1
|
Yao YM, Miodownik I, O'Hagan MP, Jbara M, Afek A. Deciphering the dynamic code: DNA recognition by transcription factors in the ever-changing genome. Transcription 2024:1-25. [PMID: 39033307 DOI: 10.1080/21541264.2024.2379161] [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: 03/15/2024] [Accepted: 07/03/2024] [Indexed: 07/23/2024] Open
Abstract
Transcription factors (TFs) intricately navigate the vast genomic landscape to locate and bind specific DNA sequences for the regulation of gene expression programs. These interactions occur within a dynamic cellular environment, where both DNA and TF proteins experience continual chemical and structural perturbations, including epigenetic modifications, DNA damage, mechanical stress, and post-translational modifications (PTMs). While many of these factors impact TF-DNA binding interactions, understanding their effects remains challenging and incomplete. This review explores the existing literature on these dynamic changes and their potential impact on TF-DNA interactions.
Collapse
Affiliation(s)
- Yumi Minyi Yao
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Irina Miodownik
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Michael P O'Hagan
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Muhammad Jbara
- School of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Ariel Afek
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot, Israel
| |
Collapse
|
2
|
Zhao B, Li Z, Yu S, Li T, Wang W, Liu R, Zhang B, Fang X, Shen Y, Han Q, Xu X, Wang K, Gong W, Li T, Li A, Zhou T, Li W, Li T. LEF1 enhances β-catenin transactivation through IDR-dependent liquid-liquid phase separation. Life Sci Alliance 2023; 6:e202302118. [PMID: 37657935 PMCID: PMC10474303 DOI: 10.26508/lsa.202302118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 08/23/2023] [Accepted: 08/23/2023] [Indexed: 09/03/2023] Open
Abstract
Wnt/β-catenin signaling plays a crucial role in cancer development, primarily activated by β-catenin forming a transcription complex with LEF/TCF in the nucleus and initiating the transcription of Wnt target genes. Here, we report that LEF1, a member of the LEF/TCF family, can form intrinsically disordered region (IDR)-dependent condensates with β-catenin both in vivo and in vitro, which is required for β-catenin-dependent transcription. Notably, LEF1 with disrupted IDR lost its promoting activity on tumor proliferation and metastasis, which can be restored by substituting with FUS IDR. Our findings provide new insight into the essential role of liquid-liquid phase separation in Wnt/β-catenin signaling and present a potential new target for cancer therapy.
Collapse
Affiliation(s)
- Bing Zhao
- National Center of Biomedical Analysis, Beijing, China
| | - Zhuoxin Li
- National Center of Biomedical Analysis, Beijing, China
| | - Shaoqing Yu
- School of Clinical Medicine, Tsinghua University, Beijing, China
| | - Tingting Li
- National Center of Biomedical Analysis, Beijing, China
- Nanhu Laboratory, Jiaxing, China
| | - Wen Wang
- National Center of Biomedical Analysis, Beijing, China
| | - Ran Liu
- National Center of Biomedical Analysis, Beijing, China
| | - Biyu Zhang
- National Center of Biomedical Analysis, Beijing, China
| | - Xiya Fang
- National Center of Biomedical Analysis, Beijing, China
| | - Yezhuang Shen
- National Center of Biomedical Analysis, Beijing, China
| | - Qiuying Han
- National Center of Biomedical Analysis, Beijing, China
- Nanhu Laboratory, Jiaxing, China
| | - Xin Xu
- National Center of Biomedical Analysis, Beijing, China
- Nanhu Laboratory, Jiaxing, China
| | - Kai Wang
- National Center of Biomedical Analysis, Beijing, China
- Nanhu Laboratory, Jiaxing, China
| | - Weili Gong
- National Center of Biomedical Analysis, Beijing, China
| | - Tao Li
- National Center of Biomedical Analysis, Beijing, China
- Nanhu Laboratory, Jiaxing, China
| | - Ailing Li
- National Center of Biomedical Analysis, Beijing, China
| | - Tao Zhou
- National Center of Biomedical Analysis, Beijing, China
- Nanhu Laboratory, Jiaxing, China
| | - Weihua Li
- National Center of Biomedical Analysis, Beijing, China
| | - Teng Li
- National Center of Biomedical Analysis, Beijing, China
- Nanhu Laboratory, Jiaxing, China
| |
Collapse
|
3
|
Hou Y, Yu W, Wu G, Wang Z, Leng S, Dong M, Li N, Chen L. Carcinogenesis promotion in oral squamous cell carcinoma: KDM4A complex-mediated gene transcriptional suppression by LEF1. Cell Death Dis 2023; 14:510. [PMID: 37553362 PMCID: PMC10409759 DOI: 10.1038/s41419-023-06024-3] [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: 02/22/2023] [Revised: 07/20/2023] [Accepted: 07/27/2023] [Indexed: 08/10/2023]
Abstract
Oral squamous cell carcinoma (OSCC) is the most prevalent cancer of the mouth, characterised by rapid progression and poor prognosis. Hence, an urgent need exists for the development of predictive targets for early diagnosis, prognosis determination, and clinical therapy. Dysregulation of lymphoid enhancer-binding factor 1 (LEF1), an important transcription factor involved in the Wnt-β-catenin pathway, contributes to the poor prognosis of OSCC. Herein, we aimed to explore the correlation between LEF1 and histone lysine demethylase 4 A (KDM4A). Results show that the KDM4A complex is recruited by LEF1 and specifically binds the LATS2 promoter region, thereby inhibiting its expression, and consequently promoting cell proliferation and impeding apoptosis in OSCC. We also established NOD/SCID mouse xenograft models using CAL-27 cells to conduct an in vivo analysis of the roles of LEF1 and KDM4A in tumour growth, and our findings show that cells stably suppressing LEF1 or KDM4A have markedly decreased tumour-initiating capacity. Overall, the results of this study demonstrate that LEF1 plays a pivotal role in OSCC development and has potential to serve as a target for early diagnosis and treatment of OSCC.
Collapse
Affiliation(s)
- Yiming Hou
- Department of Orthodontics, School and Hospital of Stomatology, Cheeloo College of Medicine, Shandong University & Shandong Key Laboratory of Oral Tissue Regeneration & Shandong Engineering Laboratory for Dental Materials and Oral Tissue Regeneration & Shandong Provincial Clinical Research Center for Oral Diseases, Jinan, Shandong, 250012, China
| | - Wenqian Yu
- Research Center of Translational Medicine, Central Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, 250013, P. R. China
- Department of Otolaryngology-Head and Neck Surgery, Shandong Provincial ENT Hospital, Shandong University, Jinan, Shandong, 250022, China
- Center of Clinical Laboratory, Shandong Second Provincial General Hospital, Jinan, Shandong, 250022, China
| | - Gaoyi Wu
- School of Stomatology, Heilongjiang Key Lab of Oral Biomedicine Materials and Clinical Application & Experimental Center for Stomatology Engineering, Jiamusi University, Jiamusi, Heilongjiang, 154007, China
| | - Zhaoling Wang
- Department of Oral and Maxillofacial Surgery, School and Hospital of Stomatology, Cheeloo College of Medicine, Shandong University & Shandong Key Laboratory of Oral Tissue Regeneration & Shandong Engineering Laboratory for Dental Materials and Oral Tissue Regeneration & Shandong Provincial Clinical Research Center for Oral Diseases, Jinan, Shandong, 250012, China
| | - Shuai Leng
- Research Center of Translational Medicine, Central Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, 250013, P. R. China
| | - Ming Dong
- School of Stomatology, Heilongjiang Key Lab of Oral Biomedicine Materials and Clinical Application & Experimental Center for Stomatology Engineering, Jiamusi University, Jiamusi, Heilongjiang, 154007, China
| | - Na Li
- Department of Otolaryngology-Head and Neck Surgery, Shandong Provincial ENT Hospital, Shandong University, Jinan, Shandong, 250022, China.
- Center of Clinical Laboratory, Shandong Second Provincial General Hospital, Jinan, Shandong, 250022, China.
| | - Lei Chen
- Department of Orthodontics, School and Hospital of Stomatology, Cheeloo College of Medicine, Shandong University & Shandong Key Laboratory of Oral Tissue Regeneration & Shandong Engineering Laboratory for Dental Materials and Oral Tissue Regeneration & Shandong Provincial Clinical Research Center for Oral Diseases, Jinan, Shandong, 250012, China.
| |
Collapse
|
4
|
Wang H, Bienz M, Yan XX, Xu W. Structural basis of the interaction between BCL9-Pygo and LDB-SSBP complexes in assembling the Wnt enhanceosome. Nat Commun 2023; 14:3702. [PMID: 37349336 PMCID: PMC10287724 DOI: 10.1038/s41467-023-39439-9] [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: 11/09/2022] [Accepted: 06/14/2023] [Indexed: 06/24/2023] Open
Abstract
The Wnt enhanceosome is responsible for transactivation of Wnt-responsive genes and a promising therapeutic target for treatment of numerous cancers with Adenomatous Polyposis Coli (APC) or β-catenin mutations. How the Wnt enhanceosome is assembled remains poorly understood. Here we show that B-cell lymphoma 9 protein (BCL9), Pygopus (Pygo), LIM domain-binding protein 1 (LDB1) and single-stranded DNA-binding protein (SSBP) form a stable core complex within the Wnt enhanceosome. Their mutual interactions rely on a highly conserved N-terminal asparagine proline phenylalanine (NPF) motif of Pygo, through which the BCL9-Pygo complex binds to the LDB-SSBP core complex. Our crystal structure of a ternary complex comprising the N-terminus of human Pygo2, LDB1 and SSBP2 reveals a single LDB1-SSBP2 complex binding simultaneously to two Pygo2 molecules via their NPF motifs. These interactions critically depend on the NPF motifs which bind to a deep groove formed between LDB1 and SSBP2, potentially constituting a binding site for drugs blocking Wnt/β-catenin signaling. Analysis of human cell lines lacking LDB or Pygo supports the functional relevance of the Pygo-LDB1-SSBP2 interaction for Wnt/β-catenin-dependent transcription.
Collapse
Affiliation(s)
- Hongyang Wang
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Mariann Bienz
- Medical Research Council Laboratory of Molecular Biology, CB2 0QH, Cambridge, United Kingdom
| | - Xiao-Xue Yan
- National Laboratory of Biomacromolecules, Chinese Academy of Sciences Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.
| | - Wenqing Xu
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China.
| |
Collapse
|
5
|
Zhang H, Liu C, Zhu D, Zhang Q, Li J. Medicinal Chemistry Strategies for the Development of Inhibitors Disrupting β-Catenin's Interactions with Its Nuclear Partners. J Med Chem 2023; 66:1-31. [PMID: 36583662 DOI: 10.1021/acs.jmedchem.2c01016] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Dysregulation of the Wnt/β-catenin signaling pathway is strongly associated with various aspects of cancer, including tumor initiation, proliferation, and metastasis as well as antitumor immunity, and presents a promising opportunity for cancer therapy. Wnt/β-catenin signaling activation increases nuclear dephosphorylated β-catenin levels, resulting in β-catenin binding to TCF and additional cotranscription factors, such as BCL9, CBP, and p300. Therefore, directly disrupting β-catenin's interactions with these nuclear partners holds promise for the effective and selective suppression of the aberrant activation of Wnt/β-catenin signaling. Herein, we summarize recent advances in biochemical techniques and medicinal chemistry strategies used to identify potent peptide-based and small-molecule inhibitors that directly disrupt β-catenin's interactions with its nuclear binding partners. We discuss the challenges involved in developing drug-like inhibitors that target the interactions of β-catenin and its nuclear binding partner into therapeutic agents.
Collapse
Affiliation(s)
- Hao Zhang
- School of Pharmacy, Fudan University, Shanghai 201203, China.,Novel Technology Center of Pharmaceutical Chemistry, Shanghai Institute of Pharmaceutical Industry Co., Ltd., China State Institute of Pharmaceutical Industry, Shanghai 201203, China
| | - Chenglong Liu
- School of Pharmacy, Fudan University, Shanghai 201203, China
| | - Di Zhu
- School of Pharmacy, Fudan University, Shanghai 201203, China.,Department of Pharmacology, School of Basic Medical Science, Fudan University, Shanghai 201100, China
| | - Qingwei Zhang
- Novel Technology Center of Pharmaceutical Chemistry, Shanghai Institute of Pharmaceutical Industry Co., Ltd., China State Institute of Pharmaceutical Industry, Shanghai 201203, China
| | - Jianqi Li
- Novel Technology Center of Pharmaceutical Chemistry, Shanghai Institute of Pharmaceutical Industry Co., Ltd., China State Institute of Pharmaceutical Industry, Shanghai 201203, China
| |
Collapse
|
6
|
The Role of PARP1 and PAR in ATP-Independent Nucleosome Reorganisation during the DNA Damage Response. Genes (Basel) 2022; 14:genes14010112. [PMID: 36672853 PMCID: PMC9859207 DOI: 10.3390/genes14010112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 12/22/2022] [Accepted: 12/23/2022] [Indexed: 12/31/2022] Open
Abstract
The functioning of the eukaryotic cell genome is mediated by sophisticated protein-nucleic-acid complexes, whose minimal structural unit is the nucleosome. After the damage to genomic DNA, repair proteins need to gain access directly to the lesion; therefore, the initiation of the DNA damage response inevitably leads to local chromatin reorganisation. This review focuses on the possible involvement of PARP1, as well as proteins acting nucleosome compaction, linker histone H1 and non-histone chromatin protein HMGB1. The polymer of ADP-ribose is considered the main regulator during the development of the DNA damage response and in the course of assembly of the correct repair complex.
Collapse
|
7
|
Yuan L, Roy B, Ratna P, Uhler C, Shivashankar GV. Lateral confined growth of cells activates Lef1 dependent pathways to regulate cell-state transitions. Sci Rep 2022; 12:17318. [PMID: 36243826 PMCID: PMC9569372 DOI: 10.1038/s41598-022-21596-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 09/29/2022] [Indexed: 01/10/2023] Open
Abstract
Long-term sustained mechano-chemical signals in tissue microenvironment regulate cell-state transitions. In recent work, we showed that laterally confined growth of fibroblasts induce dedifferentiation programs. However, the molecular mechanisms underlying such mechanically induced cell-state transitions are poorly understood. In this paper, we identify Lef1 as a critical somatic transcription factor for the mechanical regulation of de-differentiation pathways. Network optimization methods applied to time-lapse RNA-seq data identify Lef1 dependent signaling as potential regulators of such cell-state transitions. We show that Lef1 knockdown results in the down-regulation of fibroblast de-differentiation and that Lef1 directly interacts with the promoter regions of downstream reprogramming factors. We also evaluate the potential upstream activation pathways of Lef1, including the Smad4, Atf2, NFkB and Beta-catenin pathways, thereby identifying that Smad4 and Atf2 may be critical for Lef1 activation. Collectively, we describe an important mechanotransduction pathway, including Lef1, which upon activation, through progressive lateral cell confinement, results in fibroblast de-differentiation.
Collapse
Affiliation(s)
- Luezhen Yuan
- Division of Biology and Chemistry, Paul Scherrer Institut, 5232, Villigen, Switzerland
- Department of Health Sciences and Technology, ETH Zurich, 8092, Zurich, Switzerland
- Mechanobiology Institute, National University of Singapore, Singapore, 117411, Singapore
| | - Bibhas Roy
- Division of Biology and Chemistry, Paul Scherrer Institut, 5232, Villigen, Switzerland
- Mechanobiology Institute, National University of Singapore, Singapore, 117411, Singapore
- Institute of Molecular Oncology, Italian Foundation for Cancer Research, 20139, Milan, Italy
| | - Prasuna Ratna
- Mechanobiology Institute, National University of Singapore, Singapore, 117411, Singapore
| | - Caroline Uhler
- Massachusetts Institute of Technology, Cambridge, MA, USA
| | - G V Shivashankar
- Division of Biology and Chemistry, Paul Scherrer Institut, 5232, Villigen, Switzerland.
- Department of Health Sciences and Technology, ETH Zurich, 8092, Zurich, Switzerland.
- Mechanobiology Institute, National University of Singapore, Singapore, 117411, Singapore.
- Institute of Molecular Oncology, Italian Foundation for Cancer Research, 20139, Milan, Italy.
| |
Collapse
|
8
|
TCF-1 mediates chromatin intermingling during T cell development. Nat Immunol 2022; 23:1000-1001. [PMID: 35750761 DOI: 10.1038/s41590-022-01237-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
|
9
|
Wang W, Chandra A, Goldman N, Yoon S, Ferrari EK, Nguyen SC, Joyce EF, Vahedi G. TCF-1 promotes chromatin interactions across topologically associating domains in T cell progenitors. Nat Immunol 2022; 23:1052-1062. [PMID: 35726060 PMCID: PMC9728953 DOI: 10.1038/s41590-022-01232-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 05/05/2022] [Indexed: 12/12/2022]
Abstract
The high mobility group (HMG) transcription factor TCF-1 is essential for early T cell development. Although in vitro biochemical assays suggest that HMG proteins can serve as architectural elements in the assembly of higher-order nuclear organization, the contribution of TCF-1 on the control of three-dimensional (3D) genome structures during T cell development remains unknown. Here, we investigated the role of TCF-1 in 3D genome reconfiguration. Using gain- and loss-of-function experiments, we discovered that the co-occupancy of TCF-1 and the architectural protein CTCF altered the structure of topologically associating domains in T cell progenitors, leading to interactions between previously insulated regulatory elements and target genes at late stages of T cell development. The TCF-1-dependent gain in long-range interactions was linked to deposition of active enhancer mark H3K27ac and recruitment of the cohesin-loading factor NIPBL at active enhancers. These data indicate that TCF-1 has a role in controlling global genome organization during T cell development.
Collapse
Affiliation(s)
- Wenliang Wang
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA.,Institute for Immunology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA.,Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA.,Institute for Diabetes, Obesity and Metabolism, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Aditi Chandra
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA.,Institute for Immunology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA.,Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA.,Institute for Diabetes, Obesity and Metabolism, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Naomi Goldman
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA.,Institute for Immunology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA.,Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA.,Institute for Diabetes, Obesity and Metabolism, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Sora Yoon
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA.,Institute for Immunology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA.,Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA.,Institute for Diabetes, Obesity and Metabolism, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Emily K Ferrari
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA.,Institute for Immunology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA.,Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA.,Institute for Diabetes, Obesity and Metabolism, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Son C Nguyen
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA.,Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Eric F Joyce
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA.,Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Golnaz Vahedi
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA. .,Institute for Immunology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA. .,Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA. .,Institute for Diabetes, Obesity and Metabolism, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA. .,Abramson Family Cancer Research Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA.
| |
Collapse
|
10
|
Dufour W, Alawbathani S, Jourdain AS, Asif M, Baujat G, Becker C, Budde B, Gallacher L, Georgomanolis T, Ghoumid J, Höhne W, Lyonnet S, Ba-Saddik IA, Manouvrier-Hanu S, Motameny S, Noegel AA, Pais L, Vanlerberghe C, Wagle P, White SM, Willems M, Nürnberg P, Escande F, Petit F, Hussain MS. Monoallelic and biallelic variants in LEF1 are associated with a new syndrome combining ectodermal dysplasia and limb malformations caused by altered WNT signaling. Genet Med 2022; 24:1708-1721. [PMID: 35583550 DOI: 10.1016/j.gim.2022.04.022] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Revised: 04/20/2022] [Accepted: 04/20/2022] [Indexed: 11/25/2022] Open
Abstract
PURPOSE LEF1 encodes a transcription factor acting downstream of the WNT-β-catenin signaling pathway. It was recently suspected as a candidate for ectodermal dysplasia in 2 individuals carrying 4q35 microdeletions. We report on 12 individuals harboring LEF1 variants. METHODS High-throughput sequencing was employed to delineate the genetic underpinnings of the disease. Cellular consequences were characterized by immunofluorescence, immunoblotting, pulldown assays, and/or RNA sequencing. RESULTS Monoallelic variants in LEF1 were detected in 11 affected individuals from 4 unrelated families, and a biallelic variant was detected in an affected individual from a consanguineous family. The phenotypic spectrum includes various limb malformations, such as radial ray defects, polydactyly or split hand/foot, and ectodermal dysplasia. Depending on the type and location of LEF1 variants, the inheritance of this novel Mendelian condition can be either autosomal dominant or recessive. Our functional data indicate that 2 molecular mechanisms are at play: haploinsufficiency or loss of DNA binding are responsible for a mild to moderate phenotype, whereas loss of β-catenin binding caused by biallelic variants is associated with a severe phenotype. Transcriptomic studies reveal an alteration of WNT signaling. CONCLUSION Our findings establish mono- and biallelic variants in LEF1 as a cause for a novel syndrome comprising limb malformations and ectodermal dysplasia.
Collapse
Affiliation(s)
- William Dufour
- University of Lille, EA7364 RADEME, Lille, France; CHU Lille, Clinique de génétique Guy Fontaine, Lille, France
| | - Salem Alawbathani
- Cologne Center for Genomics, University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany; Center for Biochemistry, Medical Faculty, University of Cologne, Cologne, Germany
| | - Anne-Sophie Jourdain
- University of Lille, EA7364 RADEME, Lille, France; CHU Lille, Institut de Biochimie et Biologie Moléculaire, Lille, France
| | - Maria Asif
- Cologne Center for Genomics, University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany; Center for Biochemistry, Medical Faculty, University of Cologne, Cologne, Germany; Center for Molecular Medicine Cologne, University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany
| | - Geneviève Baujat
- Hôpital Necker Enfants Malades, Service de génétique, CHU Paris, Paris, France
| | - Christian Becker
- Cologne Center for Genomics, University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany
| | - Birgit Budde
- Cologne Center for Genomics, University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany
| | - Lyndon Gallacher
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Victoria, Australia; Department of Paediatrics, University of Melbourne, Melbourne, Victoria, Australia
| | - Theodoros Georgomanolis
- Cologne Center for Genomics, University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany
| | - Jamal Ghoumid
- University of Lille, EA7364 RADEME, Lille, France; CHU Lille, Clinique de génétique Guy Fontaine, Lille, France
| | - Wolfgang Höhne
- Cologne Center for Genomics, University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany
| | - Stanislas Lyonnet
- Hôpital Necker Enfants Malades, Service de génétique, CHU Paris, Paris, France
| | - Iman Ali Ba-Saddik
- Department of Pediatrics, Faculty of Medicine and Health Sciences, University of Aden, Aden, Yemen
| | - Sylvie Manouvrier-Hanu
- University of Lille, EA7364 RADEME, Lille, France; CHU Lille, Clinique de génétique Guy Fontaine, Lille, France
| | - Susanne Motameny
- Cologne Center for Genomics, University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany
| | - Angelika A Noegel
- Center for Biochemistry, Medical Faculty, University of Cologne, Cologne, Germany; Center for Molecular Medicine Cologne, University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany
| | - Lynn Pais
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA
| | - Clémence Vanlerberghe
- University of Lille, EA7364 RADEME, Lille, France; CHU Lille, Clinique de génétique Guy Fontaine, Lille, France
| | - Prerana Wagle
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases, University of Cologne, Cologne, Germany
| | - Susan M White
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Victoria, Australia; Department of Paediatrics, University of Melbourne, Melbourne, Victoria, Australia
| | - Marjolaine Willems
- Service de génétique, Hôpital Arnaud de Villeneuve, CHU de Montpellier, Montpellier, France
| | - Peter Nürnberg
- Cologne Center for Genomics, University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany; Center for Molecular Medicine Cologne, University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany
| | - Fabienne Escande
- University of Lille, EA7364 RADEME, Lille, France; CHU Lille, Institut de Biochimie et Biologie Moléculaire, Lille, France
| | - Florence Petit
- University of Lille, EA7364 RADEME, Lille, France; CHU Lille, Clinique de génétique Guy Fontaine, Lille, France.
| | - Muhammad Sajid Hussain
- Cologne Center for Genomics, University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany; Center for Biochemistry, Medical Faculty, University of Cologne, Cologne, Germany; Center for Molecular Medicine Cologne, University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany.
| |
Collapse
|
11
|
TCF-1: a maverick in T cell development and function. Nat Immunol 2022; 23:671-678. [PMID: 35487986 PMCID: PMC9202512 DOI: 10.1038/s41590-022-01194-2] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 03/22/2022] [Indexed: 02/01/2023]
Abstract
The T cell-specific DNA-binding protein TCF-1 is a central regulator of T cell development and function along multiple stages and lineages. Because it interacts with β-catenin, TCF-1 has been classically viewed as a downstream effector of canonical Wnt signaling, although there is strong evidence for β-catenin-independent TCF-1 functions. TCF-1 co-binds accessible regulatory regions containing or lacking its conserved motif and cooperates with other nuclear factors to establish context-dependent epigenetic and transcription programs that are essential for T cell development and for regulating immune responses to infection, autoimmunity and cancer. Although it has mostly been associated with positive regulation of chromatin accessibility and gene expression, TCF-1 has the potential to reduce chromatin accessibility and thereby suppress gene expression. In addition, the binding of TCF-1 bends the DNA and affects the chromatin conformation genome wide. This Review discusses the current understanding of the multiple roles of TCF-1 in T cell development and function and their mechanistic underpinnings.
Collapse
|
12
|
Morris A, Hoyle R, Pagare PP, Uz Zaman S, Ma Z, Li J, Zhang Y. Exploration of Naphthoquinone Analogs in Targeting the TCF-DNA Interaction to Inhibit the Wnt/β-catenin Signaling Pathway. Bioorg Chem 2022; 124:105812. [DOI: 10.1016/j.bioorg.2022.105812] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 04/11/2022] [Accepted: 04/12/2022] [Indexed: 11/02/2022]
|
13
|
Schneider L, Herkt S, Wang L, Feld C, Wesely J, Kuvardina ON, Meyer A, Oellerich T, Häupl B, Seifried E, Bonig H, Lausen J. PRMT6 activates cyclin D1 expression in conjunction with the transcription factor LEF1. Oncogenesis 2021; 10:42. [PMID: 34001852 PMCID: PMC8129428 DOI: 10.1038/s41389-021-00332-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Revised: 04/15/2021] [Accepted: 04/28/2021] [Indexed: 11/09/2022] Open
Abstract
The establishment of cell type specific gene expression by transcription factors and their epigenetic cofactors is central for cell fate decisions. Protein arginine methyltransferase 6 (PRMT6) is an epigenetic regulator of gene expression mainly through methylating arginines at histone H3. This way it influences cellular differentiation and proliferation. PRMT6 lacks DNA-binding capability but is recruited by transcription factors to regulate gene expression. However, currently only a limited number of transcription factors have been identified, which facilitate recruitment of PRMT6 to key cell cycle related target genes. Here, we show that LEF1 contributes to the recruitment of PRMT6 to the central cell cycle regulator CCND1 (Cyclin D1). We identified LEF1 as an interaction partner of PRMT6. Knockdown of LEF1 or PRMT6 reduces CCND1 expression. This is in line with our observation that knockdown of PRMT6 increases the number of cells in G1 phase of the cell cycle and decreases proliferation. These results improve the understanding of PRMT6 activity in cell cycle regulation. We expect that these insights will foster the rational development and usage of specific PRMT6 inhibitors for cancer therapy.
Collapse
Affiliation(s)
- Lucas Schneider
- Goethe University, Institute for Transfusion Medicine and Immunohematology, and German Red Cross Blood Service BaWüHe, Institute Frankfurt, Frankfurt, Germany
| | - Stefanie Herkt
- Goethe University, Institute for Transfusion Medicine and Immunohematology, and German Red Cross Blood Service BaWüHe, Institute Frankfurt, Frankfurt, Germany
| | - Lei Wang
- Department of Eukaryotic Genetics, Institute of Industrial Genetics, University of Stuttgart, Stuttgart, Germany
| | - Christine Feld
- Department of Eukaryotic Genetics, Institute of Industrial Genetics, University of Stuttgart, Stuttgart, Germany
| | - Josephine Wesely
- Georg-Speyer-Haus, Institute for Tumor Biology and Experimental Therapy, Frankfurt am Main, Germany.,Automated Systems and Genomics, The New York Stem Cell Foundation Research Institute, New York, USA
| | - Olga N Kuvardina
- Goethe University, Institute for Transfusion Medicine and Immunohematology, and German Red Cross Blood Service BaWüHe, Institute Frankfurt, Frankfurt, Germany
| | - Annekarin Meyer
- Goethe University, Institute for Transfusion Medicine and Immunohematology, and German Red Cross Blood Service BaWüHe, Institute Frankfurt, Frankfurt, Germany
| | - Thomas Oellerich
- Department of Medicine II, Hematology/Oncology, Goethe University, Frankfurt, Germany.,German Cancer Research Center and German Cancer Consortium, Heidelberg, Germany.,Department of Molecular Diagnostics/Translational Proteomics, Frankfurt Cancer Institute, Frankfurt, Germany
| | - Björn Häupl
- Department of Medicine II, Hematology/Oncology, Goethe University, Frankfurt, Germany.,German Cancer Research Center and German Cancer Consortium, Heidelberg, Germany.,Department of Molecular Diagnostics/Translational Proteomics, Frankfurt Cancer Institute, Frankfurt, Germany
| | - Erhard Seifried
- Goethe University, Institute for Transfusion Medicine and Immunohematology, and German Red Cross Blood Service BaWüHe, Institute Frankfurt, Frankfurt, Germany
| | - Halvard Bonig
- Goethe University, Institute for Transfusion Medicine and Immunohematology, and German Red Cross Blood Service BaWüHe, Institute Frankfurt, Frankfurt, Germany.,Department of Medicine, Division of Hematology, University of Washington, Seattle, WA, USA
| | - Joern Lausen
- Department of Eukaryotic Genetics, Institute of Industrial Genetics, University of Stuttgart, Stuttgart, Germany.
| |
Collapse
|
14
|
Cieslak A, Charbonnier G, Tesio M, Mathieu EL, Belhocine M, Touzart A, Smith C, Hypolite G, Andrieu GP, Martens JHA, Janssen-Megens E, Gut M, Gut I, Boissel N, Petit A, Puthier D, Macintyre E, Stunnenberg HG, Spicuglia S, Asnafi V. Blueprint of human thymopoiesis reveals molecular mechanisms of stage-specific TCR enhancer activation. J Exp Med 2021; 217:151947. [PMID: 32667968 PMCID: PMC7478722 DOI: 10.1084/jem.20192360] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 04/03/2020] [Accepted: 05/15/2020] [Indexed: 01/30/2023] Open
Abstract
Cell differentiation is accompanied by epigenetic changes leading to precise lineage definition and cell identity. Here we present a comprehensive resource of epigenomic data of human T cell precursors along with an integrative analysis of other hematopoietic populations. Although T cell commitment is accompanied by large scale epigenetic changes, we observed that the majority of distal regulatory elements are constitutively unmethylated throughout T cell differentiation, irrespective of their activation status. Among these, the TCRA gene enhancer (Eα) is in an open and unmethylated chromatin structure well before activation. Integrative analyses revealed that the HOXA5-9 transcription factors repress the Eα enhancer at early stages of T cell differentiation, while their decommission is required for TCRA locus activation and enforced αβ T lineage differentiation. Remarkably, the HOXA-mediated repression of Eα is paralleled by the ectopic expression of homeodomain-related oncogenes in T cell acute lymphoblastic leukemia. These results highlight an analogous enhancer repression mechanism at play in normal and cancer conditions, but imposing distinct developmental constraints.
Collapse
Affiliation(s)
- Agata Cieslak
- Université de Paris (Descartes), Institut Necker-Enfants Malades, Institut National de la Santé et de la Recherche Médicale U1151, and Laboratory of Onco-Hematology, Assistance Publique-Hôpitaux de Paris, Hôpital Necker Enfants-Malades, Paris, France
| | - Guillaume Charbonnier
- Aix-Marseille University, Institut National de la Santé et de la Recherche Médicale, Theories and Approaches of Genomic Complexity, UMR1090, Marseille, France.,Equipe Labellisée Ligue Contre le Cancer, Marseille, France
| | - Melania Tesio
- Université de Paris (Descartes), Institut Necker-Enfants Malades, Institut National de la Santé et de la Recherche Médicale U1151, and Laboratory of Onco-Hematology, Assistance Publique-Hôpitaux de Paris, Hôpital Necker Enfants-Malades, Paris, France
| | - Eve-Lyne Mathieu
- Aix-Marseille University, Institut National de la Santé et de la Recherche Médicale, Theories and Approaches of Genomic Complexity, UMR1090, Marseille, France.,Equipe Labellisée Ligue Contre le Cancer, Marseille, France
| | - Mohamed Belhocine
- Aix-Marseille University, Institut National de la Santé et de la Recherche Médicale, Theories and Approaches of Genomic Complexity, UMR1090, Marseille, France.,Equipe Labellisée Ligue Contre le Cancer, Marseille, France
| | - Aurore Touzart
- Université de Paris (Descartes), Institut Necker-Enfants Malades, Institut National de la Santé et de la Recherche Médicale U1151, and Laboratory of Onco-Hematology, Assistance Publique-Hôpitaux de Paris, Hôpital Necker Enfants-Malades, Paris, France.,Division of Cancer Epigenomics, German Cancer Research Center, Heidelberg, Germany
| | - Charlotte Smith
- Université de Paris (Descartes), Institut Necker-Enfants Malades, Institut National de la Santé et de la Recherche Médicale U1151, and Laboratory of Onco-Hematology, Assistance Publique-Hôpitaux de Paris, Hôpital Necker Enfants-Malades, Paris, France
| | - Guillaume Hypolite
- Université de Paris (Descartes), Institut Necker-Enfants Malades, Institut National de la Santé et de la Recherche Médicale U1151, and Laboratory of Onco-Hematology, Assistance Publique-Hôpitaux de Paris, Hôpital Necker Enfants-Malades, Paris, France
| | - Guillaume P Andrieu
- Université de Paris (Descartes), Institut Necker-Enfants Malades, Institut National de la Santé et de la Recherche Médicale U1151, and Laboratory of Onco-Hematology, Assistance Publique-Hôpitaux de Paris, Hôpital Necker Enfants-Malades, Paris, France
| | - Joost H A Martens
- Department of Molecular Biology, Faculties of Science and Medicine, Radboud Institute for Molecular Life Sciences, Radboud University, Nijmegen, Netherlands
| | - Eva Janssen-Megens
- Department of Molecular Biology, Faculties of Science and Medicine, Radboud Institute for Molecular Life Sciences, Radboud University, Nijmegen, Netherlands
| | - Marta Gut
- Centro Nacional de Análisis Genómico-Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain.,Universitat Pompeu Fabra, Barcelona, Spain
| | - Ivo Gut
- Centro Nacional de Análisis Genómico-Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain.,Universitat Pompeu Fabra, Barcelona, Spain
| | - Nicolas Boissel
- Université Paris Diderot, Institut Universitaire d'Hématologie, EA-3518, Assistance Publique-Hôpitaux de Paris, University Hospital Saint-Louis, Paris, France
| | - Arnaud Petit
- Department of Pediatric Hematology and Oncology, Assistance Publique-Hôpitaux de Paris, Hôpital Armand Trousseau, Paris, France
| | - Denis Puthier
- Aix-Marseille University, Institut National de la Santé et de la Recherche Médicale, Theories and Approaches of Genomic Complexity, UMR1090, Marseille, France.,Equipe Labellisée Ligue Contre le Cancer, Marseille, France
| | - Elizabeth Macintyre
- Université de Paris (Descartes), Institut Necker-Enfants Malades, Institut National de la Santé et de la Recherche Médicale U1151, and Laboratory of Onco-Hematology, Assistance Publique-Hôpitaux de Paris, Hôpital Necker Enfants-Malades, Paris, France
| | - Hendrik G Stunnenberg
- Department of Molecular Biology, Faculties of Science and Medicine, Radboud Institute for Molecular Life Sciences, Radboud University, Nijmegen, Netherlands
| | - Salvatore Spicuglia
- Aix-Marseille University, Institut National de la Santé et de la Recherche Médicale, Theories and Approaches of Genomic Complexity, UMR1090, Marseille, France.,Equipe Labellisée Ligue Contre le Cancer, Marseille, France
| | - Vahid Asnafi
- Université de Paris (Descartes), Institut Necker-Enfants Malades, Institut National de la Santé et de la Recherche Médicale U1151, and Laboratory of Onco-Hematology, Assistance Publique-Hôpitaux de Paris, Hôpital Necker Enfants-Malades, Paris, France
| |
Collapse
|
15
|
Baron RM, Kwon MY, Castano AP, Ghanta S, Riascos-Bernal DF, Lopez-Guzman S, Macias AA, Ith B, Schissel SL, Lederer JA, Reeves R, Yet SF, Layne MD, Liu X, Perrella MA. Frontline Science: Targeted expression of a dominant-negative high mobility group A1 transgene improves outcome in sepsis. J Leukoc Biol 2018; 104:677-689. [PMID: 29975792 PMCID: PMC6431081 DOI: 10.1002/jlb.4hi0817-333rr] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Revised: 05/30/2018] [Accepted: 05/31/2018] [Indexed: 01/24/2023] Open
Abstract
High mobility group (HMG) proteins are a family of architectural transcription factors, with HMGA1 playing a role in the regulation of genes involved in promoting systemic inflammatory responses. We speculated that blocking HMGA1-mediated pathways might improve outcomes from sepsis. To investigate HMGA1 further, we developed genetically modified mice expressing a dominant negative (dn) form of HMGA1 targeted to the vasculature. In dnHMGA1 transgenic (Tg) mice, endogenous HMGA1 is present, but its function is decreased due to the mutant transgene. These mice allowed us to specifically study the importance of HMGA1 not only during a purely pro-inflammatory insult of endotoxemia, but also during microbial sepsis induced by implantation of a bacterial-laden fibrin clot into the peritoneum. We found that the dnHMGA1 transgene was only present in Tg and not wild-type (WT) littermate mice, and the mutant transgene was able to interact with transcription factors (such as NF-κB), but was not able to bind DNA. Tg mice exhibited a blunted hypotensive response to endotoxemia, and less mortality in microbial sepsis. Moreover, Tg mice had a reduced inflammatory response during sepsis, with decreased macrophage and neutrophil infiltration into tissues, which was associated with reduced expression of monocyte chemotactic protein-1 and macrophage inflammatory protein-2. Collectively, these data suggest that targeted expression of a dnHMGA1 transgene is able to improve outcomes in models of endotoxin exposure and microbial sepsis, in part by modulating the immune response and suggest a novel modifiable pathway to target therapeutics in sepsis.
Collapse
Affiliation(s)
- Rebecca M. Baron
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115
| | - Min-Young Kwon
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115
| | - Ana P. Castano
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115
| | - Sailaja Ghanta
- Department of Pediatric Newborn Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115
| | - Dario F. Riascos-Bernal
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115
- Division of Cardiology, Department of Medicine, Albert Einstein College of Medicine, Bronx NY 10461
| | - Silvia Lopez-Guzman
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115
| | - Alvaro Andres Macias
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115
- Department of Anesthesiology, Perioperative and Pain Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115
| | - Bonna Ith
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115
| | - Scott L. Schissel
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115
| | - James A. Lederer
- Department of Surgery, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115
| | - Raymond Reeves
- Department of Chemistry, School of Molecular Biosciences, and Institute of Biological Chemistry, Washington State University, Pullman, WA 99164
| | - Shaw-Fang Yet
- Institute of Cellular and System Medicine, National Health Research Institutes, Zhunan, Taiwan
| | - Matthew D. Layne
- Department of Biochemistry, Boston University School of Medicine, Boston, MA 02118
| | - Xiaoli Liu
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115
- Department of Pediatric Newborn Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115
| | - Mark A. Perrella
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115
- Department of Pediatric Newborn Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115
| |
Collapse
|
16
|
Chen CL, Tsai YS, Huang YH, Liang YJ, Sun YY, Su CW, Chau GY, Yeh YC, Chang YS, Hu JT, Wu JC. Lymphoid Enhancer Factor 1 Contributes to Hepatocellular Carcinoma Progression Through Transcriptional Regulation of Epithelial-Mesenchymal Transition Regulators and Stemness Genes. Hepatol Commun 2018; 2:1392-1407. [PMID: 30411085 PMCID: PMC6211324 DOI: 10.1002/hep4.1229] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Accepted: 06/09/2018] [Indexed: 12/19/2022] Open
Abstract
Lymphoid enhancer factor 1 (LEF1) activity is associated with progression of several types of cancers. The role of LEF1 in progression of hepatocellular carcinoma (HCC) remains poorly known. We investigated LEF1 expression in HCC and its interactions with epithelial-mesenchymal transition (EMT) regulators (e.g., Snail, Slug, Twist) and stemness genes (e.g., octamer-binding transcription factor 4 [Oct4], sex determining region Y-box 2 [Sox2], Nanog homeobox [Nanog]). Microarray analysis was performed on resected tumor samples from patients with HCC with or without postoperative recurrence. LEF1 expression was associated with postoperative recurrence as validated by immunohistochemical staining in another HCC cohort. Among 74 patients, 44 displayed a relatively high percentage of LEF1 staining (>30% of HCC cells), which was associated with a reduced recurrence-free interval (P < 0.001) and overall survival (P = 0.009). In multivariate analysis, a high percentage of LEF1 staining was significantly associated with low albumin level (P = 0.035), Twist overexpression (P = 0.018), Snail overexpression (P = 0.064), co-expression of Twist and Snail (P = 0.054), and multinodular tumors (P = 0.025). Down-regulation of LEF1 by short hairpin RNA decreased tumor sphere formation, soft agar colony formation, and transwell invasiveness of HCC cell lines Mahlavu and PLC. Xenotransplant and tail vein injection experiments revealed that LEF1 down-regulation in Mahlavu reduced tumor size and metastasis. LEF1 up-regulation in Huh7 increased sphere formation, soft agar colony formation, and transwell invasiveness. LEF1 was shown to physically interact with and transcriptionally activate promoter regions of Oct4, Snail, Slug, and Twist. Furthermore, Oct4, Snail, and Twist transactivated LEF1 to form a regulatory positive-feedback loop. Conclusion: LEF1 plays a pivotal role in HCC progression through transcriptional regulation of Oct4 and EMT regulators.
Collapse
Affiliation(s)
- Chih-Li Chen
- School of Medicine, College of Medicine Fu Jen Catholic University New Taipei City Taiwan
| | - Yu-Shuen Tsai
- Center for Systems and Synthetic Biology and Institute of Biomedical Informatics National Yang-Ming University Taipei Taiwanl
| | - Yen-Hua Huang
- Center for Systems and Synthetic Biology and Institute of Biomedical Informatics National Yang-Ming University Taipei Taiwanl
| | - Yuh-Jin Liang
- Translational Research Division, Medical Research Department Taipei Veterans General Hospital Taipei Taiwan
| | - Ya-Yun Sun
- Graduate Institute of Biomedical and Pharmaceutical Science Fu Jen Catholic University New Taipei City Taiwan
| | - Chien-Wei Su
- Division of Gastroenterology and Hepatology, Department of Medicine Taipei Veterans General Hospital Taipei Taiwan.,Faculty of Medicine National Yang-Ming University School of Medicine Taipei Taiwan
| | - Gar-Yang Chau
- Department of Surgery and Department of Pathology and Laboratory Medicine Taipei Veterans General Hospital Taipei Taiwan
| | - Yi-Chen Yeh
- Department of Pathology and Laboratory Medicine Taipei Veterans General Hospital Taipei Taiwan
| | - Yung-Sheng Chang
- Institute of Clinical Medicine, School of Medicine National Yang-Ming University Taipei Taiwan
| | - Jui-Ting Hu
- School of Medicine, College of Medicine Fu Jen Catholic University New Taipei City Taiwan.,Liver Center Cathay General Hospital Taipei Taiwan
| | - Jaw-Ching Wu
- Translational Research Division, Medical Research Department Taipei Veterans General Hospital Taipei Taiwan.,Institute of Clinical Medicine, School of Medicine National Yang-Ming University Taipei Taiwan.,Cancer Progression Research Center
| |
Collapse
|
17
|
Lenka SS, Paichha M, Basu M, Samanta M. LrHMGB1 Shares Structural Similarities with Human HMGB1, and Its Expression Is Induced in Bacterial Infection, Antiviral Vaccination, and Pathogen-Associated Molecular Patterns Stimulation. DNA Cell Biol 2018; 37:708-723. [DOI: 10.1089/dna.2018.4221] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Affiliation(s)
| | - Mahismita Paichha
- Immunology Laboratory, Fish Health Management Division, Indian Council of Agricultural Research-Central Institute of Freshwater Aquaculture, Bhubaneswar, Odisha, India
| | - Madhubanti Basu
- Immunology Laboratory, Fish Health Management Division, Indian Council of Agricultural Research-Central Institute of Freshwater Aquaculture, Bhubaneswar, Odisha, India
| | - Mrinal Samanta
- Immunology Laboratory, Fish Health Management Division, Indian Council of Agricultural Research-Central Institute of Freshwater Aquaculture, Bhubaneswar, Odisha, India
| |
Collapse
|
18
|
Abstract
Gene expression is controlled by sequence-specific transcription factors (TFs), which bind to regulatory sequences in DNA. The degree to which the arrangement of motif sites within regulatory elements determines their function remains unclear. Here, we show that the positional distribution of TF motif sites within nucleosome-depleted regions of DNA fall into six distinct classes. These patterns are highly consistent across cell types and bring together factors that have similar functional and binding properties. Furthermore, the position of motif sites appears to be related to their known functions. Our results suggest that TFs play distinct roles in forming a functional enhancer, facilitated by their position within a regulatory sequence. Gene expression is controlled by sequence-specific transcription factors (TFs), which bind to regulatory sequences in DNA. TF binding occurs in nucleosome-depleted regions of DNA (NDRs), which generally encompass regions with lengths similar to those protected by nucleosomes. However, less is known about where within these regions specific TFs tend to be found. Here, we characterize the positional bias of inferred binding sites for 103 TFs within ∼500,000 NDRs across 47 cell types. We find that distinct classes of TFs display different binding preferences: Some tend to have binding sites toward the edges, some toward the center, and some at other positions within the NDR. These patterns are highly consistent across cell types, suggesting that they may reflect TF-specific intrinsic structural or functional characteristics. In particular, TF classes with binding sites at NDR edges are enriched for those known to interact with histones and chromatin remodelers, whereas TFs with central enrichment interact with other TFs and cofactors such as p300. Our results suggest distinct regiospecific binding patterns and functions of TF classes within enhancers.
Collapse
|
19
|
Li Z, Xu Z, Duan C, Liu W, Sun J, Han B. Role of TCF/LEF Transcription Factors in Bone Development and Osteogenesis. Int J Med Sci 2018; 15:1415-1422. [PMID: 30275770 PMCID: PMC6158667 DOI: 10.7150/ijms.26741] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Accepted: 07/29/2018] [Indexed: 11/05/2022] Open
Abstract
Bone formation occurs by two distinct mechanisms, namely, periosteal ossification and endochondral ossification. In both mechanisms, osteoblasts play an important role in the secretion and mineralization of bone-specific extracellular matrix. Differentiation and maturation of osteoblasts is a prerequisite to bone formation and is regulated by many factors. Recent experiments have shown that transcription factors play an important role in regulating osteoblast differentiation, proliferation, and function. Osteogenesis related transcription factors are the central targets and key mediators of the function of growth factors, such as cytokines. Transcription factors play a key role in the transformation of mesenchymal progenitor cells into functional osteoblasts. These transcription factors are closely linked with each other and in conjunction with bone-related signaling pathways form a complex network that regulates osteoblast differentiation and bone formation. In this paper, we discuss the structure of T-cell factor/lymphoid enhancer factor (TCF/LEF) and its role in embryonic skeletal development and the crosstalk with related signaling pathways and factors.
Collapse
Affiliation(s)
- Zhengqiang Li
- Department of Oral and Maxillofacial Surgery, School of Stomatology, Jilin University, Changchun 130021, China.,Stomatological Hospital of Southern Medical University & Guangdong Provincial Stomatological Hospital, Guangzhou 510280, China
| | - Zhimin Xu
- Department of Oral and Maxillofacial Surgery, School of Stomatology, Jilin University, Changchun 130021, China.,Jilin Provincial Key Laboratory of Tooth Development and Bone Remodeling, Changchun 130021, China
| | - Congcong Duan
- Department of Oral and Maxillofacial Surgery, School of Stomatology, Jilin University, Changchun 130021, China.,Jilin Provincial Key Laboratory of Tooth Development and Bone Remodeling, Changchun 130021, China
| | - Weiwei Liu
- Department of Oral and Maxillofacial Surgery, School of Stomatology, Jilin University, Changchun 130021, China.,Jilin Provincial Key Laboratory of Tooth Development and Bone Remodeling, Changchun 130021, China
| | - Jingchun Sun
- Department of Oral and Maxillofacial Surgery, School of Stomatology, Jilin University, Changchun 130021, China.,Jilin Provincial Key Laboratory of Tooth Development and Bone Remodeling, Changchun 130021, China
| | - Bing Han
- Department of Oral and Maxillofacial Surgery, School of Stomatology, Jilin University, Changchun 130021, China.,Jilin Provincial Key Laboratory of Tooth Development and Bone Remodeling, Changchun 130021, China
| |
Collapse
|
20
|
Bajpai G, Jain I, Inamdar MM, Das D, Padinhateeri R. Binding of DNA-bending non-histone proteins destabilizes regular 30-nm chromatin structure. PLoS Comput Biol 2017; 13:e1005365. [PMID: 28135276 PMCID: PMC5305278 DOI: 10.1371/journal.pcbi.1005365] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Revised: 02/13/2017] [Accepted: 01/14/2017] [Indexed: 11/18/2022] Open
Abstract
Why most of the in vivo experiments do not find the 30-nm chromatin fiber, well studied in vitro, is a puzzle. Two basic physical inputs that are crucial for understanding the structure of the 30-nm fiber are the stiffness of the linker DNA and the relative orientations of the DNA entering/exiting nucleosomes. Based on these inputs we simulate chromatin structure and show that the presence of non-histone proteins, which bind and locally bend linker DNA, destroys any regular higher order structures (e.g., zig-zag). Accounting for the bending geometry of proteins like nhp6 and HMG-B, our theory predicts phase-diagram for the chromatin structure as a function of DNA-bending non-histone protein density and mean linker DNA length. For a wide range of linker lengths, we show that as we vary one parameter, that is, the fraction of bent linker region due to non-histone proteins, the steady-state structure will show a transition from zig-zag to an irregular structure-a structure that is reminiscent of what is observed in experiments recently. Our theory can explain the recent in vivo observation of irregular chromatin having co-existence of finite fraction of the next-neighbor (i + 2) and neighbor (i + 1) nucleosome interactions.
Collapse
Affiliation(s)
- Gaurav Bajpai
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Ishutesh Jain
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Mandar M. Inamdar
- Department of Civil Engineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Dibyendu Das
- Department of Physics, Indian Institute of Technology Bombay, Mumbai, India
| | - Ranjith Padinhateeri
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
- * E-mail:
| |
Collapse
|
21
|
de Mendonça Amarante A, Jupatanakul N, de Abreu da Silva IC, Carneiro VC, Vicentino ARR, Dimopolous G, Talyuli OAC, Fantappié MR. The DNA chaperone HMGB1 potentiates the transcriptional activity of Rel1A in the mosquito Aedes aegypti. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2017; 80:32-41. [PMID: 27867076 DOI: 10.1016/j.ibmb.2016.11.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Revised: 11/16/2016] [Accepted: 11/17/2016] [Indexed: 06/06/2023]
Abstract
High Mobility Group protein 1 (HMGB1) is a non-histone, chromatin-associated nuclear protein that functions in regulating eukaryotic gene expression. We investigated the influence and mechanism of action of Aedes aegypti HMGB1 (AaHMGB1) on mosquito Rel1A-mediated transcription from target gene promoters. The DNA-binding domain (RHD) of AaRel1A was bacterially expressed and purified, and AaHMGB1 dramatically enhanced RHD binding to consensus NF-kB/Rel DNA response elements. Luciferase reporter analyses using a cecropin gene promoter showed that AaHMGB1 potentiates the transcriptional activity of AaRel1A in Aag-2 cells. Moreover, overexpression of AaHMGB1 in Aag-2 cells led to an increase in mRNA levels of antimicrobial peptide genes. In vitro GST pull-down assays revealed that the presence of DNA is a pre-requisite for assembly of a possible ternary complex containing DNA, AaHMGB1 and AaRel1A. Notably, DNA bending by AaHMGB1 enhanced the binding of AaRel1A to a DNA fragment containing a putative NF-kB/Rel response element. Importantly, AaHMGB1 was identified as a potential immune modulator in A. aegypti through AaHMGB1 overexpression or RNAi silencing in Aag-2 cells followed by bacterial challenge or through AaHMGB1 RNAi knockdown in mosquitoes followed by Dengue virus (DENV) infection. We propose a model in which AaHMGB1 bends NF-kB/Rel target DNA to recruit and allow more efficient AaRel1A binding to activate transcription of effector genes, culminating in a stronger Toll pathway-mediated response against DENV infection.
Collapse
Affiliation(s)
- Anderson de Mendonça Amarante
- Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Brazil; Instituto Nacional de Entomologia Molecular, Universidade Federal do Rio de Janeiro, Brazil
| | - Natapong Jupatanakul
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Bloomberg School of Public Health, Johns Hopkins University, United States
| | - Isabel Caetano de Abreu da Silva
- Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Brazil; Instituto Nacional de Entomologia Molecular, Universidade Federal do Rio de Janeiro, Brazil
| | - Vitor Coutinho Carneiro
- Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Brazil; Instituto Nacional de Entomologia Molecular, Universidade Federal do Rio de Janeiro, Brazil
| | - Amanda Roberta Revoredo Vicentino
- Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Brazil; Instituto Nacional de Entomologia Molecular, Universidade Federal do Rio de Janeiro, Brazil
| | - George Dimopolous
- Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Brazil; Instituto Nacional de Entomologia Molecular, Universidade Federal do Rio de Janeiro, Brazil; W. Harry Feinstone Department of Molecular Microbiology and Immunology, Bloomberg School of Public Health, Johns Hopkins University, United States
| | - Octávio Augusto C Talyuli
- Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Brazil; Instituto Nacional de Entomologia Molecular, Universidade Federal do Rio de Janeiro, Brazil
| | - Marcelo Rosado Fantappié
- Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Brazil; Instituto Nacional de Entomologia Molecular, Universidade Federal do Rio de Janeiro, Brazil.
| |
Collapse
|
22
|
Fan YH, Lin YL, Hwang YC, Yang HC, Chiu HC, Chiou SH, Jong MH, Chow KC, Lin CC. T-cell factor-4 and MHC upregulation in pigs receiving a live attenuated classical swine fever virus (CSFV) vaccine strain with interferon-gamma adjuvant. Vet J 2016; 216:148-56. [PMID: 27687943 DOI: 10.1016/j.tvjl.2016.07.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2014] [Revised: 07/13/2016] [Accepted: 07/15/2016] [Indexed: 01/15/2023]
Abstract
The effect of co-administration of interferon (IFN)-γ in pigs undergoing vaccination with an attenuated strain (LPC) of classical swine fever virus (CSFV) was investigated. Unvaccinated pigs demonstrated pyrexia and died 7-9 days after challenge with virulent CSFV. Pigs receiving the attenuated vaccine remained healthy after virus challenge, except for mild, transient pyrexia, whereas pigs receiving IFN-γ simultaneously with the vaccine demonstrated normal body temperatures after virus challenge. Examination by nested RT-PCR revealed greater viral load in the spleens of the pigs vaccinated with the attenuated CSFV, compared with those that had additionally received IFN-γ. Expression of major histocompatibility complex (MHC) class I and MHC class II molecules was upregulated in the spleens of the IFN-γ treated vaccinated pigs, demonstrated by immunohistochemistry. Based on Western blot analysis, anti-CSFV IgG2 antibodies were elevated in vaccinated pigs by co-administration of IFN-γ (IFN-γ(Hi): P < 0.01; IFN-γ(Lo): P <0.05). By employing the suppression subtractive hybridization technique, RT-PCR, in situ hybridization, and immunohistochemistry, T-cell factor-4 (Tcf-4) mRNA and protein expression were found to be upregulated in the spleens of vaccinated pigs that had received IFN-γ. This study suggests involvement of Tcf-4 in IFN-γ-mediated immune regulation following CSFV vaccination.
Collapse
Affiliation(s)
- Y-H Fan
- Graduate Institute of Microbiology and Public Health, National Chung Hsing University, Taichung 40227, Taiwan, Republic of China
| | - Y-L Lin
- Epidemiology Research Division, Animal Health Research Institute, Council of Agriculture, Executive Yuan, Tamsui, New Taipei City 251, Taiwan, Republic of China
| | - Y-C Hwang
- Graduate Institute of Microbiology and Public Health, National Chung Hsing University, Taichung 40227, Taiwan, Republic of China
| | - H-C Yang
- Graduate Institute of Microbiology and Public Health, National Chung Hsing University, Taichung 40227, Taiwan, Republic of China
| | - H-C Chiu
- Graduate Institute of Microbiology and Public Health, National Chung Hsing University, Taichung 40227, Taiwan, Republic of China
| | - S-H Chiou
- Graduate Institute of Microbiology and Public Health, National Chung Hsing University, Taichung 40227, Taiwan, Republic of China.
| | - M-H Jong
- Hog Cholera Division, Animal Health Research Institute, Council of Agriculture, Executive Yuan, Tamsui, New Taipei City 251, Taiwan, Republic of China
| | - K-C Chow
- Institute of Biomedical Sciences, National Chung Hsing University, Taichung 40227, Taiwan, Republic of China
| | - C-C Lin
- Department of Veterinary Medicine, National Chung Hsing University, Taichung 40227, Taiwan, Republic of China
| |
Collapse
|
23
|
Hrckulak D, Kolar M, Strnad H, Korinek V. TCF/LEF Transcription Factors: An Update from the Internet Resources. Cancers (Basel) 2016; 8:cancers8070070. [PMID: 27447672 PMCID: PMC4963812 DOI: 10.3390/cancers8070070] [Citation(s) in RCA: 108] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Revised: 07/11/2016] [Accepted: 07/14/2016] [Indexed: 12/18/2022] Open
Abstract
T-cell factor/lymphoid enhancer-binding factor (TCF/LEF) proteins (TCFs) from the High Mobility Group (HMG) box family act as the main downstream effectors of the Wnt signaling pathway. The mammalian TCF/LEF family comprises four nuclear factors designated TCF7, LEF1, TCF7L1, and TCF7L2 (also known as TCF1, LEF1, TCF3, and TCF4, respectively). The proteins display common structural features and are often expressed in overlapping patterns implying their redundancy. Such redundancy was indeed observed in gene targeting studies; however, individual family members also exhibit unique features that are not recapitulated by the related proteins. In the present viewpoint, we summarized our current knowledge about the specific features of individual TCFs, namely structural-functional studies, posttranslational modifications, interacting partners, and phenotypes obtained upon gene targeting in the mouse. In addition, we employed several publicly available databases and web tools to evaluate the expression patterns and production of gene-specific isoforms of the TCF/LEF family members in human cells and tissues.
Collapse
Affiliation(s)
- Dusan Hrckulak
- Department of Cell and Developmental Biology, Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Videnska 1083, Prague 4 14220, Czech Republic.
| | - Michal Kolar
- Department of Genomics and Bioinformatics, Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Videnska 1083, Prague 4 14220, Czech Republic.
| | - Hynek Strnad
- Department of Genomics and Bioinformatics, Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Videnska 1083, Prague 4 14220, Czech Republic.
| | - Vladimir Korinek
- Department of Cell and Developmental Biology, Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Videnska 1083, Prague 4 14220, Czech Republic.
| |
Collapse
|
24
|
Abstract
The temperature dependence of DNA flexibility is studied in the presence of stretching and unzipping forces. Two classes of models are considered. In one case the origin of elasticity is entropic due to the polymeric correlations, and in the other the double-stranded DNA is taken to have an intrinsic rigidity for bending. In both cases single strands are completely flexible. The change in the elastic constant for the flexible case due to thermally generated bubbles is obtained exactly. For the case of intrinsic rigidity, the elastic constant is found to be proportional to the square root of the bubble number fluctuation.
Collapse
Affiliation(s)
- Tanmoy Pal
- Institute of Physics, Bhubaneswar 751005, India
| | - Somendra M Bhattacharjee
- Institute of Physics, Bhubaneswar 751005, India.,Department of Physics, Ramakrishna Mission Vivekananda University, P.O. Belur Math, Dist. Howrah, West Bengal 711202, India
| |
Collapse
|
25
|
Ohmura S, Mizuno S, Oishi H, Ku CJ, Hermann M, Hosoya T, Takahashi S, Engel JD. Lineage-affiliated transcription factors bind the Gata3 Tce1 enhancer to mediate lineage-specific programs. J Clin Invest 2016; 126:865-78. [PMID: 26808502 DOI: 10.1172/jci83894] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2015] [Accepted: 12/10/2015] [Indexed: 01/09/2023] Open
Abstract
The transcription factor GATA3 is essential for the genesis and maturation of the T cell lineage, and GATA3 dysregulation has pathological consequences. Previous studies have shown that GATA3 function in T cell development is regulated by multiple signaling pathways and that the Notch nuclear effector, RBP-J, binds specifically to the Gata3 promoter. We previously identified a T cell-specific Gata3 enhancer (Tce1) lying 280 kb downstream from the structural gene and demonstrated in transgenic mice that Tce1 promoted T lymphocyte-specific transcription of reporter genes throughout T cell development; however, it was not clear if Tce1 is required for Gata3 transcription in vivo. Here, we determined that the canonical Gata3 promoter is insufficient for Gata3 transcriptional activation in T cells in vivo, precluding the possibility that promoter binding by a host of previously implicated transcription factors alone is responsible for Gata3 expression in T cells. Instead, we demonstrated that multiple lineage-affiliated transcription factors bind to Tce1 and that this enhancer confers T lymphocyte-specific Gata3 activation in vivo, as targeted deletion of Tce1 in a mouse model abrogated critical functions of this T cell-regulatory element. Together, our data show that Tce1 is both necessary and sufficient for critical aspects of Gata3 T cell-specific transcriptional activity.
Collapse
|
26
|
Bauman TM, Vezina CM, Ricke EA, Halberg RB, Huang W, Peterson RE, Ricke WA. Expression and colocalization of β-catenin and lymphoid enhancing factor-1 in prostate cancer progression. Hum Pathol 2016; 51:124-33. [PMID: 27067790 DOI: 10.1016/j.humpath.2015.12.024] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/19/2015] [Revised: 12/18/2015] [Accepted: 12/23/2015] [Indexed: 11/16/2022]
Abstract
The purpose of this study was to objectively investigate β-catenin and LEF1 abundance, subcellular localization, and colocalization across benign and staged prostate cancer (PCa) specimens. A tissue microarray containing tumor-adjacent histologically benign prostate tissue (BPT; n = 48 patients), high-grade prostatic intraepithelial neoplasia (HGPIN; n = 25), localized PCa (n = 42), aggressive PCa (n = 31), and metastases (n = 22) was stained using multiplexed immunohistochemistry with antibodies toward E-cadherin, β-catenin, and LEF1. Multispectral imaging was used for quantitation, and protein expression and colocalization was evaluated across PCa progression. Stromal nuclear β-catenin abundance was greater in HGPIN and PCa compared with BPT (P < .05 for both), and epithelial nuclear β-catenin abundance was lower in metastatic PCa than in BPT (P < .05 for both). Epithelial and stromal nuclear LEF1 abundance was greater in HGPIN compared with BPT, whereas epithelial nuclear LEF1 was also greater in metastases. The proportion of epithelial and stromal nuclear double-positive β-catenin(+)/LEF1(+) cells was greater in HGPIN compared with BPT. In addition, the proportion of epithelial β-catenin(+)/LEF1(+) cells was greater in localized PCa and metastases compared with BPT. A significant amount of stromal cells were positive for LEF1 but not β-catenin. β-Catenin and LEF1 abundance were negatively correlated in the epithelium (P < .0001) but not the stroma (P > .05). We conclude that β-catenin and LEF1 colocalization is increased in HGPIN and metastasis relative to BPT, suggesting a role for β-catenin/LEF1-mediated transcription in both malignant transformation and metastasis of PCa. Furthermore, our results suggest that LEF1 abundance alone is not a reliable readout for β-catenin activity in prostate tissues.
Collapse
Affiliation(s)
- Tyler M Bauman
- Division of Urologic Surgery, Washington University School of Medicine, St Louis, MO 53705
| | - Chad M Vezina
- Department of Comparative Biosciences, University of Wisconsin School of Veterinary Medicine, Madison, WI 53705; University of Wisconsin O'Brien Urology Research Center, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705
| | - Emily A Ricke
- Department of Urology, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705
| | - Richard B Halberg
- Division of Gastroenterology and Hepatology, Department of Medicine, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705
| | - Wei Huang
- University of Wisconsin O'Brien Urology Research Center, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705; Department of Pathology and Laboratory Medicine, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705
| | - Richard E Peterson
- Division of Pharmaceutical Sciences, University of Wisconsin School of Pharmacy, Madison, WI 53705
| | - William A Ricke
- University of Wisconsin O'Brien Urology Research Center, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705; Department of Urology, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705.
| |
Collapse
|
27
|
Wang Y, Zhong J, Zhang X, Liu Z, Yang Y, Gong Q, Ren B. The Role of HMGB1 in the Pathogenesis of Type 2 Diabetes. J Diabetes Res 2016; 2016:2543268. [PMID: 28101517 PMCID: PMC5215175 DOI: 10.1155/2016/2543268] [Citation(s) in RCA: 75] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Revised: 11/08/2016] [Accepted: 11/29/2016] [Indexed: 12/17/2022] Open
Abstract
Significance. With an alarming increase in recent years, diabetes mellitus has become a global challenge. Despite advances in treatment of diabetes mellitus, currently, medications available are unable to control the progression of diabetes and its complications. Growing evidence suggests that inflammation is an important pathogenic mediator in the development of diabetes mellitus. The perspectives including suggestions for new therapies involving the shift from metabolic stress to inflammation should be taken into account. Critical Issues. High-mobility group box 1 (HMGB1), a nonhistone nuclear protein regulating gene expression, was rediscovered as an endogenous danger signal molecule to trigger inflammatory responses when released into extracellular milieu in the late 1990s. Given the similarities of inflammatory response in the development of T2D, we will discuss the potential implication of HMGB1 in the pathogenesis of T2D. Importantly, we will summarize and renovate the role of HMGB1 and HMGB1-mediated inflammatory pathways in adipose tissue inflammation, insulin resistance, and islet dysfunction. Future Directions. HMGB1 and its downstream receptors RAGE and TLRs may serve as potential antidiabetic targets. Current and forthcoming projects in this territory will pave the way for prospective approaches targeting the center of HMGB1-mediated inflammation to improve T2D and its complications.
Collapse
Affiliation(s)
- Yanan Wang
- Department of Immunology, Medical School, Yangtze University, Jingzhou 434023, China
| | - Jixin Zhong
- Department of Immunology, Medical School, Yangtze University, Jingzhou 434023, China
- Department of Medicine, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Xiangzhi Zhang
- Department of Medicine, Hospital of Yangtze University, Jingzhou 434000, China
| | - Ziwei Liu
- Department of Immunology, Medical School, Yangtze University, Jingzhou 434023, China
| | - Yuan Yang
- Department of Immunology, Medical School, Yangtze University, Jingzhou 434023, China
| | - Quan Gong
- Department of Immunology, Medical School, Yangtze University, Jingzhou 434023, China
- *Quan Gong: and
| | - Boxu Ren
- Department of Immunology, Medical School, Yangtze University, Jingzhou 434023, China
- *Boxu Ren:
| |
Collapse
|
28
|
Beccari L, Marco-Ferreres R, Tabanera N, Manfredi A, Souren M, Wittbrodt B, Conte I, Wittbrodt J, Bovolenta P. A trans-Regulatory Code for the Forebrain Expression of Six3.2 in the Medaka Fish. J Biol Chem 2015; 290:26927-26942. [PMID: 26378230 PMCID: PMC4646366 DOI: 10.1074/jbc.m115.681254] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2015] [Revised: 09/11/2015] [Indexed: 12/16/2022] Open
Abstract
A well integrated and hierarchically organized gene regulatory network is responsible for the progressive specification of the forebrain. The transcription factor Six3 is one of the central components of this network. As such, Six3 regulates several components of the network, but its upstream regulators are still poorly characterized. Here we have systematically identified such regulators, taking advantage of the detailed functional characterization of the regulatory region of the medaka fish Six3.2 ortholog and of a time/cost-effective trans-regulatory screening, which complemented and overcame the limitations of in silico prediction approaches. The candidates resulting from this search were validated with dose-response luciferase assays and expression pattern criteria. Reconfirmed candidates with a matching expression pattern were also tested with chromatin immunoprecipitation and functional studies. Our results confirm the previously proposed direct regulation of Pax6 and further demonstrate that Msx2 and Pbx1 are bona fide direct regulators of early Six3.2 distribution in distinct domains of the medaka fish forebrain. They also point to other transcription factors, including Tcf3, as additional regulators of different spatial-temporal domains of Six3.2 expression. The activity of these regulators is discussed in the context of the gene regulatory network proposed for the specification of the forebrain.
Collapse
Affiliation(s)
- Leonardo Beccari
- Centro de Biología Molecular "Severo Ochoa," Consejo Superior de Investigaciones Científicas-Universidad Autónoma de Madrid, c/ Nicolas Cabrera 1, Madrid 28049, Spain,; Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), c/ Nicolas Cabrera 1, Madrid 28049, Spain; Instituto Cajal, Consejo Superior de Investigaciones Científicas, Avda. Dr. Arce 37, Madrid, 28002, Spain,.
| | - Raquel Marco-Ferreres
- Centro de Biología Molecular "Severo Ochoa," Consejo Superior de Investigaciones Científicas-Universidad Autónoma de Madrid, c/ Nicolas Cabrera 1, Madrid 28049, Spain,; Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), c/ Nicolas Cabrera 1, Madrid 28049, Spain; Instituto Cajal, Consejo Superior de Investigaciones Científicas, Avda. Dr. Arce 37, Madrid, 28002, Spain
| | - Noemi Tabanera
- Centro de Biología Molecular "Severo Ochoa," Consejo Superior de Investigaciones Científicas-Universidad Autónoma de Madrid, c/ Nicolas Cabrera 1, Madrid 28049, Spain,; Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), c/ Nicolas Cabrera 1, Madrid 28049, Spain; Instituto Cajal, Consejo Superior de Investigaciones Científicas, Avda. Dr. Arce 37, Madrid, 28002, Spain
| | - Anna Manfredi
- Instituto Cajal, Consejo Superior de Investigaciones Científicas, Avda. Dr. Arce 37, Madrid, 28002, Spain
| | - Marcel Souren
- the Centre for Organismal Studies, University of Heidelberg, Im Neuenheimer Feld 230, 69120 Heidelberg, Germany
| | - Beate Wittbrodt
- the Centre for Organismal Studies, University of Heidelberg, Im Neuenheimer Feld 230, 69120 Heidelberg, Germany
| | - Ivan Conte
- Instituto Cajal, Consejo Superior de Investigaciones Científicas, Avda. Dr. Arce 37, Madrid, 28002, Spain,; the Telethon Institute of Genetics and Medicine, Via Campi Flegrei 34, Pozzuoli, Naples, 80078, Italy
| | - Jochen Wittbrodt
- the Centre for Organismal Studies, University of Heidelberg, Im Neuenheimer Feld 230, 69120 Heidelberg, Germany
| | - Paola Bovolenta
- Centro de Biología Molecular "Severo Ochoa," Consejo Superior de Investigaciones Científicas-Universidad Autónoma de Madrid, c/ Nicolas Cabrera 1, Madrid 28049, Spain,; Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), c/ Nicolas Cabrera 1, Madrid 28049, Spain; Instituto Cajal, Consejo Superior de Investigaciones Científicas, Avda. Dr. Arce 37, Madrid, 28002, Spain,.
| |
Collapse
|
29
|
Kang JW, Kim SJ, Cho HI, Lee SM. DAMPs activating innate immune responses in sepsis. Ageing Res Rev 2015; 24:54-65. [PMID: 25816752 DOI: 10.1016/j.arr.2015.03.003] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2014] [Revised: 03/09/2015] [Accepted: 03/13/2015] [Indexed: 12/11/2022]
Abstract
Sepsis refers to the deleterious and non-resolving systemic inflammatory response of the host to microbial infection and is the leading cause of death in intensive care units. The pathogenesis of sepsis is highly complex. It is principally attributable to dysregulation of the innate immune system. Damage-associated molecular patterns (DAMPs) are actively secreted by innate immune cells and/or released passively by injured or damaged cells in response to infection or injury. In the present review, we highlight emerging evidence that supports the notion that extracellular DAMPs act as crucial proinflammatory danger signals. Furthermore, we discuss the potential of a wide array of DAMPs as therapeutic targets in sepsis.
Collapse
Affiliation(s)
- Jung-Woo Kang
- School of Pharmacy, Sungkyunkwan University, Seobu-ro 2066, Jangan-gu, Suwon, Gyeonggi-do, 440-746 South Korea
| | - So-Jin Kim
- School of Pharmacy, Sungkyunkwan University, Seobu-ro 2066, Jangan-gu, Suwon, Gyeonggi-do, 440-746 South Korea
| | - Hong-Ik Cho
- School of Pharmacy, Sungkyunkwan University, Seobu-ro 2066, Jangan-gu, Suwon, Gyeonggi-do, 440-746 South Korea
| | - Sun-Mee Lee
- School of Pharmacy, Sungkyunkwan University, Seobu-ro 2066, Jangan-gu, Suwon, Gyeonggi-do, 440-746 South Korea.
| |
Collapse
|
30
|
Osei-Sarfo K, Gudas LJ. Retinoic acid suppresses the canonical Wnt signaling pathway in embryonic stem cells and activates the noncanonical Wnt signaling pathway. Stem Cells 2015; 32:2061-71. [PMID: 24648413 DOI: 10.1002/stem.1706] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2013] [Accepted: 02/20/2014] [Indexed: 12/27/2022]
Abstract
Embryonic stem cells (ESCs) have both the ability to self-renew and to differentiate into various cell lineages. Retinoic acid (RA), a metabolite of Vitamin A, has a critical function in initiating lineage differentiation of ESCs through binding to the retinoic acid receptors. Additionally, the Wnt signaling pathway plays a role in pluripotency and differentiation, depending on the activation status of the canonical and noncanonical pathways. The activation of the canonical Wnt signaling pathway, which requires the nuclear accumulation of β-catenin and its interaction with Tcf1/Lef at Wnt response elements, is involved in ESC stemness maintenance. The noncanonical Wnt signaling pathway, through actions of Tcf3, can antagonize the canonical pathway. We show that RA activates the noncanonical Wnt signaling pathway, while concomitantly inhibiting the canonical pathway. RA increases the expression of ligands and receptors of the noncanonical Wnt pathway (Wnt 5a, 7a, Fzd2 and Fzd6), downstream signaling, and Tcf3 expression. RA reduces the phosphorylated β-catenin levels by fourfold, although total β-catenin levels do not change. We show that RA signaling increases the dissociation of Tcf1 and the association of Tcf3 at promoters of genes that regulate stemness (e.g., NR5A2, Lrh-1) or differentiation (e.g. Cyr61, Zic5). Knockdown of Tcf3 increases Lrh-1 transcript levels in mESCs and prevents the RA-associated, fourfold increase in Zic5, indicating that RA requires Tcf3 to effect changes in Zic5 levels. We demonstrate a novel role for RA in altering the activation of these two Wnt signaling pathways and show that Tcf3 mediates some actions of RA during differentiation.
Collapse
Affiliation(s)
- Kwame Osei-Sarfo
- Department of Pharmacology, Weill Cornell Medical College, New York, New York, USA; Weill Cornell Meyer Cancer Center, New York, New York, USA
| | | |
Collapse
|
31
|
Vuong LM, Chellappa K, Dhahbi JM, Deans JR, Fang B, Bolotin E, Titova NV, Hoverter NP, Spindler SR, Waterman ML, Sladek FM. Differential Effects of Hepatocyte Nuclear Factor 4α Isoforms on Tumor Growth and T-Cell Factor 4/AP-1 Interactions in Human Colorectal Cancer Cells. Mol Cell Biol 2015; 35:3471-90. [PMID: 26240283 PMCID: PMC4573706 DOI: 10.1128/mcb.00030-15] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2015] [Revised: 02/04/2015] [Accepted: 07/07/2015] [Indexed: 12/18/2022] Open
Abstract
The nuclear receptor hepatocyte nuclear factor 4α (HNF4α) is tumor suppressive in the liver but amplified in colon cancer, suggesting that it also might be oncogenic. To investigate whether this discrepancy is due to different HNF4α isoforms derived from its two promoters (P1 and P2), we generated Tet-On-inducible human colon cancer (HCT116) cell lines that express either the P1-driven (HNF4α2) or P2-driven (HNF4α8) isoform and analyzed them for tumor growth and global changes in gene expression (transcriptome sequencing [RNA-seq] and chromatin immunoprecipitation sequencing [ChIP-seq]). The results show that while HNF4α2 acts as a tumor suppressor in the HCT116 tumor xenograft model, HNF4α8 does not. Each isoform regulates the expression of distinct sets of genes and recruits, colocalizes, and competes in a distinct fashion with the Wnt/β-catenin mediator T-cell factor 4 (TCF4) at CTTTG motifs as well as at AP-1 motifs (TGAXTCA). Protein binding microarrays (PBMs) show that HNF4α and TCF4 share some but not all binding motifs and that single nucleotide polymorphisms (SNPs) in sites bound by both HNF4α and TCF4 can alter binding affinity in vitro, suggesting that they could play a role in cancer susceptibility in vivo. Thus, the HNF4α isoforms play distinct roles in colon cancer, which could be due to differential interactions with the Wnt/β-catenin/TCF4 and AP-1 pathways.
Collapse
Affiliation(s)
- Linh M Vuong
- Department of Cell Biology and Neuroscience, University of California, Riverside, Riverside, California, USA
| | - Karthikeyani Chellappa
- Department of Cell Biology and Neuroscience, University of California, Riverside, Riverside, California, USA
| | - Joseph M Dhahbi
- Department of Biochemistry, University of California, Riverside, Riverside, California, USA
| | - Jonathan R Deans
- Department of Cell Biology and Neuroscience, University of California, Riverside, Riverside, California, USA
| | - Bin Fang
- Department of Cell Biology and Neuroscience, University of California, Riverside, Riverside, California, USA
| | - Eugene Bolotin
- Department of Cell Biology and Neuroscience, University of California, Riverside, Riverside, California, USA
| | - Nina V Titova
- Department of Cell Biology and Neuroscience, University of California, Riverside, Riverside, California, USA
| | - Nate P Hoverter
- Department of Microbiology and Molecular Genetics, University of California, Irvine, Irvine, California, USA
| | - Stephen R Spindler
- Department of Biochemistry, University of California, Riverside, Riverside, California, USA
| | - Marian L Waterman
- Department of Microbiology and Molecular Genetics, University of California, Irvine, Irvine, California, USA
| | - Frances M Sladek
- Department of Cell Biology and Neuroscience, University of California, Riverside, Riverside, California, USA
| |
Collapse
|
32
|
Fiedler M, Graeb M, Mieszczanek J, Rutherford TJ, Johnson CM, Bienz M. An ancient Pygo-dependent Wnt enhanceosome integrated by Chip/LDB-SSDP. eLife 2015; 4:e09073. [PMID: 26312500 PMCID: PMC4571689 DOI: 10.7554/elife.09073] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Accepted: 08/26/2015] [Indexed: 12/15/2022] Open
Abstract
TCF/LEF factors are ancient context-dependent enhancer-binding proteins that are activated by β-catenin following Wnt signaling. They control embryonic development and adult stem cell compartments, and their dysregulation often causes cancer. β-catenin-dependent transcription relies on the NPF motif of Pygo proteins. Here, we use a proteomics approach to discover the Chip/LDB-SSDP (ChiLS) complex as the ligand specifically binding to NPF. ChiLS also recognizes NPF motifs in other nuclear factors including Runt/RUNX2 and Drosophila ARID1, and binds to Groucho/TLE. Studies of Wnt-responsive dTCF enhancers in the Drosophila embryonic midgut indicate how these factors interact to form the Wnt enhanceosome, primed for Wnt responses by Pygo. Together with previous evidence, our study indicates that ChiLS confers context-dependence on TCF/LEF by integrating multiple inputs from lineage and signal-responsive factors, including enhanceosome switch-off by Notch. Its pivotal function in embryos and stem cells explain why its integrity is crucial in the avoidance of cancer.
Collapse
Affiliation(s)
- Marc Fiedler
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Michael Graeb
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Juliusz Mieszczanek
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Trevor J Rutherford
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Christopher M Johnson
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Mariann Bienz
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge, United Kingdom
| |
Collapse
|
33
|
Hermkens DMA, van Impel A, Urasaki A, Bussmann J, Duckers HJ, Schulte-Merker S. Sox7 controls arterial specification in conjunction with hey2 and efnb2 function. Development 2015; 142:1695-704. [PMID: 25834021 DOI: 10.1242/dev.117275] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2014] [Accepted: 03/06/2015] [Indexed: 12/22/2022]
Abstract
SoxF family members have been linked to arterio-venous specification events and human pathological conditions, but in contrast to Sox17 and Sox18, a detailed in vivo analysis of a Sox7 mutant model is still lacking. In this study we generated zebrafish sox7 mutants to understand the role of Sox7 during vascular development. By in vivo imaging of transgenic zebrafish lines we show that sox7 mutants display a short circulatory loop around the heart as a result of aberrant connections between the lateral dorsal aorta (LDA) and either the venous primary head sinus (PHS) or the common cardinal vein (CCV). In situ hybridization and live observations in flt4:mCitrine transgenic embryos revealed increased expression levels of flt4 in arterial endothelial cells at the exact location of the aberrant vascular connections in sox7 mutants. An identical circulatory short loop could also be observed in newly generated mutants for hey2 and efnb2. By genetically modulating levels of sox7, hey2 and efnb2 we demonstrate a genetic interaction of sox7 with hey2 and efnb2. The specific spatially confined effect of loss of Sox7 function can be rescued by overexpressing the Notch intracellular domain (NICD) in arterial cells of sox7 mutants, placing Sox7 upstream of Notch in this aspect of arterial development. Hence, sox7 levels are crucial in arterial specification in conjunction with hey2 and efnb2 function, with mutants in all three genes displaying shunt formation and an arterial block.
Collapse
Affiliation(s)
- Dorien M A Hermkens
- Hubrecht Institute - Royal Netherlands Academy of Arts and Sciences and University Medical Centre Utrecht, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands Erasmus MC Rotterdam, 's-Gravendijkwal 230, 3015 CE Rotterdam, The Netherlands
| | - Andreas van Impel
- Hubrecht Institute - Royal Netherlands Academy of Arts and Sciences and University Medical Centre Utrecht, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Akihiro Urasaki
- Hubrecht Institute - Royal Netherlands Academy of Arts and Sciences and University Medical Centre Utrecht, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Jeroen Bussmann
- Hubrecht Institute - Royal Netherlands Academy of Arts and Sciences and University Medical Centre Utrecht, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Henricus J Duckers
- Erasmus MC Rotterdam, 's-Gravendijkwal 230, 3015 CE Rotterdam, The Netherlands
| | - Stefan Schulte-Merker
- Hubrecht Institute - Royal Netherlands Academy of Arts and Sciences and University Medical Centre Utrecht, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands Cells-in-Motion Cluster of Excellence (EXC 1003 - CiM), University of Münster, 48149 Münster, Germany Institute for Cardiovascular Organogenesis and Regeneration, Faculty of Medicine, Westfälische Wilhelms-Universität Münster (WWU), Mendelstrasse 7, 48149 Münster, Germany
| |
Collapse
|
34
|
Kang J, Malhotra N. Transcription factor networks directing the development, function, and evolution of innate lymphoid effectors. Annu Rev Immunol 2015; 33:505-38. [PMID: 25650177 PMCID: PMC4674156 DOI: 10.1146/annurev-immunol-032414-112025] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Mammalian lymphoid immunity is mediated by fast and slow responders to pathogens. Fast innate lymphocytes are active within hours after infections in mucosal tissues. Slow adaptive lymphocytes are conventional T and B cells with clonal antigen receptors that function days after pathogen exposure. A transcription factor (TF) regulatory network guiding early T cell development is at the core of effector function diversification in all innate lymphocytes, and the kinetics of immune responses is set by developmental programming. Operational units within the innate lymphoid system are not classified by the types of pathogen-sensing machineries but rather by discrete effector functions programmed by regulatory TF networks. Based on the evolutionary history of TFs of the regulatory networks, fast effectors likely arose earlier in the evolution of animals to fortify body barriers, and in mammals they often develop in fetal ontogeny prior to the establishment of fully competent adaptive immunity.
Collapse
Affiliation(s)
- Joonsoo Kang
- Department of Pathology, University of Massachusetts Medical School, Worcester, Massachusetts 01655;
| | | |
Collapse
|
35
|
Allette YM, Due MR, Wilson SM, Feldman P, Ripsch MS, Khanna R, White FA. Identification of a functional interaction of HMGB1 with Receptor for Advanced Glycation End-products in a model of neuropathic pain. Brain Behav Immun 2014; 42:169-77. [PMID: 25014009 PMCID: PMC4560334 DOI: 10.1016/j.bbi.2014.06.199] [Citation(s) in RCA: 75] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/20/2013] [Revised: 06/25/2014] [Accepted: 06/27/2014] [Indexed: 10/25/2022] Open
Abstract
Recent studies indicate that the release of high mobility group box 1 (HMGB1) following nerve injury may play a central role in the pathogenesis of neuropathic pain. HMGB1 is known to influence cellular responses within the nervous system via two distinct receptor families; the Receptor for Advanced Glycation End-products (RAGE) and Toll-like receptors (TLRs). The degree to which HMGB1 activates a receptor is thought to be dependent upon the oxidative state of the ligand, resulting in the functional isoforms of all-thiol HMGB1 (at-HMGB1) acting through RAGE, and disufide HMGB1 (ds-HMGB1) interacting with TLR4. Though it is known that dorsal root ganglia (DRG) sensory neurons exposed to HMGB1 and TLR4 agonists can influence excitation, the degree to which at-HMGB1 signaling through neuronal RAGE contributes to neuropathic pain is unknown. Here we demonstrate that at-HMGB1 activation of nociceptive neurons is dependent on RAGE and not TLR4. To distinguish the possible role of RAGE on neuropathic pain, we characterized the changes in RAGE mRNA expression up to one month after tibial nerve injury (TNI). RAGE mRNA expression in lumbar dorsal root ganglion (DRG) is substantially increased by post-injury day (PID) 28 when compared with sham injured rodents. Protein expression at PID28 confirms this injury-induced event in the DRG. Moreover, a single exposure to monoclonal antibody to RAGE (RAGE Ab) failed to abrogate pain behavior at PID 7, 14 and 21. However, RAGE Ab administration produced reversal of mechanical hyperalgesia on PID28. Thus, at-HMGB1 activation through RAGE may be responsible for sensory neuron sensitization and mechanical hyperalgesia associated with chronic neuropathic pain states.
Collapse
Affiliation(s)
- Yohance M Allette
- Medical Science Training Program, Department of Anatomy, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Michael R Due
- Department of Anesthesia, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Sarah M Wilson
- Program in Medical Neurosciences, Paul and Carole Stark Neurosciences Research Institute, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Polina Feldman
- Program in Medical Neurosciences, Paul and Carole Stark Neurosciences Research Institute, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Matthew S Ripsch
- Department of Anesthesia, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Rajesh Khanna
- Program in Medical Neurosciences, Paul and Carole Stark Neurosciences Research Institute, Indiana University School of Medicine, Indianapolis, IN, United States; Department of Pharmacology and Toxicology, United States; Department of Biochemistry and Molecular Biology, United States
| | - Fletcher A White
- Department of Anesthesia, Indiana University School of Medicine, Indianapolis, IN, United States; Program in Medical Neurosciences, Paul and Carole Stark Neurosciences Research Institute, Indiana University School of Medicine, Indianapolis, IN, United States.
| |
Collapse
|
36
|
Abstract
With growing accounts of inflammatory diseases such as sepsis, greater understanding the immune system and the mechanisms of cellular immunity have become primary objectives in immunology studies. High mobility group box 1 (HMGB1) is a ubiquitous nuclear protein that is implicated in various aspects of the innate immune system as a damage-associated molecular pattern molecule and a late mediator of inflammation, as well as in principal cellular processes, such as autophagy and apoptosis. HMGB1 functions in the nucleus as a DNA chaperone; however, it exhibits cytokine-like activity when secreted by injurious or infectious stimuli. Extracellular HMGB1 acts through specific receptors to promote activation of the NF-κB signaling pathway, leading to production of cytokines and chemokines. These findings further implicate HMGB1 in lethal inflammatory diseases as a crucial regulator of inflammatory, injurious, and infectious responses. In this paper, we summarize the role of HMGB1 in inflammatory and non-inflammatory states and assess potential therapeutic approaches targeting HMGB1 in inflammatory diseases.
Collapse
Affiliation(s)
- Shin-Ae Lee
- Department of Microbiology, Yonsei University College of Medicine, Seoul, Korea
| | - Man Sup Kwak
- Department of Microbiology, Yonsei University College of Medicine, Seoul, Korea
| | - Sol Kim
- Department of Microbiology, Yonsei University College of Medicine, Seoul, Korea
| | - Jeon-Soo Shin
- Department of Microbiology, Yonsei University College of Medicine, Seoul, Korea. ; Brain Korea 21 PLUS for Medical Science, Yonsei University College of Medicine, Seoul, Korea. ; Severance Biomedical Science Institute and Institute for Immunology and Immunological Diseases, Yonsei University College of Medicine, Seoul, Korea
| |
Collapse
|
37
|
Liu Z, Liu J, Wang J, Xu J, Liu Y, Sun X, Su L, Wang JH, Jiang Y. Role of testis-specific high-mobility-group protein in transcriptional regulation of inducible nitric oxide synthase expression in the liver of endotoxic shock mice. FEBS J 2014; 281:2202-13. [PMID: 24605775 DOI: 10.1111/febs.12774] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2013] [Revised: 02/24/2014] [Accepted: 02/26/2014] [Indexed: 01/13/2023]
Abstract
Inducible nitric oxide synthase (iNOS) plays a central role in tissue damage during endotoxic shock. However, the underlying mechanisms that control transcription of iNOS are not completely defined. A screening strategy with DNA pull-down technology and two-dimensional difference in gel electrophorcsis (2D-DIGE) analysis was used to identify regulators that interact with the iNOS promoter. We found 14 proteins that bind to the iNOS promoter in the liver of endotoxic shock mice. After matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF MS) analysis, one of these proteins was identified as testis-specific high-mobility-group protein (tsHMG), an alternative splicing isoform encoded by the mitochondrial transcription factor A gene. We identified the binding sites of tsHMG on the iNOS promoter using a LiquiChip system, and further confirmed interactions between tsHMG and iNOS by RT-PCR, western blotting and immunofluorescence. Functional analysis by over-expression and RNA interference of tsHMG revealed that tsHMG regulates lipopolysaccharide-stimulated iNOS expression. These results indicate that tsHMG participates in modulation of iNOS expression in the early stage of endotoxic shock.
Collapse
Affiliation(s)
- Zhifeng Liu
- Key Laboratory of Functional Proteomics of Guangdong Province, Department of Pathophysiology, Southern Medical University, Guangzhou, China; Department of Intensive Care Unit, General Hospital of Guangzhou Military Command, Guangzhou, China
| | | | | | | | | | | | | | | | | |
Collapse
|
38
|
Ohnesorg T, Vilain E, Sinclair AH. The genetics of disorders of sex development in humans. Sex Dev 2014; 8:262-72. [PMID: 24504012 DOI: 10.1159/000357956] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
One of the defining events during human embryonic development with the most far-reaching effects for the individual is whether the embryo develops as male or female. The crucial step in this process is the differentiation of the bipotential embryonic gonads into either testes or ovaries. If the embryo inherits X and Y sex chromosomes, the Y-linked SRY (sex determining region in Y) gene initiates a network of genes that results in a functional testis and ultimately a male phenotype. By contrast, in an embryo with 2 X chromosomes, the undifferentiated gonad develops as an ovary resulting in a female phenotype. Perturbation of any of the genes in either the testicular or ovarian developmental pathway can result in individuals with disorders of sex development. In this review, we provide a summary of known components of testicular or ovarian pathways and their antagonistic actions and give a brief overview of new technologies currently used to identify the missing pieces of the sex development network.
Collapse
Affiliation(s)
- Thomas Ohnesorg
- Murdoch Children's Research Institute and Department of Paediatrics, The University of Melbourne, Royal Children's Hospital, Melbourne, Vic., Australia
| | | | | |
Collapse
|
39
|
Ait Benkhali J, Coppin E, Brun S, Peraza-Reyes L, Martin T, Dixelius C, Lazar N, van Tilbeurgh H, Debuchy R. A network of HMG-box transcription factors regulates sexual cycle in the fungus Podospora anserina. PLoS Genet 2013; 9:e1003642. [PMID: 23935511 PMCID: PMC3730723 DOI: 10.1371/journal.pgen.1003642] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2012] [Accepted: 06/03/2013] [Indexed: 12/14/2022] Open
Abstract
High-mobility group (HMG) B proteins are eukaryotic DNA-binding proteins characterized by the HMG-box functional motif. These transcription factors play a pivotal role in global genomic functions and in the control of genes involved in specific developmental or metabolic pathways. The filamentous ascomycete Podospora anserina contains 12 HMG-box genes. Of these, four have been previously characterized; three are mating-type genes that control fertilization and development of the fruit-body, whereas the last one encodes a factor involved in mitochondrial DNA stability. Systematic deletion analysis of the eight remaining uncharacterized HMG-box genes indicated that none were essential for viability, but that seven were involved in the sexual cycle. Two HMG-box genes display striking features. PaHMG5, an ortholog of SpSte11 from Schizosaccharomyces pombe, is a pivotal activator of mating-type genes in P. anserina, whereas PaHMG9 is a repressor of several phenomena specific to the stationary phase, most notably hyphal anastomoses. Transcriptional analyses of HMG-box genes in HMG-box deletion strains indicated that PaHMG5 is at the hub of a network of several HMG-box factors that regulate mating-type genes and mating-type target genes. Genetic analyses revealed that this network also controls fertility genes that are not regulated by mating-type transcription factors. This study points to the critical role of HMG-box members in sexual reproduction in fungi, as 11 out of 12 members were involved in the sexual cycle in P. anserina. PaHMG5 and SpSte11 are conserved transcriptional regulators of mating-type genes, although P. anserina and S. pombe diverged 550 million years ago. Two HMG-box genes, SOX9 and its upstream regulator SRY, also play an important role in sex determination in mammals. The P. anserina and S. pombe mating-type genes and their upstream regulatory factor form a module of HMG-box genes analogous to the SRY/SOX9 module, revealing a commonality of sex regulation in animals and fungi. Podospora anserina, a coprophilous fungus, is used extensively as a model organism to address questions of sexual development and mating-type functions. Its mating-type locus contains three HMGB genes that encode transcription factors involved in fertilization and fruit-body development. We present the functional characterization of the remaining HMGB genes, which revealed that 11 of 12 HMGB genes were involved in sexual development. An analysis of the relationships between these genes uncovered a regulatory network governing the expression of mating-type genes. PaHMG5 is a key transcription factor that operates upstream of mating-type genes in this network. A homolog of PaHMG5 performs a similar function in the fission yeast Schizosaccharomyces pombe, which diverged from P. anserina 550 million years ago. The conservation of a regulatory circuit over such a prolonged timeframe is a striking exception to the general observation that sex developmental pathways are highly variable, even across closely related lineages. A module consisting of two HMGB transcription factors (Sry and Sox9) is a key regulator of sex determination in mammals. We propose that the module containing PaHMG5 and mating-type HMGB genes is the fungal counterpart of the mammalian module, revealing a commonality of sex regulation in animals and fungi.
Collapse
Affiliation(s)
- Jinane Ait Benkhali
- Université Paris-Sud, Institut de Génétique et Microbiologie UMR8621, Orsay, France
- CNRS, Institut de Génétique et Microbiologie UMR8621, Orsay, France
| | - Evelyne Coppin
- Université Paris-Sud, Institut de Génétique et Microbiologie UMR8621, Orsay, France
- CNRS, Institut de Génétique et Microbiologie UMR8621, Orsay, France
| | - Sylvain Brun
- Université Paris-Sud, Institut de Génétique et Microbiologie UMR8621, Orsay, France
- CNRS, Institut de Génétique et Microbiologie UMR8621, Orsay, France
- Université Paris Diderot, Sorbonne Paris Cité, Institut des Energies de Demain (IED), Paris, France
| | - Leonardo Peraza-Reyes
- Université Paris-Sud, Institut de Génétique et Microbiologie UMR8621, Orsay, France
- CNRS, Institut de Génétique et Microbiologie UMR8621, Orsay, France
| | - Tom Martin
- Department of Plant Biology and Forest Genetics, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala, Sweden
| | - Christina Dixelius
- Department of Plant Biology and Forest Genetics, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala, Sweden
| | - Noureddine Lazar
- Université Paris-Sud, Institut de Biochimie et de Biophysique Moléculaire et Cellulaire, UMR8619, Orsay, France
| | - Herman van Tilbeurgh
- Université Paris-Sud, Institut de Biochimie et de Biophysique Moléculaire et Cellulaire, UMR8619, Orsay, France
| | - Robert Debuchy
- Université Paris-Sud, Institut de Génétique et Microbiologie UMR8621, Orsay, France
- CNRS, Institut de Génétique et Microbiologie UMR8621, Orsay, France
- * E-mail:
| |
Collapse
|
40
|
GRG5/AES interacts with T-cell factor 4 (TCF4) and downregulates Wnt signaling in human cells and zebrafish embryos. PLoS One 2013; 8:e67694. [PMID: 23840876 PMCID: PMC3698143 DOI: 10.1371/journal.pone.0067694] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2011] [Accepted: 05/22/2013] [Indexed: 12/27/2022] Open
Abstract
Transcriptional control by TCF/LEF proteins is crucial in key developmental processes such as embryo polarity, tissue architecture and cell fate determination. TCFs associate with β-catenin to activate transcription in the presence of Wnt signaling, but in its absence act as repressors together with Groucho-family proteins (GRGs). TCF4 is critical in vertebrate intestinal epithelium, where TCF4-β-catenin complexes are necessary for the maintenance of a proliferative compartment, and their abnormal formation initiates tumorigenesis. However, the extent of TCF4-GRG complexes' roles in development and the mechanisms by which they repress transcription are not completely understood. Here we characterize the interaction between TCF4 and GRG5/AES, a Groucho family member whose functional relationship with TCFs has been controversial. We map the core GRG interaction region in TCF4 to a 111-amino acid fragment and show that, in contrast to other GRGs, GRG5/AES-binding specifically depends on a 4-amino acid motif (LVPQ) present only in TCF3 and some TCF4 isoforms. We further demonstrate that GRG5/AES represses Wnt-mediated transcription both in human cells and zebrafish embryos. Importantly, we provide the first evidence of an inherent repressive function of GRG5/AES in dorsal-ventral patterning during early zebrafish embryogenesis. These results improve our understanding of TCF-GRG interactions, have significant implications for models of transcriptional repression by TCF-GRG complexes, and lay the groundwork for in depth direct assessment of the potential role of Groucho-family proteins in both normal and abnormal development.
Collapse
|
41
|
Bidwell JP, Childress P, Alvarez MB, Hood M, He Y, Pavalko FM, Kacena MA, Yang FC. Nmp4/CIZ closes the parathyroid hormone anabolic window. Crit Rev Eukaryot Gene Expr 2012; 22:205-18. [PMID: 23140162 DOI: 10.1615/critreveukargeneexpr.v22.i3.40] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Chronic degenerative diseases are increasing with the aging U.S. population. One consequence of this phenomenon is the need for long-term osteoporosis therapies. Parathyroid hormone (PTH), the only FDA-approved treatment that adds bone to the aged skeleton, loses its potency within two years of initial treatment but the mechanism regulating its limited "anabolic window" is unknown. We have discovered that disabling the nucleocytoplasmic shuttling transcription factor nuclear matrix protein 4/cas interacting zinc finger protein (Nmp4/CIZ) in mice extends the PTH bone-forming capacity. Nmp4 was discovered during our search for nuclear matrix transcription factors that couple this hormone's impact on osteoblast cytoskeletal and nuclear organization with its anabolic capacity. CIZ was independently discovered as a protein that associates with the focal adhesion-associated mechanosensor p130Cas. The Nmp4/CIZ-knockout (KO) skeletal phenotype exhibits a modestly enhanced bone mineral density but manifests an exaggerated response to both PTH and to BMP2 and is resistant to disuse-induced bone loss. The cellular basis of the global Nmp4/CIZ-KO skeletal phenotype remains to be elucidated but may involve an expansion of the bone marrow osteoprogenitor population along with modestly enhanced osteoblast and osteoclast activities supporting anabolic bone turnover. As a shuttling Cys(2)His(2) zinc finger protein, Nmp4/CIZ acts as a repressive transcription factor perhaps associated with epigenetic remodeling complexes, but the functional significance of its interaction with p130Cas is not known. Despite numerous remaining questions, Nmp4/CIZ provides insights into how the anabolic window is regulated, and itself may provide an adjuvant therapy target for the treatment of osteoporosis by extending PTH anabolic efficacy.
Collapse
Affiliation(s)
- Joseph P Bidwell
- Department of Anatomy and Cell Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA.
| | | | | | | | | | | | | | | |
Collapse
|
42
|
Abstract
Proteins in the HMG family are important transcription factors. They recognize cisplatin-damaged DNA lesions with a structure-specific preference and account for more than 70% of all proteins that interact with the cisplatin 1,2-intrastrand d(GpG) cross-link. HMGB4, a new member of the mammalian HMGB protein family expressed preferentially in the testis, was generated recombinantly, and its interactions with cisplatin-modified DNA were investigated in vitro. The binding affinities of the two individual DNA-binding domains of HMGB4 to DNA carrying a cisplatin 1,2-intrastrand d(GpG) cross-link are weaker than those of the DNA-binding domains of HMGB1. Full-length HMGB4, however, has a 28-fold stronger binding affinity (K(d) = 4.35 nM) for the platinated adduct compared to that of HMGB1 (K(d) = 120 nM), presumably because the former lacks a C-terminal acidic tail. The residue Phe37 plays a critical role in stabilizing the binding complex of HMGB4 with the cisplatin-modified DNA, as it does for HMGB1. Hydroxyl radical footprinting analysis of the HMGB4/platinated DNA complex reveals a footprinting pattern very different from that of HMGB1, however, revealing very little binding asymmetry with respect to the platinated lesion. An in vitro repair assay revealed that HMGB4, at 1 μM, interferes with repair of cisplatin 1,2-intrastrand cross-link damage by >90% compared to control, whereas HMGB1 at the same concentration inhibits repair by 45%. This repair inhibition capability is highly dependent on both the binding affinity and the size of the proteins. The putative role of HMGB4 in the mechanism of action of cisplatin, and especially its potential relevance to the hypersensitivity of testicular germ cell tumors to cisplatin, are discussed.
Collapse
Affiliation(s)
- Semi Park
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139-4307, USA
| | | |
Collapse
|
43
|
Jash A, Yun K, Sahoo A, So JS, Im SH. Looping mediated interaction between the promoter and 3' UTR regulates type II collagen expression in chondrocytes. PLoS One 2012; 7:e40828. [PMID: 22815835 PMCID: PMC3397959 DOI: 10.1371/journal.pone.0040828] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2012] [Accepted: 06/13/2012] [Indexed: 11/18/2022] Open
Abstract
Type II collagen is the major component of articular cartilage and is mainly synthesized by chondrocytes. Repeated sub-culturing of primary chondrocytes leads to reduction of type II collagen gene (Col2a1) expression, which mimics the process of chondrocyte dedifferentiation. Although the functional importance of Col2a1 expression has been extensively investigated, mechanism of transcriptional regulation during chondrocyte dedifferentiation is still unclear. In this study, we have investigated the crosstalk between cis-acting DNA element and transcription factor on Col2a1 expression in primary chondrocytes. Bioinformatic analysis revealed the potential regulatory regions in the Col2a1 genomic locus. Among them, promoter and 3′ untranslated region (UTR) showed highly accessible chromatin architecture with enriched recruitment of active chromatin markers in primary chondrocytes. 3′ UTR has a potent enhancer function which recruits Lef1 (Lymphoid enhancer binding factor 1) transcription factor, leading to juxtaposition of the 3′ UTR with the promoter through gene looping resulting in up-regulation of Col2a1 gene transcription. Knock-down of endogenous Lef1 level significantly reduced the gene looping and subsequently down-regulated Col2a1 expression. However, these regulatory loci become inaccessible due to condensed chromatin architecture as chondrocytes dedifferentiate which was accompanied by a reduction of gene looping and down-regulation of Col2a1 expression. Our results indicate that Lef1 mediated looping between promoter and 3′ UTR under the permissive chromatin architecture upregulates Col2a1 expression in primary chondrocytes.
Collapse
Affiliation(s)
- Arijita Jash
- School of Life Sciences and Immune Synapse Research Center, Gwangju Institute of Science and Technology (GIST), Gwangju, Korea
| | - Kangsun Yun
- School of Life Sciences and Immune Synapse Research Center, Gwangju Institute of Science and Technology (GIST), Gwangju, Korea
| | - Anupama Sahoo
- School of Life Sciences and Immune Synapse Research Center, Gwangju Institute of Science and Technology (GIST), Gwangju, Korea
| | - Jae-Seon So
- School of Life Sciences and Immune Synapse Research Center, Gwangju Institute of Science and Technology (GIST), Gwangju, Korea
| | - Sin-Hyeog Im
- School of Life Sciences and Immune Synapse Research Center, Gwangju Institute of Science and Technology (GIST), Gwangju, Korea
- * E-mail:
| |
Collapse
|
44
|
Abstract
Disorders of sex development (DSD) are congenital conditions in which the development of chromosomal, gonadal, or anatomical sex is atypical. Many of the genes required for gonad development have been identified by analysis of DSD patients. However, the use of knockout and transgenic mouse strains have contributed enormously to the study of gonad gene function and interactions within the development network. Although the genetic basis of mammalian sex determination and differentiation has advanced considerably in recent years, a majority of 46,XY gonadal dysgenesis patients still cannot be provided with an accurate diagnosis. Some of these unexplained DSD cases may be due to mutations in novel DSD genes or genomic rearrangements affecting regulatory regions that lead to atypical gene expression. Here, we review our current knowledge of mammalian sex determination drawing on insights from human DSD patients and mouse models.
Collapse
Affiliation(s)
- Stefanie Eggers
- Murdoch Children’s Research Institute, Royal Children’s Hospital and Department of Paediatrics, The University of Melbourne, Melbourne, VIC Australia
| | - Andrew Sinclair
- Murdoch Children’s Research Institute, Royal Children’s Hospital and Department of Paediatrics, The University of Melbourne, Melbourne, VIC Australia
| |
Collapse
|
45
|
Yáñez-Cuna JO, Dinh HQ, Kvon EZ, Shlyueva D, Stark A. Uncovering cis-regulatory sequence requirements for context-specific transcription factor binding. Genome Res 2012; 22:2018-30. [PMID: 22534400 PMCID: PMC3460196 DOI: 10.1101/gr.132811.111] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The regulation of gene expression is mediated at the transcriptional level by enhancer regions that are bound by sequence-specific transcription factors (TFs). Recent studies have shown that the in vivo binding sites of single TFs differ between developmental or cellular contexts. How this context-specific binding is encoded in the cis-regulatory DNA sequence has, however, remained unclear. We computationally dissect context-specific TF binding sites in Drosophila, Caenorhabditis elegans, mouse, and human and find distinct combinations of sequence motifs for partner factors, which are predictive and reveal specific motif requirements of individual binding sites. We predict that TF binding in the early Drosophila embryo depends on motifs for the early zygotic TFs Vielfaltig (also known as Zelda) and Tramtrack. We validate experimentally that the activity of Twist-bound enhancers and Twist binding itself depend on Vielfaltig motifs, suggesting that Vielfaltig is more generally important for early transcription. Our finding that the motif content can predict context-specific binding and that the predictions work across different Drosophila species suggests that characteristic motif combinations are shared between sites, revealing context-specific motif codes (cis-regulatory signatures), which appear to be conserved during evolution. Taken together, this study establishes a novel approach to derive predictive cis-regulatory motif requirements for individual TF binding sites and enhancers. Importantly, the method is generally applicable across different cell types and organisms to elucidate cis-regulatory sequence determinants and the corresponding trans-acting factors from the increasing number of tissue- and cell-type-specific TF binding studies.
Collapse
|
46
|
Qin F, Ye W, Chen Y, Chen X, Li Y, Zhang J, Chen HF. Specific recognition between intrinsically disordered LEF and DNA. Phys Chem Chem Phys 2012; 14:538-45. [DOI: 10.1039/c1cp22610j] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
|
47
|
Archbold HC, Yang YX, Chen L, Cadigan KM. How do they do Wnt they do?: regulation of transcription by the Wnt/β-catenin pathway. Acta Physiol (Oxf) 2012; 204:74-109. [PMID: 21624092 DOI: 10.1111/j.1748-1716.2011.02293.x] [Citation(s) in RCA: 101] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Wnt/β-catenin signalling is known to play many roles in metazoan development and tissue homeostasis. Misregulation of the pathway has also been linked to many human diseases. In this review, specific aspects of the pathway's involvement in these processes are discussed, with an emphasis on how Wnt/β-catenin signalling regulates gene expression in a cell and temporally specific manner. The T-cell factor (TCF) family of transcription factors, which mediate a large portion of Wnt/β-catenin signalling, will be discussed in detail. Invertebrates contain a single TCF gene that contains two DNA-binding domains, the high mobility group (HMG) domain and the C-clamp, which increases the specificity of DNA binding. In vertebrates, the situation is more complex, with four TCF genes producing many isoforms that contain the HMG domain, but only some of which possess a C-clamp. Vertebrate TCFs have been reported to act in concert with many other transcription factors, which may explain how they obtain sufficient specificity for specific DNA sequences, as well as how they achieve a wide diversity of transcriptional outputs in different cells.
Collapse
Affiliation(s)
- H C Archbold
- Program in Cell and Molecular Biology, University of Michigan, Ann Arbor, 48109-1048, USA
| | | | | | | |
Collapse
|
48
|
Wu J, Richards MH, Huang J, Al-Harthi L, Xu X, Lin R, Xie F, Gibson AW, Edberg JC, Kimberly RP. Human FasL gene is a target of β-catenin/T-cell factor pathway and complex FasL haplotypes alter promoter functions. PLoS One 2011; 6:e26143. [PMID: 22022540 PMCID: PMC3191176 DOI: 10.1371/journal.pone.0026143] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2011] [Accepted: 09/20/2011] [Indexed: 01/01/2023] Open
Abstract
FasL expression on human immune cells and cancer cells plays important roles in immune homeostasis and in cancer development. Our previous study suggests that polymorphisms in the FasL promoter can significantly affect the gene expression in human cells. In addition to the functional FasL SNP -844C>T (rs763110), three other SNPs (SNP -756A>G or rs2021837, SNP -478A>T or rs41309790, and SNP -205 C>G or rs74124371) exist in the proximal FasL promoter. In the current study, we established three major FasL hyplotypes in humans. Interestingly, a transcription motif search revealed that the FasL promoter possessed two consensus T-cell factor (TCF/LEF1) binding elements (TBEs), which is either polymorphic (SNP -205C>G) or close to the functional SNP -844C>T. Subsequently, we demonstrate that both FasL TBEs formed complexes with the TCF-4 and β-catenin transcription factors in vitro and in vivo. Co-transfection of LEF-1 and β-catenin transcription factors significantly increased FasL promoter activities, suggesting that FasL is a target gene of the β-catenin/T-cell factor pathway. More importantly, we found that the rare allele (-205G) of the polymorphic FasL TBE (SNP -205C>G) failed to bind the TCF-4 transcription factor and that SNP -205 C>G significantly affected the promoter activity. Furthermore, promoter reporter assays revealed that FasL SNP haplotypes influenced promoter activities in human colon cancer cells and in human T cells. Finally, β-catenin knockdown significantly decreased the FasL expression in human SW480 colon cancer cells. Collectively, our data suggest that β-catenin may be involved in FasL gene regulation and that FasL expression is influenced by FasL SNP haplotypes, which may have significant implications in immune response and tumorigenesis.
Collapse
Affiliation(s)
- Jianming Wu
- Department of Veterinary and Biomedical Sciences, University of Minnesota, St. Paul, Minnesota, United States of America.
| | | | | | | | | | | | | | | | | | | |
Collapse
|
49
|
Zhou F, Zhang L, van Laar T, van Dam H, Ten Dijke P. GSK3β inactivation induces apoptosis of leukemia cells by repressing the function of c-Myb. Mol Biol Cell 2011; 22:3533-40. [PMID: 21795403 PMCID: PMC3172276 DOI: 10.1091/mbc.e11-06-0483] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
The level of c-Myb is a determining factor in the response of leukemia cells to GSK3β kinase inhibiton, which is of particular interest for the therapy of leukemia and cancers that have c-Myb amplifications. Glycogen synthase kinase 3β (GSK3β) regulates diverse physiological processes, including metabolism, development, oncogenesis, and neuroprotection. GSK3β kinase activity has been reported to be critical for various types of cancer cells, but the mechanism has remained elusive. In this study we examine the mechanism by which GSK3β regulates the survival of leukemia cells. We demonstrate that upon GSK3β kinase inhibition different types of leukemia cells show severe proliferation defects as a result of apoptosis. The transcription factor c-Myb is found to be the main target of GSK3β inhibition in cell survival. GSK3β inactivation reduces the expression of c-Myb by promoting its ubiquitination-mediated degradation, thereby inhibiting the expression of c-Myb–dependent antiapoptotic genes Bcl2 and survivin. Coimmunoprecipitation, reporter assays, chromatin immunoprecipitation, and knockdown studies show that c-Myb needs to interact and cooperate with transcription factor LEF-1 in the activation of Bcl2 and survivin and that both transcription factors are required for cell survival. These data reveal an as-yet-unknown mechanism by which GSK3β controls cell survival.
Collapse
Affiliation(s)
- Fangfang Zhou
- Department of Molecular Cell Biology and Centre for Biomedical Genetics, Leiden University Medical Center, 2300 RC Leiden, Netherlands
| | | | | | | | | |
Collapse
|
50
|
Gracz AD, Magness ST. Sry-box (Sox) transcription factors in gastrointestinal physiology and disease. Am J Physiol Gastrointest Liver Physiol 2011; 300:G503-15. [PMID: 21292996 PMCID: PMC3302185 DOI: 10.1152/ajpgi.00489.2010] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
The genetic mechanisms underlying tissue maintenance of the gastrointestinal tract are critical for the proper function of the digestive system under normal physiological stress. The identification of transcription factors and related signal transduction pathways that regulate stem cell maintenance and lineage allocation is attractive from a clinical standpoint in that it may provide targets for novel cell- or drug-based therapies. Sox [sex-determining region Y (Sry) box-containing] factors are a family of transcription factors that are emerging as potent regulators of stem cell maintenance and cell fate decisions in multiple organ systems and might provide valuable insight toward the understanding of these processes in endodermally derived tissues of the gastrointestinal tract. In this review, we focus on the known genetic functions of Sox factors and their roles in epithelial tissues of the esophagus, stomach, intestine, colon, pancreas, and liver. Additionally, we discuss pathological conditions in the gastrointestinal tract that are associated with a dysregulation of Sox factors. Further study of Sox factors and their role in gastrointestinal physiology and pathophysiology may lead to advances that facilitate control of tissue maintenance and development of advanced clinical therapies.
Collapse
Affiliation(s)
- A. D. Gracz
- 1Department of Medicine, Division of Gastroenterology and Hepatology, and ,2Department of Cell and Molecular Physiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - S. T. Magness
- 1Department of Medicine, Division of Gastroenterology and Hepatology, and
| |
Collapse
|