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Wang M, Pan B, Hu Y, Gao J, Hou L, Yu Z, Li M, Zhao Z. STIL facilitates the development and malignant progression of triple-negative breast cancer through activation of Fanconi anemia pathway via interacting with KLF16. Transl Oncol 2024; 46:102010. [PMID: 38823260 PMCID: PMC11177054 DOI: 10.1016/j.tranon.2024.102010] [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: 07/30/2023] [Revised: 05/08/2024] [Accepted: 05/25/2024] [Indexed: 06/03/2024] Open
Abstract
BACKGROUND STIL is an important cell cycle-regulating protein specifically recruited to the mitotic centrosome to promote the replication of centrioles in dividing cells. However, the potential role of STIL in the regulation of the biological functions of triple-negative breast cancer remains still unclear. METHODS We screened for differentially expressed STIL in the Cancer Genome Atlas database. The expression of STIL protein in 10 pairs of breast cancer tissues and adjacent normal tissues was further assessed by western blotting. Functionally, the knockdown and overexpression of STIL have been used to explore the effects of STIL on breast cancer cell proliferation, migration, and invasion. Mechanistically, RNA-seq, dual-luciferase reporter assay, chromatin immunoprecipitation assay, mass spectrometry, immunoprecipitation assay, and DNA pull-down assay were performed. RESULTS Breast cancer tissues and cells have higher STIL expression than normal tissues and cells. STIL knockdown impairs breast cancer cell growth, migration, and invasion, whereas STIL overexpression accelerates these processes. STIL promotes breast cancer progression by regulating FANCD2 expression, and exploration of its molecular mechanism demonstrated that STIL interacts with KLF16 to regulate the expression of FANCD2. CONCLUSIONS Collectively, our findings identified STIL as a critical promoter of breast cancer progression that interacts with KLF16 to regulate Fanconi anemia pathway protein FANCD2. In summary, STIL is a potential novel biomarker and therapeutic target for breast cancer.
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Affiliation(s)
- Meiling Wang
- Department of Breast Surgery & Department of Oncology, The Second Hospital of Dalian Medical University, Dalian, 116023 China
| | - Bo Pan
- Department of Breast Surgery & Department of Oncology, The Second Hospital of Dalian Medical University, Dalian, 116023 China
| | - Ye Hu
- Department of Breast Surgery & Department of Oncology, The Second Hospital of Dalian Medical University, Dalian, 116023 China
| | - Jiyue Gao
- Department of Breast Surgery & Department of Oncology, The Second Hospital of Dalian Medical University, Dalian, 116023 China
| | - Lu Hou
- Department of Breast Surgery & Department of Oncology, The Second Hospital of Dalian Medical University, Dalian, 116023 China
| | - Zhenlong Yu
- College of Pharmacy, Dalian Medical University, Dalian, China.
| | - Man Li
- Department of Breast Surgery & Department of Oncology, The Second Hospital of Dalian Medical University, Dalian, 116023 China.
| | - Zuowei Zhao
- Department of Breast Surgery & Department of Oncology, The Second Hospital of Dalian Medical University, Dalian, 116023 China.
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2
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Shwab EK, Gingerich DC, Man Z, Gamache J, Garrett ME, Crawford GE, Ashley-Koch AE, Serrano GE, Beach TG, Lutz MW, Chiba-Falek O. Single-nucleus multi-omics of Parkinson's disease reveals a glutamatergic neuronal subtype susceptible to gene dysregulation via alteration of transcriptional networks. Acta Neuropathol Commun 2024; 12:111. [PMID: 38956662 PMCID: PMC11218415 DOI: 10.1186/s40478-024-01803-1] [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: 05/22/2024] [Accepted: 05/27/2024] [Indexed: 07/04/2024] Open
Abstract
The genetic architecture of Parkinson's disease (PD) is complex and multiple brain cell subtypes are involved in the neuropathological progression of the disease. Here we aimed to advance our understanding of PD genetic complexity at a cell subtype precision level. Using parallel single-nucleus (sn)RNA-seq and snATAC-seq analyses we simultaneously profiled the transcriptomic and chromatin accessibility landscapes in temporal cortex tissues from 12 PD compared to 12 control subjects at a granular single cell resolution. An integrative bioinformatic pipeline was developed and applied for the analyses of these snMulti-omics datasets. The results identified a subpopulation of cortical glutamatergic excitatory neurons with remarkably altered gene expression in PD, including differentially-expressed genes within PD risk loci identified in genome-wide association studies (GWAS). This was the only neuronal subtype showing significant and robust overexpression of SNCA. Further characterization of this neuronal-subpopulation showed upregulation of specific pathways related to axon guidance, neurite outgrowth and post-synaptic structure, and downregulated pathways involved in presynaptic organization and calcium response. Additionally, we characterized the roles of three molecular mechanisms in governing PD-associated cell subtype-specific dysregulation of gene expression: (1) changes in cis-regulatory element accessibility to transcriptional machinery; (2) changes in the abundance of master transcriptional regulators, including YY1, SP3, and KLF16; (3) candidate regulatory variants in high linkage disequilibrium with PD-GWAS genomic variants impacting transcription factor binding affinities. To our knowledge, this study is the first and the most comprehensive interrogation of the multi-omics landscape of PD at a cell-subtype resolution. Our findings provide new insights into a precise glutamatergic neuronal cell subtype, causal genes, and non-coding regulatory variants underlying the neuropathological progression of PD, paving the way for the development of cell- and gene-targeted therapeutics to halt disease progression as well as genetic biomarkers for early preclinical diagnosis.
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Affiliation(s)
- E Keats Shwab
- Division of Translational Brain Sciences, Department of Neurology, Duke University School of Medicine, Duke University Medical Center, Durham, NC, 27710, USA
- Center for Genomic and Computational Biology, Duke University Medical Center, Durham, NC, 27708, USA
| | - Daniel C Gingerich
- Division of Translational Brain Sciences, Department of Neurology, Duke University School of Medicine, Duke University Medical Center, Durham, NC, 27710, USA
- Center for Genomic and Computational Biology, Duke University Medical Center, Durham, NC, 27708, USA
| | - Zhaohui Man
- Division of Translational Brain Sciences, Department of Neurology, Duke University School of Medicine, Duke University Medical Center, Durham, NC, 27710, USA
- Center for Genomic and Computational Biology, Duke University Medical Center, Durham, NC, 27708, USA
| | - Julia Gamache
- Division of Translational Brain Sciences, Department of Neurology, Duke University School of Medicine, Duke University Medical Center, Durham, NC, 27710, USA
- Center for Genomic and Computational Biology, Duke University Medical Center, Durham, NC, 27708, USA
| | - Melanie E Garrett
- Duke Molecular Physiology Institute, Duke University Medical Center, Durham, NC, 27701, USA
| | - Gregory E Crawford
- Center for Genomic and Computational Biology, Duke University Medical Center, Durham, NC, 27708, USA
- Division of Medical Genetics, Department of Pediatrics, Duke University Medical Center, Durham, NC, 27708, USA
- Center for Advanced Genomic Technologies, Duke University Medical Center, Durham, NC, 27708, USA
| | - Allison E Ashley-Koch
- Duke Molecular Physiology Institute, Duke University Medical Center, Durham, NC, 27701, USA
- Department of Medicine, Duke University Medical Center, Durham, NC, 27708, USA
| | - Geidy E Serrano
- Banner Sun Health Research Institute, Sun City, AZ, 85351, USA
| | - Thomas G Beach
- Banner Sun Health Research Institute, Sun City, AZ, 85351, USA
| | - Michael W Lutz
- Division of Translational Brain Sciences, Department of Neurology, Duke University School of Medicine, Duke University Medical Center, Durham, NC, 27710, USA
| | - Ornit Chiba-Falek
- Division of Translational Brain Sciences, Department of Neurology, Duke University School of Medicine, Duke University Medical Center, Durham, NC, 27710, USA.
- Center for Genomic and Computational Biology, Duke University Medical Center, Durham, NC, 27708, USA.
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3
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Gui LK, Liu HJ, Jin LJ, Peng XC. Krüpple-like factors in cardiomyopathy: emerging player and therapeutic opportunities. Front Cardiovasc Med 2024; 11:1342173. [PMID: 38516000 PMCID: PMC10955087 DOI: 10.3389/fcvm.2024.1342173] [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: 11/22/2023] [Accepted: 02/23/2024] [Indexed: 03/23/2024] Open
Abstract
Cardiomyopathy, a heterogeneous pathological condition characterized by changes in cardiac structure or function, represents a significant risk factor for the prevalence and mortality of cardiovascular disease (CVD). Research conducted over the years has led to the modification of definition and classification of cardiomyopathy. Herein, we reviewed seven of the most common types of cardiomyopathies, including Arrhythmogenic Right Ventricular Cardiomyopathy (ARVC), diabetic cardiomyopathy, Dilated Cardiomyopathy (DCM), desmin-associated cardiomyopathy, Hypertrophic Cardiomyopathy (HCM), Ischemic Cardiomyopathy (ICM), and obesity cardiomyopathy, focusing on their definitions, epidemiology, and influencing factors. Cardiomyopathies manifest in various ways ranging from microscopic alterations in cardiomyocytes, to tissue hypoperfusion, cardiac failure, and arrhythmias caused by electrical conduction abnormalities. As pleiotropic Transcription Factors (TFs), the Krüppel-Like Factors (KLFs), a family of zinc finger proteins, are involved in regulating the setting and development of cardiomyopathies, and play critical roles in associated biological processes, including Oxidative Stress (OS), inflammatory reactions, myocardial hypertrophy and fibrosis, and cellular autophagy and apoptosis, particularly in diabetic cardiomyopathy. However, research into KLFs in cardiomyopathy is still in its early stages, and the pathophysiologic mechanisms of some KLF members in various types of cardiomyopathies remain unclear. This article reviews the roles and recent research advances in KLFs, specifically those targeting and regulating several cardiomyopathy-associated processes.
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Affiliation(s)
- Le-Kun Gui
- Department of Cardiology, The First Affiliated Hospital of Yangtze University, Jingzhou, Hubei, China
- School of Medicine, Yangtze University, Jingzhou, Hubei, China
| | - Huang-Jun Liu
- Department of Cardiology, The First Affiliated Hospital of Yangtze University, Jingzhou, Hubei, China
| | - Li-Jun Jin
- Department of Cardiology, The First Affiliated Hospital of Yangtze University, Jingzhou, Hubei, China
| | - Xiao-Chun Peng
- Department of Pathophysiology, School of Basic Medicine, Health Science Center, Yangtze University, Jingzhou, Hubei, China
- Laboratory of Oncology, School of Basic Medicine, Center for Molecular Medicine, Health Science Center, Yangtze University, Jingzhou, Hubei, China
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4
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Ru Y, Ma M, Zhou X, Kriti D, Cohen N, D’Souza S, Schaniel C, Motch Perrine SM, Kuo S, Pinto D, Housman G, Wu M, Holmes G, Schadt E, van Bakel H, Zhang B, Jabs EW. Transcriptomic landscape of human induced pluripotent stem cell-derived osteogenic differentiation identifies a regulatory role of KLF16. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.11.579844. [PMID: 38405902 PMCID: PMC10888757 DOI: 10.1101/2024.02.11.579844] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
Osteogenic differentiation is essential for bone development and metabolism, but the underlying gene regulatory networks have not been well investigated. We differentiated mesenchymal stem cells, derived from 20 human induced pluripotent stem cell lines, into preosteoblasts and osteoblasts, and performed systematic RNA-seq analyses of 60 samples for differential gene expression. We noted a highly significant correlation in expression patterns and genomic proximity among transcription factor (TF) and long noncoding RNA (lncRNA) genes. We identified TF-TF regulatory networks, regulatory roles of lncRNAs on their neighboring coding genes for TFs and splicing factors, and differential splicing of TF, lncRNA, and splicing factor genes. TF-TF regulatory and gene co-expression network analyses suggested an inhibitory role of TF KLF16 in osteogenic differentiation. We demonstrate that in vitro overexpression of human KLF16 inhibits osteogenic differentiation and mineralization, and in vivo Klf16+/- mice exhibit increased bone mineral density, trabecular number, and cortical bone area. Thus, our model system highlights the regulatory complexity of osteogenic differentiation and identifies novel osteogenic genes.
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Affiliation(s)
- Ying Ru
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Meng Ma
- Mount Sinai Genomics, Sema4, Stamford, CT, 06902, USA
| | - Xianxiao Zhou
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Divya Kriti
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Ninette Cohen
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Present address: Division of Cytogenetics and Molecular Pathology, Zucker School of Medicine at Hofstra/Northwell, Northwell Health Laboratories, Lake Success, NY, 11030, USA
| | - Sunita D’Souza
- Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Present address: St Jude Children’s Research Hospital, Memphis, TN, 38105, USA
| | - Christoph Schaniel
- Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Medicine, Division of Hematology and Medical Oncology, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Mount Sinai Institute for Systems Biomedicine, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Susan M. Motch Perrine
- Department of Anthropology, Pennsylvania State University, University Park, PA, 16802, USA
| | - Sharon Kuo
- Department of Anthropology, Pennsylvania State University, University Park, PA, 16802, USA
- Department of Biomedical Sciences, University of Minnesota, Duluth, MN, 55812, USA
| | - Dalila Pinto
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Genevieve Housman
- Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL, 60637, USA
- Department of Primate Behavior and Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, 04103, Germany
| | - Meng Wu
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Clinical Genomics, Mayo Clinic, Rochester, MN, 55905
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, 55905
| | - Greg Holmes
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Eric Schadt
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Harm van Bakel
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Bin Zhang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Ethylin Wang Jabs
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Clinical Genomics, Mayo Clinic, Rochester, MN, 55905
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, 55905
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5
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Yang Y, Bhargava D, Chen X, Zhou T, Dursuk G, Jiang W, Wang J, Zong Z, Katz SI, Lomberk GA, Urrutia RA, Katz JP. KLF5 and p53 comprise an incoherent feed-forward loop directing cell-fate decisions following stress. Cell Death Dis 2023; 14:299. [PMID: 37130837 PMCID: PMC10154356 DOI: 10.1038/s41419-023-05731-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Revised: 03/01/2023] [Accepted: 03/13/2023] [Indexed: 05/04/2023]
Abstract
In response to stress, cells make a critical decision to arrest or undergo apoptosis, mediated in large part by the tumor suppressor p53. Yet the mechanisms of these cell fate decisions remain largely unknown, particularly in normal cells. Here, we define an incoherent feed-forward loop in non-transformed human squamous epithelial cells involving p53 and the zinc-finger transcription factor KLF5 that dictates responses to differing levels of cellular stress from UV irradiation or oxidative stress. In normal unstressed human squamous epithelial cells, KLF5 complexes with SIN3A and HDAC2 repress TP53, allowing cells to proliferate. With moderate stress, this complex is disrupted, and TP53 is induced; KLF5 then acts as a molecular switch for p53 function by transactivating AKT1 and AKT3, which direct cells toward survival. By contrast, severe stress results in KLF5 loss, such that AKT1 and AKT3 are not induced, and cells preferentially undergo apoptosis. Thus, in human squamous epithelial cells, KLF5 gates the response to UV or oxidative stress to determine the p53 output of growth arrest or apoptosis.
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Affiliation(s)
- Yizeng Yang
- Division of Gastroenterology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104, USA
| | - Dharmendra Bhargava
- Division of Gastroenterology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104, USA
| | - Xiao Chen
- Department of Radiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104, USA
| | - Taicheng Zhou
- Division of Gastroenterology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104, USA
| | - Gizem Dursuk
- Division of Gastroenterology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104, USA
| | - Wenpeng Jiang
- Division of Gastroenterology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104, USA
| | - Jinshen Wang
- Division of Gastroenterology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104, USA
| | - Zhen Zong
- Division of Gastroenterology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104, USA
| | - Sharyn I Katz
- Department of Radiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104, USA
| | - Gwen A Lomberk
- Department of Surgery, Medical College of Wisconsin, Milwaukee, WI, 53226, USA
| | - Raul A Urrutia
- Department of Surgery, Medical College of Wisconsin, Milwaukee, WI, 53226, USA
- Genomic Sciences and Precision Medicine Center, Medical College of Wisconsin, Milwaukee, WI, 53226, USA
| | - Jonathan P Katz
- Division of Gastroenterology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104, USA.
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6
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KLF16 enhances stress tolerance of colorectal carcinomas by modulating nucleolar homeostasis and translational reprogramming. Mol Ther 2022; 30:2828-2843. [PMID: 35524408 PMCID: PMC9372374 DOI: 10.1016/j.ymthe.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: 11/07/2021] [Revised: 04/25/2022] [Accepted: 04/29/2022] [Indexed: 12/22/2022] Open
Abstract
Translational reprogramming is part of the unfolded protein response (UPR) during endoplasmic reticulum (ER) stress, which acts to the advantage of cancer growth and development in different stress conditions. But the mechanism of ER stress-related translational reprogramming in colorectal carcinoma (CRC) progression remains unclear. Here, we identified that Krüppel-Like Factor 16 (KLF16) can promote CRC progression and stress tolerance through translational reprogramming. The expression of KLF16 was upregulated in CRC tissues and associated with poor prognosis for CRC patients. We found that ER stress inducers can recruit KLF16 to the nucleolus and increase its interaction with two essential proteins for nucleolar homeostasis, nucleophosmin1 (NPM1) and fibrillarin (FBL). Moreover, knockdown of KLF16 can dysregulate nucleolar homeostasis in CRC cells. Translation-reporter system and polysome profiling assays further showed that KLF16 can effectively promote cap-independent translation of ATF4, which can enhance ER-phagy and proliferation of CRC cells. Overall, our study unveils a previously unrecognized role for KLF16 as an ER stress regulator through mediating translational reprogramming to enhance stress tolerance of CRC cells and provides a potential therapeutic vulnerability.
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7
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Zakeri S, Aminian H, Sadeghi S, Esmaeilzadeh-Gharehdaghi E, Razmara E. Krüppel-like factors in bone biology. Cell Signal 2022; 93:110308. [PMID: 35301064 DOI: 10.1016/j.cellsig.2022.110308] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2022] [Revised: 03/07/2022] [Accepted: 03/09/2022] [Indexed: 12/27/2022]
Abstract
The krüppel-like factor (KLF) family is a group of zinc finger transcription factors and contributes to different cellular processes such as differentiation, proliferation, migration, and apoptosis. While different studies show the roles of this family in skeletal development-specifically in chondrocyte and osteocyte development and bone homeostasis-there are few reviews summarizing their importance. To fill this gap, this review discusses current knowledge on different functions of the KLF family during skeletal development, including their roles in stem cell maintenance and differentiation, cell apoptosis, and cell cycle. To understand the importance of the KLF family, we also review genotype-phenotype correlations in different animal models. We also discuss how KLF proteins function through different signaling pathways and display their paramount importance in skeletal development. To highlight their roles in cartilage- or bone-related cells, we also use single-cell RNA sequencing publicly available data on mouse hindlimb. We also challenge our knowledge of how the KLF family is epigenetically regulated-e.g., using DNA methylation, histone modifications, and noncoding RNAs-during chondrocyte and osteocyte development.
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Affiliation(s)
- Sina Zakeri
- Department of Veterinary Science, Faculty of Veterinary Medicine, Urmia University, Urmia, Iran
| | - Hesam Aminian
- Department of Biology, Faculty of Sciences, Nour Danesh Institute of Higher Education, Meymeh, Isfahan, Iran
| | - Soheila Sadeghi
- Department of Biology, Faculty of Basic Sciences, Sanandaj Branch, Islamic Azad University, Kurdistan, Iran
| | | | - Ehsan Razmara
- Department of Medical Genetics, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran.
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8
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Ye L, Liu R, Lin P, Wang W. Krüppel-like transcription factor 16 transcriptional up-regulation of cellular retinoic acid-binding proteins-2 promotes the invasion and migration and inhibits apoptosis of retinoblastoma cells by regulating integrin-β1/focal adhesion kinase /extracellular signal-regulated kinase pathway. Bioengineered 2022; 13:3694-3706. [PMID: 35671035 PMCID: PMC8973949 DOI: 10.1080/21655979.2021.2024977] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
As a common intraocular malignancy in pediatrics, retinoblastoma (RB) has high prevalence worldwide. We conducted this study, aiming to explore the molecular mechanism of Krüppel-like transcription factor 16 (KLF16)/cellular retinoic acid-binding proteins-2 (CRABP2) in regulating the invasion and migration and apoptosis of RB cells via integrin-β1/focal adhesion kinase (FAK)/extracellular signal-regulated kinase (ERK) pathway. With the adoption of real-time quantitative polymerase chain reaction (RT-qPCR) and Western blot, the mRNA and protein expression of CRABP2 and KLF16 were measured. In addition, the proliferation, clone formation ability and migration were detected with methyl thiazolyl tetrazolium (MTT), clone formation and wound healing assays, respectively. Furthermore, the invasion and apoptosis of transfected WERI-RB1 cells were evaluated with transwell and Tunel assays. With the application of Western blot, the expressions of proliferation-, apoptosis- and pathway-related proteins were assayed. The combination of KLF16 and CRABP2 was confirmed by dual-luciferase reporter assay and chromatin immunoprecipitation (ChIP). In this study, we found that CRABP2 gained a huge growth in RB cells and its silence promoted apoptosis but suppressed the proliferation, migration and invasiveness of WERI-RB1 cells. In addition, KLF16 could bind to CRABP2. It was also found that KLF16 overexpression reversed the effects of CRABP2 silence on the proliferation, migration and apoptosis of WERI-RB1 cells. What is more, CRABP2 silence blocked integrin-β1/FAK/ERK signaling pathway. In conclusion, KLF16 transcriptional up-regulation of CRABP2 promoted proliferation, invasion and migration but inhibited apoptosis of RB cells by activating integrin-β1/FAK/ERK pathway.
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Affiliation(s)
- Lu Ye
- Optometry Center, Shaanxi Eye Hospital, Xi’an People’s Hospital (Xi’an Fourth Hospital), Affiliated Guangren Hospital, School of Medicine, Xi’an Jiaotong University, Xi’an, Shaanxi Province, China
| | - Ru Liu
- Department of Ophthalmology, The First People’s Hospital of Chenzhou, Chenzhou, Hunan Province, China
| | - Ping Lin
- Department of Ophthalmology, Xi’an Children’s Hospital, Xi’an, Shaanxi Province, China
| | - Wenjun Wang
- Optometry Center, Shaanxi Eye Hospital, Xi’an People’s Hospital (Xi’an Fourth Hospital), Affiliated Guangren Hospital, School of Medicine, Xi’an Jiaotong University, Xi’an, Shaanxi Province, China
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9
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Yang L, Shi YL, Ma Y, Ren WW, Pang GM, Liu J. Silencing KLF16 inhibits oral squamous cell carcinoma cell proliferation by arresting the cell cycle and inducing apoptosis. APMIS 2021; 130:43-52. [PMID: 34779529 DOI: 10.1111/apm.13194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Accepted: 11/11/2021] [Indexed: 11/29/2022]
Abstract
Krüppel-like factor 16 (KLF16), a member of the Krüppel-like factor (KLF) family, has been extensively investigated in multiple cancer types. However, the role of KLF16 in oral squamous cell carcinoma (OSCC) remains unknown. Thus, we conducted this study to investigate its related mechanism. KLF16 expression in OSCC cell lines was quantified by western blotting. Then, OECM1 and OC3 cells were divided into Blank, siCtrl, siKLF16#1 and siKLF16#2 groups. Subsequently, cell proliferation was detected using 3-[4,5-dimethylthiazol-2-yl]-2,5 diphenyl tetrazolium bromide (MTT) assays, cell migration and invasion were detected with wound healing and Transwell assays, and cell cycle distribution and cell apoptosis were detected via flow cytometry. KLF16, p21, CDK4, Cyclin D1 and p-Rb expression was detected by western blotting. Finally, xenograft models were established in nude mice to observe the in vivo effects of KLF16 on OSCC. KLF16 protein expression was upregulated in OSCC cells. Compared to the cells in the Blank group, the OECM1 and OC3 cells in the siKLF16#1 group and siKLF16#2 group exhibited a sharp decrease in proliferation but a remarkable increase in apoptosis. Moreover, the proportion of cells in the G0/G1 phase notably increased and that in the S phase decreased, with evident decreases in cell invasion and migration. Moreover, KLF16, cyclin-dependent kinase 4 (CDK4), Cyclin D1 and p-Rb protein expression was upregulated, but p21 expression was downregulated. The mice in the siKLF16#1 and siKLF16#2 xenograft model groups exhibited slower tumour growth and smaller tumours with evident downregulation of Ki67 expression compared to the mice in the Blank group. KLF16 expression was upregulated in OSCC cells, and interfering with KLF16 led to cell cycle arrest, inhibited OSCC cell growth and promoted cell apoptosis.
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Affiliation(s)
- Lei Yang
- Department of Orthodontics, Dongfeng Stomatological Hospital, Hubei University of Medicine, Shiyan, Hubei Province, China
| | - You-Ling Shi
- Department of Orthodontics, Dongfeng Stomatological Hospital, Hubei University of Medicine, Shiyan, Hubei Province, China
| | - Yan Ma
- Department of Orthodontics, Dongfeng Stomatological Hospital, Hubei University of Medicine, Shiyan, Hubei Province, China
| | - Wei-Wei Ren
- Department of Pediatric Stomatology, Dongfeng Stomatological Hospital, Hubei University of Medicine, Shiyan, Hubei Province, China
| | - Guang-Ming Pang
- Department of Orthodontics, Dongfeng Stomatological Hospital, Hubei University of Medicine, Shiyan, Hubei Province, China
| | - Jiao Liu
- Department of Pediatric Stomatology, Dongfeng Stomatological Hospital, Hubei University of Medicine, Shiyan, Hubei Province, China
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10
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Sun N, Shen C, Zhang L, Wu X, Yu Y, Yang X, Yang C, Zhong C, Gao Z, Miao W, Yang Z, Gao W, Hu L, Williams K, Liu C, Chang Y, Gao Y. Hepatic Krüppel-like factor 16 (KLF16) targets PPARα to improve steatohepatitis and insulin resistance. Gut 2021; 70:2183-2195. [PMID: 33257471 PMCID: PMC8515101 DOI: 10.1136/gutjnl-2020-321774] [Citation(s) in RCA: 60] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/10/2020] [Revised: 10/20/2020] [Accepted: 11/08/2020] [Indexed: 12/16/2022]
Abstract
OBJECTIVE Impaired hepatic fatty acids oxidation results in lipid accumulation and redox imbalance, promoting the development of fatty liver diseases and insulin resistance. However, the underlying pathogenic mechanism is poorly understood. Krüppel-like factor 16 (KLF16) is a transcription factor that abounds in liver. We explored whether and by what mechanisms KLF16 affects hepatic lipid catabolism to improve hepatosteatosis and insulin resistance. DESIGN KLF16 expression was determined in patients with non-alcoholic fatty liver disease (NAFLD) and mice models. The role of KLF16 in the regulation of lipid metabolism was investigated using hepatocyte-specific KLF16-deficient mice fed a high-fat diet (HFD) or using an adenovirus/adeno-associated virus to alter KLF16 expression in mouse primary hepatocytes (MPHs) and in vivo livers. RNA-seq, luciferase reporter gene assay and ChIP analysis served to explore the molecular mechanisms involved. RESULTS KLF16 expression was decreased in patients with NAFLD, mice models and oleic acid and palmitic acid (OA and PA) cochallenged hepatocytes. Hepatic KLF16 knockout impaired fatty acid oxidation, aggravated mitochondrial stress, ROS burden, advancing hepatic steatosis and insulin resistance. Conversely, KLF16 overexpression reduced lipid deposition and improved insulin resistance via directly binding the promoter of peroxisome proliferator-activated receptor α (PPARα) to accelerate fatty acids oxidation and attenuate mitochondrial stress, oxidative stress in db/db and HFD mice. PPARα deficiency diminished the KLF16-evoked protective effects against lipid deposition in MPHs. Hepatic-specific PPARα overexpression effectively rescued KLF16 deficiency-induced hepatic steatosis, altered redox balance and insulin resistance. CONCLUSIONS These findings prove that a direct KLF16-PPARα pathway closely links hepatic lipid homeostasis and redox balance, whose dysfunction promotes insulin resistance and hepatic steatosis.
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Affiliation(s)
- Nannan Sun
- Science and Technology Innovation Center, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Chuangpeng Shen
- Department of Endocrinology, The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China
| | - Lei Zhang
- Department of Physiology and Pathophysiology, Tianjin Medical University, Tianjin, China
| | - Xiaojie Wu
- Central Lab of Binzhou People’s Hospital, Central Lab of Binzhou People’s Hospital, Shandong, China
| | - Yuanyuan Yu
- Artemisinin Research Center, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China
| | - Xiaoying Yang
- Jiangsu Key Laboratory of Immunity and Metabolism, Department of Pathogen Biology and Immunology, Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Chen Yang
- School of Pharmaceutical, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China
| | - Chong Zhong
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China
| | - Zhao Gao
- Guangdong Provincial Institute of Sports Science, Guangzhou, Guangdong, China
| | - Wei Miao
- Science and Technology Innovation Center, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Zehong Yang
- Science and Technology Innovation Center, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Weihang Gao
- Science and Technology Innovation Center, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Ling Hu
- Science and Technology Innovation Center, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Kevin Williams
- Division of Hypothalamic Research, University of Texas Southwestern Medical Center at Dallas, Dallas, Texas, USA
| | - Changhui Liu
- School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China
| | - Yongsheng Chang
- Department of Physiology and Pathophysiology, Tianjin Medical University, Tianjin, China
| | - Yong Gao
- Science and Technology Innovation Center, Guangzhou University of Chinese Medicine, Guangzhou, China .,Division of Hypothalamic Research, University of Texas Southwestern Medical Center at Dallas, Dallas, Texas, USA
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11
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Bang S, Li J, Zhang M, Cui R, Wu X, Xin Z, Ma D, Zhang J, Zhang H. The Clinical Relevance and Function of Krüppel-Like Factor 16 in Breast Cancer. Cancer Manag Res 2020; 12:6373-6383. [PMID: 32821156 PMCID: PMC7419641 DOI: 10.2147/cmar.s256490] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Accepted: 06/25/2020] [Indexed: 12/15/2022] Open
Abstract
Background Krüppel-like factor 16 (KLF16), a member of the KLF family, is involved in metabolism and regulation of the endocrine system and has emerging roles in tumor progression. However, the expression of KLF16 and its role in breast cancer are elusive. Methods We investigated the expression and prognostic value of KLFs in breast cancer using data acquired from the TCGA BRCA dataset and the Kaplan–Meier plotter dataset. The protein levels of KLF16 in breast specimens were detected by immunohistochemistry (IHC). KLF16 silencing using shRNAs was performed to explore the effects of KLF16 on breast cancer cell growth, migration, and invasion. The expression of EMT markers in cells manipulated for KLF16 expression was assessed by Western blotting. Results Using publicly available dataset and specimens from breast cancer patients, we found that the expression levels of KLF16 were significantly higher in tumor tissues and that high levels of KLF16 were associated with poor prognosis in breast cancer patients. Moreover, KLF16 expression levels had relation to several clinicopathological parameters of breast cancer, including the molecular subtype and histological grade. Importantly, knockdown of KLF16 dramatically suppressed cell proliferation both in vitro and in vivo. Also, KLF16 deletion impaired migration, and invasion in breast cancer cells, and suppressed epithelial–mesenchymal transition (EMT). Conclusion Our results suggest that KLF16 has important oncogenic functions in breast cancer and that the expression levels of KLF16 are associated with prognosis in breast cancer patients. Our findings also suggest that KLF16 is involved in proliferation, migration, and invasion in breast cancer cells. Thus, KLF16 might be a promising prognostic marker and a therapeutic target for breast cancer.
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Affiliation(s)
- Soyeon Bang
- Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, People's Republic of China
| | - Junhong Li
- Department of Urology, Shanghai Fifth People's Hospital, Fudan University, Shanghai, People's Republic of China
| | - Meiqin Zhang
- Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, People's Republic of China
| | - Renjie Cui
- Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, People's Republic of China
| | - Xingwen Wu
- Department of Dentistry, Zhongshan Hospital, Fudan University, Shanghai, People's Republic of China
| | - Zhaochen Xin
- Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, People's Republic of China
| | - Duan Ma
- Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, People's Republic of China.,Children's Hospital, Fudan University, Shanghai, People's Republic of China
| | - Jin Zhang
- Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, People's Republic of China
| | - Hongwei Zhang
- Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, People's Republic of China
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12
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Zhang J, Yu W, Wang X, Hu B, Wu D, Shi G. KLF16 Affects the MYC Signature and Tumor Growth in Prostate Cancer. Onco Targets Ther 2020; 13:1303-1310. [PMID: 32103997 PMCID: PMC7025737 DOI: 10.2147/ott.s233495] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2019] [Accepted: 01/18/2020] [Indexed: 11/23/2022] Open
Abstract
Background KLF16, a member of the Kruppel-like factor (KLF) family, functions in the regulation of dopaminergic transmission, metabolism, and endocrinology. However, the role of KLF16 in prostate cancer (PCa) remains unknown. Methods We screened the expression of KLFs in PCa based on bioinformatics analysis. The protein levels of KLF16 in PCa specimens were confirmed by immunohistochemistry. Inhibiting KLF16 by RNA interference with shRNA was used to determine the effects of KLF16 on PCa cell growth in vitro and in vivo. RNA sequencing was used to investigate the signaling regulated by KLF16 in PCa. Bioinformatics analysis was also used to determine the possible correlations of KLF16 and signaling in PCa cohorts. Results Bioinformatics analysis showed that KLF16 may be required for PCa development. Notably, the expression of KLF16 was elevated in human PCa tissues. In vitro and in vivo experiments both demonstrated that depleting KLF16 significantly inhibited the growth of PCa cells. Downregulation of KLF16 significantly decreased the expression of MYC signaling in PCa cells. Furthermore, KLF16 expression was correlated with MYC signaling activity. Conclusion KLF16 was overexpressed in PCa tissues compared to normal tissues. KLF16 knockdown suppressed PCa cell growth in vitro and in vivo, and a deficiency of KLF16 inhibited activation of MYC signaling.
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Affiliation(s)
- Jun Zhang
- Department of Urology, Tongji Hospital, Tongji University School of Medicine, Shanghai 200065, People's Republic of China.,Department of Urology, The Fifth People's Hospital of Shanghai, Fudan University, Shanghai 200240, People's Republic of China
| | - Wandong Yu
- Department of Urology, The Fifth People's Hospital of Shanghai, Fudan University, Shanghai 200240, People's Republic of China
| | - Xilong Wang
- Department of Urology, The Fifth People's Hospital of Shanghai, Fudan University, Shanghai 200240, People's Republic of China
| | - Bo Hu
- Department of Urology, The Fifth People's Hospital of Shanghai, Fudan University, Shanghai 200240, People's Republic of China
| | - Denglong Wu
- Department of Urology, Tongji Hospital, Tongji University School of Medicine, Shanghai 200065, People's Republic of China
| | - Guowei Shi
- Department of Urology, The Fifth People's Hospital of Shanghai, Fudan University, Shanghai 200240, People's Republic of China
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13
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Suh Y, Noh SJ, Lee S, Suh BK, Lee SB, Choi J, Jeong J, Kim S, Park SK. Dopamine D1 Receptor (D1R) Expression Is Controlled by a Transcriptional Repressor Complex Containing DISC1. Mol Neurobiol 2019; 56:6725-6735. [PMID: 30915712 PMCID: PMC6728282 DOI: 10.1007/s12035-019-1566-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2018] [Accepted: 03/13/2019] [Indexed: 11/26/2022]
Abstract
Disrupted-in-Schizophrenia 1 (DISC1) is a scaffold protein implicated in various psychiatric diseases. Dysregulation of the dopamine system has been associated with DISC1 deficiency, while the molecular mechanism is unclear. In this study, we propose a novel molecular mechanism underlying the transcriptional regulation of the dopamine D1 receptor (D1R) in the striatum via DISC1. We verified the increase in D1R at the transcriptional level in the striatum of DISC1-deficient mouse models and altered histone acetylation status at the D1r locus. We identified a functional interaction between DISC1 and Krüppel-like factor 16 (KLF16). KLF16 translocates DISC1 into the nucleus and forms a regulatory complex by recruiting SIN3A corepressor complexes to the D1r locus. Moreover, DISC1-deficient mice have altered D1R-mediated signaling in the striatum and exhibit hyperlocomotion in response to cocaine; the blockade of D1R suppresses these effects. Taken together, our results suggest that nuclear DISC1 plays a critical role in the transcriptional regulation of D1R in the striatal neuron, providing a mechanistic link between DISC1 and dopamine-related psychiatric symptoms.
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Affiliation(s)
- Yeongjun Suh
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, 37673, Republic of Korea
| | - Su-Jin Noh
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, 37673, Republic of Korea
| | - Saebom Lee
- The Russell H. Morgan Department of Radiology and Radiological Sciences, The Johns Hopkins University of School of Medicine, Baltimore, MD, USA
- The Center for Nanomedicine at Wilmer Eye Institute, The Johns Hopkins University of School of Medicine, Baltimore, MD, USA
| | - Bo Kyoung Suh
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, 37673, Republic of Korea
| | - Su Been Lee
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, 37673, Republic of Korea
| | - Jinhyuk Choi
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, 37673, Republic of Korea
| | - Jaehoon Jeong
- National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Sangjune Kim
- Neurodegeneration and Stem Cell Programs, Institute for Cell Engineering, The Johns Hopkins University of School of Medicine, Baltimore, MD, USA
- Department of Neurology, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Sang Ki Park
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, 37673, Republic of Korea.
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14
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Nagaprashantha LD, Singhal J, Chikara S, Gugiu G, Horne D, Awasthi S, Salgia R, Singhal SS. 2′-Hydroxyflavanone induced changes in the proteomic profile of breast cancer cells. J Proteomics 2019; 192:233-245. [DOI: 10.1016/j.jprot.2018.09.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Revised: 09/03/2018] [Accepted: 09/10/2018] [Indexed: 12/12/2022]
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15
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Rane MJ, Zhao Y, Cai L. Krϋppel-like factors (KLFs) in renal physiology and disease. EBioMedicine 2019; 40:743-750. [PMID: 30662001 PMCID: PMC6414320 DOI: 10.1016/j.ebiom.2019.01.021] [Citation(s) in RCA: 94] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2018] [Revised: 01/08/2019] [Accepted: 01/08/2019] [Indexed: 12/20/2022] Open
Abstract
Dysregulated Krϋppel-like factor (KLF) gene expression appears in many disease-associated pathologies. In this review, we discuss physiological functions of KLFs in the kidney with a focus on potential pharmacological modulation/therapeutic applications of these KLF proteins. KLF2 is critical to maintaining endothelial barrier integrity and preventing gap formations and in prevention of glomerular endothelial cell and podocyte damage in diabetic mice. KLF4 is renoprotective in the setting of AKI and is a critical regulator of proteinuria in mice and humans. KLF6 expression in podocytes preserves mitochondrial function and prevents podocyte apoptosis, while KLF5 expression prevents podocyte apoptosis by blockade of ERK/p38 MAPK pathways. KLF15 is a critical regulator of podocyte differentiation and is protective against podocyte injury. Loss of KLF4 and KLF15 promotes renal fibrosis, while fibrotic kidneys have increased KLF5 and KLF6 expression. For therapeutic modulation of KLFs, continued screening of small molecules will promote drug discoveries targeting KLF proteins.
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Affiliation(s)
- Madhavi J Rane
- Department of Medicine, Division Nephrology, Department of Biochemistry and Molecular Genetics, University of Louisville, Louisville, KY 40292, USA.
| | - Yuguang Zhao
- Cancer Center, The First Hospital of Jilin University, Changchun, Jilin, 130021, China
| | - Lu Cai
- Pediatric Research Institute, Department of Pediatrics, Radiation Oncology, Pharmacology and Toxicology, University of Louisville, Louisville, KY 40292, USA.
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16
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Tripodi IJ, Allen MA, Dowell RD. Detecting Differential Transcription Factor Activity from ATAC-Seq Data. Molecules 2018; 23:molecules23051136. [PMID: 29748466 PMCID: PMC6099720 DOI: 10.3390/molecules23051136] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2018] [Revised: 05/05/2018] [Accepted: 05/06/2018] [Indexed: 02/06/2023] Open
Abstract
Transcription factors are managers of the cellular factory, and key components to many diseases. Many non-coding single nucleotide polymorphisms affect transcription factors, either by directly altering the protein or its functional activity at individual binding sites. Here we first briefly summarize high-throughput approaches to studying transcription factor activity. We then demonstrate, using published chromatin accessibility data (specifically ATAC-seq), that the genome-wide profile of TF recognition motifs relative to regions of open chromatin can determine the key transcription factor altered by a perturbation. Our method of determining which TFs are altered by a perturbation is simple, is quick to implement, and can be used when biological samples are limited. In the future, we envision that this method could be applied to determine which TFs show altered activity in response to a wide variety of drugs and diseases.
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Affiliation(s)
- Ignacio J Tripodi
- Computer Science, University of Colorado, Boulder, CO 80305, USA.
- BioFrontiers Institute, University of Colorado, Boulder, CO 80303, USA.
| | - Mary A Allen
- BioFrontiers Institute, University of Colorado, Boulder, CO 80303, USA.
| | - Robin D Dowell
- Computer Science, University of Colorado, Boulder, CO 80305, USA.
- BioFrontiers Institute, University of Colorado, Boulder, CO 80303, USA.
- Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, CO 80305, USA.
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17
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Pollak NM, Hoffman M, Goldberg IJ, Drosatos K. Krüppel-like factors: Crippling and un-crippling metabolic pathways. JACC Basic Transl Sci 2018; 3:132-156. [PMID: 29876529 PMCID: PMC5985828 DOI: 10.1016/j.jacbts.2017.09.001] [Citation(s) in RCA: 68] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Revised: 09/05/2017] [Accepted: 09/06/2017] [Indexed: 12/20/2022]
Abstract
Krüppel-like factors (KLFs) are DNA-binding transcriptional factors that regulate various pathways that control metabolism and other cellular mechanisms. Various KLF isoforms have been associated with cellular, organ or systemic metabolism. Altered expression or activation of KLFs has been linked to metabolic abnormalities, such as obesity and diabetes, as well as with heart failure. In this review article we summarize the metabolic functions of KLFs, as well as the networks of different KLF isoforms that jointly regulate metabolism in health and disease.
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Affiliation(s)
- Nina M. Pollak
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland, Australia
| | - Matthew Hoffman
- Metabolic Biology Laboratory, Center for Translational Medicine, Department of Pharmacology, Lewis Katz School of Medicine at Temple University, Philadelphia, Pennsylvania
| | - Ira J. Goldberg
- Division of Endocrinology, Diabetes and Metabolism, New York University School of Medicine, New York, New York
| | - Konstantinos Drosatos
- Metabolic Biology Laboratory, Center for Translational Medicine, Department of Pharmacology, Lewis Katz School of Medicine at Temple University, Philadelphia, Pennsylvania
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18
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Khan Z, Zheng Y, Jones TL, Delaney AA, Correa LF, Shenoy CC, Khazaie K, Daftary GS. Epigenetic Therapy: Novel Translational Implications for Arrest of Environmental Dioxin-Induced Disease in Females. Endocrinology 2018; 159:477-489. [PMID: 29165700 DOI: 10.1210/en.2017-00860] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Accepted: 11/14/2017] [Indexed: 02/07/2023]
Abstract
Increased toxicant exposure and resultant environmentally induced diseases are a tradeoff of industrial productivity. Dioxin [2,3,7,8 tetrachlorodibenzo-p-dioxin (TCDD)], a ubiquitous byproduct, is associated with a spectrum of diseases including endometriosis, a common, chronic disease in women. TCDD activates cytochrome (CYP) p450 metabolic enzymes that alter organ function to cause disease. In contrast, the transcription factor, Krüppel-like factor (KLF) 11, represses these enzymes via epigenetic mechanisms. In this study, we characterized these opposing mechanisms in vitro and in vivo as well as determining potential translational implications of epigenetic inhibitor therapy. KLF11 antagonized TCDD-mediated activation of CYP3A4 gene expression and function in endometrial cells. The repression was pharmacologically replicated by selective use of an epigenetic histone acetyltransferase inhibitor (HATI). We further showed phenotypic relevance of this mechanism using an animal model for endometriosis. Fibrotic extent in TCDD-exposed wild-type animals was similar to that previously observed in Klf11-/- animals. When TCDD-exposed animals were treated with a HATI, Cyp3 messenger RNA levels and protein expression decreased along with disease progression. Fibrotic progression is ubiquitous in environmentally induced chronic, untreatable diseases; this report shows that relentless disease progression can be arrested through targeted epigenetic modulation of protective mechanisms.
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Affiliation(s)
- Zaraq Khan
- Laboratory of Translational Epigenetics in Reproduction, Department of Obstetrics and Gynecology, Mayo Clinic, Rochester, Minnesota
| | - Ye Zheng
- Laboratory of Translational Epigenetics in Reproduction, Department of Obstetrics and Gynecology, Mayo Clinic, Rochester, Minnesota
| | - Tiffanny L Jones
- Laboratory of Translational Epigenetics in Reproduction, Department of Obstetrics and Gynecology, Mayo Clinic, Rochester, Minnesota
| | - Abigail A Delaney
- Laboratory of Translational Epigenetics in Reproduction, Department of Obstetrics and Gynecology, Mayo Clinic, Rochester, Minnesota
| | - Luiz F Correa
- Laboratory of Translational Epigenetics in Reproduction, Department of Obstetrics and Gynecology, Mayo Clinic, Rochester, Minnesota
| | - Chandra C Shenoy
- Laboratory of Translational Epigenetics in Reproduction, Department of Obstetrics and Gynecology, Mayo Clinic, Rochester, Minnesota
| | - Khashayarsha Khazaie
- Laboratory of Translational Epigenetics in Reproduction, Department of Obstetrics and Gynecology, Mayo Clinic, Rochester, Minnesota
- Department of Immunology, Mayo Clinic, Rochester, Minnesota
| | - Gaurang S Daftary
- Laboratory of Translational Epigenetics in Reproduction, Department of Obstetrics and Gynecology, Mayo Clinic, Rochester, Minnesota
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19
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Bialkowska AB, Yang VW, Mallipattu SK. Krüppel-like factors in mammalian stem cells and development. Development 2017; 144:737-754. [PMID: 28246209 DOI: 10.1242/dev.145441] [Citation(s) in RCA: 79] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Krüppel-like factors (KLFs) are a family of zinc-finger transcription factors that are found in many species. Recent studies have shown that KLFs play a fundamental role in regulating diverse biological processes such as cell proliferation, differentiation, development and regeneration. Of note, several KLFs are also crucial for maintaining pluripotency and, hence, have been linked to reprogramming and regenerative medicine approaches. Here, we review the crucial functions of KLFs in mammalian embryogenesis, stem cell biology and regeneration, as revealed by studies of animal models. We also highlight how KLFs have been implicated in human diseases and outline potential avenues for future research.
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Affiliation(s)
- Agnieszka B Bialkowska
- Division of Gastroenterology, Department of Medicine, Stony Brook University School of Medicine, Stony Brook, NY 11794-8176, USA
| | - Vincent W Yang
- Division of Gastroenterology, Department of Medicine, Stony Brook University School of Medicine, Stony Brook, NY 11794-8176, USA.,Department of Physiology and Biophysics, Stony Brook University School of Medicine, Stony Brook, NY 11794-8176, USA
| | - Sandeep K Mallipattu
- Division of Nephrology, Department of Medicine, Stony Brook University School of Medicine, Stony Brook, NY 11794-8176, USA
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20
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Anbalagan M, Sheng M, Fleischer B, Zhang Y, Gao Y, Hoang V, Matossian M, Burks HE, Burow ME, Collins-Burow BM, Hangauer D, Rowan BG. Dual Src Kinase/Pretubulin Inhibitor KX-01, Sensitizes ERα-negative Breast Cancers to Tamoxifen through ERα Reexpression. Mol Cancer Res 2017; 15:1491-1502. [PMID: 28751463 DOI: 10.1158/1541-7786.mcr-16-0297-t] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Revised: 02/22/2017] [Accepted: 07/19/2017] [Indexed: 12/20/2022]
Abstract
Unlike breast cancer that is positive for estrogen receptor-α (ERα), there are no targeted therapies for triple-negative breast cancer (TNBC). ERα is silenced in TNBC through epigenetic changes including DNA methylation and histone acetylation. Restoring ERα expression in TNBC may sensitize patients to endocrine therapy. Expression of c-Src and ERα are inversely correlated in breast cancer suggesting that c-Src inhibition may lead to reexpression of ERα in TNBC. KX-01 is a peptide substrate-targeted Src/pretubulin inhibitor in clinical trials for solid tumors. KX-01 (1 mg/kg body weight-twice daily) inhibited growth of tamoxifen-resistant MDA-MB-231 and MDA-MB-157 TNBC xenografts in nude mice that was correlated with Src kinase inhibition. KX-01 also increased ERα mRNA and protein, as well as increased the ERα targets progesterone receptor (PR), pS2 (TFF1), cyclin D1 (CCND1), and c-myc (MYC) in MDA-MB-231 and MDA-MB-468, but not MDA-MB-157 xenografts. MDA-MB-231 and MDA-MB-468 tumors exhibited reduction in mesenchymal markers (vimentin, β-catenin) and increase in epithelial marker (E-cadherin) suggesting mesenchymal-to-epithelial transition (MET). KX-01 sensitized MDA-MB-231 and MDA-MB-468 tumors to tamoxifen growth inhibition and tamoxifen repression of the ERα targets pS2, cyclin D1, and c-myc. Chromatin immunoprecipitation (ChIP) of the ERα promoter in KX-01-treated tumors demonstrated enrichment of active transcription marks (acetyl-H3, acetyl-H3Lys9), dissociation of HDAC1, and recruitment of RNA polymerase II. Methylation-specific PCR and bisulfite sequencing demonstrated no alteration in ERα promoter methylation by KX-01. These data demonstrate that in addition to Src kinase inhibition, peptidomimetic KX-01 restores ERα expression in TNBC through changes in histone acetylation that sensitize tumors to tamoxifen.Implications: Src kinase/pretubulin inhibitor KX-01 restores functional ERα expression in ERα- breast tumors, a novel treatment strategy to treat triple-negative breast cancer. Mol Cancer Res; 15(11); 1491-502. ©2017 AACR.
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Affiliation(s)
- Muralidharan Anbalagan
- Department of Structural and Cellular Biology, Tulane University School of Medicine, New Orleans, Louisiana
| | - Mei Sheng
- Department of Structural and Cellular Biology, Tulane University School of Medicine, New Orleans, Louisiana
| | - Brian Fleischer
- Department of Structural and Cellular Biology, Tulane University School of Medicine, New Orleans, Louisiana
| | - Yifang Zhang
- Department of Structural and Cellular Biology, Tulane University School of Medicine, New Orleans, Louisiana.,Department of Obstetrics and Gynecology, Affiliated Hospital of Taishan Medical University, Taishan, Shandong, China
| | - Yuanjun Gao
- Department of Structural and Cellular Biology, Tulane University School of Medicine, New Orleans, Louisiana.,Department of Gastroenterology, Taihe Hospital, Hubei University of Medicine, Hubei, China
| | - Van Hoang
- Department of Medicine, Section of Hematology and Medical Oncology, Tulane University School of Medicine, New Orleans, Louisiana
| | - Margarite Matossian
- Department of Medicine, Section of Hematology and Medical Oncology, Tulane University School of Medicine, New Orleans, Louisiana
| | - Hope E Burks
- Department of Medicine, Section of Hematology and Medical Oncology, Tulane University School of Medicine, New Orleans, Louisiana
| | - Matthew E Burow
- Department of Medicine, Section of Hematology and Medical Oncology, Tulane University School of Medicine, New Orleans, Louisiana
| | - Bridgette M Collins-Burow
- Department of Medicine, Section of Hematology and Medical Oncology, Tulane University School of Medicine, New Orleans, Louisiana
| | - David Hangauer
- Athenex Pharmaceuticals LLC, New York State Center of Excellence in Bioinformatics and Life Sciences, Buffalo, New York
| | - Brian G Rowan
- Department of Structural and Cellular Biology, Tulane University School of Medicine, New Orleans, Louisiana.
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21
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Ma P, Sun CQ, Wang YF, Pan YT, Chen QN, Liu WT, Liu J, Zhao CH, Shu YQ, Li W. KLF16 promotes proliferation in gastric cancer cells via regulating p21 and CDK4. Am J Transl Res 2017; 9:3027-3036. [PMID: 28670390 PMCID: PMC5489902] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Accepted: 05/09/2017] [Indexed: 06/07/2023]
Abstract
Krüppel-like factors (KLFs), such as KLF4, KLF2, KLF5 and KLF15, have been extensively investigated in multi-cancers. However, KLF16, a member of KLFs, hasn't been well identified in cancer, especially in gastric cancer (GC). Here, we investigated the roles of KLF16 in GC. In present study, we found that KLF16 expression levels were significantly up-regulated in GC tissues compared to adjacent normal tissues both in protein and mRNA levels by using immunohistochemistry assays (IHC) and real-time quantitative PCR (qPCR). And KLF16 expression levels were positively correlated to tumor size, invasion depth, lymphatic metastasis and TNM stage. Furthermore, KLF16 expression also could predict prognosis in patients with GC. Moreover, the knock-down of KLF16 could significantly suppress proliferation via increasing p21 expression and decreasing CDK4 expression in GC cell lines. In summary, these findings demonstrate that KLF16 plays a significant role in GC progression and could be a new therapeutic target for GC patients.
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Affiliation(s)
- Pei Ma
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical UniversityNanjing, People’s Republic of China
| | - Chong-Qi Sun
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical UniversityNanjing, People’s Republic of China
| | - Yan-Fen Wang
- Department of Pathology, Yangzhou No.1 People’s HospitalYangzhou, People’s Republic of China
| | - Yu-Tian Pan
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical UniversityNanjing, People’s Republic of China
| | - Qin-Nan Chen
- Department of Oncology, The Second Affiliated Hospital of Nanjing Medical UniversityNanjing, People’s Republic of China
| | - Wei-Tao Liu
- Department of Pathology, Nanjing Medical UniversityNanjing, People’s Republic of China
| | - Jie Liu
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical UniversityNanjing, People’s Republic of China
| | - Chen-Hui Zhao
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical UniversityNanjing, People’s Republic of China
| | - Yong-Qian Shu
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical UniversityNanjing, People’s Republic of China
- Department of Medical Oncology, Affiliated Sir Run Run Hospital of Nanjing Medical UniversityNanjing, People’s Republic of China
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center For Cancer Personalized Medicine, Nanjing Medical UniversityNanjing, People’s Republic of China
| | - Wei Li
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical UniversityNanjing, People’s Republic of China
- Department of Medical Oncology, Affiliated Sir Run Run Hospital of Nanjing Medical UniversityNanjing, People’s Republic of China
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Correa LF, Zheng Y, Delaney AA, Khan Z, Shenoy CC, Daftary GS. TGF-β Induces Endometriotic Progression via a Noncanonical, KLF11-Mediated Mechanism. Endocrinology 2016; 157:3332-43. [PMID: 27384304 DOI: 10.1210/en.2016-1194] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Endometriosis, a chronic disease of heterogeneous etiopathology affects 10% of young women and is characterized by ectopic implantation of endometrial cells. Growth and spread of endometriosis lesions involves biological interplay between intrinsic lesion-driven and extrinsic host-responsive mechanisms. We propose a role for TGFβ and its target transcription factor Krüppel-like factor 11 (KLF11) in mediating such mechanisms. Although TGFβ, a pleiotropic cytokine implicated in endometriosis potentially, mediates its pathological phenotypes, KLF11 is associated with endocrine and reproductive tract diseases, specifically progression of endometriosis. In Ishikawa cells, TGFβ1 treatment resulted in noncanonical SMAD-mediated transient up-regulation and sustained repression of KLF11. KLF11 recruits histone deacetylases to epigenetically repress multiple synthetic and metabolic cytochrome P450 (CYP) enzymes such as CYP3A4, which affects endometrial metabolism and pathophysiology. In contrast to KLF11, TGFβ1 treatment caused transient repression and sustained activation of CYP3A4 expression. CYP3A4 increased endometrial cell proliferation and was also increased in human endometriosis lesions compared with eutopic endometrium. To determine whether dysregulation of TGFβ/Klf11/Cyp3a signaling affected endometriotic progression, we treated wild-type control and Klf11-/- mice with a Tgfβ type 1 receptor inhibitor (TGFβR1I) that inhibits Tgfβ signaling upstream of the canonical Smad proteins or a combination of TGFβR1I and a histone acetyltransferase inhibitor that additionally inhibits Klf11 signaling. Disease progression and lesional Cyp3a expression was diminished in TGFβR1I-treated animals and more so in animals treated synergistically with TGFβR1I and histone acetyltransferase inhibitor. TGFβ and KLF11 thus mediate critical, translationally relevant host and lesion-driven responses that enable establishment and progression of endometriosis.
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Affiliation(s)
- Luiz F Correa
- Laboratory of Translational Epigenetics in Reproduction, Department of Obstetrics and Gynecology, Mayo Clinic, Rochester, Minnesota 55905
| | - Ye Zheng
- Laboratory of Translational Epigenetics in Reproduction, Department of Obstetrics and Gynecology, Mayo Clinic, Rochester, Minnesota 55905
| | - Abigail A Delaney
- Laboratory of Translational Epigenetics in Reproduction, Department of Obstetrics and Gynecology, Mayo Clinic, Rochester, Minnesota 55905
| | - Zaraq Khan
- Laboratory of Translational Epigenetics in Reproduction, Department of Obstetrics and Gynecology, Mayo Clinic, Rochester, Minnesota 55905
| | - Chandra C Shenoy
- Laboratory of Translational Epigenetics in Reproduction, Department of Obstetrics and Gynecology, Mayo Clinic, Rochester, Minnesota 55905
| | - Gaurang S Daftary
- Laboratory of Translational Epigenetics in Reproduction, Department of Obstetrics and Gynecology, Mayo Clinic, Rochester, Minnesota 55905
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23
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Delaney AA, Khan Z, Zheng Y, Correa LF, Zanfagnin V, Shenoy CC, Schoolmeester JK, Saadalla AM, El-Nashar S, Famuyide AO, Subramaniam M, Hawse JR, Khazaie K, Daftary GS. KLF10 Mediated Epigenetic Dysregulation of Epithelial CD40/CD154 Promotes Endometriosis. Biol Reprod 2016; 95:62. [PMID: 27488034 PMCID: PMC5333936 DOI: 10.1095/biolreprod.116.140764] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2016] [Accepted: 07/27/2016] [Indexed: 12/11/2022] Open
Abstract
Endometriosis is a highly prevalent, chronic, heterogeneous, fibro-inflammatory disease that remains recalcitrant to conventional therapy. We previously showed that loss of KLF11, a transcription factor implicated in uterine disease, results in progression of endometriosis. Despite extensive homology, co-expression, and human disease association, loss of the paralog Klf10 causes a unique inflammatory, cystic endometriosis phenotype in contrast to fibrotic progression seen with loss of Klf11. We identify here for the first time a novel role for KLF10 in endometriosis. In an animal endometriosis model, unlike wild-type controls, Klf10−/− animals developed cystic lesions with massive immune infiltrate and minimal peri-lesional fibrosis. The Klf10−/− disease progression phenotype also contrasted with prolific fibrosis and minimal immune cell infiltration seen in Klf11−/− animals. We further found that lesion genotype rather than that of the host determined each unique disease progression phenotype. Mechanistically, KLF10 regulated CD40/CD154-mediated immune pathways. Both inflammatory as well as fibrotic phenotypes are the commonest clinical manifestations in chronic fibro-inflammatory diseases such as endometriosis. The complementary, paralogous Klf10 and Klf11 models therefore offer novel insights into the mechanisms of inflammation and fibrosis in a disease-relevant context. Our data suggests that divergence in underlying gene dysregulation critically determines disease-phenotype predominance rather than the conventional paradigm of inflammation being precedent to fibrotic scarring. Heterogeneity in clinical progression and treatment response are thus likely from disparate gene regulation profiles. Characterization of disease phenotype-associated gene dysregulation offers novel approaches for developing targeted, individualized therapy for recurrent and recalcitrant chronic disease.
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Affiliation(s)
- Abigail A Delaney
- Laboratory of Translational Epigenetics in Reproduction, Mayo Clinic, Rochester, Minnesota Department of Obstetrics and Gynecology, Mayo Clinic, Rochester, Minnesota
| | - Zaraq Khan
- Laboratory of Translational Epigenetics in Reproduction, Mayo Clinic, Rochester, Minnesota Department of Obstetrics and Gynecology, Mayo Clinic, Rochester, Minnesota
| | - Ye Zheng
- Laboratory of Translational Epigenetics in Reproduction, Mayo Clinic, Rochester, Minnesota Department of Obstetrics and Gynecology, Mayo Clinic, Rochester, Minnesota
| | - Luiz F Correa
- Laboratory of Translational Epigenetics in Reproduction, Mayo Clinic, Rochester, Minnesota Department of Obstetrics and Gynecology, Mayo Clinic, Rochester, Minnesota
| | - Valentina Zanfagnin
- Laboratory of Translational Epigenetics in Reproduction, Mayo Clinic, Rochester, Minnesota Department of Obstetrics and Gynecology, Mayo Clinic, Rochester, Minnesota
| | - Chandra C Shenoy
- Laboratory of Translational Epigenetics in Reproduction, Mayo Clinic, Rochester, Minnesota Department of Obstetrics and Gynecology, Mayo Clinic, Rochester, Minnesota
| | - John K Schoolmeester
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | | | - Sherif El-Nashar
- Laboratory of Translational Epigenetics in Reproduction, Mayo Clinic, Rochester, Minnesota
| | - Abimbola O Famuyide
- Laboratory of Translational Epigenetics in Reproduction, Mayo Clinic, Rochester, Minnesota
| | | | - John R Hawse
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, Minnesota
| | | | - Gaurang S Daftary
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota Department of Obstetrics and Gynecology, Mayo Clinic, Rochester, Minnesota
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24
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Wang J, Galvao J, Beach KM, Luo W, Urrutia RA, Goldberg JL, Otteson DC. Novel Roles and Mechanism for Krüppel-like Factor 16 (KLF16) Regulation of Neurite Outgrowth and Ephrin Receptor A5 (EphA5) Expression in Retinal Ganglion Cells. J Biol Chem 2016; 291:18084-95. [PMID: 27402841 DOI: 10.1074/jbc.m116.732339] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Indexed: 11/06/2022] Open
Abstract
Regenerative medicine holds great promise for the treatment of degenerative retinal disorders. Krüppel-like factors (KLFs) are transcription factors that have recently emerged as key tools in regenerative medicine because some of them can function as epigenetic reprogrammers in stem cell biology. Here, we show that KLF16, one of the least understood members of this family, is a POU4F2 independent transcription factor in retinal ganglion cells (RGCs) as early as embryonic day 15. When overexpressed, KLF16 inhibits RGC neurite outgrowth and enhances RGC growth cone collapse in response to exogenous ephrinA5 ligands. Ephrin/EPH signaling regulates RGC connectivity. The EphA5 promoter contains multiple GC- and GT-rich KLF-binding sites, which, as shown by ChIP-assays, bind KLF16 in vivo In electrophoretic mobility shift assays, KLF16 binds specifically to a single KLF site near the EphA5 transcription start site that is required for KLF16 transactivation. Interestingly, methylation of only six of 98 CpG dinucleotides within the EphA5 promoter blocks its transactivation by KLF16 but enables transactivation by KLF2 and KLF15. These data demonstrate a role for KLF16 in regulation of RGC neurite outgrowth and as a methylation-sensitive transcriptional regulator of EphA5 expression. Together, these data identify differential low level methylation as a novel mechanism for regulating KLF16-mediated EphA5 expression across the retina. Because of the critical role of ephrin/EPH signaling in patterning RGC connectivity, understanding the role of KLFs in regulating neurite outgrowth and Eph receptor expression will be vital for successful restoration of functional vision through optic nerve regenerative therapies.
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Affiliation(s)
- Jianbo Wang
- From the Departments of Physiological Optics and Vision Science and
| | - Joana Galvao
- the Byers Eye Institute, School of Medicine, Stanford University, Palo Alto, California 94303, the Shiley Eye Institute, University of California San Diego, La Jolla, California 92093, and
| | - Krista M Beach
- From the Departments of Physiological Optics and Vision Science and
| | - Weijia Luo
- Biology and Biochemistry, University of Houston, Houston, Texas 77204
| | - Raul A Urrutia
- the Laboratory of Epigenetics and Chromatin Dynamics, Gastroenterology Research Unit, Epigenomics Translational Program, Center for Individualized Medicine, Departments of Medicine, Biochemistry and Molecular Biology, Mayo Clinic, Rochester, Minnesota 55905
| | - Jeffrey L Goldberg
- the Byers Eye Institute, School of Medicine, Stanford University, Palo Alto, California 94303, the Shiley Eye Institute, University of California San Diego, La Jolla, California 92093, and
| | - Deborah C Otteson
- From the Departments of Physiological Optics and Vision Science and Biology and Biochemistry, University of Houston, Houston, Texas 77204,
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25
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Zheng Y, Khan Z, Zanfagnin V, Correa LF, Delaney AA, Daftary GS. Epigenetic Modulation of Collagen 1A1: Therapeutic Implications in Fibrosis and Endometriosis1. Biol Reprod 2016; 94:87. [DOI: 10.1095/biolreprod.115.138115] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Accepted: 02/25/2016] [Indexed: 01/08/2023] Open
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26
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Human cancer: Is it linked to dysfunctional lipid metabolism? Biochim Biophys Acta Gen Subj 2015; 1850:352-64. [DOI: 10.1016/j.bbagen.2014.11.004] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2014] [Revised: 10/27/2014] [Accepted: 11/03/2014] [Indexed: 11/23/2022]
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27
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Zheng Y, Tabbaa ZM, Khan Z, Schoolmeester JK, El-Nashar S, Famuyide A, Keeney GL, Daftary GS. Epigenetic regulation of uterine biology by transcription factor KLF11 via posttranslational histone deacetylation of cytochrome p450 metabolic enzymes. Endocrinology 2014; 155:4507-20. [PMID: 25076120 DOI: 10.1210/en.2014-1139] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Endocrine regulation of uterine biology is critical for embryo receptivity and human reproduction. Uterine endometrium depends on extrinsic sex steroid input and hence likely has mechanisms that enable adaptation to hormonal variation. Emerging evidence suggests that sex steroid bioavailability in the endometrium is determined by adjusting their metabolic rate and fate via regulation of cytochrome (CYP) p450 enzymes. The CYP enzymes are targeted by ubiquitously expressed Sp/Krüppel-like (Sp/KLF) transcription factors. Specifically, KLF11 is highly expressed in reproductive tissues, regulates an array of endocrine/metabolic pathways via epigenetic histone-based mechanisms and, when aberrantly expressed, is associated with diabetes and reproductive tract diseases, such as leiomyoma and endometriosis. Using KLF11 as a model to investigate epigenetic regulation of endometrial first-pass metabolism, we evaluated the expression of a comprehensive array of metabolic enzymes in Ishikawa cells. KLF11 repressed most endometrial CYP enzymes. To characterize KLF11-recruited epigenetic regulatory mechanisms, we focused on the estrogen-metabolizing enzyme CYP3A4. KLF11 expression declined in secretory phase endometrial epithelium associated with increased CYP3A4 expression. Additionally, KLF11 bound to CYP3A4 promoter GC elements and thereby repressed promoter, message, protein as well as enzymatic function. This repression was epigenetically mediated, because KLF11 colocalized with and recruited the corepressor SIN3A/histone deacetylase resulting in selective deacetylation of the CYP3A4 promoter. Repression was reversed by a mutation in KLF11 that abrogated cofactor recruitment and binding. This repression was also pharmacologically reversible with an histone deacetylase inhibitor. Pharmacological alteration of endometrial metabolism could have long-term translational implications on human reproduction and uterine disease.
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Affiliation(s)
- Ye Zheng
- Laboratory of Translational Epigenetics in Reproduction (Y.Z., Z.M.T., Z.K., G.S.D.) and Departments of Laboratory Medicine and Pathology (J.K.S., G.L.K.) and Obstetrics and Gynecology (Y.Z., Z.M.T., Z.K., S.E.-N., A.F., G.S.D.), Mayo Clinic, Rochester, Minnesota 55905
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28
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Koh KH, Pan X, Zhang W, McLachlan A, Urrutia R, Jeong H. Krüppel-like factor 9 promotes hepatic cytochrome P450 2D6 expression during pregnancy in CYP2D6-humanized mice. Mol Pharmacol 2014; 86:727-35. [PMID: 25217496 DOI: 10.1124/mol.114.093666] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Cytochrome P450 2D6 (CYP2D6), a major drug-metabolizing enzyme, is responsible for metabolism of approximately 25% of marketed drugs. Clinical evidence indicates that metabolism of CYP2D6 substrates is increased during pregnancy, but the underlying mechanisms remain unclear. To identify transcription factors potentially responsible for CYP2D6 induction during pregnancy, a panel of genes differentially expressed in the livers of pregnant versus nonpregnant CYP2D6-humanized (tg-CYP2D6) mice was compiled via microarray experiments followed by real-time quantitative reverse-transcription polymerase chain reaction(qRT-PCR) verification. As a result, seven transcription factors-activating transcription factor 5 (ATF5), early growth response 1 (EGR1), forkhead box protein A3 (FOXA3), JUNB, Krüppel-like factor 9 (KLF9), KLF10, and REV-ERBα-were found to be up-regulated in liver during pregnancy. Results from transient transfection and promoter reporter gene assays indicate that KLF9 itself is a weak transactivator of CYP2D6 promoter but significantly enhances CYP2D6 promoter transactivation by hepatocyte nuclear factor 4 (HNF4α), a known transcriptional activator of CYP2D6 expression. The results from deletion and mutation analysis of CYP2D6 promoter activity identified a KLF9 putative binding motif at -22/-14 region to be critical in the potentiation of HNF4α-induced transactivation of CYP2D6. Electrophoretic mobility shift assays revealed a direct binding of KLF9 to the putative KLF binding motif. Results from chromatin immunoprecipitation assay showed increased recruitment of KLF9 to CYP2D6 promoter in the livers of tg-CYP2D6 mice during pregnancy. Taken together, our data suggest that increased KLF9 expression is in part responsible for CYP2D6 induction during pregnancy via the potentiation of HNF4α transactivation of CYP2D6.
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Affiliation(s)
- Kwi Hye Koh
- Department of Pharmacy Practice (K.H.K., H.J.), Department of Biopharmaceutical Sciences (X.P., H.J.), College of Pharmacy, and Department of Pediatrics (W.Z.) and Department of Microbiology and Immunology (A.M.), College of Medicine, University of Illinois at Chicago, Chicago, Illinois; and Laboratory of Epigenetics and Chromatin Dynamics, and Departments of Biology and Molecular Biology, Epigenomics Translational Program, Mayo Clinic Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota (R.U.)
| | - Xian Pan
- Department of Pharmacy Practice (K.H.K., H.J.), Department of Biopharmaceutical Sciences (X.P., H.J.), College of Pharmacy, and Department of Pediatrics (W.Z.) and Department of Microbiology and Immunology (A.M.), College of Medicine, University of Illinois at Chicago, Chicago, Illinois; and Laboratory of Epigenetics and Chromatin Dynamics, and Departments of Biology and Molecular Biology, Epigenomics Translational Program, Mayo Clinic Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota (R.U.)
| | - Wei Zhang
- Department of Pharmacy Practice (K.H.K., H.J.), Department of Biopharmaceutical Sciences (X.P., H.J.), College of Pharmacy, and Department of Pediatrics (W.Z.) and Department of Microbiology and Immunology (A.M.), College of Medicine, University of Illinois at Chicago, Chicago, Illinois; and Laboratory of Epigenetics and Chromatin Dynamics, and Departments of Biology and Molecular Biology, Epigenomics Translational Program, Mayo Clinic Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota (R.U.)
| | - Alan McLachlan
- Department of Pharmacy Practice (K.H.K., H.J.), Department of Biopharmaceutical Sciences (X.P., H.J.), College of Pharmacy, and Department of Pediatrics (W.Z.) and Department of Microbiology and Immunology (A.M.), College of Medicine, University of Illinois at Chicago, Chicago, Illinois; and Laboratory of Epigenetics and Chromatin Dynamics, and Departments of Biology and Molecular Biology, Epigenomics Translational Program, Mayo Clinic Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota (R.U.)
| | - Raul Urrutia
- Department of Pharmacy Practice (K.H.K., H.J.), Department of Biopharmaceutical Sciences (X.P., H.J.), College of Pharmacy, and Department of Pediatrics (W.Z.) and Department of Microbiology and Immunology (A.M.), College of Medicine, University of Illinois at Chicago, Chicago, Illinois; and Laboratory of Epigenetics and Chromatin Dynamics, and Departments of Biology and Molecular Biology, Epigenomics Translational Program, Mayo Clinic Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota (R.U.)
| | - Hyunyoung Jeong
- Department of Pharmacy Practice (K.H.K., H.J.), Department of Biopharmaceutical Sciences (X.P., H.J.), College of Pharmacy, and Department of Pediatrics (W.Z.) and Department of Microbiology and Immunology (A.M.), College of Medicine, University of Illinois at Chicago, Chicago, Illinois; and Laboratory of Epigenetics and Chromatin Dynamics, and Departments of Biology and Molecular Biology, Epigenomics Translational Program, Mayo Clinic Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota (R.U.)
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29
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Krüppel-like factor 5 as potential molecular marker in cervical cancer and the KLF family profile expression. Tumour Biol 2014; 35:11399-407. [PMID: 25119587 DOI: 10.1007/s13277-014-2380-4] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2014] [Accepted: 07/22/2014] [Indexed: 12/19/2022] Open
Abstract
Cervical cancer (CC) as other cancer types, presents molecular deregulations, such as the alterations of transcription factors. Krüppel-like factors (KLF) are a family of transcriptional regulators. They are involved in diverse cellular processes, such as proliferation, apoptosis, and angiogenesis among others. Here, we analyzed the expression of all 17 KLF members at messenger RNA (mRNA) level, and protein expression of the two most commonly altered KLF5 and KLF6 in cervical tissues. Fifty-nine cervical tissues ranging from normal tissue to CC were evaluated for KLF1-17 mRNA expression by end-point RT-PCR and KLF5 by qRT-PCR. For KLF5 and KLF6 protein analysis, a tissue microarray was constructed containing the 59 cases and subjected for immunohistochemistry assay and KLF6 IVS1-27G>A single nucleotide polymorphism by direct DNA sequencing. KLF2-16 expressions were present in normal tissue, whereas all 17 were present in Low-Grade Squamous Intraepithelial Lesion, High-Grade-SIL and CC, unrelated to presence of human papillomavirus (HPV). KLF5 mRNA expression gradually increased throughout the subgroups and overexpressed in CC (p=0.01). KLF5 and KLF6 proteins were immunodetected in all samples. For the KLF6 SNP analysis, 80% of the CC population analyzed presented GG genotype and the remaining 20% presented GA genotype (p=0.491). Our present data show that KLFs expression could not be related to HPV presence, at least at transcriptional level, and KLF5 mRNA overexpression could represent a potential molecular marker for CC; KLF6 SNP has no relation to increased risk of CC.
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30
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Xiong Y, Svingen PA, Sarmento OO, Smyrk TC, Dave M, Khanna S, Lomberk GA, Urrutia RA, Faubion WA. Differential coupling of KLF10 to Sin3-HDAC and PCAF regulates the inducibility of the FOXP3 gene. Am J Physiol Regul Integr Comp Physiol 2014; 307:R608-20. [PMID: 24944246 DOI: 10.1152/ajpregu.00085.2014] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Inducible gene expression, which requires chromatin remodeling on gene promoters, underlies the epigenetically inherited differentiation program of most immune cells. However, chromatin-mediated mechanisms that underlie these events in T regulatory cells remain to be fully characterized. Here, we report that inducibility of FOXP3, a key transcription factor for the development of T regulatory cells, depends upon Kruppel-like factor 10 (KLF10) interacting with two antagonistic histone-modifying systems. We utilized chromatin immunoprecipitation, genome-integrated reporter assays, and functional domain KLF10 mutant proteins, to characterize reciprocal interactions between this transcription factor and either the Sin3-histone deacetylase complex or the histone acetyltransferase, p300/CBP-associated factor (PCAF). We characterize a Sin3-interacting repressor domain on the NH2 terminus of KLF10, which works to limit the activating function of this transcription factor. Indeed, inactivation of this Sin3-interacting domain renders KLF10 able to physically associate with PCAF as to induce FOXP3 gene transcription. We show that this biochemical data derived from studying our genome-integrated reporter cell system are recapitulated in primary murine lymphocytes. Collectively, these results advance our understanding of how a single transcription factor, namely KLF10, functions as a toggle to integrate antagonistic signals regulating FOXP3 and, thus, immune activation.
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Affiliation(s)
- Yuning Xiong
- Epigenetics and Chromatin Dynamics Laboratory, Mayo Clinic, Rochester, Minnesota; Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
| | - Phyllis A Svingen
- Epigenetics and Chromatin Dynamics Laboratory, Mayo Clinic, Rochester, Minnesota; Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
| | - Olga O Sarmento
- Epigenetics and Chromatin Dynamics Laboratory, Mayo Clinic, Rochester, Minnesota; Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
| | - Thomas C Smyrk
- Department of Anatomic Pathology, Mayo Clinic, Rochester, Minnesota
| | - Maneesh Dave
- Epigenetics and Chromatin Dynamics Laboratory, Mayo Clinic, Rochester, Minnesota; Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
| | - Sahil Khanna
- Epigenetics and Chromatin Dynamics Laboratory, Mayo Clinic, Rochester, Minnesota; Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
| | - Gwen A Lomberk
- Epigenetics and Chromatin Dynamics Laboratory, Mayo Clinic, Rochester, Minnesota; Translational Epigenomic Program, Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota; and
| | - Raul A Urrutia
- Epigenetics and Chromatin Dynamics Laboratory, Mayo Clinic, Rochester, Minnesota; Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota; Translational Epigenomic Program, Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota; and
| | - William A Faubion
- Epigenetics and Chromatin Dynamics Laboratory, Mayo Clinic, Rochester, Minnesota; Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota; Translational Epigenomic Program, Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota; and
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31
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de Assuncao TM, Lomberk G, Cao S, Yaqoob U, Mathison A, Simonetto DA, Huebert RC, Urrutia RA, Shah VH. New role for Kruppel-like factor 14 as a transcriptional activator involved in the generation of signaling lipids. J Biol Chem 2014; 289:15798-809. [PMID: 24759103 DOI: 10.1074/jbc.m113.544346] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Sphingosine kinase 1 (SK1) is an FGF-inducible gene responsible for generation of sphingosine-1-phosphate, a critical lipid signaling molecule implicated in diverse endothelial cell functions. In this study, we identified SK1 as a target of the canonical FGF2/FGF receptor 1 activation pathway in endothelial cells and sought to identify novel transcriptional pathways that mediate lipid signaling. Studies using the 1.9-kb SK1 promoter and deletion mutants revealed that basal and FGF2-stimulated promoter activity occurred through two GC-rich regions located within 633 bp of the transcription start site. Screening for GC-rich binding transcription factors that could activate this site demonstrated that KLF14, a gene implicated in obesity and the metabolic syndrome, binds to this region. Congruently, overexpression of KLF14 increased basal and FGF2-stimulated SK1 promoter activity by 3-fold, and this effect was abrogated after mutation of the GC-rich sites. In addition, KLF14 siRNA transfection decreased SK1 mRNA and protein levels by 3-fold. Congruently, SK1 mRNA and protein levels were decreased in livers from KLF14 knock-out mice. Combined, luciferase, gel shift, and chromatin immunoprecipitation assays showed that KLF14 couples to p300 to increase the levels of histone marks associated with transcriptional activation (H4K8ac and H3K14ac), while decreasing repressive marks (H3K9me3 and H3K27me3). Collectively, the results demonstrate a novel mechanism whereby SK1 lipid signaling is regulated by epigenetic modifications conferred by KLF14 and p300. Thus, this is the first description of the activity and mechanisms underlying the function of KLF14 as an activator protein and novel regulator of lipid signaling.
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Affiliation(s)
- Thiago M de Assuncao
- From the Gastroenterology Research Unit, Departments of Biochemistry and Molecular Biology, Physiology and Biophysics, and Medicine and
| | - Gwen Lomberk
- From the Gastroenterology Research Unit, Departments of Biochemistry and Molecular Biology, Physiology and Biophysics, and Medicine and the Epigenomics Translational Program, Mayo Clinic Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota 55905
| | - Sheng Cao
- From the Gastroenterology Research Unit, Departments of Biochemistry and Molecular Biology, Physiology and Biophysics, and Medicine and
| | - Usman Yaqoob
- From the Gastroenterology Research Unit, Departments of Biochemistry and Molecular Biology, Physiology and Biophysics, and Medicine and
| | - Angela Mathison
- From the Gastroenterology Research Unit, Departments of Biochemistry and Molecular Biology, Physiology and Biophysics, and Medicine and
| | - Douglas A Simonetto
- From the Gastroenterology Research Unit, Departments of Biochemistry and Molecular Biology, Physiology and Biophysics, and Medicine and
| | - Robert C Huebert
- From the Gastroenterology Research Unit, Departments of Biochemistry and Molecular Biology, Physiology and Biophysics, and Medicine and
| | - Raul A Urrutia
- From the Gastroenterology Research Unit, Departments of Biochemistry and Molecular Biology, Physiology and Biophysics, and Medicine and the Epigenomics Translational Program, Mayo Clinic Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota 55905
| | - Vijay H Shah
- From the Gastroenterology Research Unit, Departments of Biochemistry and Molecular Biology, Physiology and Biophysics, and Medicine and
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Liu Y, Olanrewaju YO, Zheng Y, Hashimoto H, Blumenthal RM, Zhang X, Cheng X. Structural basis for Klf4 recognition of methylated DNA. Nucleic Acids Res 2014; 42:4859-67. [PMID: 24520114 PMCID: PMC4005678 DOI: 10.1093/nar/gku134] [Citation(s) in RCA: 72] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
Transcription factor Krüppel-like factor 4 (Klf4), one of the factors directing cellular reprogramming, recognizes the CpG dinucleotide (whether methylated or unmodified) within a specific G/C-rich sequence. The binding affinity of the mouse Klf4 DNA-binding domain for methylated DNA is only slightly stronger than that for an unmodified oligonucleotide. The structure of the C-terminal three Krüppel-like zinc fingers (ZnFs) of mouse Klf4, in complex with fully methylated DNA, was determined at 1.85 Å resolution. An arginine and a glutamate interact with the methyl group. By comparison with two other recently characterized structures of ZnF protein complexes with methylated DNA, we propose a common principle of recognition of methylated CpG by C2H2 ZnF proteins, which involves a spatially conserved Arg–Glu pair.
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Affiliation(s)
- Yiwei Liu
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA, New England Biolabs, 240 County Road, Ipswich, MA 01938, USA and Department of Medical Microbiology and Immunology and Program in Bioinformatics, The University of Toledo College of Medicine and Life Sciences, Toledo, OH 43614, USA
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Tabbaa ZM, Zheng Y, Daftary GS. KLF11 epigenetically regulates glycodelin-A, a marker of endometrial biology via histone-modifying chromatin mechanisms. Reprod Sci 2013; 21:319-28. [PMID: 24060634 DOI: 10.1177/1933719113503407] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Endometrial biology is characterized by programmed proliferation and differentiation that is synchronous with ovarian folliculogenesis to maximize the chance of pregnancy. Glycodelin-A, an endometrial secretory protein, promotes pregnancy mostly through immunomodulatory mechanisms. Glycodelin-A is repressed during the proliferative and early secretory phase and activated thereafter. Progesterone activates glycodelin via the Sp1 (Specificity Protein 1) transactivator. We identify a novel role for Kruppel-like transcription factor 11 (KLF11) as a glycodelin-A repressor. Although KLF11 bound 2 distinct regulatory elements, it regulated glycodelin promoter activity differentially through each element. Whereas KLF11 weakly activated glycodelin promoter activity via a region that also bound Sp1, the dominant effect of KLF11 was repression of promoter activity, messenger RNA (mRNA), and protein expression via a novel, specific binding element. KLF11 mediated this repression by recruiting the SIN3/histone deacetylase (HDAC) corepressor complex to the glycodelin promoter. KLF11 may solely, or by competing with Sp1, repress glycodelin-A levels and thereby influence its role in the endometrium.
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Affiliation(s)
- Zaid M Tabbaa
- 1Laboratory of Translational Epigenetics in Reproduction, Department of Obstetrics and Gynecology, Mayo Clinic, Rochester, MN, USA
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Lomberk G, Grzenda A, Mathison A, Escande C, Zhang JS, Calvo E, Miller LJ, Iovanna J, Chini EN, Fernandez-Zapico ME, Urrutia R. Krüppel-like factor 11 regulates the expression of metabolic genes via an evolutionarily conserved protein interaction domain functionally disrupted in maturity onset diabetes of the young. J Biol Chem 2013; 288:17745-58. [PMID: 23589285 PMCID: PMC3682574 DOI: 10.1074/jbc.m112.434670] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The function of Krüppel-like factor 11 (KLF11) in the regulation of metabolic pathways is conserved from flies to human. Alterations in KLF11 function result in maturity onset diabetes of the young 7 (MODY7) and neonatal diabetes; however, the mechanisms underlying the role of this protein in metabolic disorders remain unclear. Here, we investigated how the A347S genetic variant, present in MODY7 patients, modulates KLF11 transcriptional activity. A347S affects a previously identified transcriptional regulatory domain 3 (TRD3) for which co-regulators remain unknown. Structure-oriented sequence analyses described here predicted that the KLF11 TRD3 represents an evolutionarily conserved protein domain. Combined yeast two-hybrid and protein array experiments demonstrated that the TRD3 binds WD40, WWI, WWII, and SH3 domain-containing proteins. Using one of these proteins as a model, guanine nucleotide-binding protein β2 (Gβ2), we investigated the functional consequences of KLF11 coupling to a TRD3 binding partner. Combined immunoprecipitation and biomolecular fluorescence complementation assays confirmed that activation of three different metabolic G protein-coupled receptors (β-adrenergic, secretin, and cholecystokinin) induces translocation of Gβ2 to the nucleus where it directly binds KLF11 in a manner that is disrupted by the MODY7 A347S variant. Using genome-wide expression profiles, we identified metabolic gene networks impacted upon TRD3 disruption. Furthermore, A347S disrupted KLF11-mediated increases in basal insulin levels and promoter activity and blunted glucose-stimulated insulin secretion. Thus, this study characterizes a novel protein/protein interaction domain disrupted in a KLF gene variant that associates to MODY7, contributing to our understanding of gene regulation events in complex metabolic diseases.
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Affiliation(s)
- Gwen Lomberk
- Laboratory of Epigenetics and Chromatin Dynamics, Epigenomics Translational Program, Mayo Clinic Center for Individualized Medicine, Division of Gastroenterology and Hepatology, and Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, Minnesota 55905, USA
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A novel role of the Sp/KLF transcription factor KLF11 in arresting progression of endometriosis. PLoS One 2013; 8:e60165. [PMID: 23555910 PMCID: PMC3610699 DOI: 10.1371/journal.pone.0060165] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2013] [Accepted: 02/22/2013] [Indexed: 12/20/2022] Open
Abstract
Endometriosis affects approximately 10% of young, reproductive-aged women. Disease associated pelvic pain; infertility and sexual dysfunction have a significant adverse clinical, social and financial impact. As precise disease etiology has remained elusive, current therapeutic strategies are empiric, unfocused and often unsatisfactory. Lack of a suitable genetic model has impaired further translational research in the field. In this study, we evaluated the role of the Sp/KLF transcription factor KLF11/Klf11 in the pathogenesis of endometriosis. KLF11, a human disease-associated gene is etiologically implicated in diabetes, uterine fibroids and cancer. We found that KLF11 expression was diminished in human endometriosis implants and further investigated its pathogenic role in Klf11-/- knockout mice with surgically induced endometriotic lesions. Lesions in Klf11-/- animals were large and associated with prolific fibrotic adhesions resembling advanced human disease in contrast to wildtype controls. To determine phenotype-specificity, endometriosis was also generated in Klf9-/- animals. Unlike in Klf11-/- mice, lesions in Klf9-/- animals were neither large, nor associated with a significant fibrotic response. KLF11 also bound to specific elements located in the promoter regions of key fibrosis-related genes from the Collagen, MMP and TGF-β families in endometrial stromal cells. KLF11 binding resulted in transcriptional repression of these genes. In summary, we identify a novel pathogenic role for KLF11 in preventing de novo disease-associated fibrosis in endometriosis. Our model validates in vivo the phenotypic consequences of dysregulated Klf11 signaling. Additionally, it provides a robust means not only for further detailed mechanistic investigation but also the ability to test any emergent translational ramifications thereof, so as to expand the scope and capability for treatment of endometriosis.
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Heard ME, Pabona JMP, Clayberger C, Krensky AM, Simmen FA, Simmen RCM. The reproductive phenotype of mice null for transcription factor Krüppel-like factor 13 suggests compensatory function of family member Krüppel-like factor 9 in the peri-implantation uterus. Biol Reprod 2012; 87:115. [PMID: 22993382 DOI: 10.1095/biolreprod.112.102251] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The ovarian hormones estrogen and progesterone promote uterine receptivity and successful pregnancy through their cognate receptors functioning in concert with context-dependent nuclear coregulators. Previously, we showed that the transcription factor Krüppel-like factor (KLF) 9 is a progesterone receptor (PGR) coactivator in the uterus and that mice null for Klf9 exhibit subfertility and reduced progesterone sensitivity. The highly related family member KLF13 displays increased expression in uteri of pregnant and nonpregnant Klf9 null mice and similarly regulates PGR-mediated transactivation in endometrial stromal cells. However, a uterine phenotype with loss of Klf13 has not been reported. In the present study, we demonstrate that Klf13 deficiency in mice did not compromise female fertility and pregnancy outcome. Klf13 null females had litter sizes, numbers of implanting embryos, uterine morphology, and ovarian steroid hormone production comparable to those of wild-type (WT) counterparts. Further, pregnant WT and Klf13 null females at Day Postcoitum (DPC) 3.5 had similar uterine Pgr, estrogen receptor, and Wnt-signaling component transcript levels. Nuclear levels of KLF9 were higher in Klf13 null than in WT uteri at DPC 3.5, albeit whole-tissue KLF9 protein and transcript levels did not differ between genotypes. The lack of a similar induction of nuclear KLF9 levels in uteri of virgin Klf13((-/-)) mice relative to WT uteri was associated with lower stromal PGR expression. In differentiating human endometrial stromal cells, coincident KLF9/KLF13 knockdown by small interfering RNA targeting reduced decidualization-associated PRL expression, whereas KLF9 and KLF13 knockdowns alone reduced transcript levels of WNT4 and BMP2, respectively. Results suggest that KLF9 and KLF13 functionally compensate in peri-implantation uterus for pregnancy success.
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Affiliation(s)
- Melissa E Heard
- Department of Physiology & Biophysics, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA
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