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Wang Z, Liu Z, Zhou P, Niu X, Sun Z, He H, Zhu Z. The involvement of krüppel-like transcription factor 2 in megakaryocytic differentiation induction by phorbol 12-myrestrat 13-acetate. Biomark Res 2024; 12:65. [PMID: 39014479 PMCID: PMC11253501 DOI: 10.1186/s40364-024-00614-9] [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: 02/23/2024] [Accepted: 07/05/2024] [Indexed: 07/18/2024] Open
Abstract
BACKGROUND Megakaryocytic differentiation is a complicated process regulated by a series of transcription factors in a context- and stage-dependent manner. Recent studies have suggested that krüppel-like transcription factor 2 (KLF2) is involved in the control of embryonic erythroid precursor cell differentiation and maturation. However, the function and mechanism of KLF2 in regulating megakaryocytic differentiation remain unclear. METHODS The expression patterns of krüppel-like transcription factors (KLFs) during megakaryocytic differentiation were identified from public databases. Phorbol 12-myristate 13-acetate (PMA) treatment of the myeloid-erythroid-leukemic cell lines K562 and HEL were used as cellular megakaryocytic differentiation models. A lentiviral transduction system was utilized to achieve the goal of amplifying or reducing KLF2. The expression of KLF2 was examined using real-time PCR and western blot. The impact of KLF2 on the megakaryocytic differentiation of K562 cells was examined by flow cytometry, Giemsa staining, Phalloidin staining and western blot. RNA-sequencing (RNA-seq) and chromatin immunoprecipitation-sequencing (ChIP-seq) technologies were used to identify the KLF2-regulated targets. RESULTS KLF2 is increased in the maturation process of megakaryocytes. KLF2 overexpression accelerated the PMA-induced megakaryocytic differentiation, as reflected by an increased percentage of CD41/CD61 cells, an increased number of polyploid cells, and an elevated expression of P21 and P27. KLF2 knockdown exhibited the opposite results, indicating that KLF2 knockdown suppressed the megakaryocytic differentiation. Further, combination of the RNA-seq and ChIP-seq results suggested that chimerin 1 (CHN1) and potassium voltage-gated channel subfamily Q member 5 (KCNQ5) may be target genes regulated of KLF2. Both CHN1 and KCNQ5 knockdown could block the megakaryocytic differentiation to some content. CONCLUSION This study implicated a regulatory role of KLF2 in megakaryocytic differentiation, which may suggest KLF2 as a target for illness with abnormal megakaryocytic differentiation.
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Affiliation(s)
- Zhen Wang
- Department of Hematology, Zhengzhou University People's Hospital, Henan Provincial People's Hospital, Zhengzhou, Henan, China.
- Henan University, Kaifeng, Henan, China.
- Zhengzhou University, Zhengzhou, Henan, China.
| | - Zhongwen Liu
- Department of Hematology, Zhengzhou University People's Hospital, Henan Provincial People's Hospital, Zhengzhou, Henan, China
- Henan University, Kaifeng, Henan, China
- Zhengzhou University, Zhengzhou, Henan, China
| | - Pan Zhou
- Department of Hematology, Zhengzhou University People's Hospital, Henan Provincial People's Hospital, Zhengzhou, Henan, China
| | - Xiaona Niu
- Department of Hematology, Zhengzhou University People's Hospital, Henan Provincial People's Hospital, Zhengzhou, Henan, China
- Henan University, Kaifeng, Henan, China
- Zhengzhou University, Zhengzhou, Henan, China
| | | | - Huan He
- Zhengzhou University, Zhengzhou, Henan, China
| | - Zunmin Zhu
- Department of Hematology, Zhengzhou University People's Hospital, Henan Provincial People's Hospital, Zhengzhou, Henan, China.
- Henan University, Kaifeng, Henan, China.
- Zhengzhou University, Zhengzhou, Henan, China.
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Bieker JJ, Philipsen S. Erythroid Krüppel-Like Factor (KLF1): A Surprisingly Versatile Regulator of Erythroid Differentiation. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2024; 1459:217-242. [PMID: 39017846 DOI: 10.1007/978-3-031-62731-6_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/18/2024]
Abstract
Erythroid Krüppel-like factor (KLF1), first discovered in 1992, is an erythroid-restricted transcription factor (TF) that is essential for terminal differentiation of erythroid progenitors. At face value, KLF1 is a rather inconspicuous member of the 26-strong SP/KLF TF family. However, 30 years of research have revealed that KLF1 is a jack of all trades in the molecular control of erythropoiesis. Initially described as a one-trick pony required for high-level transcription of the adult HBB gene, we now know that it orchestrates the entire erythroid differentiation program. It does so not only as an activator but also as a repressor. In addition, KLF1 was the first TF shown to be directly involved in enhancer/promoter loop formation. KLF1 variants underlie a wide range of erythroid phenotypes in the human population, varying from very mild conditions such as hereditary persistence of fetal hemoglobin and the In(Lu) blood type in the case of haploinsufficiency, to much more serious non-spherocytic hemolytic anemias in the case of compound heterozygosity, to dominant congenital dyserythropoietic anemia type IV invariably caused by a de novo variant in a highly conserved amino acid in the KLF1 DNA-binding domain. In this chapter, we present an overview of the past and present of KLF1 research and discuss the significance of human KLF1 variants.
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Affiliation(s)
- James J Bieker
- Department of Cell, Developmental, and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
| | - Sjaak Philipsen
- Department of Cell Biology, Erasmus MC, Rotterdam, The Netherlands.
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Frith MC, Ni S. DNA Conserved in Diverse Animals Since the Precambrian Controls Genes for Embryonic Development. Mol Biol Evol 2023; 40:msad275. [PMID: 38085182 PMCID: PMC10735318 DOI: 10.1093/molbev/msad275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2023] [Revised: 11/13/2023] [Accepted: 12/06/2023] [Indexed: 12/23/2023] Open
Abstract
DNA that controls gene expression (e.g. enhancers, promoters) has seemed almost never to be conserved between distantly related animals, like vertebrates and arthropods. This is mysterious, because development of such animals is partly organized by homologous genes with similar complex expression patterns, termed "deep homology." Here, we report 25 regulatory DNA segments conserved across bilaterian animals, of which 7 are also conserved in cnidaria (coral and sea anemone). They control developmental genes (e.g. Nr2f, Ptch, Rfx1/3, Sall, Smad6, Sp5, Tbx2/3), including six homeobox genes: Gsx, Hmx, Meis, Msx, Six1/2, and Zfhx3/4. The segments contain perfectly or near-perfectly conserved CCAAT boxes, E-boxes, and other sequences recognized by regulatory proteins. More such DNA conservation will surely be found soon, as more genomes are published and sequence comparison is optimized. This reveals a control system for animal development conserved since the Precambrian.
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Affiliation(s)
- Martin C Frith
- Artificial Intelligence Research Center, AIST, Tokyo, Japan
- Graduate School of Frontier Sciences, University of Tokyo, Chiba, Japan
- Computational Bio Big Data Open Innovation Laboratory, AIST, Tokyo, Japan
| | - Shengliang Ni
- Graduate School of Frontier Sciences, University of Tokyo, Chiba, Japan
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Han X, Wu W, Wang S. Krüppel-like factor 15 counteracts endoplasmic reticulum stress and suppresses lung fibroblast proliferation and extracellular matrix accumulation. Tissue Cell 2023; 84:102183. [PMID: 37531874 DOI: 10.1016/j.tice.2023.102183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 07/12/2023] [Accepted: 07/25/2023] [Indexed: 08/04/2023]
Abstract
The incidence of pulmonary fibrosis is on the rise, and existing treatments have limited efficacy in improving patient survival. The purpose of this study was to reveal the potential of Krüppel-like factor (KLF)15 activation in alleviating pulmonary fibrosis. Transforming growth factor beta (TGF-β) was utilized to induce lung fibroblasts to establish an in vitro model of pulmonary fibrosis. The impacts of TGF-β and KLF15 level on cell proliferation, migration, extracellular matrix (ECM) accumulation, and endoplasmic reticulum stress (ERS) were assessed. Additionally, tunicamycin, an ERS agonist, was used to investigate the role of ERS in KLF15 regulation. The results showed that KLF15 was dropped in response to TGF-β treatment. However, KLF15 overexpression reduced cell proliferation, migration, ECM accumulation, and ERS, alleviating the effects of TGF-β stimulation. Subsequent treatment with tunicamycin diminished the effects of KLF15 overexpression, demonstrating that ERS mediated the modulation of KLF15. KLF15 acts against ERS and suppresses excessive proliferation and ECM accumulation in lung fibroblast. These findings suggest that activating KLF15 is a promising strategy for alleviating pulmonary fibrosis.
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Affiliation(s)
- Xiang Han
- Department of Emergency, The Affiliated Huaian No.1 People's Hospital of Nanjing Medical University, Huai'an, Jiangsu 223300, China.
| | - Weiqin Wu
- Department of Emergency, The Affiliated Huaian No.1 People's Hospital of Nanjing Medical University, Huai'an, Jiangsu 223300, China
| | - Shuming Wang
- Department of Hepatobiliary and Pancreatic Surgery, The Affiliated Huaian No.1 People's Hospital of Nanjing Medical University, Huai'an, Jiangsu 223300, China.
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Chen R, Hao X, Chen J, Zhang C, Fan H, Lian F, Chen X, Wang C, Xia Y. Integrated multi-omics analyses reveal Jorunnamycin A as a novel suppressor for muscle-invasive bladder cancer by targeting FASN and TOP1. J Transl Med 2023; 21:549. [PMID: 37587470 PMCID: PMC10428641 DOI: 10.1186/s12967-023-04400-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 07/29/2023] [Indexed: 08/18/2023] Open
Abstract
BACKGROUND Bladder cancer is a urological carcinoma with high incidence, among which muscle invasive bladder cancer (MIBC) is a malignant carcinoma with high mortality. There is an urgent need to develop new drugs with low toxicity and high efficiency for MIBC because existing medication has defects, such as high toxicity, poor efficacy, and side effects. Jorunnamycin A (JorA), a natural marine compound, has been found to have a high efficiency anticancer effect, but its anticancer function and mechanism on bladder cancer have not been studied. METHODS To examine the anticancer effect of JorA on MIBC, Cell Counting Kit 8, EdU staining, and colony formation analyses were performed. Moreover, a xenograft mouse model was used to verify the anticancer effect in vivo. To investigate the pharmacological mechanism of JorA, high-throughput quantitative proteomics, transcriptomics, RT-qPCR, western blotting, immunofluorescence staining, flow cytometry, pulldown assays, and molecular docking were performed. RESULTS JorA inhibited the proliferation of MIBC cells, and the IC50 of T24 and UM-UC-3 was 0.054 and 0.084 μM, respectively. JorA-induced significantly changed proteins were enriched in "cancer-related pathways" and "EGFR-related signaling pathways", which mainly manifested by inhibiting cell proliferation and promoting cell apoptosis. Specifically, JorA dampened the DNA synthesis rate, induced phosphatidylserine eversion, and inhibited cell migration. Furthermore, it was discovered that fatty acid synthase (FASN) and topoisomerase 1 (TOP1) are the JorA interaction proteins. Using DockThor software, the 3D docking structures of JorA binding to FASN and TOP1 were obtained (the binding affinities were - 8.153 and - 7.264 kcal/mol, respectively). CONCLUSIONS The marine compound JorA was discovered to have a specific inhibitory effect on MIBC, and its potential pharmacological mechanism was revealed for the first time. This discovery makes an important contribution to the development of new high efficiency and low toxicity drugs for bladder cancer therapy.
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Affiliation(s)
- Ruijiao Chen
- Medical Laboratory of Jining Medical University, Jining Medical University, Jining, 272067, Shandong, China
| | - Xiaopeng Hao
- Institute of Precision Medicine, Jining Medical University, No. 133 Hehua Road, Taibaihu District, Jining, 272067, Shandong, China
| | - Jingyuan Chen
- Institute of Precision Medicine, Jining Medical University, No. 133 Hehua Road, Taibaihu District, Jining, 272067, Shandong, China
| | - Changyue Zhang
- Medical Laboratory of Jining Medical University, Jining Medical University, Jining, 272067, Shandong, China
- School of Pharmacy, Binzhou Medical University, Yantai, 264003, Shandong, China
| | - Huixia Fan
- Institute of Precision Medicine, Jining Medical University, No. 133 Hehua Road, Taibaihu District, Jining, 272067, Shandong, China
| | - Fuming Lian
- Institute of Precision Medicine, Jining Medical University, No. 133 Hehua Road, Taibaihu District, Jining, 272067, Shandong, China
| | - Xiaochuan Chen
- Key Laboratory of Green Chemistry and Technology of Ministry of Education, College of Chemistry, Sichuan University, Chengdu, 610064, China.
| | - Chao Wang
- Department of Urology, Jining No. 1 People's Hospital, Jining, 272106, Shandong, China.
| | - Yong Xia
- Medical Laboratory of Jining Medical University, Jining Medical University, Jining, 272067, Shandong, China.
- Institute of Precision Medicine, Jining Medical University, No. 133 Hehua Road, Taibaihu District, Jining, 272067, Shandong, China.
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Catta-Preta R, Lindtner S, Ypsilanti A, Price J, Abnousi A, Su-Feher L, Wang Y, Juric I, Jones IR, Akiyama JA, Hu M, Shen Y, Visel A, Pennacchio LA, Dickel D, Rubenstein JLR, Nord AS. Combinatorial transcription factor binding encodes cis-regulatory wiring of forebrain GABAergic neurogenesis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.28.546894. [PMID: 37425940 PMCID: PMC10327028 DOI: 10.1101/2023.06.28.546894] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
Transcription factors (TFs) bind combinatorially to genomic cis-regulatory elements (cREs), orchestrating transcription programs. While studies of chromatin state and chromosomal interactions have revealed dynamic neurodevelopmental cRE landscapes, parallel understanding of the underlying TF binding lags. To elucidate the combinatorial TF-cRE interactions driving mouse basal ganglia development, we integrated ChIP-seq for twelve TFs, H3K4me3-associated enhancer-promoter interactions, chromatin and transcriptional state, and transgenic enhancer assays. We identified TF-cREs modules with distinct chromatin features and enhancer activity that have complementary roles driving GABAergic neurogenesis and suppressing other developmental fates. While the majority of distal cREs were bound by one or two TFs, a small proportion were extensively bound, and these enhancers also exhibited exceptional evolutionary conservation, motif density, and complex chromosomal interactions. Our results provide new insights into how modules of combinatorial TF-cRE interactions activate and repress developmental expression programs and demonstrate the value of TF binding data in modeling gene regulatory wiring.
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Affiliation(s)
- Rinaldo Catta-Preta
- Department of Neurobiology, Physiology and Behavior, and Department of Psychiatry and Behavioral Sciences, University of California, Davis, Davis, CA 95618, USA
- Current Address: Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Susan Lindtner
- Nina Ireland Laboratory of Developmental Neurobiology, Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Athena Ypsilanti
- Nina Ireland Laboratory of Developmental Neurobiology, Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - James Price
- Nina Ireland Laboratory of Developmental Neurobiology, Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Armen Abnousi
- Department of Quantitative Health Sciences, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH 44106, USA
- Current Address: NovaSignal, Los Angeles, CA 90064, USA
| | - Linda Su-Feher
- Department of Neurobiology, Physiology and Behavior, and Department of Psychiatry and Behavioral Sciences, University of California, Davis, Davis, CA 95618, USA
| | - Yurong Wang
- Department of Neurobiology, Physiology and Behavior, and Department of Psychiatry and Behavioral Sciences, University of California, Davis, Davis, CA 95618, USA
| | - Ivan Juric
- Department of Quantitative Health Sciences, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH 44106, USA
| | - Ian R Jones
- Institute for Human Genetics, Department of Neurology, University of California, San Francisco, San Francisco, CA 94143, USA
- Department of Neurology, University of California, San Francisco, CA 94143, USA
| | - Jennifer A Akiyama
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Ming Hu
- Department of Quantitative Health Sciences, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH 44106, USA
| | - Yin Shen
- Institute for Human Genetics, Department of Neurology, University of California, San Francisco, San Francisco, CA 94143, USA
- Department of Neurology, University of California, San Francisco, CA 94143, USA
| | - Axel Visel
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- U.S. Department of Energy Joint Genome Institute, Walnut Creek, CA 94598, USA
- School of Natural Sciences, University of California, Merced, Merced, CA 95343, USA
| | - Len A Pennacchio
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- U.S. Department of Energy Joint Genome Institute, Walnut Creek, CA 94598, USA
- Comparative Biochemistry Program, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Diane Dickel
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - John L R Rubenstein
- Nina Ireland Laboratory of Developmental Neurobiology, Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Alex S Nord
- Department of Neurobiology, Physiology and Behavior, and Department of Psychiatry and Behavioral Sciences, University of California, Davis, Davis, CA 95618, USA
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Tsytsykova AV, Wiley G, Li C, Pelikan RC, Garman L, Acquah FA, Mooers BH, Tsitsikov EN, Dunn IF. Mutated KLF4(K409Q) in meningioma binds STRs and activates FGF3 gene expression. iScience 2022; 25:104839. [PMID: 35996584 PMCID: PMC9391581 DOI: 10.1016/j.isci.2022.104839] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 07/04/2022] [Accepted: 07/21/2022] [Indexed: 11/30/2022] Open
Abstract
Krüppel-like factor 4 (KLF4) is a transcription factor that has been proven necessary for both induction and maintenance of pluripotency and self-renewal. Whole-genome sequencing defined a unique mutation in KLF4 (KLF4K409Q) in human meningiomas. However, the molecular mechanism of this tumor-specific KLF4 mutation is unknown. Using genome-wide high-throughput and focused quantitative transcriptional approaches in human cell lines, primary meningeal cells, and meningioma tumor tissue, we found that a change in the evolutionarily conserved DNA-binding domain of KLF4 alters its DNA recognition preference, resulting in a shift in downstream transcriptional activity. In the KLF4K409Q-specific targets, the normally silent fibroblast growth factor 3 (FGF3) is activated. We demonstrated a neomorphic function of KLF4K409Q in stimulating FGF3 transcription through binding to its promoter and in using short tandem repeats (STRs) located within the locus as enhancers.
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Affiliation(s)
- Alla V. Tsytsykova
- Department of Neurosurgery, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | - Graham Wiley
- Clinical Genomics Center, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104, USA
| | - Chuang Li
- Oklahoma Medical Research Foundation, Genes & Human Disease Research Program, Oklahoma City, OK 73104, USA
| | - Richard C. Pelikan
- Oklahoma Medical Research Foundation, Genes & Human Disease Research Program, Oklahoma City, OK 73104, USA
| | - Lori Garman
- Oklahoma Medical Research Foundation, Genes & Human Disease Research Program, Oklahoma City, OK 73104, USA
| | - Francis A. Acquah
- Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | - Blaine H.M. Mooers
- Peggy and Charles Stephenson Cancer Center, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
- Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | - Erdyni N. Tsitsikov
- Department of Neurosurgery, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | - Ian F. Dunn
- Department of Neurosurgery, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
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Vanni V, Salonna M, Gasparini F, Martini M, Anselmi C, Gissi C, Manni L. Yamanaka Factors in the Budding Tunicate Botryllus schlosseri Show a Shared Spatio-Temporal Expression Pattern in Chordates. Front Cell Dev Biol 2022; 10:782722. [PMID: 35342743 PMCID: PMC8948423 DOI: 10.3389/fcell.2022.782722] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Accepted: 02/09/2022] [Indexed: 01/22/2023] Open
Abstract
In vertebrates, the four transcription factors Sox2, c-Myc, Pou5f1 and Klf4 are involved in the differentiation of several tissues during vertebrate embryogenesis; moreover, they are normally co-expressed in embryonic stem cells and play roles in pluripotency, self-renewal, and maintenance of the undifferentiated state in adult cells. The in vitro forced co-expression of these factors, named Yamanaka factors (YFs), induces pluripotency in human or mouse fibroblasts. Botryllus schlosseri is a colonial tunicate undergoing continuous stem cell-mediated asexual development, providing a valuable model system for the study of pluripotency in the closest living relatives of vertebrates. In this study, we identified B. schlosseri orthologs of human Sox2 and c-Myc genes, as well as the closest homologs of the vertebrate-specific Pou5f1 gene, through an in-depth evolutionary analysis of the YF gene families in tunicates and other deuterostomes. Then, we studied the expression of these genes during the asexual cycle of B. schlosseri using in situ hybridization in order to investigate their possible involvement in tissue differentiation and in pluripotency maintenance. Our results show a shared spatio-temporal expression pattern consistent with the reported functions of these genes in invertebrate and vertebrate embryogenesis. Moreover, Myc, SoxB1 and Pou3 were expressed in candidate stem cells residing in their niches, while Pou2 was found expressed exclusively in the immature previtellogenic oocytes, both in gonads and circulating in the colonial vascular system. Our data suggest that Myc, SoxB1 and Pou3 may be individually involved in the differentiation of the same territories seen in other chordates, and that, together, they may play a role in stemness even in this colonial ascidian.
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Affiliation(s)
- Virginia Vanni
- Department of Biology, University of Padova, Padova, Italy
| | - Marika Salonna
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari "Aldo Moro", Bari, Italy
| | | | | | - Chiara Anselmi
- Stanford University, Hopkins Marine Station, Pacific Grove, CA, United States.,Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, United States
| | - Carmela Gissi
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari "Aldo Moro", Bari, Italy.,IBIOM, Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, Consiglio Nazionale Delle Ricerche, Bari, Italy.,CoNISMa, Consorzio Nazionale Interuniversitario per le Scienze Del Mare, Roma, Italy
| | - Lucia Manni
- Department of Biology, University of Padova, Padova, Italy
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Jiang Z, Elsarrag SZ, Duan Q, LaGory EL, Wang Z, Alexanian M, McMahon S, Rulifson IC, Winchester S, Wang Y, Vaisse C, Brown JD, Quattrocelli M, Lin CY, Haldar SM. KLF15 cistromes reveal a hepatocyte pathway governing plasma corticosteroid transport and systemic inflammation. SCIENCE ADVANCES 2022; 8:eabj2917. [PMID: 35263131 PMCID: PMC8906731 DOI: 10.1126/sciadv.abj2917] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2021] [Accepted: 01/13/2022] [Indexed: 05/15/2023]
Abstract
Circulating corticosteroids orchestrate stress adaptation, including inhibition of inflammation. While pathways governing corticosteroid biosynthesis and intracellular signaling are well understood, less is known about mechanisms controlling plasma corticosteroid transport. Here, we show that hepatocyte KLF15 (Kruppel-like factor 15) controls plasma corticosteroid transport and inflammatory responses through direct transcriptional activation of Serpina6, which encodes corticosteroid-binding globulin (CBG). Klf15-deficient mice have profoundly low CBG, reduced plasma corticosteroid binding capacity, and heightened mortality during inflammatory stress. These defects are completely rescued by reconstituting CBG, supporting that KLF15 works primarily through CBG to control plasma corticosterone homeostasis. To understand transcriptional mechanisms, we generated the first KLF15 cistromes using newly engineered Klf153xFLAG mice. Unexpectedly, liver KLF15 is predominantly promoter enriched, including Serpina6, where it binds a palindromic GC-rich motif, opens chromatin, and transactivates genes with minimal associated direct gene repression. Overall, we provide critical mechanistic insight into KLF15 function and identify a hepatocyte-intrinsic transcriptional module that potently regulates systemic corticosteroid transport and inflammation.
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Affiliation(s)
- Zhen Jiang
- Amgen Research, South San Francisco, CA 94080, USA
- Gladstone Institutes, San Francisco, CA 94158, USA
| | - Selma Z. Elsarrag
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Medical Scientist Training Program and Quantitative and Computational Biosciences Graduate Program, Baylor College of Medicine, Houston, TX 77030, USA
| | - Qiming Duan
- Gladstone Institutes, San Francisco, CA 94158, USA
| | | | - Zhe Wang
- Amgen Research, South San Francisco, CA 94080, USA
| | | | - Sarah McMahon
- Gladstone Institutes, San Francisco, CA 94158, USA
- Biomedical Sciences Graduate Program, UCSF School of Medicine, San Francisco, CA 94143, USA
| | | | | | - Yi Wang
- UCSF Diabetes Center and Department of Medicine, UCSF School of Medicine, San Francisco, CA 94143, USA
| | - Christian Vaisse
- UCSF Diabetes Center and Department of Medicine, UCSF School of Medicine, San Francisco, CA 94143, USA
| | - Jonathan D. Brown
- Division of Cardiovascular Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Mattia Quattrocelli
- Molecular Cardiovascular Biology Division, Heart Institute, Cincinnati Children’s Hospital Medical Center and Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
| | - Charles Y. Lin
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Kronos Bio Inc., Cambridge, MA 02142, USA
| | - Saptarsi M. Haldar
- Amgen Research, South San Francisco, CA 94080, USA
- Gladstone Institutes, San Francisco, CA 94158, USA
- Cardiology Division, Department of Medicine, UCSF School of Medicine, San Francisco, CA 94143, USA
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10
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Smith CEL, Whitehouse LLE, Poulter JA, Wilkinson Hewitt L, Nadat F, Jackson BR, Manfield IW, Edwards TA, Rodd HD, Inglehearn CF, Mighell AJ. A missense variant in specificity protein 6 (SP6) is associated with amelogenesis imperfecta. Hum Mol Genet 2021; 29:1417-1425. [PMID: 32167558 PMCID: PMC7268548 DOI: 10.1093/hmg/ddaa041] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 03/03/2020] [Accepted: 03/04/2020] [Indexed: 01/01/2023] Open
Abstract
Amelogenesis is the process of enamel formation. For amelogenesis to proceed, the cells of the inner enamel epithelium (IEE) must first proliferate and then differentiate into the enamel-producing ameloblasts. Amelogenesis imperfecta (AI) is a heterogeneous group of genetic conditions that result in defective or absent tooth enamel. We identified a 2 bp variant c.817_818GC>AA in SP6, the gene encoding the SP6 transcription factor, in a Caucasian family with autosomal dominant hypoplastic AI. The resulting missense protein change, p.(Ala273Lys), is predicted to alter a DNA-binding residue in the first of three zinc fingers. SP6 has been shown to be crucial to both proliferation of the IEE and to its differentiation into ameloblasts. SP6 has also been implicated as an AI candidate gene through its study in rodent models. We investigated the effect of the missense variant in SP6 (p.(Ala273Lys)) using surface plasmon resonance protein-DNA binding studies. We identified a potential SP6 binding motif in the AMBN proximal promoter sequence and showed that wild-type (WT) SP6 binds more strongly to it than the mutant protein. We hypothesize that SP6 variants may be a very rare cause of AI due to the critical roles of SP6 in development and that the relatively mild effect of the missense variant identified in this study is sufficient to affect amelogenesis causing AI, but not so severe as to be incompatible with life. We suggest that current AI cohorts, both with autosomal recessive and dominant disease, be screened for SP6 variants.
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Affiliation(s)
- Claire E L Smith
- Division of Molecular Medicine, Leeds Institute of Medical Research, Faculty of Medicine and Health, St James's University Hospital, University of Leeds, Leeds LS9 7TF, UK
| | - Laura L E Whitehouse
- School of Dentistry, Faculty of Medicine and Health, University of Leeds, Leeds LS2 9LU, UK
| | - James A Poulter
- Division of Molecular Medicine, Leeds Institute of Medical Research, Faculty of Medicine and Health, St James's University Hospital, University of Leeds, Leeds LS9 7TF, UK
| | - Laura Wilkinson Hewitt
- Protein Production Facility, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Fatima Nadat
- Protein Production Facility, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Brian R Jackson
- Protein Production Facility, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Iain W Manfield
- Centre for Biomolecular Interactions Technology Facility, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds LS2 9JT, UK
| | - Thomas A Edwards
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Helen D Rodd
- Academic Unit of Oral Health Dentistry and Society, School of Clinical Dentistry, University of Sheffield, Sheffield, S10 2TA, UK
| | - Chris F Inglehearn
- Division of Molecular Medicine, Leeds Institute of Medical Research, Faculty of Medicine and Health, St James's University Hospital, University of Leeds, Leeds LS9 7TF, UK
| | - Alan J Mighell
- School of Dentistry, Faculty of Medicine and Health, University of Leeds, Leeds LS2 9LU, UK
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11
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Chen L, Huang R, Li Y, Li Y, Li Y, Liao L, He L, Zhu Z, Wang Y. Genome-wide identification, evolution of Krüppel-like factors (klfs) and their expressions during GCRV challenge in grass carp (Ctenopharyngodonidella). DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2021; 120:104062. [PMID: 33667530 DOI: 10.1016/j.dci.2021.104062] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 02/25/2021] [Accepted: 02/25/2021] [Indexed: 06/12/2023]
Abstract
The Krüppel-like factors (KLFs) are a family of transcription factors containing three highly conserved tandem zinc finger structures, and each member participates in multiple physiological and pathological processes. The publication of genome sequences and the application of bioinformatics tools have led to the discovery of numerous gene families in fishes. Here, 24 klf genes were re-annotated in grass carp. Subsequently, the number of klf family members were investigated in some representative vertebrate species. Then, a series of bioinformatics analysis showed that grass carp klfs in the same subfamily had similar genome structure patterns and conserved distribution patterns of motifs, which supported their molecular evolutionary relationships. Furthermore, the mRNA expression profiles showed that 24 grass carp klfs were ubiquitously expressed in 11 different tissues, and some of them displayed tissue-enriched expression patterns. Finally, the expressions of the evolutionarily expanded klf members (klf2a, 2b, 2l, 5a, 5b, 5l, 6a, 6b, 7a, 7b, 11a, 11b, 12a, 12b, 15 and 15l) during GCRV infection were also analyzed. The results suggested that grass carp klf genes with common evolutionary sources may share functional diversity and conservation. In conclusion, this study provides preliminary clues for further researches on grass carp klf members and their underlying transcriptional regulatory mechanisms during GCRV infection.
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Affiliation(s)
- Liangming Chen
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Rong Huang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China.
| | - Yangyang Li
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yangyu Li
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yongming Li
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Lanjie Liao
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Libo He
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Zuoyan Zhu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Yaping Wang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
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12
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Meta-Analysis of Transcriptome Data Detected New Potential Players in Response to Dioxin Exposure in Humans. Int J Mol Sci 2020; 21:ijms21217858. [PMID: 33113971 PMCID: PMC7672605 DOI: 10.3390/ijms21217858] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 10/18/2020] [Accepted: 10/21/2020] [Indexed: 12/26/2022] Open
Abstract
Dioxins are one of the most potent anthropogenic poisons, causing systemic disorders in embryonic development and pathologies in adults. The mechanism of dioxin action requires an aryl hydrocarbon receptor (AhR), but the downstream mechanisms are not yet precisely clear. Here, we performed a meta-analysis of all available transcriptome datasets taken from human cell cultures exposed to 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD). Differentially expressed genes from different experiments overlapped partially, but there were a number of those genes that were systematically affected by TCDD. Some of them have been linked to toxic dioxin effects, but we also identified other attractive targets. Among the genes that were affected by TCDD, there are functionally related gene groups that suggest an interplay between retinoic acid, AhR, and Wnt signaling pathways. Next, we analyzed the upstream regions of differentially expressed genes and identified potential transcription factor (TF) binding sites overrepresented in the genes responding to TCDD. Intriguingly, the dioxin-responsive element (DRE), the binding site of AhR, was not overrepresented as much as other cis-elements were. Bioinformatics analysis of the AhR binding profile unveils potential cooperation of AhR with E2F2, CTCFL, and ZBT14 TFs in the dioxin response. We discuss the potential implication of these predictions for further dioxin studies.
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13
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McCulloch KJ, Koenig KM. Krüppel-like factor/specificity protein evolution in the Spiralia and the implications for cephalopod visual system novelties. Proc Biol Sci 2020; 287:20202055. [PMID: 33081641 PMCID: PMC7661307 DOI: 10.1098/rspb.2020.2055] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The cephalopod visual system is an exquisite example of convergence in biological complexity. However, we have little understanding of the genetic and molecular mechanisms underpinning its elaboration. The generation of new genetic material is considered a significant contributor to the evolution of biological novelty. We sought to understand if this mechanism may be contributing to cephalopod-specific visual system novelties. Specifically, we identified duplications in the Krüppel-like factor/specificity protein (KLF/SP) sub-family of C2H2 zinc-finger transcription factors in the squid Doryteuthis pealeii. We cloned and analysed gene expression of the KLF/SP family, including two paralogs of the DpSP6-9 gene. These duplicates showed overlapping expression domains but one paralog showed unique expression in the developing squid lens, suggesting a neofunctionalization of DpSP6-9a. To better understand this neofunctionalization, we performed a thorough phylogenetic analysis of SP6-9 orthologues in the Spiralia. We find multiple duplications and losses of the SP6-9 gene throughout spiralian lineages and at least one cephalopod-specific duplication. This work supports the hypothesis that gene duplication and neofunctionalization contribute to novel traits like the cephalopod image-forming eye and to the diversity found within Spiralia.
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Affiliation(s)
- Kyle J McCulloch
- Department of Organismic and Evolutionary Biology, Harvard University Cambridge, MA 02138, USA.,John Harvard Distinguished Science Fellows, Harvard University, Cambridge, MA 02138, USA
| | - Kristen M Koenig
- Department of Organismic and Evolutionary Biology, Harvard University Cambridge, MA 02138, USA.,John Harvard Distinguished Science Fellows, Harvard University, Cambridge, MA 02138, USA
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14
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Liu S, Huang J, Wang X, Ma Y. Transcription factors regulate adipocyte differentiation in beef cattle. Anim Genet 2020; 51:351-357. [PMID: 32253788 DOI: 10.1111/age.12931] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/08/2020] [Indexed: 12/13/2022]
Abstract
Intramuscular fat (IMF) content is a critical factor affecting meat flavor, juiciness, tenderness, and color. Therefore, the improvement of IMF content is one of the hotspots of animal science research. Fat deposition is the result of a combination of increased number of fat cells and cellular hypertrophy. In addition, transcription factors can influence the number of adipocytes and regulate lipid metabolism. The progress of the transcription factors regulating adipocyte differentiation in beef cattle, including IMF cell sources, and promoting or inhibiting adipogenic differentiation of transcription factors is reviewed in this paper.
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Affiliation(s)
- S Liu
- School of Agriculture, Ningxia University, Helan Mountain West Road 489, 750021, Yin Chuan, Ningxia Hui Autonomous Region, China
| | - J Huang
- College of Life Sciences, Xinyang Normal University, Nanhu Road 237, 464000, Xinyang, Henan Province, China
| | - X Wang
- School of Agriculture, Ningxia University, Helan Mountain West Road 489, 750021, Yin Chuan, Ningxia Hui Autonomous Region, China
| | - Y Ma
- School of Agriculture, Ningxia University, Helan Mountain West Road 489, 750021, Yin Chuan, Ningxia Hui Autonomous Region, China.,College of Life Sciences, Xinyang Normal University, Nanhu Road 237, 464000, Xinyang, Henan Province, China
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15
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Turpaev KT. Transcription Factor KLF2 and Its Role in the Regulation of Inflammatory Processes. BIOCHEMISTRY (MOSCOW) 2020; 85:54-67. [PMID: 32079517 DOI: 10.1134/s0006297920010058] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
KLF2 is a member of the Krüppel-like transcription factor family of proteins containing highly conserved DNA-binding zinc finger domains. KLF2 participates in the differentiation and regulation of the functional activity of monocytes, T lymphocytes, adipocytes, and vascular endothelial cells. The activity of KLF2 is controlled by several regulatory systems, including the MEKK2,3/MEK5/ERK5/MEF2 MAP kinase cascade, Rho family G-proteins, histone acetyltransferases CBP and p300, and histone deacetylases HDAC4 and HDAC5. Activation of KLF2 in endothelial cells induces eNOS expression and provides vasodilatory effect. Many KLF2-dependent genes participate in the suppression of blood coagulation and aggregation of T cells and macrophages with the vascular endothelium, thereby preventing atherosclerosis progression. KLF2 can have a dual effect on the gene transcription. Thus, it induces expression of multiple genes, but suppresses transcription of NF-κB-dependent genes. Transcription factors KLF2 and NF-κB are reciprocal antagonists. KLF2 inhibits induction of NF-κB-dependent genes, whereas NF-κB downregulates KLF2 expression. KLF2-mediated inhibition of NF-κB signaling leads to the suppression of cell response to the pro-inflammatory cytokines IL-1β and TNFα and results in the attenuation of inflammatory processes.
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Affiliation(s)
- K T Turpaev
- Center for Theoretical Problems of Physicochemical Pharmacology, Russian Academy of Sciences, Moscow, 119991, Russia.
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16
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Chen X, Shi W, Zhang H. The role of KLF14 in multiple disease processes. Biofactors 2020; 46:276-282. [PMID: 31925990 DOI: 10.1002/biof.1612] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Accepted: 10/31/2019] [Indexed: 12/13/2022]
Abstract
Kruppel-like factor 14 (KLF14) is a newly identified member of the KLF family. Expression of KLF14 is induced by TGF-β in intrauterine and ectodermal tissue. Initial researches on KLF14 focused on its role in lipid and glucose metabolism. In recent years, however, the role of KLF14 in regulating cell signaling pathways, cell proliferation and differentiation has been explored. Moreover, the research has gradually extended into the field of tumorigenesis and immune regulation. This paper aims to briefly review the functions of KLF14 in physiologyical and pathological process.
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Affiliation(s)
- Xiaoyan Chen
- Department of Gastroenterology, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Wenjie Shi
- Department of Gastroenterology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Heng Zhang
- Department of Gastroenterology, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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17
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Host Transcription Factors in Hepatitis B Virus RNA Synthesis. Viruses 2020; 12:v12020160. [PMID: 32019103 PMCID: PMC7077322 DOI: 10.3390/v12020160] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Revised: 01/27/2020] [Accepted: 01/28/2020] [Indexed: 02/06/2023] Open
Abstract
The hepatitis B virus (HBV) chronically infects over 250 million people worldwide and is one of the leading causes of liver cancer and hepatocellular carcinoma. HBV persistence is due in part to the highly stable HBV minichromosome or HBV covalently closed circular DNA (cccDNA) that resides in the nucleus. As HBV replication requires the help of host transcription factors to replicate, focusing on host protein–HBV genome interactions may reveal insights into new drug targets against cccDNA. The structural details on such complexes, however, remain poorly defined. In this review, the current literature regarding host transcription factors’ interactions with HBV cccDNA is discussed.
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18
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Shao M, Ge GZ, Liu WJ, Xiao J, Xia HJ, Fan Y, Zhao F, He BL, Chen C. Characterization and phylogenetic analysis of Krüppel-like transcription factor (KLF) gene family in tree shrews (Tupaia belangeri chinensis). Oncotarget 2017; 8:16325-16339. [PMID: 28032601 PMCID: PMC5369966 DOI: 10.18632/oncotarget.13883] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Accepted: 12/05/2016] [Indexed: 11/25/2022] Open
Abstract
Krüppel-like factors (KLFs) are a family of zinc finger transcription factors regulating embryonic development and diseases. The phylogenetics of KLFs has not been studied in tree shrews, an animal lineage with a closer relationship to primates than rodents. Here, we identified 17 KLFs from Chinese tree shrew (Tupaia belangeri chinensis). KLF proteins are highly conserved among humans, monkeys, rats, mice and tree shrews compared to zebrafish and chickens. The CtBP binding site, Sin3A binding site and nuclear localization signals are largely conserved between tree shrews and human beings. Tupaia belangeri (Tb) KLF5 contains several conserved post-transcriptional modification motifs. Moreover, the mRNA and protein expression patterns of multiple tbKLFs are tissue-specific. TbKLF5, like hKLF5, significantly promotes NIH3T3 cell proliferation in vitro. These results provide insight for future studies regarding the structure and function of the tbKLF gene family.
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Affiliation(s)
- Ming Shao
- Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China.,Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan, China
| | - Guang-Zhe Ge
- Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China.,Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan, China
| | - Wen-Jing Liu
- Medical Faculty, Kunming University of Science and Technology, Kunming, Yunnan, China.,Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Ji Xiao
- Medical Faculty, Kunming University of Science and Technology, Kunming, Yunnan, China.,Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Hou-Jun Xia
- Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Yu Fan
- Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Feng Zhao
- Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Bao-Li He
- Department of Laboratory Animal Science, Kunming Medical University, Kunming, Yunnan 650500, China
| | - Ceshi Chen
- Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
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19
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Dailey SC, Kozmikova I, Somorjai IM. Amphioxus Sp5 is a member of a conserved Specificity Protein complement and is modulated by Wnt/β-catenin signalling. THE INTERNATIONAL JOURNAL OF DEVELOPMENTAL BIOLOGY 2017; 61:723-732. [PMID: 29319119 PMCID: PMC5777634 DOI: 10.1387/ijdb.170205is] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
A cluster of three Specificity Protein (Sp) genes (Sp1-4, Sp5 and Sp6-9) is thought to be ancestral in both chordates and the wider Eumetazoa. Sp5 and Sp6-9 gene groups are associated with embryonic growth zones, such as tailbuds, and are both Wnt/β-catenin signalling pathway members and targets. Currently, there are conflicting reports as to the number and identity of Sp genes in the cephalochordates, the sister group to the vertebrates and urochordates. We confirm the SP complement of Branchiostoma belcheri and Branchiostoma lanceolatum, as well as their genomic arrangement, protein domain structure and residue frequency. We assay Sp5 expression in B. lanceolatum embryos, and determine its response to pharmacologically increased β-catenin signalling. Branchiostoma possesses three Sp genes, located on the same genomic scaffold. Phylogenetic and domain structure analyses are consistent with their identification as SP1-4, SP5 and SP6-9, although SP1-4 contains a novel glutamine-rich N-terminal region. SP5 is expressed in axial mesoderm and neurectoderm, and marks the cerebral vesicle and presumptive pharynx. Early exposure to increased β-catenin caused ubiquitous SP5 expression in late gastrula, while later treatment at gastrula stages reduced SP5 expression in the posterior growth zone during axis elongation. Amphioxus possess a typical invertebrate eumetazoan SP complement, and SP5 expression in embryos is well conserved with vertebrate homologues. Its expression in the tailbud, a posterior growth zone, is consistent with expression seen in other bilaterians. Branchiostoma SP5 shows a dynamic response to Wnt/β-catenin signalling.
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Affiliation(s)
- Simon C. Dailey
- University of St Andrews, Biomedical Sciences Research Complex, North Haugh, St Andrews, UK
- Scottish Oceans Institute, East Sands, St Andrews, UK
| | - Iryna Kozmikova
- Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Ildikó M.L. Somorjai
- University of St Andrews, Biomedical Sciences Research Complex, North Haugh, St Andrews, UK
- Scottish Oceans Institute, East Sands, St Andrews, UK
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20
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Hashimoto H, Zhang X, Zheng Y, Wilson GG, Cheng X. Denys-Drash syndrome associated WT1 glutamine 369 mutants have altered sequence-preferences and altered responses to epigenetic modifications. Nucleic Acids Res 2016; 44:10165-10176. [PMID: 27596598 PMCID: PMC5137435 DOI: 10.1093/nar/gkw766] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Revised: 08/19/2016] [Accepted: 08/23/2016] [Indexed: 01/10/2023] Open
Abstract
Mutations in human zinc-finger transcription factor WT1 result in abnormal development of the kidneys and genitalia and an array of pediatric problems including nephropathy, blastoma, gonadal dysgenesis and genital discordance. Several overlapping phenotypes are associated with WT1 mutations, including Wilms tumors, Denys-Drash syndrome (DDS), Frasier syndrome (FS) and WAGR syndrome (Wilms tumor, aniridia, genitourinary malformations, and mental retardation). These conditions vary in severity from individual to individual; they can be fatal in early childhood, or relatively benign into adulthood. DDS mutations cluster predominantly in zinc fingers (ZF) 2 and 3 at the C-terminus of WT1, which together with ZF4 determine the sequence-specificity of DNA binding. We examined three DDS associated mutations in ZF2 of human WT1 where the normal glutamine at position 369 is replaced by arginine (Q369R), lysine (Q369K) or histidine (Q369H). These mutations alter the sequence-specificity of ZF2, we find, changing its affinity for certain bases and certain epigenetic forms of cytosine. X-ray crystallography of the DNA binding domains of normal WT1, Q369R and Q369H in complex with preferred sequences revealed the molecular interactions responsible for these affinity changes. DDS is inherited in an autosomal dominant fashion, implying a gain of function by mutant WT1 proteins. This gain, we speculate, might derive from the ability of the mutant proteins to sequester WT1 into unproductive oligomers, or to erroneously bind to variant target sequences.
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Affiliation(s)
- Hideharu Hashimoto
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Xing Zhang
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Yu Zheng
- RGENE, Inc., 953 Indiana Street, San Francisco, CA 94107, USA
| | | | - Xiaodong Cheng
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA
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