/s10875-021-00967-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Accepted: 01/06/2021] [Indexed: 12/11/2022]
Abstract
Human nude SCID is a rare autosomal recessive inborn error of immunity (IEI) characterized by congenital athymia, alopecia, and nail dystrophy. Few cases have been reported to date. However, the recent introduction of newborn screening for IEIs and high-throughput sequencing has led to the identification of novel and atypical cases. Moreover, immunological alterations have been recently described in patients carrying heterozygous mutations. The aim of this paper is to describe the extended phenotype associated with FOXN1 homozygous, compound heterozygous, or heterozygous mutations. We collected clinical and laboratory information of a cohort of 11 homozygous, 2 compound heterozygous, and 5 heterozygous patients with recurrent severe infections. All, except one heterozygous patient, had signs of CID or SCID. Nail dystrophy and alopecia, that represent the hallmarks of the syndrome, were not always present, while almost 50% of the patients developed Omenn syndrome. One patient with hypomorphic compound heterozygous mutations had a late-onset atypical phenotype. A SCID-like phenotype was observed in 4 heterozygous patients coming from the same family. A spectrum of clinical manifestations may be associated with different mutations. The severity of the clinical phenotype likely depends on the amount of residual activity of the gene product, as previously observed for other SCID-related genes. The severity of the manifestations in this heterozygous family may suggest a mechanism of negative dominance of the specific mutation or the presence of additional mutations in noncoding regions.
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12
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Kreins AY, Maio S, Dhalla F. Inborn errors of thymic stromal cell development and function. Semin Immunopathol 2020; 43:85-100. [PMID: 33257998 PMCID: PMC7925491 DOI: 10.1007/s00281-020-00826-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Accepted: 11/09/2020] [Indexed: 12/31/2022]
Abstract
As the primary site for T cell development, the thymus is responsible for the production and selection of a functional, yet self-tolerant T cell repertoire. This critically depends on thymic stromal cells, derived from the pharyngeal apparatus during embryogenesis. Thymic epithelial cells, mesenchymal and vascular elements together form the unique and highly specialised microenvironment required to support all aspects of thymopoiesis and T cell central tolerance induction. Although rare, inborn errors of thymic stromal cells constitute a clinically important group of conditions because their immunological consequences, which include autoimmune disease and T cell immunodeficiency, can be life-threatening if unrecognised and untreated. In this review, we describe the molecular and environmental aetiologies of the thymic stromal cell defects known to cause disease in humans, placing particular emphasis on those with a propensity to cause thymic hypoplasia or aplasia and consequently severe congenital immunodeficiency. We discuss the principles underpinning their diagnosis and management, including the use of novel tools to aid in their identification and strategies for curative treatment, principally transplantation of allogeneic thymus tissue.
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Affiliation(s)
- Alexandra Y Kreins
- UCL Great Ormond Street Institute of Child Health, London, UK.,Department of Immunology, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Stefano Maio
- Developmental Immunology, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Fatima Dhalla
- Developmental Immunology, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK. .,Department of Clinical Immunology, Oxford University Hospitals, Oxford, UK.
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13
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Dai S, Li J, Zhang H, Chen X, Guo M, Chen Z, Chen Y. Structural Basis for DNA Recognition by FOXG1 and the Characterization of Disease-causing FOXG1 Mutations. J Mol Biol 2020; 432:6146-6156. [PMID: 33058871 DOI: 10.1016/j.jmb.2020.10.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 09/22/2020] [Accepted: 10/07/2020] [Indexed: 12/22/2022]
Abstract
Forkhead box G1 (FOXG1) is a transcription factor mainly expressed in the brain that plays a critical role in the development and regionalization of the forebrain. Aberrant expression of FOXG1 has implications in FOXG1 syndrome, a serious neurodevelopmental disorder. Here, we report the crystal structure of the FOXG1 DNA-binding domain (DBD) in complex with the forkhead consensus DNA site DBE2 at the resolution of 1.6 Å. FOXG1-DBD adopts a typical winged helix fold. Compared to those of other FOX-DBD/DBE2 structures, the N terminus, H3 helix and wing2 region of FOXG1-DBD exhibit differences in DNA recognition. The FOXG1-DBD wing2 region adopts a unique architecture composed of two β-strands that differs from all other known FOX-DBD wing2 folds. Mutation assays revealed that the disease-causing mutations within the FOXG1-DBD affect DNA binding, protein thermal stability, or both. Our report provides initial insight into how FOXG1 binds DNA and sheds light on how disease-causing mutations in FOXG1-DBD affect its DNA-binding ability.
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Affiliation(s)
- Shuyan Dai
- Department of Oncology, NHC Key Laboratory of Cancer Proteomics, Laboratory of Structural Biology, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Jun Li
- Department of Oncology, NHC Key Laboratory of Cancer Proteomics, Laboratory of Structural Biology, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China.
| | - Huajun Zhang
- Department of Oncology, NHC Key Laboratory of Cancer Proteomics, Laboratory of Structural Biology, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Xiaojuan Chen
- Department of Oncology, NHC Key Laboratory of Cancer Proteomics, Laboratory of Structural Biology, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Ming Guo
- Department of Oncology, NHC Key Laboratory of Cancer Proteomics, Laboratory of Structural Biology, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Zhuchu Chen
- Department of Oncology, NHC Key Laboratory of Cancer Proteomics, Laboratory of Structural Biology, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Yongheng Chen
- Department of Oncology, NHC Key Laboratory of Cancer Proteomics, Laboratory of Structural Biology, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China.
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Bhalla P, Wysocki CA, van Oers NSC. Molecular Insights Into the Causes of Human Thymic Hypoplasia With Animal Models. Front Immunol 2020; 11:830. [PMID: 32431714 PMCID: PMC7214791 DOI: 10.3389/fimmu.2020.00830] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Accepted: 04/14/2020] [Indexed: 12/30/2022] Open
Abstract
22q11.2 deletion syndrome (DiGeorge), CHARGE syndrome, Nude/SCID and otofaciocervical syndrome type 2 (OTFCS2) are distinct clinical conditions in humans that can result in hypoplasia and occasionally, aplasia of the thymus. Thymic hypoplasia/aplasia is first suggested by absence or significantly reduced numbers of recent thymic emigrants, revealed in standard-of-care newborn screens for T cell receptor excision circles (TRECs). Subsequent clinical assessments will often indicate whether genetic mutations are causal to the low T cell output from the thymus. However, the molecular mechanisms leading to the thymic hypoplasia/aplasia in diverse human syndromes are not fully understood, partly because the problems of the thymus originate during embryogenesis. Rodent and Zebrafish models of these clinical syndromes have been used to better define the underlying basis of the clinical presentations. Results from these animal models are uncovering contributions of different cell types in the specification, differentiation, and expansion of the thymus. Cell populations such as epithelial cells, mesenchymal cells, endothelial cells, and thymocytes are variably affected depending on the human syndrome responsible for the thymic hypoplasia. In the current review, findings from the diverse animal models will be described in relation to the clinical phenotypes. Importantly, these results are suggesting new strategies for regenerating thymic tissue in patients with distinct congenital disorders.
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Affiliation(s)
- Pratibha Bhalla
- Department of Immunology, The University of Texas Southwestern Medical Center, Dallas, TX, United States
| | - Christian A. Wysocki
- Department of Pediatrics, The University of Texas Southwestern Medical Center, Dallas, TX, United States
| | - Nicolai S. C. van Oers
- Department of Immunology, The University of Texas Southwestern Medical Center, Dallas, TX, United States
- Department of Pediatrics, The University of Texas Southwestern Medical Center, Dallas, TX, United States
- Department of Microbiology, The University of Texas Southwestern Medical Center, Dallas, TX, United States
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Schmitt-Ney M. The FOXO's Advantages of Being a Family: Considerations on Function and Evolution. Cells 2020; 9:E787. [PMID: 32214027 PMCID: PMC7140813 DOI: 10.3390/cells9030787] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2020] [Revised: 03/16/2020] [Accepted: 03/23/2020] [Indexed: 12/12/2022] Open
Abstract
The nematode Caenorhabditis elegans possesses a unique (with various isoforms) FOXO transcription factor DAF-16, which is notorious for its role in aging and its regulation by the insulin-PI3K-AKT pathway. In humans, five genes (including a protein-coding pseudogene) encode for FOXO transcription factors that are targeted by the PI3K-AKT axis, such as in C. elegans. This common regulation and highly conserved DNA-binding domain are the pillars of this family. In this review, I will discuss the possible meaning of possessing a group of very similar proteins and how it can generate additional functionality to more complex organisms. I frame this discussion in relation to the much larger super family of Forkhead proteins to which they belong. FOXO members are very often co-expressed in the same cell type. The overlap of function and expression creates a certain redundancy that might be a safeguard against the accidental loss of FOXO function, which could otherwise lead to disease, particularly, cancer. This is one of the points that will be examined in this "family affair" report.
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Affiliation(s)
- Michel Schmitt-Ney
- Molecular Biotechnology Center, University of Torino, Via Nizza 52, 10126 Torino, Italy
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