1
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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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2
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Wang B, Bian Q. Regulation of 3D genome organization during T cell activation. FEBS J 2024. [PMID: 38944686 DOI: 10.1111/febs.17211] [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: 01/04/2024] [Revised: 04/23/2024] [Accepted: 06/14/2024] [Indexed: 07/01/2024]
Abstract
Within the three-dimensional (3D) nuclear space, the genome organizes into a series of orderly structures that impose important influences on gene regulation. T lymphocytes, crucial players in adaptive immune responses, undergo intricate transcriptional remodeling upon activation, leading to differentiation into specific effector and memory T cell subsets. Recent evidence suggests that T cell activation is accompanied by dynamic changes in genome architecture at multiple levels, providing a unique biological context to explore the functional relevance and molecular mechanisms of 3D genome organization. Here, we summarize recent advances that link the reorganization of genome architecture to the remodeling of transcriptional programs and conversion of cell fates during T cell activation and differentiation. We further discuss how various chromatin architecture regulators, including CCCTC-binding factor and several transcription factors, collectively modulate the genome architecture during this process.
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Affiliation(s)
- Bao Wang
- Shanghai lnstitute of Precision Medicine, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, China
- Shanghai Key Laboratory of Reproductive Medicine, Shanghai Jiao Tong University School of Medicine, China
| | - Qian Bian
- Shanghai lnstitute of Precision Medicine, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, China
- Shanghai Key Laboratory of Reproductive Medicine, Shanghai Jiao Tong University School of Medicine, China
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3
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Kolimi N, Ballard J, Peulen T, Goutam R, Duffy FX, Ramírez-Sarmiento CA, Babul J, Medina E, Sanabria H. DNA controls the dimerization of the human FoxP1 forkhead domain. CELL REPORTS. PHYSICAL SCIENCE 2024; 5:101854. [PMID: 38585429 PMCID: PMC10997372 DOI: 10.1016/j.xcrp.2024.101854] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
Transcription factors (TFs) regulate gene expression by binding to specific DNA sequences and gating access to genes. Even when the binding of TFs and their cofactors to DNA is reversible, indicating a reversible control of gene expression, there is little knowledge about the molecular effect DNA has on TFs. Using single-molecule multiparameter fluorescence spectroscopy, molecular dynamics simulations, and biochemical assays, we find that the monomeric form of the forkhead (FKH) domain of the human FoxP1 behaves as a disordered protein and increases its folded population when it dimerizes. Notably, DNA binding promotes a disordered FKH dimer bound to DNA, negatively controlling the stability of the dimeric FoxP1:DNA complex. The DNA-mediated reversible regulation on FKH dimers suggests that FoxP1-dependent gene suppression is unstable, and it must require the presence of other dimerization domains or cofactors to revert the negative impact exerted by the DNA.
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Affiliation(s)
- Narendar Kolimi
- Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, USA
| | - Jake Ballard
- Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, USA
| | - Thomas Peulen
- Rudolf-Virchow-Zentrum – Center for Integrative and Translational Bioimaging, Haus D15, Josef-Schneider-Straße 2, 97080 Würzburg Germany
| | - Rajen Goutam
- Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, USA
| | - Francis X. Duffy
- Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, USA
| | - César A. Ramírez-Sarmiento
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences, Pontificia Universidad Católica de Chile, Santiago 7820436, Chile
- ANID – Millennium Science Initiative Program – Millennium Institute for Integrative Biology (iBio), Santiago 8331150, Chile
| | - Jorge Babul
- Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Casilla 653, Santiago 7800003, Chile
| | - Exequiel Medina
- Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, USA
- Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Casilla 653, Santiago 7800003, Chile
| | - Hugo Sanabria
- Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, USA
- Lead contact
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4
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Gao C, Zhu H, Gong P, Wu C, Xu X, Zhu X. The functions of FOXP transcription factors and their regulation by post-translational modifications. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2023; 1866:194992. [PMID: 37797785 DOI: 10.1016/j.bbagrm.2023.194992] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 09/26/2023] [Accepted: 09/30/2023] [Indexed: 10/07/2023]
Abstract
The forkhead box subfamily P (FOXP) of transcription factors, consisting of FOXP1, FOXP2, FOXP3, and FOXP4, is involved in the regulation of multisystemic functioning. Disruption of the transcriptional activity of FOXP proteins leads to neurodevelopmental disorders and immunological diseases, as well as the suppression or promotion of carcinogenesis. The transcriptional activities of FOXP proteins are directly or indirectly regulated by diverse post-translational modifications, including phosphorylation, ubiquitination, SUMOylation, acetylation, O-GlcNAcylation, and methylation. Here, we discuss how post-translational modifications modulate the multiple functions of FOXP proteins and examine the implications for tumorigenesis and cancer therapy.
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Affiliation(s)
- Congwen Gao
- Guangdong Key Laboratory for Genome Stability & Disease Prevention and Marshall Laboratory of Biomedical Engineering, Shenzhen University Medical School, Shenzhen, Guangdong 518060, China; College of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding 071002, China
| | - Honglin Zhu
- Guangdong Key Laboratory for Genome Stability & Disease Prevention and Marshall Laboratory of Biomedical Engineering, Shenzhen University Medical School, Shenzhen, Guangdong 518060, China
| | - Peng Gong
- Department of General Surgery & Institute of Precision Diagnosis and Treatment of Gastrointestinal Tumors & Carson International Cancer Center, Shenzhen University General Hospital, Shenzhen University Medical School, Shenzhen, Guangdong 518060, China
| | - Chen Wu
- College of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding 071002, China
| | - Xingzhi Xu
- Guangdong Key Laboratory for Genome Stability & Disease Prevention and Marshall Laboratory of Biomedical Engineering, Shenzhen University Medical School, Shenzhen, Guangdong 518060, China.
| | - Xuefei Zhu
- Department of General Surgery & Institute of Precision Diagnosis and Treatment of Gastrointestinal Tumors & Carson International Cancer Center, Shenzhen University General Hospital, Shenzhen University Medical School, Shenzhen, Guangdong 518060, China.
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5
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Liu Z, Zheng Y. An immune-cell transcription factor tethers DNA together. Nature 2023; 624:255-256. [PMID: 38030764 DOI: 10.1038/d41586-023-03628-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2023]
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6
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Zhang W, Leng F, Wang X, Ramirez RN, Park J, Benoist C, Hur S. FOXP3 recognizes microsatellites and bridges DNA through multimerization. Nature 2023; 624:433-441. [PMID: 38030726 PMCID: PMC10719092 DOI: 10.1038/s41586-023-06793-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Accepted: 10/27/2023] [Indexed: 12/01/2023]
Abstract
FOXP3 is a transcription factor that is essential for the development of regulatory T cells, a branch of T cells that suppress excessive inflammation and autoimmunity1-5. However, the molecular mechanisms of FOXP3 remain unclear. Here we here show that FOXP3 uses the forkhead domain-a DNA-binding domain that is commonly thought to function as a monomer or dimer-to form a higher-order multimer after binding to TnG repeat microsatellites. The cryo-electron microscopy structure of FOXP3 in a complex with T3G repeats reveals a ladder-like architecture, whereby two double-stranded DNA molecules form the two 'side rails' bridged by five pairs of FOXP3 molecules, with each pair forming a 'rung'. Each FOXP3 subunit occupies TGTTTGT within the repeats in a manner that is indistinguishable from that of FOXP3 bound to the forkhead consensus motif (TGTTTAC). Mutations in the intra-rung interface impair TnG repeat recognition, DNA bridging and the cellular functions of FOXP3, all without affecting binding to the forkhead consensus motif. FOXP3 can tolerate variable inter-rung spacings, explaining its broad specificity for TnG-repeat-like sequences in vivo and in vitro. Both FOXP3 orthologues and paralogues show similar TnG repeat recognition and DNA bridging. These findings therefore reveal a mode of DNA recognition that involves transcription factor homomultimerization and DNA bridging, and further implicates microsatellites in transcriptional regulation and diseases.
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Affiliation(s)
- Wenxiang Zhang
- Howard Hughes Medical Institute and Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Fangwei Leng
- Howard Hughes Medical Institute and Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Xi Wang
- Howard Hughes Medical Institute and Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Ricardo N Ramirez
- Department of Immunology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Jinseok Park
- Department of Immunology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Christophe Benoist
- Department of Immunology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Sun Hur
- Howard Hughes Medical Institute and Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA.
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA.
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7
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Zhang W, Leng F, Wang X, Ramirez RN, Park J, Benoist C, Hur S. FoxP3 recognizes microsatellites and bridges DNA through multimerization. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.12.548762. [PMID: 37986949 PMCID: PMC10659269 DOI: 10.1101/2023.07.12.548762] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
FoxP3 is a transcription factor (TF) essential for development of regulatory T cells (Tregs), a branch of T cells that suppress excessive inflammation and autoimmunity 1-5 . Molecular mechanisms of FoxP3, however, remain elusive. We here show that FoxP3 utilizes the Forkhead domain--a DNA binding domain (DBD) that is commonly thought to function as a monomer or dimer--to form a higher-order multimer upon binding to T n G repeat microsatellites. A cryo-electron microscopy structure of FoxP3 in complex with T 3 G repeats reveals a ladder-like architecture, where two double-stranded DNA molecules form the two "side rails" bridged by five pairs of FoxP3 molecules, with each pair forming a "rung". Each FoxP3 subunit occupies TGTTTGT within the repeats in the manner indistinguishable from that of FoxP3 bound to the Forkhead consensus motif (FKHM; TGTTTAC). Mutations in the "intra-rung" interface impair T n G repeat recognition, DNA bridging and cellular functions of FoxP3, all without affecting FKHM binding. FoxP3 can tolerate variable "inter-rung" spacings, explaining its broad specificity for T n G repeat-like sequences in vivo and in vitro . Both FoxP3 orthologs and paralogs show similar T n G repeat recognition and DNA bridging. These findings thus reveal a new mode of DNA recognition that involves TF homo-multimerization and DNA bridging, and further implicates microsatellites in transcriptional regulation and diseases.
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8
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Liu Z, Lee DS, Liang Y, Zheng Y, Dixon JR. Foxp3 orchestrates reorganization of chromatin architecture to establish regulatory T cell identity. Nat Commun 2023; 14:6943. [PMID: 37932264 PMCID: PMC10628232 DOI: 10.1038/s41467-023-42647-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 10/09/2023] [Indexed: 11/08/2023] Open
Abstract
Chromatin conformation reorganization is emerging as an important layer of regulation for gene expression and lineage specification. Yet, how lineage-specific transcription factors contribute to the establishment of cell type-specific 3D chromatin architecture in the immune cells remains unclear, especially for the late stages of T cell subset differentiation and maturation. Regulatory T cells (Treg) are mainly generated in the thymus as a subpopulation of T cells specializing in suppressing excessive immune responses. Here, by comprehensively mapping 3D chromatin organization during Treg cell differentiation, we show that Treg-specific chromatin structures were progressively established during its lineage specification, and highly associated with Treg signature gene expression. Additionally, the binding sites of Foxp3, a Treg lineage specifying transcription factor, were highly enriched at Treg-specific chromatin loop anchors. Further comparison of the chromatin interactions between wide-type Tregs versus Treg cells from Foxp3 knock-in/knockout or newly-generated Foxp3 domain-swap mutant mouse revealed that Foxp3 was essential for the establishment of Treg-specific 3D chromatin architecture, although it was not dependent on the formation of the Foxp3 domain-swapped dimer. These results highlighted an underappreciated role of Foxp3 in modulating Treg-specific 3D chromatin structure formation.
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Affiliation(s)
- Zhi Liu
- Shanghai Immune Therapy Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- NOMIS Center for Immunobiology and Microbial Pathogenesis, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Dong-Sung Lee
- Gene Expression Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA
- Department of Life Sciences, University of Seoul, Seoul, South Korea
| | - Yuqiong Liang
- NOMIS Center for Immunobiology and Microbial Pathogenesis, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Ye Zheng
- NOMIS Center for Immunobiology and Microbial Pathogenesis, Salk Institute for Biological Studies, La Jolla, CA, USA.
| | - Jesse R Dixon
- Gene Expression Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA.
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9
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Vaseghi-Shanjani M, Yousefi P, Sharma M, Samra S, Sifuentes E, Turvey SE, Biggs CM. Transcription factor defects in inborn errors of immunity with atopy. FRONTIERS IN ALLERGY 2023; 4:1237852. [PMID: 37727514 PMCID: PMC10505736 DOI: 10.3389/falgy.2023.1237852] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2023] [Accepted: 08/08/2023] [Indexed: 09/21/2023] Open
Abstract
Transcription factors (TFs) are critical components involved in regulating immune system development, maintenance, and function. Monogenic defects in certain TFs can therefore give rise to inborn errors of immunity (IEIs) with profound clinical implications ranging from infections, malignancy, and in some cases severe allergic inflammation. This review examines TF defects underlying IEIs with severe atopy as a defining clinical phenotype, including STAT3 loss-of-function, STAT6 gain-of-function, FOXP3 deficiency, and T-bet deficiency. These disorders offer valuable insights into the pathophysiology of allergic inflammation, expanding our understanding of both rare monogenic and common polygenic allergic diseases. Advances in genetic testing will likely uncover new IEIs associated with atopy, enriching our understanding of molecular pathways involved in allergic inflammation. Identification of monogenic disorders profoundly influences patient prognosis, treatment planning, and genetic counseling. Hence, the consideration of IEIs is essential for patients with severe, early-onset atopy. This review highlights the need for continued investigation into TF defects to enhance our understanding and management of allergic diseases.
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Affiliation(s)
- Maryam Vaseghi-Shanjani
- British Columbia Children’s Hospital, Department of Pediatrics, The University of British Columbia, Vancouver, BC, Canada
- Experimental Medicine Program, Faculty of Medicine, The University of British Columbia, Vancouver, BC, Canada
| | - Pariya Yousefi
- British Columbia Children’s Hospital, Department of Pediatrics, The University of British Columbia, Vancouver, BC, Canada
| | - Mehul Sharma
- British Columbia Children’s Hospital, Department of Pediatrics, The University of British Columbia, Vancouver, BC, Canada
| | - Simran Samra
- British Columbia Children’s Hospital, Department of Pediatrics, The University of British Columbia, Vancouver, BC, Canada
- Experimental Medicine Program, Faculty of Medicine, The University of British Columbia, Vancouver, BC, Canada
| | - Erika Sifuentes
- British Columbia Children’s Hospital, Department of Pediatrics, The University of British Columbia, Vancouver, BC, Canada
| | - Stuart E. Turvey
- British Columbia Children’s Hospital, Department of Pediatrics, The University of British Columbia, Vancouver, BC, Canada
| | - Catherine M. Biggs
- British Columbia Children’s Hospital, Department of Pediatrics, The University of British Columbia, Vancouver, BC, Canada
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10
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Gu Q, Zhao X, Guo J, Jin Q, Wang T, Xu W, Li L, Zhang J, Zhang W, Hong S, Zhang F, Hou B, Zhou X. The splicing isoform Foxp3Δ2 differentially regulates tTreg and pTreg homeostasis. Cell Rep 2023; 42:112877. [PMID: 37498744 DOI: 10.1016/j.celrep.2023.112877] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 06/09/2023] [Accepted: 07/12/2023] [Indexed: 07/29/2023] Open
Abstract
Foxp3 is the master transcription factor for regulatory T cells (Tregs). Alternative splicing of human Foxp3 results in the expression of two isoforms: the full length and an exon 2-deleted protein. Here, AlphaFold2 predictions and in vitro experiments demonstrate that the N-terminal domain of Foxp3 inhibits DNA binding by moving toward the C terminus and that this movement is mediated by exon 2. Consequently, we find that Foxp3Δ2-bearing thymus-derived Tregs (tTregs) in the peripheral lymphoid organ are less sensitive to T cell receptor (TCR) stimulation due to the enhanced binding of Foxp3Δ2 to the Batf promoter and are hyporesponsive to interleukin-2 (IL-2). In contrast, among RORγt+ peripherally induced Tregs (pTregs) in the large intestine, Foxp3Δ2 pTregs express many more RORγt-related genes, conferring a competitive advantage. Together, our results reveal that alternative splicing of exon 2 generates an active form of Foxp3, which plays a differential role in regulating tTreg and pTreg homeostasis.
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Affiliation(s)
- Qianchong Gu
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Science (CAS), Beijing 100101, China; Department of Savaid Medical School, University of Chinese Academy of Sciences (CAS), Beijing 100049, China
| | - Xiufeng Zhao
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Science (CAS), Beijing 100101, China; Department of Savaid Medical School, University of Chinese Academy of Sciences (CAS), Beijing 100049, China
| | - Jie Guo
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Science (CAS), Beijing 100101, China
| | - Qiuzhu Jin
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Science (CAS), Beijing 100101, China; Department of Savaid Medical School, University of Chinese Academy of Sciences (CAS), Beijing 100049, China
| | - Ting Wang
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Science (CAS), Beijing 100101, China; Department of Savaid Medical School, University of Chinese Academy of Sciences (CAS), Beijing 100049, China
| | - Wei Xu
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Science (CAS), Beijing 100101, China; Department of Savaid Medical School, University of Chinese Academy of Sciences (CAS), Beijing 100049, China
| | - Liping Li
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Science (CAS), Beijing 100101, China; Department of Savaid Medical School, University of Chinese Academy of Sciences (CAS), Beijing 100049, China
| | - Jianhua Zhang
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Science (CAS), Beijing 100101, China
| | - Wei Zhang
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Science (CAS), Beijing 100101, China
| | - Sheng Hong
- Key Laboratory of Infection and Immunity, Institute of Biophysics, Chinese Academy of Sciences (CAS), Beijing 100101, China
| | - Fuping Zhang
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Science (CAS), Beijing 100101, China; Department of Savaid Medical School, University of Chinese Academy of Sciences (CAS), Beijing 100049, China
| | - Baidong Hou
- Key Laboratory of Infection and Immunity, Institute of Biophysics, Chinese Academy of Sciences (CAS), Beijing 100101, China
| | - Xuyu Zhou
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Science (CAS), Beijing 100101, China; Department of Savaid Medical School, University of Chinese Academy of Sciences (CAS), Beijing 100049, China.
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11
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Leon J, Chowdhary K, Zhang W, Ramirez RN, André I, Hur S, Mathis D, Benoist C. Mutations from patients with IPEX ported to mice reveal different patterns of FoxP3 and Treg dysfunction. Cell Rep 2023; 42:113018. [PMID: 37605532 PMCID: PMC10565790 DOI: 10.1016/j.celrep.2023.113018] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 07/26/2023] [Accepted: 08/04/2023] [Indexed: 08/23/2023] Open
Abstract
Mutations of the transcription factor FoxP3 in patients with "IPEX" (immune dysregulation, polyendocrinopathy, enteropathy, X-linked syndrome) disrupt regulatory T cells (Treg), causing an array of multiorgan autoimmunity. To understand the functional impact of mutations across FoxP3 domains, without genetic and environmental confounders, six human FOXP3 missense mutations are engineered into mice. Two classes of mutations emerge from combined immunologic and genomic analyses. A mutation in the DNA-binding domain shows the same lymphoproliferation and multiorgan infiltration as complete FoxP3 knockouts but delayed by months. Tregs expressing this mutant FoxP3 are destabilized by normal Tregs in heterozygous females compared with hemizygous males. Mutations in other domains affect chromatin opening differently, involving different cofactors and provoking more specific autoimmune pathology (dermatitis, colitis, diabetes), unmasked by immunological challenges or incrossing NOD autoimmune-susceptibility alleles. This work establishes that IPEX disease heterogeneity results from the actual mutations, combined with genetic and environmental perturbations, explaining then the intra-familial variation in IPEX.
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Affiliation(s)
- Juliette Leon
- Department of Immunology, Harvard Medical School, Boston, MA, USA; INSERM UMR 1163, University of Paris, Imagine Institute, Paris, France
| | | | - Wenxiang Zhang
- Howard Hughes Medical Institute, Program in Cellular and Molecular Medicine, Boston Children's Hospital, Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | | | - Isabelle André
- INSERM UMR 1163, University of Paris, Imagine Institute, Paris, France
| | - Sun Hur
- Howard Hughes Medical Institute, Program in Cellular and Molecular Medicine, Boston Children's Hospital, Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Diane Mathis
- Department of Immunology, Harvard Medical School, Boston, MA, USA
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12
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Coñuecar R, Asela I, Rivera M, Galaz-Davison P, González-Higueras J, Hamilton GL, Engelberger F, Ramírez-Sarmiento CA, Babul J, Sanabria H, Medina E. DNA facilitates heterodimerization between human transcription factors FoxP1 and FoxP2 by increasing their conformational flexibility. iScience 2023; 26:107228. [PMID: 37485372 PMCID: PMC10362293 DOI: 10.1016/j.isci.2023.107228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 05/15/2023] [Accepted: 06/20/2023] [Indexed: 07/25/2023] Open
Abstract
Transcription factors regulate gene expression by binding to DNA. They have disordered regions and specific DNA-binding domains. Binding to DNA causes structural changes, including folding and interactions with other molecules. The FoxP subfamily of transcription factors in humans is unique because they can form heterotypic interactions without DNA. However, it is unclear how they form heterodimers and how DNA binding affects their function. We used computational and experimental methods to study the structural changes in FoxP1's DNA-binding domain when it forms a heterodimer with FoxP2. We found that FoxP1 has complex and diverse conformational dynamics, transitioning between compact and extended states. Surprisingly, DNA binding increases the flexibility of FoxP1, contrary to the typical folding-upon-binding mechanism. In addition, we observed a 3-fold increase in the rate of heterodimerization after FoxP1 binds to DNA. These findings emphasize the importance of structural flexibility in promoting heterodimerization to form transcriptional complexes.
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Affiliation(s)
- Ricardo Coñuecar
- Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago 7800003, Chile
| | - Isabel Asela
- Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago 7800003, Chile
| | - Maira Rivera
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences, Pontificia Universidad Católica de Chile, Santiago 7820436, Chile
- ANID – Millennium Science Initiative Program – Millennium Institute for Integrative Biology (iBio), Santiago 8331150, Chile
| | - Pablo Galaz-Davison
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences, Pontificia Universidad Católica de Chile, Santiago 7820436, Chile
- ANID – Millennium Science Initiative Program – Millennium Institute for Integrative Biology (iBio), Santiago 8331150, Chile
| | - Jorge González-Higueras
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences, Pontificia Universidad Católica de Chile, Santiago 7820436, Chile
- ANID – Millennium Science Initiative Program – Millennium Institute for Integrative Biology (iBio), Santiago 8331150, Chile
| | - George L. Hamilton
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY, USA
| | - Felipe Engelberger
- Institute for Drug Discovery, Leipzig University Medical School, 04107 Leipzig, Germany
| | - César A. Ramírez-Sarmiento
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences, Pontificia Universidad Católica de Chile, Santiago 7820436, Chile
- ANID – Millennium Science Initiative Program – Millennium Institute for Integrative Biology (iBio), Santiago 8331150, Chile
| | - Jorge Babul
- Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago 7800003, Chile
| | - Hugo Sanabria
- Department of Physics & Astronomy, Clemson University, Clemson, SC 29634, USA
| | - Exequiel Medina
- Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago 7800003, Chile
- Department of Physics & Astronomy, Clemson University, Clemson, SC 29634, USA
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13
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Villalobos P, Carvajal AI, Castro-Fernández V, Babul J, Ramírez-Sarmiento CA, Medina E. Unraveling the folding and dimerization properties of the human FoxP subfamily of transcription factors. FEBS Lett 2023; 597:1894-1905. [PMID: 37199668 DOI: 10.1002/1873-3468.14665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 04/20/2023] [Accepted: 05/09/2023] [Indexed: 05/19/2023]
Abstract
Human FoxP proteins share a highly conserved DNA-binding domain that dimerizes via three-dimensional domain swapping, although showing varying oligomerization propensities among its members. Here, we present an experimental and computational characterization of all human FoxP proteins to unravel how their amino acid substitutions impact their folding and dimerization mechanism. We solved the crystal structure of the forkhead domain of FoxP4 to then perform a comparison across all members, finding that their sequence changes impact not only the structural heterogeneity of their forkhead domains but also the protein-protein association energy barrier. Lastly, we demonstrate that the accumulation of a monomeric intermediate is an oligomerization-dependent feature rather than a common aspect of monomers and dimers in this protein subfamily.
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Affiliation(s)
- Pablo Villalobos
- Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Alonso I Carvajal
- Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | | | - Jorge Babul
- Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago, 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
| | - Exequiel Medina
- Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
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14
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Műzes G, Sipos F. CAR-Based Therapy for Autoimmune Diseases: A Novel Powerful Option. Cells 2023; 12:1534. [PMID: 37296654 PMCID: PMC10252902 DOI: 10.3390/cells12111534] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 05/29/2023] [Accepted: 05/31/2023] [Indexed: 06/12/2023] Open
Abstract
The pervasive application of chimeric antigen receptor (CAR)-based cellular therapies in the treatment of oncological diseases has long been recognized. However, CAR T cells can target and eliminate autoreactive cells in autoimmune and immune-mediated diseases. By doing so, they can contribute to an effective and relatively long-lasting remission. In turn, CAR Treg interventions may have a highly effective and durable immunomodulatory effect via a direct or bystander effect, which may have a positive impact on the course and prognosis of autoimmune diseases. CAR-based cellular techniques have a complex theoretical foundation and are difficult to implement in practice, but they have a remarkable capacity to suppress the destructive functions of the immune system. This article provides an overview of the numerous CAR-based therapeutic options developed for the treatment of immune-mediated and autoimmune diseases. We believe that well-designed, rigorously tested cellular therapies could provide a promising new personalized treatment strategy for a significant number of patients with immune-mediated disorders.
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Affiliation(s)
- Györgyi Műzes
- Immunology Division, Department of Internal Medicine and Hematology, Semmelweis University, 1088 Budapest, Hungary;
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15
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Cruz P, Paredes N, Asela I, Kolimi N, Molina JA, Ramírez-Sarmiento CA, Goutam R, Huang G, Medina E, Sanabria H. Domain tethering impacts dimerization and DNA-mediated allostery in the human transcription factor FoxP1. J Chem Phys 2023; 158:2890482. [PMID: 37184020 DOI: 10.1063/5.0138782] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 04/25/2023] [Indexed: 05/16/2023] Open
Abstract
Transcription factors are multidomain proteins with specific DNA binding and regulatory domains. In the human FoxP subfamily (FoxP1, FoxP2, FoxP3, and FoxP4) of transcription factors, a 90 residue-long disordered region links a Leucine Zipper (ZIP)-known to form coiled-coil dimers-and a Forkhead (FKH) domain-known to form domain swapping dimers. We used replica exchange discrete molecular dynamics simulations, single-molecule fluorescence experiments, and other biophysical tools to understand how domain tethering in FoxP1 impacts dimerization at ZIP and FKH domains and how DNA binding allosterically regulates their dimerization. We found that domain tethering promotes FoxP1 dimerization but inhibits a FKH domain-swapped structure. Furthermore, our findings indicate that the linker mediates the mutual organization and dynamics of ZIP and FKH domains, forming closed and open states with and without interdomain contacts, thus highlighting the role of the linkers in multidomain proteins. Finally, we found that DNA allosterically promotes structural changes that decrease the dimerization propensity of FoxP1. We postulate that, upon DNA binding, the interdomain linker plays a crucial role in the gene regulatory function of FoxP1.
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Affiliation(s)
- Perla Cruz
- Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Casilla 653, Santiago 7800003, Chile
| | - Nicolás Paredes
- Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Casilla 653, Santiago 7800003, Chile
| | - Isabel Asela
- Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Casilla 653, Santiago 7800003, Chile
| | - Narendar Kolimi
- Department of Physics and Astronomy, Clemson University, Clemson, South Carolina 29634, USA
| | - José Alejandro Molina
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences, Pontificia Universidad Católica de Chile, Av. Vicuña Mackenna 4860, Santiago 7820436, Chile
- ANID - Millennium Science Initiative Program - Millennium Institute for Integrative Biology (iBio), Santiago 7820436, Chile
| | - César A Ramírez-Sarmiento
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences, Pontificia Universidad Católica de Chile, Av. Vicuña Mackenna 4860, Santiago 7820436, Chile
- ANID - Millennium Science Initiative Program - Millennium Institute for Integrative Biology (iBio), Santiago 7820436, Chile
| | - Rajen Goutam
- Department of Physics and Astronomy, Clemson University, Clemson, South Carolina 29634, USA
| | - Gangton Huang
- Department of Physics and Astronomy, Clemson University, Clemson, South Carolina 29634, USA
| | - Exequiel Medina
- Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Casilla 653, Santiago 7800003, Chile
| | - Hugo Sanabria
- Department of Physics and Astronomy, Clemson University, Clemson, South Carolina 29634, USA
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16
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Dolsten GA, Pritykin Y. Genomic Analysis of Foxp3 Function in Regulatory T Cells. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2023; 210:880-887. [PMID: 36947819 PMCID: PMC10037560 DOI: 10.4049/jimmunol.2200864] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 01/23/2023] [Indexed: 03/24/2023]
Abstract
Regulatory T (Treg) cells are critical for tolerance to self-antigens and for preventing autoimmunity. Foxp3 has been identified as a Treg cell lineage-defining transcription factor controlling Treg cell differentiation and function. In this article, we review the current mechanistic and systemic understanding of Foxp3 function enabled by experimental and computational advances in high-throughput genomics.
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Affiliation(s)
- Gabriel A Dolsten
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
- Quantitative and Computational Biology Graduate Program, Princeton University, Princeton, NJ, USA
| | - Yuri Pritykin
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
- Department of Computer Science, Princeton University, Princeton, NJ, USA
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17
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Liu Z, Lee DS, Liang Y, Zheng Y, Dixon JR. Foxp3 Orchestrates Reorganization of Chromatin Architecture to Establish Regulatory T Cell Identity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.22.529589. [PMID: 36865315 PMCID: PMC9980151 DOI: 10.1101/2023.02.22.529589] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/25/2023]
Abstract
Chromatin conformation reorganization is emerging as an important layer of regulation for gene expression and lineage specification. Yet, how lineage-specific transcription factors contribute to the establishment of cell type-specific 3D chromatin architecture in the immune cells remains unclear, especially for the late stages of T cell subset differentiation and maturation. Regulatory T cells (Treg) are mainly generated in the thymus as a subpopulation of T cells specializing in suppressing excessive immune responses. Here, by comprehensively mapping 3D chromatin organization during Treg cell differentiation, we show that Treg-specific chromatin structures were progressively established during its lineage specification, and highly associated with Treg signature gene expression. Additionally, the binding sites of Foxp3, a Treg lineage specifying transcription factor, were highly enriched at Treg-specific chromatin loop anchors. Further comparison of the chromatin interactions between wide-type Tregs versus Treg cells from Foxp3 knock-in/knockout or newly-generated Foxp3 domain-swap mutant mouse revealed that Foxp3 was essential for the establishment of Treg-specific 3D chromatin architecture, although it was not dependent on the formation of the Foxp3 domain-swapped dimer. These results highlighted an underappreciated role of Foxp3 in modulating Treg-specific 3D chromatin structure formation.
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Affiliation(s)
- Zhi Liu
- NOMIS Center for Immunobiology and Microbial Pathogenesis, Salk Institute for Biological Studies, La Jolla, CA, USA
- Shanghai Immune Therapy Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Dong-Sung Lee
- Gene Expression Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA
- Department of Life Sciences, University of Seoul, Seoul, South Korea
| | - Yuqiong Liang
- NOMIS Center for Immunobiology and Microbial Pathogenesis, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Ye Zheng
- NOMIS Center for Immunobiology and Microbial Pathogenesis, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Jesse R Dixon
- Gene Expression Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA
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18
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Decreased ratio of FOXP3 +/FOXP3 -CD45RA +CD4 + T cells in peripheral blood is associated with unexplained infertility and ART failure. J Reprod Immunol 2023; 155:103793. [PMID: 36603467 DOI: 10.1016/j.jri.2022.103793] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 12/17/2022] [Accepted: 12/29/2022] [Indexed: 01/01/2023]
Abstract
Unexplained infertility has a huge social impact and is a significant challenge for both clinicians and researchers. Previous studies have shown the involvement of multiple factors in infertility. Among these, the subset of regulatory T cells is of particular interest for the maternal tolerance towards the semi-allogenic fetus. We investigated circulating CD45RA+ regulatory and non-regulatory CD4+ T cells in healthy women and patients with unexplained infertility in the context of thymic output and peripheral proliferation. The proportion of FOXP3+ and FOXP3-CD45RA+CD4+ T cells in peripheral blood was studied in control groups of healthy parous and nulliparous (never-pregnant) women and in patients with unexplained infertility. In the same groups thymic output and peripheral proliferation were defined by the sj/βTREC ratio, and signal joint T-cell receptor excision circles (sjTREC) and Ki67 expression, respectively. In parous women a decrease in sjTREC/105 cells and CD45RA+ T lymphocytes, compared to nulliparous group was found. At the same time, the proportion of FOXP3-CD45RA+CD4+ cells, but not FOXP3+CD45RA+ Tregs was reduced. In contrast, in patients with unsuccessful pregnancy, proportions of both regulatory and non-regulatory T cell counterparts were lower. Taken together, our results provide evidence for group-specific properties in the CD45RA+ T cell compartment between healthy parous, nulliparous and women with unexplained infertility.
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19
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Nakajima A, Murakami R, Hori S. Functional Analysis of Foxp3 and Its Mutants by Retroviral Transduction of Murine Primary CD4 + T Cells. Methods Mol Biol 2023; 2559:79-94. [PMID: 36180628 DOI: 10.1007/978-1-0716-2647-4_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
The transcription factor Foxp3/FOXP3 orchestrates regulatory T (Treg) cell development and function by interacting with numerous target genes and partner proteins. Functional analysis of naturally occurring or engineered Foxp3/FOXP3 mutations has provided important insights into how the complex Foxp3/FOXP3-centered molecular network operates. Here, we describe detailed protocols for retroviral transduction of murine primary conventional CD4+ T cells to determine the impacts of Foxp3 mutations on the Treg-cell-like phenotype and function conferred by Foxp3.
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Affiliation(s)
- Akira Nakajima
- Laboratory of Immunology and Microbiology, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan
| | - Ryuichi Murakami
- Laboratory of Immunology and Microbiology, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan
| | - Shohei Hori
- Laboratory of Immunology and Microbiology, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan.
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20
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Narula M, Lakshmanan U, Borna S, Schulze JJ, Holmes TH, Harre N, Kirkey M, Ramachandran A, Tagi VM, Barzaghi F, Grunebaum E, Upton JEM, Hong-Diep Kim V, Wysocki C, Dimitriades VR, Weinberg K, Weinacht KG, Gernez Y, Sathi BK, Schelotto M, Johnson M, Olek S, Sachsenmaier C, Roncarolo MG, Bacchetta R. Epigenetic and immunological indicators of IPEX disease in subjects with FOXP3 gene mutation. J Allergy Clin Immunol 2023; 151:233-246.e10. [PMID: 36152823 DOI: 10.1016/j.jaci.2022.09.013] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 08/16/2022] [Accepted: 09/09/2022] [Indexed: 02/04/2023]
Abstract
BACKGROUND Forkhead box protein 3 (FOXP3) is the master transcription factor in CD4+CD25hiCD127lo regulatory T (Treg) cells. Mutations in FOXP3 result in IPEX (immune dysregulation, polyendocrinopathy, enteropathy, X-linked) syndrome. Clinical presentation of IPEX syndrome is broader than initially described, challenging the understanding of the disease, its evolution, and treatment choice. OBJECTIVE We sought to study the type and extent of immunologic abnormalities that remain ill-defined in IPEX, across genetic and clinical heterogeneity. METHODS We performed Treg-cell-specific epigenetic quantification and immunologic characterization of severe "typical" (n = 6) and "atypical" or asymptomatic (n = 9) patients with IPEX. RESULTS Increased number of cells with Treg-cell-Specific Demethylated Region demethylation in FOXP3 is a consistent feature in patients with IPEX, with (1) highest values in those with typical IPEX, (2) increased values in subjects with pathogenic FOXP3 but still no symptoms, and (3) gradual increase over the course of disease progression. Large-scale profiling using Luminex identified plasma inflammatory signature of macrophage activation and TH2 polarization, with cytokines previously not associated with IPEX pathology, including CCL22, CCL17, CCL15, and IL-13, and the inflammatory markers TNF-α, IL-1A, IL-8, sFasL, and CXCL9. Similarly, both Treg-cell and Teff compartments, studied by Mass Cytometry by Time-Of-Flight, were skewed toward the TH2 compartment, especially in typical IPEX. CONCLUSIONS Elevated TSDR-demethylated cells, combined with elevation of plasmatic and cellular markers of a polarized type 2 inflammatory immune response, extends our understanding of IPEX diagnosis and heterogeneity.
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Affiliation(s)
- Mansi Narula
- Department of Pediatrics, Division of Hematology, Oncology, Stem Cell Transplantation and Regenerative Medicine, Stanford University School of Medicine, Stanford, Calif
| | - Uma Lakshmanan
- Department of Pediatrics, Division of Hematology, Oncology, Stem Cell Transplantation and Regenerative Medicine, Stanford University School of Medicine, Stanford, Calif
| | - Simon Borna
- Department of Pediatrics, Division of Hematology, Oncology, Stem Cell Transplantation and Regenerative Medicine, Stanford University School of Medicine, Stanford, Calif
| | | | - Tyson H Holmes
- Human Immune Monitoring Center, Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, Calif
| | - Nicholas Harre
- Department of Pediatrics, Division of Hematology, Oncology, Stem Cell Transplantation and Regenerative Medicine, Stanford University School of Medicine, Stanford, Calif
| | - Matthew Kirkey
- Department of Pediatrics, Division of Hematology, Oncology, Stem Cell Transplantation and Regenerative Medicine, Stanford University School of Medicine, Stanford, Calif
| | - Akshaya Ramachandran
- Department of Pediatrics, Division of Hematology, Oncology, Stem Cell Transplantation and Regenerative Medicine, Stanford University School of Medicine, Stanford, Calif
| | - Veronica Maria Tagi
- San Raffaele Telethon Institute for Gene Therapy, Pediatric Immunohematology and Bone Marrow Transplantation Unit, IRCCS San Raffaele Scientific Institute Milan, Milan, Italy
| | - Federica Barzaghi
- San Raffaele Telethon Institute for Gene Therapy, Pediatric Immunohematology and Bone Marrow Transplantation Unit, IRCCS San Raffaele Scientific Institute Milan, Milan, Italy
| | - Eyal Grunebaum
- Division of Immunology and Allergy, The Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada
| | - Julia E M Upton
- Division of Immunology and Allergy, The Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada
| | - Vy Hong-Diep Kim
- Division of Immunology and Allergy, The Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada
| | - Christian Wysocki
- Department of Internal Medicine, Pediatrics, Allergy and Immunology, UT Southwestern Medical Center, Dallas, Tex
| | - Victoria R Dimitriades
- Department of Pediatrics, Division of Allergy, Immunology and Rheumatology, UC Davis Health Medical Center, Sacramento, Calif
| | - Kenneth Weinberg
- Department of Pediatrics, Division of Hematology, Oncology, Stem Cell Transplantation and Regenerative Medicine, Stanford University School of Medicine, Stanford, Calif
| | - Katja G Weinacht
- Department of Pediatrics, Division of Hematology, Oncology, Stem Cell Transplantation and Regenerative Medicine, Stanford University School of Medicine, Stanford, Calif
| | - Yael Gernez
- Department of Pediatrics, Division of Allergy, Immunology, and Rheumatology, Stanford University School of Medicine, Stanford, Calif
| | | | | | - Matthew Johnson
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, Exeter, United Kingdom
| | - Sven Olek
- Ivana Turbachova Laboratory of Epigenetics, Precision for Medicine GmbH, Berlin, Germany
| | | | - Maria-Grazia Roncarolo
- Department of Pediatrics, Division of Hematology, Oncology, Stem Cell Transplantation and Regenerative Medicine, Stanford University School of Medicine, Stanford, Calif; Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, Calif; Center for Definitive and Curative Medicine, Stanford University School of Medicine, Stanford, Calif
| | - Rosa Bacchetta
- Department of Pediatrics, Division of Hematology, Oncology, Stem Cell Transplantation and Regenerative Medicine, Stanford University School of Medicine, Stanford, Calif; Center for Definitive and Curative Medicine, Stanford University School of Medicine, Stanford, Calif.
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21
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Cassidy MF, Herbert ZT, Moulton VR. Splicing factor SRSF1 controls autoimmune-related molecular pathways in regulatory T cells distinct from FoxP3. Mol Immunol 2022; 152:140-152. [PMID: 36368121 DOI: 10.1016/j.molimm.2022.10.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 10/26/2022] [Accepted: 10/30/2022] [Indexed: 11/09/2022]
Abstract
Regulatory T cells (Tregs) are vital for maintaining immune self-tolerance, and their impaired function leads to autoimmune disease. Mutations in FoxP3, the master transcriptional regulator of Tregs, leads to immune dysregulation, polyendocrinopathy, enteropathy, X-linked (IPEX) syndrome in humans and the early lethal "scurfy" phenotype with multi-organ autoimmune disease in mice. We recently identified serine/arginine-rich splicing factor 1 (SRSF1) as an indispensable regulator of Treg homeostasis and function. Intriguingly, Treg-conditional SRSF1-deficient mice exhibit early lethal systemic autoimmunity with multi-organ inflammation reminiscent of the scurfy mice. Importantly, SRSF1 is decreased in T cells from patients with the autoimmune disease systemic lupus erythematosus (SLE), and low SRSF1 levels inversely correlate with disease severity. Given that the Treg-specific deficiency of SRSF1 causes similarly profound autoimmune disease outcomes in mice as the deficiency/mutation in FoxP3, we aimed to evaluate the genes and molecular pathways controlled by these two indispensable regulatory proteins. We performed comparative bioinformatic analyses of transcriptomic profiles of Tregs from Srsf1-knockout mice and two Foxp3 mutant mice--the FoxP3-deficient ΔFoxp3 and the Foxp3 M370I mutant mice. We identified 132 differentially expressed genes (DEGs) unique to Srsf1-ko Tregs, 503 DEGs unique to Foxp3 M370I Tregs, and 1367 DEGs unique to ΔFoxp3 Tregs. Gene set enrichment and pathway analysis of DEGs unique to Srsf1-ko Tregs indicate that SRSF1 controls cytokine and immune response pathways. Conversely, FoxP3 controls pathways involved in DNA replication and cell cycle. Besides the distinct gene signatures, we identified only 30 shared genes between all three Treg mutants, mostly contributing to cytokine and immune defense pathways. Prominent genes included the chemokines CXCR6 and CCL1 and the checkpoint inhibitors FASLG and PDCD1. Thus, we demonstrate that SRSF1 and FoxP3 control common and distinct molecular pathways implicated in autoimmunity. Our analyses suggest that SRSF1 controls crucial immune functions in Tregs contributing to immune tolerance, and perturbations in its levels lead to systemic autoimmunity via mechanisms that are largely distinct from FoxP3.
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Affiliation(s)
- Michael F Cassidy
- Division of Rheumatology and Clinical Immunology, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, United States; Tufts University School of Medicine, Boston, MA, United States.
| | - Zachary T Herbert
- Molecular Biology Core Facilities, Dana Farber Cancer Institute, Harvard Medical School, Boston, MA, United States
| | - Vaishali R Moulton
- Division of Rheumatology and Clinical Immunology, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, United States
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22
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Pluta R, Aragón E, Prescott NA, Ruiz L, Mees RA, Baginski B, Flood JR, Martin-Malpartida P, Massagué J, David Y, Macias MJ. Molecular basis for DNA recognition by the maternal pioneer transcription factor FoxH1. Nat Commun 2022; 13:7279. [PMID: 36435807 PMCID: PMC9701222 DOI: 10.1038/s41467-022-34925-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 11/10/2022] [Indexed: 11/28/2022] Open
Abstract
Forkhead box H1 (FoxH1) is an essential maternal pioneer factor during embryonic development that binds to specific GG/GT-containing DNA target sequences. Here we have determined high-resolution structures of three FoxH1 proteins (from human, frog and fish species) and four DNAs to clarify the way in which FoxH1 binds to these sites. We found that the protein-DNA interactions extend to both the minor and major DNA grooves and are thus almost twice as extensive as those of other FOX family members. Moreover, we identified two specific amino acid changes in FoxH1 that allowed the recognition of GG/GT motifs. Consistent with the pioneer factor activity of FoxH1, we found that its affinity for nucleosomal DNA is even higher than for linear DNA fragments. The structures reported herein illustrate how FoxH1 binding to distinct DNA sites provides specificity and avoids cross-regulation by other FOX proteins that also operate during the maternal-zygotic transition and select canonical forkhead sites.
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Affiliation(s)
- Radoslaw Pluta
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Barcelona, 08028, Spain
| | - Eric Aragón
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Barcelona, 08028, Spain
| | - Nicholas A Prescott
- Tri-Institutional PhD Program in Chemical Biology, New York, NY, USA
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Lidia Ruiz
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Barcelona, 08028, Spain
| | - Rebeca A Mees
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Barcelona, 08028, Spain
| | - Blazej Baginski
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Barcelona, 08028, Spain
| | - Julia R Flood
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Pau Martin-Malpartida
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Barcelona, 08028, Spain
| | - Joan Massagué
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Yael David
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
- Department of Pharmacology, Weill Cornell Medicine, New York, NY, 10065, USA
- Department of Physiology, Biophysics and Systems Biology, Weill Cornell Medicine, New York, NY, 10065, USA
| | - Maria J Macias
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Barcelona, 08028, Spain.
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Passeig Lluís Companys 23, Barcelona, 08010, Spain.
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23
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Inhibition of FOXP3 by stapled alpha-helical peptides dampens regulatory T cell function. Proc Natl Acad Sci U S A 2022; 119:e2209044119. [PMID: 36227917 PMCID: PMC9586281 DOI: 10.1073/pnas.2209044119] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Therapies and preclinical probes designed to drug and better understand the specific functions of intracellular protein–protein interactions (PPIs) remain an area of unmet need. This study describes the development of prototype therapeutics against the FOXP3 homodimer, a PPI essential for regulatory T cell suppressive capacity. We demonstrate that hydrocarbon stapled peptides designed to block this interaction can dampen regulatory T cell (Treg cell) suppressive function and lead to genetic signatures of immune reactivation. This work provides strong scientific justification for continued development of FOXP3-specific peptide-based inhibitors and provides mechanistic insights into the design and delivery of specific inhibitors of the coiled-coil region of FOXP3. These studies ultimately could lead to new immunotherapeutic strategies to amplify immune responsiveness in a number of settings. Despite continuing advances in the development of novel cellular-, antibody-, and chemotherapeutic-based strategies to enhance immune reactivity, the presence of regulatory T cells (Treg cells) remains a complicating factor for their clinical efficacy. To overcome dosing limitations and off-target effects from antibody-based Treg cell deletional strategies or small molecule drugging, we investigated the ability of hydrocarbon stapled alpha-helical (SAH) peptides to target FOXP3, the master transcription factor regulator of Treg cell development, maintenance, and suppressive function. Using the crystal structure of the FOXP3 homodimer as a guide, we developed SAHs in the likeness of a portion of the native FOXP3 antiparallel coiled-coil homodimerization domain (SAH-FOXP3) to block this key FOXP3 protein-protein interaction (PPI) through molecular mimicry. We describe the design, synthesis, and biochemical evaluation of single- and double-stapled SAHs covering the entire coiled-coil expanse. We show that lead SAH-FOXP3s bind FOXP3, are cell permeable and nontoxic to T cells, induce dose-dependent transcript and protein level alterations of FOXP3 target genes, impede Treg cell function, and lead to Treg cell gene expression changes in vivo consistent with FOXP3 dysfunction. These results demonstrate a proof of concept for rationally designed FOXP3-directed peptide therapeutics that could be used as approaches to amplify endogenous immune responsiveness.
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Riet T, Chmielewski M. Regulatory CAR-T cells in autoimmune diseases: Progress and current challenges. Front Immunol 2022; 13:934343. [PMID: 36032080 PMCID: PMC9399761 DOI: 10.3389/fimmu.2022.934343] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Accepted: 07/19/2022] [Indexed: 11/13/2022] Open
Abstract
CAR (Chimeric Antigen Receptor) T-cell therapy has revolutionized the field of oncology in recent years. This innovative shift in cancer treatment also provides the opportunity to improve therapies for many patients suffering from various autoimmune diseases. Recent studies have confirmed the therapeutic suppressive potential of regulatory T cells (Tregs) to modulate immune response in autoimmune diseases. However, the polyclonal character of regulatory T cells and their unknown TCR specificity impaired their therapeutic potency in clinical implementation. Genetical engineering of these immune modulating cells to express antigen-specific receptors and using them therapeutically is a logical step on the way to overcome present limitations of the Treg strategy for the treatment of autoimmune diseases. Encouraging preclinical studies successfully demonstrated immune modulating properties of CAR Tregs in various mouse models. Still, there are many concerns about targeted Treg therapies relating to CAR target selectivity, suppressive functions, phenotype stability and safety aspects. Here, we summarize recent developments in CAR design, Treg biology and future strategies and perspectives in CAR Treg immunotherapy aiming at clinical translation.
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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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Bekere I, de Oliveira Mann CC. FoxP3 forkhead dimer: Don’t swap me now. Immunity 2022; 55:1329-1331. [DOI: 10.1016/j.immuni.2022.07.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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Fueyo-González F, McGinty M, Ningoo M, Anderson L, Cantarelli C, Andrea Angeletti, Demir M, Llaudó I, Purroy C, Marjanovic N, Heja D, Sealfon SC, Heeger PS, Cravedi P, Fribourg M. Interferon-β acts directly on T cells to prolong allograft survival by enhancing regulatory T cell induction through Foxp3 acetylation. Immunity 2022; 55:459-474.e7. [PMID: 35148827 PMCID: PMC8917088 DOI: 10.1016/j.immuni.2022.01.011] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 06/18/2021] [Accepted: 01/13/2022] [Indexed: 12/19/2022]
Abstract
Type I interferons (IFNs) are pleiotropic cytokines with potent antiviral properties that also promote protective T cell and humoral immunity. Paradoxically, type I IFNs, including the widely expressed IFNβ, also have immunosuppressive properties, including promoting persistent viral infections and treating T-cell-driven, remitting-relapsing multiple sclerosis. Although associative evidence suggests that IFNβ mediates these immunosuppressive effects by impacting regulatory T (Treg) cells, mechanistic links remain elusive. Here, we found that IFNβ enhanced graft survival in a Treg-cell-dependent murine transplant model. Genetic conditional deletion models revealed that the extended allograft survival was Treg cell-mediated and required IFNβ signaling on T cells. Using an in silico computational model and analysis of human immune cells, we found that IFNβ directly promoted Treg cell induction via STAT1- and P300-dependent Foxp3 acetylation. These findings identify a mechanistic connection between the immunosuppressive effects of IFNβ and Treg cells, with therapeutic implications for transplantation, autoimmunity, and malignancy.
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Affiliation(s)
- Francisco Fueyo-González
- Division of Nephrology, Department of Medicine, Translational Transplant Research Center, Icahn School of Medicine at Mount Sinai, New York City, NY, USA; Immunology Institute Icahn School of Medicine at Mount Sinai, New York City, NY, USA
| | - Mitchell McGinty
- Carter Immunology Center, University of Virginia, Charlottesville, VA 22903, USA
| | - Mehek Ningoo
- Division of Nephrology, Department of Medicine, Translational Transplant Research Center, Icahn School of Medicine at Mount Sinai, New York City, NY, USA; Immunology Institute Icahn School of Medicine at Mount Sinai, New York City, NY, USA
| | - Lisa Anderson
- Division of Nephrology, Department of Medicine, Translational Transplant Research Center, Icahn School of Medicine at Mount Sinai, New York City, NY, USA; Immunology Institute Icahn School of Medicine at Mount Sinai, New York City, NY, USA
| | - Chiara Cantarelli
- UO Nefrologia, Azienda Ospedaliero-Universitaria Parma, Parma, Italy
| | - Andrea Angeletti
- Division of Nephrology, Dialysis, Transplantation, IRCCS Giannina Gaslini, Genoa, Italy
| | - Markus Demir
- Department of Anesthesiology, University of Cologne, Cologne, Germany
| | - Inés Llaudó
- Division of Nephrology, Department of Medicine, Translational Transplant Research Center, Icahn School of Medicine at Mount Sinai, New York City, NY, USA; Immunology Institute Icahn School of Medicine at Mount Sinai, New York City, NY, USA
| | - Carolina Purroy
- Department of Nephrology, Complejo Hospitalario de Navarra, Navarra, Spain
| | - Nada Marjanovic
- Immunology Institute Icahn School of Medicine at Mount Sinai, New York City, NY, USA; Department of Neurology, Icahn School of Medicine at Mount Sinai, New York City, NY, USA
| | - David Heja
- Division of Nephrology, Department of Medicine, Translational Transplant Research Center, Icahn School of Medicine at Mount Sinai, New York City, NY, USA; Immunology Institute Icahn School of Medicine at Mount Sinai, New York City, NY, USA
| | - Stuart C Sealfon
- Immunology Institute Icahn School of Medicine at Mount Sinai, New York City, NY, USA; Department of Neurology, Icahn School of Medicine at Mount Sinai, New York City, NY, USA
| | - Peter S Heeger
- Division of Nephrology, Department of Medicine, Translational Transplant Research Center, Icahn School of Medicine at Mount Sinai, New York City, NY, USA; Immunology Institute Icahn School of Medicine at Mount Sinai, New York City, NY, USA
| | - Paolo Cravedi
- Division of Nephrology, Department of Medicine, Translational Transplant Research Center, Icahn School of Medicine at Mount Sinai, New York City, NY, USA; Immunology Institute Icahn School of Medicine at Mount Sinai, New York City, NY, USA
| | - Miguel Fribourg
- Division of Nephrology, Department of Medicine, Translational Transplant Research Center, Icahn School of Medicine at Mount Sinai, New York City, NY, USA; Immunology Institute Icahn School of Medicine at Mount Sinai, New York City, NY, USA.
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TCR-induced FOXP3 expression by CD8 + T cells impairs their anti-tumor activity. Cancer Lett 2022; 528:45-58. [PMID: 34973390 DOI: 10.1016/j.canlet.2021.12.030] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 12/09/2021] [Accepted: 12/25/2021] [Indexed: 11/23/2022]
Abstract
Adoptive cell transfer therapy using CD8+ T lymphocytes showed promising results eradicating metastatic malignancies. However, several regulatory mechanisms limit its efficacy. We studied the role of the expression of the transcription factor FOXP3 on CD8+ T cell function and anti-tumor immunity. Here we show that suboptimal T cell receptor stimulation of CD8+ T cells upregulates FOXP3 in vitro. Similarly, CD8 T cells transferred into tumor-bearing mice upregulate FOXP3 in vivo. Cell-intrinsic loss of FOXP3 by CD8+ T cells resulted in improved functionality after TCR stimulation and better antitumor responses in vivo. Inhibition of the FOXP3/NFAT interaction likewise improved CD8+ T cell functionality. Transcriptomic analysis of cells after TCR stimulation revealed an enrichment of genes implicated in the response to IFN-γ, IFN-α, inflammatory response, IL-6/JAK/STAT, G2M checkpoint and IL-2/STAT signaling in FOXP3-deficient CD8+ T cells with respect to FOXP3-wt CD8+ T cells. Our results suggest that transient expression of FOXP3 by CD8+ T cells in the tumor microenvironment restrains their anti-tumor activity, with clear implications for improving T cell responses during immunotherapy.
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K 2P18.1 translates T cell receptor signals into thymic regulatory T cell development. Cell Res 2022; 32:72-88. [PMID: 34702947 PMCID: PMC8547300 DOI: 10.1038/s41422-021-00580-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Accepted: 08/25/2021] [Indexed: 02/07/2023] Open
Abstract
It remains largely unclear how thymocytes translate relative differences in T cell receptor (TCR) signal strength into distinct developmental programs that drive the cell fate decisions towards conventional (Tconv) or regulatory T cells (Treg). Following TCR activation, intracellular calcium (Ca2+) is the most important second messenger, for which the potassium channel K2P18.1 is a relevant regulator. Here, we identify K2P18.1 as a central translator of the TCR signal into the thymus-derived Treg (tTreg) selection process. TCR signal was coupled to NF-κB-mediated K2P18.1 upregulation in tTreg progenitors. K2P18.1 provided the driving force for sustained Ca2+ influx that facilitated NF-κB- and NFAT-dependent expression of FoxP3, the master transcription factor for Treg development and function. Loss of K2P18.1 ion-current function induced a mild lymphoproliferative phenotype in mice, with reduced Treg numbers that led to aggravated experimental autoimmune encephalomyelitis, while a gain-of-function mutation in K2P18.1 resulted in increased Treg numbers in mice. Our findings in human thymus, recent thymic emigrants and multiple sclerosis patients with a dominant-negative missense K2P18.1 variant that is associated with poor clinical outcomes indicate that K2P18.1 also plays a role in human Treg development. Pharmacological modulation of K2P18.1 specifically modulated Treg numbers in vitro and in vivo. Finally, we identified nitroxoline as a K2P18.1 activator that led to rapid and reversible Treg increase in patients with urinary tract infections. Conclusively, our findings reveal how K2P18.1 translates TCR signals into thymic T cell fate decisions and Treg development, and provide a basis for the therapeutic utilization of Treg in several human disorders.
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Bustamante A, Rivera R, Floor M, Babul J, Baez M. Single-molecule optical tweezers reveals folding steps of the domain swapping mechanism of a protein. Biophys J 2021; 120:4809-4818. [PMID: 34555362 PMCID: PMC8595740 DOI: 10.1016/j.bpj.2021.09.026] [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: 12/14/2020] [Revised: 05/15/2021] [Accepted: 09/15/2021] [Indexed: 11/18/2022] Open
Abstract
Domain swapping is a mechanism of protein oligomerization by which two or more subunits exchange structural elements to generate an intertwined complex. Numerous studies support a diversity of swapping mechanisms in which structural elements can be exchanged at different stages of the folding pathway of a subunit. Here, we used single-molecule optical tweezers technique to analyze the swapping mechanism of the forkhead DNA-binding domain of human transcription factor FoxP1. FoxP1 populates folded monomers in equilibrium with a swapped dimer. We generated a fusion protein linking two FoxP1 domains in tandem to obtain repetitive mechanical folding and unfolding trajectories. Thus, by stretching the same molecule several times, we detected either the independent folding of each domain or the elusive swapping step between domains. We found that a swapped dimer can be formed directly from fully or mostly folded monomer. In this situation, the interaction between the monomers in route to the domain-swapped dimer is the rate-limiting step. This approach is a useful strategy to test the different proposed domain swapping mechanisms for proteins with relevant physiological functions.
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Affiliation(s)
- Andres Bustamante
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Santiago, Chile
| | - Rodrigo Rivera
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Santiago, Chile
| | - Martin Floor
- Bioinformatics and Medical Statistics Group, Faculty of Science and Technology, Universitat de Vic - Universitat Central de Catalunya, Vic, Spain; Department of Basic Sciences, Faculty of Medicine and Health Sciences, Universitat Internacional de Catalunya, Sant Cugat del Vallès, Spain
| | - Jorge Babul
- Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Mauricio Baez
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Santiago, Chile.
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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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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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Hori S, Murakami R. The adaptability of regulatory T cells and Foxp3. Int Immunol 2021; 33:803-807. [PMID: 34297100 DOI: 10.1093/intimm/dxab045] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Accepted: 07/22/2021] [Indexed: 12/11/2022] Open
Abstract
Regulatory T (Treg) cells that express the lineage-defining transcription factor Foxp3 play a pivotal role in establishing and maintaining immune and tissue homeostasis. Foxp3 serves as a highly connected "hub", interacting with numerous genomic sites and partner proteins, in the molecular network that orchestrates multiple facets of Treg cell differentiation and function. Treg cells are distributed throughout the body from lymphoid tissues to most non-lymphoid tissues, where they exert anti-inflammatory and protective functions appropriate for the tissue and immune environment. They are thus capable of adapting to diverse and changing environments by dynamically integrating extrinsic cues with the intrinsic molecular network. In this review, we discuss recent advances in our understanding of the cell-intrinsic and -extrinsic mechanisms underlying the adaptability of Treg cells and we propose a crucial role for the Foxp3-centered molecular network, which operates in a multimodal and adaptive manner in response to environmental signals.
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Affiliation(s)
- Shohei Hori
- Laboratory of Immunology and Microbiology, Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Ryuichi Murakami
- Laboratory of Immunology and Microbiology, Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
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Hernández Vásquez MN, Ulvmar MH, González-Loyola A, Kritikos I, Sun Y, He L, Halin C, Petrova TV, Mäkinen T. Transcription factor FOXP2 is a flow-induced regulator of collecting lymphatic vessels. EMBO J 2021; 40:e107192. [PMID: 33934370 PMCID: PMC8204859 DOI: 10.15252/embj.2020107192] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 03/26/2021] [Accepted: 03/30/2021] [Indexed: 12/26/2022] Open
Abstract
The lymphatic system is composed of a hierarchical network of fluid absorbing lymphatic capillaries and transporting collecting vessels. Despite distinct functions and morphologies, molecular mechanisms that regulate the identity of the different vessel types are poorly understood. Through transcriptional analysis of murine dermal lymphatic endothelial cells (LECs), we identified Foxp2, a member of the FOXP family of transcription factors implicated in speech development, as a collecting vessel signature gene. FOXP2 expression was induced after initiation of lymph flow in vivo and upon shear stress on primary LECs in vitro. Loss of FOXC2, the major flow-responsive transcriptional regulator of lymphatic valve formation, abolished FOXP2 induction in vitro and in vivo. Genetic deletion of Foxp2 in mice using the endothelial-specific Tie2-Cre or the tamoxifen-inducible LEC-specific Prox1-CreERT2 line resulted in enlarged collecting vessels and defective valves characterized by loss of NFATc1 activity. Our results identify FOXP2 as a new flow-induced transcriptional regulator of collecting lymphatic vessel morphogenesis and highlight the existence of unique transcription factor codes in the establishment of vessel-type-specific endothelial cell identities.
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Affiliation(s)
| | - Maria H Ulvmar
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Alejandra González-Loyola
- Vascular and Tumor Biology Laboratory, Department of Oncology UNIL CHUV, Ludwig Institute for Cancer Research Lausanne, Lausanne, Switzerland
| | - Ioannis Kritikos
- Institute of Pharmaceutical Sciences, ETH Zürich, Zürich, Switzerland
| | - Ying Sun
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Liqun He
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Cornelia Halin
- Institute of Pharmaceutical Sciences, ETH Zürich, Zürich, Switzerland
| | - Tatiana V Petrova
- Vascular and Tumor Biology Laboratory, Department of Oncology UNIL CHUV, Ludwig Institute for Cancer Research Lausanne, Lausanne, Switzerland
| | - Taija Mäkinen
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
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Li J, Dai S, Chen X, Liang X, Qu L, Jiang L, Guo M, Zhou Z, Wei H, Zhang H, Chen Z, Chen L, Chen Y. Mechanism of forkhead transcription factors binding to a novel palindromic DNA site. Nucleic Acids Res 2021; 49:3573-3583. [PMID: 33577686 PMCID: PMC8034652 DOI: 10.1093/nar/gkab086] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Revised: 01/21/2021] [Accepted: 02/02/2021] [Indexed: 12/15/2022] Open
Abstract
Forkhead transcription factors bind a canonical consensus DNA motif, RYAAAYA (R = A/G, Y = C/T), as a monomer. However, the molecular mechanisms by which forkhead transcription factors bind DNA as a dimer are not well understood. In this study, we show that FOXO1 recognizes a palindromic DNA element DIV2, and mediates transcriptional regulation. The crystal structure of FOXO1/DIV2 reveals that the FOXO1 DNA binding domain (DBD) binds the DIV2 site as a homodimer. The wing1 region of FOXO1 mediates the dimerization, which enhances FOXO1 DNA binding affinity and complex stability. Further biochemical assays show that FOXO3, FOXM1 and FOXI1 also bind the DIV2 site as homodimer, while FOXC2 can only bind this site as a monomer. Our structural, biochemical and bioinformatics analyses not only provide a novel mechanism by which FOXO1 binds DNA as a homodimer, but also shed light on the target selection of forkhead transcription factors.
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Affiliation(s)
- 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
| | - 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
| | - 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
| | - Xujun Liang
- 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
| | - Lingzhi 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
| | - Longying Jiang
- 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
| | - Zhan Zhou
- 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
| | - Hudie Wei
- 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
| | - 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
| | - Lin Chen
- Molecular and Computational Biology Program, Department of Biological Sciences and Department of Chemistry, University of Southern California, Los Angeles, California 90089, United States
| | - 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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Ben-Skowronek I. IPEX Syndrome: Genetics and Treatment Options. Genes (Basel) 2021; 12:323. [PMID: 33668198 PMCID: PMC7995986 DOI: 10.3390/genes12030323] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 02/17/2021] [Accepted: 02/19/2021] [Indexed: 12/03/2022] Open
Abstract
(1) Background: IPEX (immune dysregulation, polyendocrinopathy, enteropathy, X-linked) syndrome characterizes a complex autoimmune reaction beginning in the perinatal period, caused by a dysfunction of the transcription factor forkhead box P3 (FOXP3). (2) Objectives: Studies have shown the clinical, immunological, and molecular heterogeneity of patients with IPEX syndrome. The symptoms, treatment, and survival were closely connected to the genotype of the IPEX syndrome. Recognition of the kind of mutation is important for the diagnostics of IPEX syndrome in newborns and young infants, as well as in prenatal screening. The method of choice for treatment is hematopoietic stem cell transplantation and immunosuppressive therapy. In children, supportive therapy for refractory diarrhea is very important, as well as replacement therapy of diabetes mellitus type 1 (DMT1) and other endocrinopathies. In the future, genetic engineering methods may be of use in the successful treatment of IPEX syndrome. (3) Conclusions: The genetic defects determine a diagnostic approach and prognosis, making the knowledge of the genetics of IPEX syndrome fundamental to introducing novel treatment methods.
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MESH Headings
- Allografts
- Animals
- Diabetes Mellitus, Type 1/congenital
- Diabetes Mellitus, Type 1/diagnosis
- Diabetes Mellitus, Type 1/genetics
- Diabetes Mellitus, Type 1/metabolism
- Diabetes Mellitus, Type 1/therapy
- Diarrhea/diagnosis
- Diarrhea/genetics
- Diarrhea/metabolism
- Diarrhea/therapy
- Female
- Forkhead Transcription Factors/genetics
- Forkhead Transcription Factors/metabolism
- Genetic Diseases, X-Linked/diagnosis
- Genetic Diseases, X-Linked/genetics
- Genetic Diseases, X-Linked/metabolism
- Genetic Diseases, X-Linked/therapy
- Hematopoietic Stem Cell Transplantation
- Humans
- Immune System Diseases/congenital
- Immune System Diseases/diagnosis
- Immune System Diseases/genetics
- Immune System Diseases/metabolism
- Immune System Diseases/therapy
- Infant
- Infant, Newborn
- Male
- Mutation
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Affiliation(s)
- Iwona Ben-Skowronek
- Department of Pediatric Endocrinology and Diabetology, Medical University, 20-093 Lublin, Poland
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Searching for Peptide Inhibitors of T Regulatory Cell Activity by Targeting Specific Domains of FOXP3 Transcription Factor. Biomedicines 2021; 9:biomedicines9020197. [PMID: 33671179 PMCID: PMC7922534 DOI: 10.3390/biomedicines9020197] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 02/13/2021] [Accepted: 02/14/2021] [Indexed: 12/03/2022] Open
Abstract
(1) Background: The ability of cancer cells to evade the immune system is due in part to their capacity to induce and recruit T regulatory cells (Tregs) to the tumor microenvironment. Strategies proposed to improve antitumor immunity by depleting Tregs generally lack specificity and raise the possibility of autoimmunity. Therefore, we propose to control Tregs by their functional inactivation rather than depletion. Tregs are characterized by the expression of the Forkhead box protein 3 (FOXP3) transcription factor, which is considered their “master regulator”. Its interaction with DNA is assisted primarily by its interaction with other proteins in the so-called “Foxp3 interactome”, which elicits much of the characteristic Treg cell transcriptional signature. We speculated that the disruption of such a protein complex by using synthetic peptides able to bind Foxp3 might have an impact on the functionality of Treg cells and thus have a therapeutic potential in cancer treatment. (2) Methods: By using a phage-displayed peptide library, or short synthetic peptides encompassing Foxp3 fragments, or by studying the crystal structure of the Foxp3:NFAT complex, we have identified a series of peptides that are able to bind Foxp3 and inhibit Treg activity. (3) Results: We identified some peptides encompassing fragments of the leuzin zipper or the C terminal domain of Foxp3 with the capacity to inhibit Treg activity in vitro. The acetylation/amidation of linear peptides, head-to-tail cyclization, the incorporation of non-natural aminoacids, or the incorporation of cell-penetrating peptide motifs increased in some cases the Foxp3 binding capacity and Treg inhibitory activity of the identified peptides. Some of them have shown antitumoral activity in vivo. (4) Conclusions: Synthetic peptides constitute an alternative to inhibit Foxp3 protein–protein interactions intracellularly and impair Treg immunosuppressive activity. These peptides might be considered as potential hit compounds on the design of new immunotherapeutic approaches against cancer.
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Kim DH, Kim HY, Cho S, Yoo SJ, Kim WJ, Yeon HR, Choi K, Choi JM, Kang SW, Lee WW. Induction of the IL-1RII decoy receptor by NFAT/FOXP3 blocks IL-1β-dependent response of Th17 cells. eLife 2021; 10:61841. [PMID: 33507149 PMCID: PMC7872515 DOI: 10.7554/elife.61841] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Accepted: 01/28/2021] [Indexed: 12/29/2022] Open
Abstract
Derived from a common precursor cell, the balance between Th17 and Treg cells must be maintained within immune system to prevent autoimmune diseases. IL-1β-mediated IL-1 receptor (IL-1R) signaling is essential for Th17-cell biology. Fine-tuning of IL-1R signaling is controlled by two receptors, IL-1RI and IL-RII, IL-1R accessory protein, and IL-1R antagonist. We demonstrate that the decoy receptor, IL-1RII, is important for regulating IL-17 responses in TCR-stimulated CD4+ T cells expressing functional IL-1RI via limiting IL-1β responsiveness. IL-1RII expression is regulated by NFAT via its interaction with Foxp3. The NFAT/FOXP3 complex binds to the IL-1RII promoter and is critical for its transcription. Additionally, IL-1RII expression is dysregulated in CD4+ T cells from patients with rheumatoid arthritis. Thus, differential expression of IL-1Rs on activated CD4+ T cells defines unique immunological features and a novel molecular mechanism underlies IL-1RII expression. These findings shed light on the modulatory effects of IL-1RII on Th17 responses.
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Affiliation(s)
- Dong Hyun Kim
- Laboratory of Autoimmunity and Inflammation (LAI), Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Hee Young Kim
- Laboratory of Autoimmunity and Inflammation (LAI), Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Republic of Korea.,Department of Microbiology and Immunology, Seoul National University College of Medicine, Seoul, Republic of Korea.,Cancer Research Institute and Institute of Infectious Diseases, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Sunjung Cho
- Department of Microbiology and Immunology, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Su-Jin Yoo
- Department of Internal Medicine, Chungnam National University School of Medicine, 282 Munhwa-ro, Jung-gu, Daejeon, Republic of Korea
| | - Won-Ju Kim
- Department of Life Science, College of Natural Sciences and Research Institute for Natural Sciences, Hanyang University, Seoul, Republic of Korea
| | - Hye Ran Yeon
- Department of Biochemistry and Molecular Biology, Department of Biomedical Sciences, and Cancer Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Kyungho Choi
- Department of Biochemistry and Molecular Biology, Department of Biomedical Sciences, and Cancer Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Je-Min Choi
- Department of Life Science, College of Natural Sciences and Research Institute for Natural Sciences, Hanyang University, Seoul, Republic of Korea
| | - Seong Wook Kang
- Department of Internal Medicine, Chungnam National University School of Medicine, 282 Munhwa-ro, Jung-gu, Daejeon, Republic of Korea
| | - Won-Woo Lee
- Laboratory of Autoimmunity and Inflammation (LAI), Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Republic of Korea.,Department of Microbiology and Immunology, Seoul National University College of Medicine, Seoul, Republic of Korea.,Cancer Research Institute and Institute of Infectious Diseases, Seoul National University College of Medicine, Seoul, Republic of Korea.,Ischemic/Hypoxic Disease Institute, Seoul National University College of Medicine; Seoul National University Hospital Biomedical Research Institute, Seoul, Republic of Korea
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The influence of various regions of the FOXP2 sequence on its structure and DNA-binding function. Biosci Rep 2021; 41:227301. [PMID: 33319247 PMCID: PMC7789814 DOI: 10.1042/bsr20202128] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 12/09/2020] [Accepted: 12/11/2020] [Indexed: 12/18/2022] Open
Abstract
FOX proteins are a superfamily of transcription factors which share a DNA-binding domain referred to as the forkhead domain. Our focus is on the FOXP subfamily members, which are involved in language and cognition amongst other things. The FOXP proteins contain a conserved zinc finger and a leucine zipper motif in addition to the forkhead domain. The remainder of the sequence is predicted to be unstructured and includes an acidic C-terminal tail. In the present study, we aim to investigate how both the structured and unstructured regions of the sequence cooperate so as to enable FOXP proteins to perform their function. We do this by studying the effect of these regions on both oligomerisation and DNA binding. Structurally, the FOXP proteins appear to be comparatively globular with a high proportion of helical structure. The proteins multimerise via the leucine zipper, and the stability of the multimers is controlled by the unstructured interlinking sequence including the acid rich tail. FOXP2 is more compact than FOXP1, has a greater propensity to form higher order oligomers, and binds DNA with stronger affinity. We conclude that while the forkhead domain is necessary for DNA binding, the affinity of the binding event is attributable to the leucine zipper, and the unstructured regions play a significant role in the specificity of binding. The acid rich tail forms specific contacts with the forkhead domain which may influence oligomerisation and DNA binding, and therefore the acid rich tail may play an important regulatory role in FOXP transcription.
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Wright WE, Li C, Zheng CX, Tucker HO. FOXP1 Interacts with MyoD to Repress its Transcription and Myoblast Conversion. JOURNAL OF CELLULAR SIGNALING 2021; 2:9-26. [PMID: 33554216 PMCID: PMC7861563] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Abstract
Forkhead transcription factors (TFs) often dimerize outside their extensive family, whereas bHLH transcription factors typically dimerize with E12/E47. Based on structural similarities, we predicted that a member of the former, Forkhead Box P1 (FOXP1), might heterodimerize with a member of the latter, MYOD1 (MyoD). Data shown here support this hypothesis and further demonstrate the specificity of this forkhead/myogenic interaction among other myogenic regulatory factors. We found that FOXP1-MyoD heterodimerization compromises the ability of MyoD to bind to E-boxes and to transactivate E box- containing promoters. We observed that FOXP1 is required for the full ability of MyoD to convert fibroblasts into myotubules. We provide a model in which FOXP1 displaces ID and E12/E47 to repress MyoD during the proliferative phase of myoblast differentiation. These data identify FOXP1 as a hitherto unsuspected transcriptional repressor of MyoD. We suggest that isolation of paired E-box and forkhead sites within 1 turn helical spacings provides potential for cooperative interactions among heretofore distinct classes of transcription factors.
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Affiliation(s)
- Woodring E. Wright
- Department of Cell Biology, UT Southwestern Medical School,
Dallas TX 75235, USA
| | - Chuan Li
- Department of Microbiology, University of Texas
Southwestern Medical Center, Dallas TX 75235, USA
| | - Chang-xue Zheng
- Department of Molecular Biosciences, the University of
Texas at Austin, Austin TX 78712, USA
| | - Haley O. Tucker
- Department of Molecular Biosciences, the University of
Texas at Austin, Austin TX 78712, USA,Correspondence should be addressed to Haley O.
Tucker;
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41
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Grover P, Goel PN, Piccirillo CA, Greene MI. FOXP3 and Tip60 Structural Interactions Relevant to IPEX Development Lead to Potential Therapeutics to Increase FOXP3 Dependent Suppressor T Cell Functions. Front Pediatr 2021; 9:607292. [PMID: 33614551 PMCID: PMC7888439 DOI: 10.3389/fped.2021.607292] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Accepted: 01/05/2021] [Indexed: 12/21/2022] Open
Abstract
Regulatory T (Treg) cells play a role in the maintenance of immune homeostasis and are critical mediators of immune tolerance. The Forkhead box P3 (FOXP3) protein acts as a regulator for Treg development and function. Mutations in the FOXP3 gene can lead to autoimmune diseases such as Immunodysregulation, polyendocrinopathy, enteropathy, and X-linked (IPEX) syndrome in humans, often resulting in death within the first 2 years of life and a scurfy like phenotype in Foxp3 mutant mice. We discuss biochemical features of the FOXP3 ensemble including its regulation at various levels (epigenetic, transcriptional, and post-translational modifications) and molecular functions. The studies also highlight the interactions of FOXP3 and Tat-interacting protein 60 (Tip60), a principal histone acetylase enzyme that acetylates FOXP3 and functions as an essential subunit of the FOXP3 repression ensemble complex. Lastly, we have emphasized the role of allosteric modifiers that help stabilize FOXP3:Tip60 interactions and discuss targeting this interaction for the therapeutic manipulation of Treg activity.
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Affiliation(s)
- Payal Grover
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Peeyush N Goel
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Ciriaco A Piccirillo
- Department of Microbiology and Immunology, McGill University, Montréal, QC, Canada.,Program in Infectious Diseases and Immunology in Global Health, The Research Institute of the McGill University Health Centre, Montréal, QC, Canada.,Centre of Excellence in Translational Immunology (CETI), Montréal, QC, Canada
| | - Mark I Greene
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
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42
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Medina E, Villalobos P, Hamilton GL, Komives EA, Sanabria H, Ramírez-Sarmiento CA, Babul J. Intrinsically Disordered Regions of the DNA-Binding Domain of Human FoxP1 Facilitate Domain Swapping. J Mol Biol 2020; 432:5411-5429. [PMID: 32735805 PMCID: PMC7663421 DOI: 10.1016/j.jmb.2020.07.017] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Revised: 07/21/2020] [Accepted: 07/22/2020] [Indexed: 01/01/2023]
Abstract
Forkhead box P (FoxP) proteins are unique transcription factors that spatiotemporally regulate gene expression by tethering two chromosome loci together via functional domain-swapped dimers formed through their DNA-binding domains. Further, the differential kinetics on this dimerization mechanism underlie an intricate gene regulation network at physiological conditions. Nonetheless, poor understanding of the structural dynamics and steps of the association process impedes to link the functional domain swapping to human-associated diseases. Here, we have characterized the DNA-binding domain of human FoxP1 by integrating single-molecule Förster resonance energy transfer and hydrogen-deuterium exchange mass spectrometry data with molecular dynamics simulations. Our results confirm the formation of a previously postulated domain-swapped (DS) FoxP1 dimer in solution and reveal the presence of highly populated, heterogeneous, and locally disordered dimeric intermediates along the dimer dissociation pathway. The unique features of FoxP1 provide a glimpse of how intrinsically disordered regions can facilitate domain swapping oligomerization and other tightly regulated association mechanisms relevant in biological processes.
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Affiliation(s)
- Exequiel Medina
- Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Casilla 653, Santiago 7800003, Chile
| | - Pablo Villalobos
- Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Casilla 653, Santiago 7800003, Chile
| | - George L Hamilton
- Department of Physics & Astronomy, Clemson University, Clemson, SC 29634, USA
| | - Elizabeth A Komives
- Department of Chemistry & Biochemistry, University of California San Diego, La Jolla, CA, USA
| | - Hugo Sanabria
- Department of Physics & Astronomy, Clemson University, Clemson, SC 29634, USA.
| | - César A Ramírez-Sarmiento
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile; Millennium Institute for Integrative Biology (iBio), Santiago, Chile.
| | - Jorge Babul
- Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Casilla 653, Santiago 7800003, Chile.
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43
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Bartalucci N, Guglielmelli P, Vannucchi AM. Polycythemia vera: the current status of preclinical models and therapeutic targets. Expert Opin Ther Targets 2020; 24:615-628. [PMID: 32366208 DOI: 10.1080/14728222.2020.1762176] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
INTRODUCTION Polycythemia vera (PV) is the most common myeloproliferative neoplasm (MPN). PV is characterized by erythrocytosis, leukocytosis, thrombocytosis, increased hematocrit, and hemoglobin in the peripheral blood. Splenomegaly and myelofibrosis often occur in PV patients. Almost all PV patients harbor a mutation in the JAK2 gene, mainly represented by the JAK2V617F point mutation. AREAS COVERED This article examines the recent in vitro and in vivo available models of PV and moreover, it offers insights on emerging biomarkers and therapeutic targets. The evidence from mouse models, resembling a PV-like phenotype generated by different technical approaches, is discussed. The authors searched PubMed, books, and clinicaltrials.gov for original and review articles and drugs development status including the terms Myeloproliferative Neoplasms, Polycythemia Vera, erythrocytosis, hematocrit, splenomegaly, bone marrow fibrosis, JAK2V617F, Hematopoietic Stem Cells, MPN cytoreductive therapy, JAK2 inhibitor, histone deacetylase inhibitor, PV-like phenotype, JAK2V617F BMT, transgenic JAK2V617F mouse, JAK2 physiologic promoter. EXPERT OPINION Preclinical models of PV are valuable tools for enabling an understanding of the pathophysiology and the molecular mechanisms of the disease. These models provide new biological insights on the contribution of concomitant mutations and the efficacy of novel drugs in a 'more faithful' setting. This may facilitate an enhanced understanding of pathogenetic mechanisms and targeted therapy.
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Affiliation(s)
- Niccolò Bartalucci
- Department of Experimental and Clinical Medicine, Center Research and Innovation of Myeloproliferative Neoplasms - CRIMM, Azienda Ospedaliera Universitaria Careggi, University of Florence , Florence, Italy
| | - Paola Guglielmelli
- Department of Experimental and Clinical Medicine, Center Research and Innovation of Myeloproliferative Neoplasms - CRIMM, Azienda Ospedaliera Universitaria Careggi, University of Florence , Florence, Italy
| | - Alessandro M Vannucchi
- Department of Experimental and Clinical Medicine, Center Research and Innovation of Myeloproliferative Neoplasms - CRIMM, Azienda Ospedaliera Universitaria Careggi, University of Florence , Florence, Italy
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Shi L, Peng P, Zheng J, Wang Q, Tian Z, Wang H, Li T. I-Motif/miniduplex hybrid structures bind benzothiazole dyes with unprecedented efficiencies: a generic light-up system for label-free DNA nanoassemblies and bioimaging. Nucleic Acids Res 2020; 48:1681-1690. [PMID: 31950160 PMCID: PMC7039006 DOI: 10.1093/nar/gkaa020] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Revised: 12/17/2019] [Accepted: 01/06/2020] [Indexed: 12/21/2022] Open
Abstract
I-motif DNAs have been widely employed as robust modulating components to construct reconfigurable DNA nanodevices that function well in acidic cellular environments. However, they generally display poor interactivity with fluorescent ligands under these complex conditions, illustrating a major difficulty in utilizing i-motifs as the light-up system for label-free DNA nanoassemblies and bioimaging. Towards addressing this challenge, here we devise new types of i-motif/miniduplex hybrid structures that display an unprecedentedly high interactivity with commonly-used benzothiazole dyes (e.g. thioflavin T). A well-chosen tetranucleotide, whose optimal sequence depends on the used ligand, is appended to the 5′-terminals of diverse i-motifs and forms a minimal parallel duplex thereby creating a preferential site for binding ligands, verified by molecular dynamics simulation. In this way, the fluorescence of ligands can be dramatically enhanced by the i-motif/miniduplex hybrids under complex physiological conditions. This provides a generic light-up system with a high signal-to-background ratio for programmable DNA nanoassemblies, illustrated through utilizing it for a pH-driven framework nucleic acid nanodevice manipulated in acidic cellular membrane microenvironments. It enables label-free fluorescence bioimaging in response to extracellular pH change.
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Affiliation(s)
- Lili Shi
- Department of Chemistry, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui 230026, China
| | - Pai Peng
- Department of Chemistry, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui 230026, China
| | - Jiao Zheng
- Department of Chemistry, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui 230026, China
| | - Qiwei Wang
- Department of Chemistry, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui 230026, China
| | - Zhijin Tian
- Department of Chemistry, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui 230026, China
| | - Huihui Wang
- Department of Chemistry, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui 230026, China
| | - Tao Li
- Department of Chemistry, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui 230026, China
- To whom correspondence should be addressed. Tel: +86 551 63601813;
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45
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Huang Q, Liu X, Zhang Y, Huang J, Li D, Li B. Molecular feature and therapeutic perspectives of immune dysregulation, polyendocrinopathy, enteropathy, X-linked syndrome. J Genet Genomics 2020; 47:17-26. [PMID: 32081609 DOI: 10.1016/j.jgg.2019.11.011] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Revised: 11/02/2019] [Accepted: 11/10/2019] [Indexed: 01/01/2023]
Abstract
Regulatory T (Treg) cells, a subtype of immunosuppressive CD4+ T cells, are vital for maintaining immune homeostasis in healthy people. Forkhead box protein P3 (FOXP3), a member of the forkhead-winged-helix family, is the pivotal transcriptional factor of Treg cells. The expression, post-translational modifications, and protein complex of FOXP3 present a great impact on the functional stability and immune plasticity of Treg cells in vivo. In particular, the mutation of FOXP3 can result in immune dysregulation, polyendocrinopathy, enteropathy, X-linked (IPEX) syndrome, which is a rare genetic disease mostly diagnosed in early childhood and can soon be fatal. IPEX syndrome is related to several manifestations, including dermatitis, enteropathy, type 1 diabetes, thyroiditis, and so on. Here, we summarize some recent findings on FOXP3 regulation and Treg cell function. We also review the current knowledge about the underlying mechanism of FOXP3 mutant-induced IPEX syndrome and some latest clinical prospects. At last, this review offers a novel insight into the role played by the FOXP3 complex in potential therapeutic applications in IPEX syndrome.
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Affiliation(s)
- Qianru Huang
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, Shanghai Jiao Tong University, Shanghai, 200025, China
| | - Xu Liu
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, Shanghai Jiao Tong University, Shanghai, 200025, China
| | - Yujia Zhang
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, Shanghai Jiao Tong University, Shanghai, 200025, China
| | - Jingyao Huang
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, Shanghai Jiao Tong University, Shanghai, 200025, China
| | - Dan Li
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, Shanghai Jiao Tong University, Shanghai, 200025, China.
| | - Bin Li
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, Shanghai Jiao Tong University, Shanghai, 200025, China.
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46
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Jin Y, Liang Z, Lou H. The Emerging Roles of Fox Family Transcription Factors in Chromosome Replication, Organization, and Genome Stability. Cells 2020; 9:cells9010258. [PMID: 31968679 PMCID: PMC7016735 DOI: 10.3390/cells9010258] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Revised: 01/13/2020] [Accepted: 01/14/2020] [Indexed: 12/13/2022] Open
Abstract
The forkhead box (Fox) transcription factors (TFs) are widespread from yeast to humans. Their mutations and dysregulation have been linked to a broad spectrum of malignant neoplasias. They are known as critical players in DNA repair, metabolism, cell cycle control, differentiation, and aging. Recent studies, especially those from the simple model eukaryotes, revealed unexpected contributions of Fox TFs in chromosome replication and organization. More importantly, besides functioning as a canonical TF in cell signaling cascades and gene expression, Fox TFs can directly participate in DNA replication and determine the global replication timing program in a transcription-independent mechanism. Yeast Fox TFs preferentially recruit the limiting replication factors to a subset of early origins on chromosome arms. Attributed to their dimerization capability and distinct DNA binding modes, Fkh1 and Fkh2 also promote the origin clustering and assemblage of replication elements (replication factories). They can mediate long-range intrachromosomal and interchromosomal interactions and thus regulate the four-dimensional chromosome organization. The novel aspects of Fox TFs reviewed here expand their roles in maintaining genome integrity and coordinating the multiple essential chromosome events. These will inevitably be translated to our knowledge and new treatment strategies of Fox TF-associated human diseases including cancer.
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Huang J, Wang S, Jia Y, Zhang Y, Dai X, Li B. Targeting FOXP3 complex ensemble in drug discovery. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2020; 121:143-168. [PMID: 32312420 DOI: 10.1016/bs.apcsb.2019.11.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Forkhead Box P3 (FOXP3) is a key transcriptional regulator of regulatory T cells (Tregs), especially for its function of immune suppression. The special immune suppression function of Tregs plays an important role in maintaining immune homeostasis, and is related to several diseases including cancer, and autoimmune diseases. At the same time, FOXP3 takes a place in a large transcriptional complex, whose stability and functions can be controlled by various post-translational modification. More and more researches have suggested that targeting FOXP3 or its partners might be a feasible solution to immunotherapy. In this review, we focus on the transcription factor FOXP3 in Tregs, Treg functions in diseases and the FOXP3 targets.
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Affiliation(s)
- Jingyao Huang
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Shuoyang Wang
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Yuxin Jia
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Yujia Zhang
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Xueyu Dai
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Bin Li
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, Shanghai Jiao Tong University, Shanghai, China
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Scherm MG, Daniel C. miRNA-Mediated Immune Regulation in Islet Autoimmunity and Type 1 Diabetes. Front Endocrinol (Lausanne) 2020; 11:606322. [PMID: 33329406 PMCID: PMC7731293 DOI: 10.3389/fendo.2020.606322] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 10/27/2020] [Indexed: 12/15/2022] Open
Abstract
The important role of microRNAs as major modulators of various physiological processes, including immune regulation and homeostasis, has been increasingly recognized. Consequently, aberrant miRNA expression contributes to the defective regulation of T cell development, differentiation, and function. This can result in immune activation and impaired tolerance mechanisms, which exert a cardinal function for the onset of islet autoimmunity and the progression to T1D. The specific impact of miRNAs for immune regulation and how miRNAs and their downstream targets are involved in the pathogenesis of islet autoimmunity and T1D has been investigated recently. These studies revealed that increased expression of individual miRNAs is involved in several layers of tolerance impairments, such as inefficient Treg induction and Treg instability. The targeted modulation of miRNAs using specific inhibitors, resulting in improved immune homeostasis, as well as improved methods for the targeting of miRNAs, suggest that miRNAs, especially in T cells, are a promising target for the reestablishment of immune tolerance.
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Affiliation(s)
- Martin G. Scherm
- Institute of Diabetes Research, Group Immune Tolerance in Type 1 Diabetes, Helmholtz Diabetes Center at Helmholtz Zentrum München, Munich, Germany
- Deutsches Zentrum für Diabetesforschung (DZD), Munich-Neuherberg, Germany
| | - Carolin Daniel
- Institute of Diabetes Research, Group Immune Tolerance in Type 1 Diabetes, Helmholtz Diabetes Center at Helmholtz Zentrum München, Munich, Germany
- Deutsches Zentrum für Diabetesforschung (DZD), Munich-Neuherberg, Germany
- Division of Clinical Pharmacology, Department of Medicine IV, Ludwig-Maximilians-Universität München, Munich, Germany
- *Correspondence: Carolin Daniel,
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Qiu Q, Yu X, Yao C, Hao Y, Fan L, Li C, Xu P, An G, Li Z, He Z. FOXP3 pathogenic variants cause male infertility through affecting the proliferation and apoptosis of human spermatogonial stem cells. Aging (Albany NY) 2019; 11:12581-12599. [PMID: 31855573 PMCID: PMC6949051 DOI: 10.18632/aging.102589] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Accepted: 11/26/2019] [Indexed: 12/11/2022]
Abstract
Genetic causes of male infertility that is associated with aging are largely unknown. This study was designed to identify novel pathogenic variants of FOXP3 gene causing azoospermia. One homozygous (c.155 G > T) pathogenic variant of FOXP3 was identified in nine non-obstructive azoospermia patients, and one heterozygous (c.691 C > A) of FOXP3 was found in one non-obstructive azoospermia patient. Pedigrees studies indicated that the homozygous (c.155 G > T) FOXP3 pathogenic variant was inherited, while heterozygous (c.691 C > A) FOXP3 pathogenic variant was acquired. Human testis carrying pathogenic variant exhibited abnormal spermatogenesis. FOXP3 protein was expressed at a lower level or undetected in spermatocytes of mutant testis of non-obstructive azoospermia patients compared to obstructive azoospermia patients. FOXP3 stimulated the proliferation and inhibited the apoptosis of human spermatogonial stem cells, and we further analyzed the targets of FOXP3. We have identified two new pathogenic variants of FOXP3 in non-obstructive azoospermia patients with high incidence, and FOXP3 silencing inhibits the proliferation and enhances the apoptosis of human spermatogonial stem cells. This study provides new insights into the etiology of azoospermia and offers novel pathogenic variants for gene targeting of male infertility.
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Affiliation(s)
- Qianqian Qiu
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Xing Yu
- Hunan Normal University School of Medicine, Changsha, Hunan, China
| | - Chencheng Yao
- Department of Andrology, The Center for Men's Health, Urologic Medical Center, Shanghai Key Laboratory of Reproductive Medicine, Shanghai General Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Yujun Hao
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Liqing Fan
- Institute of Reproductive and Stem Cell Engineering, School of Basic Medical Science, Central South University, Changsha, China.,Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha, China
| | - Chunyi Li
- Fertility Center, Shenyang Dongfang Jinghua Hospital, Shenyang, Liaoning, China
| | - Peng Xu
- Fertility Center, Shenyang Dongfang Jinghua Hospital, Shenyang, Liaoning, China
| | - Geng An
- Department of Reproductive Medicine, Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Zheng Li
- Department of Andrology, The Center for Men's Health, Urologic Medical Center, Shanghai Key Laboratory of Reproductive Medicine, Shanghai General Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Zuping He
- Hunan Normal University School of Medicine, Changsha, Hunan, China.,Renji-Med X Clinical Stem Cell Research Center, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,Shanghai Key Laboratory of Reproductive Medicine, Shanghai, China
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50
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Mulero MC, Wang VYF, Huxford T, Ghosh G. Genome reading by the NF-κB transcription factors. Nucleic Acids Res 2019; 47:9967-9989. [PMID: 31501881 PMCID: PMC6821244 DOI: 10.1093/nar/gkz739] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Revised: 08/05/2019] [Accepted: 08/21/2019] [Indexed: 12/25/2022] Open
Abstract
The NF-κB family of dimeric transcription factors regulates transcription by selectively binding to DNA response elements present within promoters or enhancers of target genes. The DNA response elements, collectively known as κB sites or κB DNA, share the consensus 5'-GGGRNNNYCC-3' (where R, Y and N are purine, pyrimidine and any nucleotide base, respectively). In addition, several DNA sequences that deviate significantly from the consensus have been shown to accommodate binding by NF-κB dimers. X-ray crystal structures of NF-κB in complex with diverse κB DNA have helped elucidate the chemical principles that underlie target selection in vitro. However, NF-κB dimers encounter additional impediments to selective DNA binding in vivo. Work carried out during the past decades has identified some of the barriers to sequence selective DNA target binding within the context of chromatin and suggests possible mechanisms by which NF-κB might overcome these obstacles. In this review, we first highlight structural features of NF-κB:DNA complexes and how distinctive features of NF-κB proteins and DNA sequences contribute to specific complex formation. We then discuss how native NF-κB dimers identify DNA binding targets in the nucleus with support from additional factors and how post-translational modifications enable NF-κB to selectively bind κB sites in vivo.
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Affiliation(s)
- Maria Carmen Mulero
- Department of Chemistry and Biochemistry, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Vivien Ya-Fan Wang
- Faculty of Health Sciences, University of Macau, Avenida da Universidade, Taipa, Macau SAR, China
| | - Tom Huxford
- Structural Biochemistry Laboratory, Department of Chemistry and Biochemistry, San Diego State University, 5500 Campanile Drive, San Diego, CA 92182, USA
| | - Gourisankar Ghosh
- Department of Chemistry and Biochemistry, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
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