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Wan B, Zhang W, Deng X, Lu Y, Zhang Z, Yang Y. Molecular Expression and Prognostic Implications of Krüppel-Like Factor 3 (KLF3) in Clear Cell Renal Cell Carcinoma. Crit Rev Eukaryot Gene Expr 2024; 34:45-59. [PMID: 38073441 DOI: 10.1615/critreveukaryotgeneexpr.2023049010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2023]
Abstract
A major subtype of renal cancer is clear cell renal cell carcinoma (ccRCC). Krüppel-like factor 3 (KLF3) dysfunction is also revealed leading to poor prognosis in multiple cancer types. However, dysregulation and molecular dynamics of KLF3 underlying ccRCC progression still remains elusive. Here KLF3 gene and protein expressions in ccRCC were explored using data cohorts from The Cancer Genome Atlas (TCGA), Human Protein Atlas (HPA), Clinical Proteomic Tumor Analysis Consortium (CPTAC) and verified them in our patient cohort. Correlations of KLF3 expression with clinicopathological features, epigenetic modification, and immune microenvironment characteristics were further investigated. KLF3 was significantly down-regulated expressed in ccRCC tissues compared to adjacent normal controls. Adverse pathological parameters and poor prognosis were associated with lower expression of KLF3. Mechanically, KLF3 regulation was mainly attributed to CpG island methylation. KLF3-high expression subgroup was significantly enriched in cell signaling pathways most associated with EMT markers, angiogenesis, inflammatory response, apoptosis, TGF-β, degradation of ECM, G2M checkpoint, and PI3K-AKT-mTOR. Based on GDSC database, KLF3 upregulation was identified to be associated with higher sensitivities towards PI3K-Akt-mTOR pathway inhibitors such as PI-103, PIK-93, and OSI-027. In addition, patients with down-regulated KLF3 expressions were found more sensitive towards Trametinib, Cetuximab, and Erlotinib. Collectively, our findings suggest that KLF3 may act as a suitable biomarker for prognosis prediction, tumor microenvironment (TME) phenotype identification, thereby helping ccRCC patients to make better therapeutic decisions.
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Affiliation(s)
- Bin Wan
- Department of Urology, The First People's Hospital of Jiujiang in Jiangxi Province, Jiujiang City, 332000, Jiangxi Province, China
| | - Wensheng Zhang
- Department of Urology, The First People's Hospital of Jiujiang in Jiangxi Province, Jiujiang City, 332000, Jiangxi Province, China
| | - Xinxi Deng
- Department of Urology, The First People's Hospital of Jiujiang in Jiangxi Province, Jiujiang City, 332000, Jiangxi Province, China
| | - Yigang Lu
- Department of Urology, The First People's Hospital of Jiujiang in Jiangxi Province, Jiujiang City, 332000, Jiangxi Province, China
| | - Zhuo Zhang
- Department of Urology, The First People's Hospital of Jiujiang in Jiangxi Province, Jiujiang City, 332000, Jiangxi Province, China
| | - Yang Yang
- Department of Urology, The First People's Hospital of Jiujiang in Jiangxi Province, Jiujiang City, 332000, Jiangxi Province, China
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2
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Ly LC, Yang Y, Li F, Crossley M, Shi Y, Quinlan KGR. Protocols for protein-DNA binding analysis of a zinc finger transcription factor bound to its cognate promoter. STAR Protoc 2022; 3:101598. [PMID: 35928006 PMCID: PMC9344028 DOI: 10.1016/j.xpro.2022.101598] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Affiliation(s)
- Lana C Ly
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia.
| | - Yang Yang
- School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230026, China; Ministry of Education Key Laboratory for Membraneless Organelles and Cellular Dynamics, University of Science and Technology of China, Hefei, China
| | - Fudong Li
- Ministry of Education Key Laboratory for Membraneless Organelles and Cellular Dynamics, University of Science and Technology of China, Hefei, China
| | - Merlin Crossley
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Yunyu Shi
- School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230026, China; Ministry of Education Key Laboratory for Membraneless Organelles and Cellular Dynamics, University of Science and Technology of China, Hefei, China.
| | - Kate G R Quinlan
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia.
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Ravi NS, Wienert B, Wyman SK, Bell HW, George A, Mahalingam G, Vu JT, Prasad K, Bandlamudi BP, Devaraju N, Rajendiran V, Syedbasha N, Pai AA, Nakamura Y, Kurita R, Narayanasamy M, Balasubramanian P, Thangavel S, Marepally S, Velayudhan SR, Srivastava A, DeWitt MA, Crossley M, Corn JE, Mohankumar KM. Identification of novel HPFH-like mutations by CRISPR base editing that elevate the expression of fetal hemoglobin. eLife 2022; 11:65421. [PMID: 35147495 PMCID: PMC8865852 DOI: 10.7554/elife.65421] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 02/11/2022] [Indexed: 11/29/2022] Open
Abstract
Naturally occurring point mutations in the HBG promoter switch hemoglobin synthesis from defective adult beta-globin to fetal gamma-globin in sickle cell patients with hereditary persistence of fetal hemoglobin (HPFH) and ameliorate the clinical severity. Inspired by this natural phenomenon, we tiled the highly homologous HBG proximal promoters using adenine and cytosine base editors that avoid the generation of large deletions and identified novel regulatory regions including a cluster at the –123 region. Base editing at –123 and –124 bp of HBG promoter induced fetal hemoglobin (HbF) to a higher level than disruption of well-known BCL11A binding site in erythroblasts derived from human CD34+ hematopoietic stem and progenitor cells (HSPC). We further demonstrated in vitro that the introduction of –123T > C and –124T > C HPFH-like mutations drives gamma-globin expression by creating a de novo binding site for KLF1. Overall, our findings shed light on so far unknown regulatory elements within the HBG promoter and identified additional targets for therapeutic upregulation of fetal hemoglobin.
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Affiliation(s)
- Nithin Sam Ravi
- Centre for Stem Cell Research, Christian Medical College, Vellore, India
| | - Beeke Wienert
- Institute of Data Science and Biotechnology, Gladstone Institutes, San Francisco, United States
| | - Stacia K Wyman
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, United States
| | - Henry William Bell
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, Australia
| | - Anila George
- Centre for Stem Cell Research, Christian Medical College, Vellore, India
| | | | - Jonathan T Vu
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, United States
| | - Kirti Prasad
- Centre for Stem Cell Research, Christian Medical College, Vellore, India
| | | | | | - Vignesh Rajendiran
- Centre for Stem Cell Research, Christian Medical College, Vellore, India
| | - Nazar Syedbasha
- Centre for Stem Cell Research, Christian Medical College, Vellore, India
| | - Aswin Anand Pai
- Department of Haematology, Christian Medical College & Hospital, Vellore, India
| | - Yukio Nakamura
- Cell Engineering Division, RIKEN BioResource Center, Ibaraki, Japan
| | - Ryo Kurita
- Research and Development Department, Central Blood Institute Blood Service Headquarters, Japanese Red Cross Society, Japan, Tokyo, Japan
| | | | | | | | - Srujan Marepally
- Centre for Stem Cell Research, Christian Medical College, Vellore, India
| | - Shaji R Velayudhan
- Department of Haematology, Christian Medical College & Hospital, Vellore, India
| | - Alok Srivastava
- Department of Haematology, Christian Medical College & Hospital, Vellore, India
| | - Mark A DeWitt
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, Los Angeles, United States
| | - Merlin Crossley
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Kensington, Australia
| | - Jacob E Corn
- Department of Biology, ETH Zurich, Zurich, Switzerland
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4
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Yang Y, Ren R, Ly LC, Horton JR, Li F, Quinlan KGR, Crossley M, Shi Y, Cheng X. Structural basis for human ZBTB7A action at the fetal globin promoter. Cell Rep 2021; 36:109759. [PMID: 34592153 PMCID: PMC8553545 DOI: 10.1016/j.celrep.2021.109759] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 08/09/2021] [Accepted: 09/02/2021] [Indexed: 12/02/2022] Open
Abstract
Elevated levels of fetal globin protect against β-hemoglobinopathies, such as sickle cell disease and β-thalassemia. Two zinc-finger (ZF) repressors, BCL11A and ZBTB7A/LRF, bind directly to the fetal globin promoter elements positioned at −115 and −200, respectively. Here, we describe X-ray structures of the ZBTB7A DNA-binding domain, consisting of four adjacent ZFs, in complex with the −200 sequence element, which contains two copies of four consecutive C:G base pairs. ZF1 and ZF2 recognize the 5′ C:G quadruple, and ZF4 contacts the 3′ C:G quadruple. Natural non-coding DNA mutations associated with hereditary persistence of fetal hemoglobin (HPFH) impair ZBTB7A DNA binding, with the most severe disruptions resulting from mutations in the base pairs recognized by ZF1 and ZF2. Our results firmly establish ZBTB7A/LRF as a key molecular regulator of fetal globin expression and inform genome-editing strategies that inhibit repressor binding and boost fetal globin expression to treat hemoglobinopathies. Yang et al. show that the transcription factor ZBTB7A has features that deviate from conventional one finger-three bases recognition. Among the four fingers, ZF1 and ZF2 each contact two DNA bases. ZF3 does not make base-specific contacts but serves as a spacer to position ZF4 into the right location.
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Affiliation(s)
- Yang Yang
- Hefei National Laboratory for Physical Sciences at Microscale, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230026, China; Ministry of Education Key Laboratory for Membraneless Organelles and Cellular Dynamics, University of Science and Technology of China, Hefei, China
| | - Ren Ren
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Lana C Ly
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney 2052, Australia
| | - John R Horton
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Fudong Li
- Ministry of Education Key Laboratory for Membraneless Organelles and Cellular Dynamics, University of Science and Technology of China, Hefei, China
| | - Kate G R Quinlan
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney 2052, Australia
| | - Merlin Crossley
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney 2052, Australia.
| | - Yunyu Shi
- Hefei National Laboratory for Physical Sciences at Microscale, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230026, China; Ministry of Education Key Laboratory for Membraneless Organelles and Cellular Dynamics, University of Science and Technology of China, Hefei, China.
| | - Xiaodong Cheng
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
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miR-21-5p Regulates the Proliferation and Differentiation of Skeletal Muscle Satellite Cells by Targeting KLF3 in Chicken. Genes (Basel) 2021; 12:genes12060814. [PMID: 34073601 PMCID: PMC8227323 DOI: 10.3390/genes12060814] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 05/21/2021] [Accepted: 05/25/2021] [Indexed: 01/04/2023] Open
Abstract
The proliferation and differentiation of skeletal muscle satellite cells (SMSCs) play an important role in the development of skeletal muscle. Our previous sequencing data showed that miR-21-5p is one of the most abundant miRNAs in chicken skeletal muscle. Therefore, in this study, the spatiotemporal expression of miR-21-5p and its effects on skeletal muscle development of chickens were explored using in vitro cultured SMSCs as a model. The results in this study showed that miR-21-5p was highly expressed in the skeletal muscle of chickens. The overexpression of miR-21-5p promoted the proliferation of SMSCs as evidenced by increased cell viability, increased cell number in the proliferative phase, and increased mRNA and protein expression of proliferation markers including PCNA, CDK2, and CCND1. Moreover, it was revealed that miR-21-5p promotes the formation of myotubes by modulating the expression of myogenic markers including MyoG, MyoD, and MyHC, whereas knockdown of miR-21-5p showed the opposite result. Gene prediction and dual fluorescence analysis confirmed that KLF3 was one of the direct target genes of miR-21-5p. We confirmed that, contrary to the function of miR-21-5p, KLF3 plays a negative role in the proliferation and differentiation of SMSCs. Si-KLF3 promotes cell number and proliferation activity, as well as the cell differentiation processes. Our results demonstrated that miR-21-5p promotes the proliferation and differentiation of SMSCs by targeting KLF3. Collectively, the results obtained in this study laid a foundation for exploring the mechanism through which miR-21-5p regulates SMSCs.
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6
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Lan X, Ren R, Feng R, Ly LC, Lan Y, Zhang Z, Aboreden N, Qin K, Horton JR, Grevet JD, Mayuranathan T, Abdulmalik O, Keller CA, Giardine B, Hardison RC, Crossley M, Weiss MJ, Cheng X, Shi J, Blobel GA. ZNF410 Uniquely Activates the NuRD Component CHD4 to Silence Fetal Hemoglobin Expression. Mol Cell 2020; 81:239-254.e8. [PMID: 33301730 DOI: 10.1016/j.molcel.2020.11.006] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Revised: 10/26/2020] [Accepted: 11/02/2020] [Indexed: 01/08/2023]
Abstract
Metazoan transcription factors typically regulate large numbers of genes. Here we identify via a CRISPR-Cas9 genetic screen ZNF410, a pentadactyl DNA-binding protein that in human erythroid cells directly activates only a single gene, the NuRD component CHD4. Specificity is conveyed by two highly evolutionarily conserved clusters of ZNF410 binding sites near the CHD4 gene with no counterparts elsewhere in the genome. Loss of ZNF410 in adult-type human erythroid cell culture systems and xenotransplantation settings diminishes CHD4 levels and derepresses the fetal hemoglobin genes. While previously known to be silenced by CHD4, the fetal globin genes are exposed here as among the most sensitive to reduced CHD4 levels.. In vitro DNA binding assays and crystallographic studies reveal the ZNF410-DNA binding mode. ZNF410 is a remarkably selective transcriptional activator in erythroid cells, and its perturbation might offer new opportunities for treatment of hemoglobinopathies.
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Affiliation(s)
- Xianjiang Lan
- Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Ren Ren
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Ruopeng Feng
- Department of Hematology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Lana C Ly
- School of Biotechnology and Biomolecular Sciences, University of New South Wales (UNSW) Sydney, Sydney, NSW 2052, Australia
| | - Yemin Lan
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Zhe Zhang
- Department of Biomedical and Health Informatics, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Nicholas Aboreden
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Kunhua Qin
- Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - John R Horton
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Jeremy D Grevet
- Department of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | | | - Osheiza Abdulmalik
- Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Cheryl A Keller
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Belinda Giardine
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Ross C Hardison
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Merlin Crossley
- School of Biotechnology and Biomolecular Sciences, University of New South Wales (UNSW) Sydney, Sydney, NSW 2052, Australia
| | - Mitchell J Weiss
- Department of Hematology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Xiaodong Cheng
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Junwei Shi
- Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
| | - Gerd A Blobel
- Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
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7
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Jones J, Chen Y, Tiwari M, Li J, Ling J, Sen GL. KLF3 Mediates Epidermal Differentiation through the Epigenomic Writer CBP. iScience 2020; 23:101320. [PMID: 32659720 PMCID: PMC7358749 DOI: 10.1016/j.isci.2020.101320] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 06/02/2020] [Accepted: 06/24/2020] [Indexed: 12/24/2022] Open
Abstract
Impairments in the differentiation process can lead to skin diseases that can afflict ∼20% of the population. Thus, it is of utmost importance to understand the factors that promote the differentiation process. Here we identify the transcription factor KLF3 as a regulator of epidermal differentiation. Knockdown of KLF3 results in reduced differentiation gene expression and increased cell cycle gene expression. Over half of KLF3's genomic binding sites occur at active enhancers. KLF3 binds to active enhancers proximal to differentiation genes that are dependent upon KLF3 for expression. KLF3's genomic binding sites also highly overlaps with CBP, a histone acetyltransferase necessary for activating enhancers. Depletion of KLF3 causes reduced CBP localization at enhancers proximal to differentiation gene clusters, which leads to loss of enhancer activation but not priming. Our results suggest that KLF3 is necessary to recruit CBP to activate enhancers and drive epidermal differentiation gene expression.
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Affiliation(s)
- Jackson Jones
- Department of Dermatology, Department of Cellular and Molecular Medicine, UCSD Stem Cell Program, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0869, USA
| | - Yifang Chen
- Department of Dermatology, Department of Cellular and Molecular Medicine, UCSD Stem Cell Program, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0869, USA
| | - Manisha Tiwari
- Department of Dermatology, Department of Cellular and Molecular Medicine, UCSD Stem Cell Program, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0869, USA
| | - Jingting Li
- Department of Dermatology, Department of Cellular and Molecular Medicine, UCSD Stem Cell Program, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0869, USA
| | - Ji Ling
- Department of Dermatology, Department of Cellular and Molecular Medicine, UCSD Stem Cell Program, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0869, USA
| | - George L Sen
- Department of Dermatology, Department of Cellular and Molecular Medicine, UCSD Stem Cell Program, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0869, USA.
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Yang L, Chen Z, Stout ES, Delerue F, Ittner LM, Wilkins MR, Quinlan KGR, Crossley M. Methylation of a CGATA element inhibits binding and regulation by GATA-1. Nat Commun 2020; 11:2560. [PMID: 32444652 PMCID: PMC7244756 DOI: 10.1038/s41467-020-16388-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Accepted: 04/29/2020] [Indexed: 02/07/2023] Open
Abstract
Alterations in DNA methylation occur during development, but the mechanisms by which they influence gene expression remain uncertain. There are few examples where modification of a single CpG dinucleotide directly affects transcription factor binding and regulation of a target gene in vivo. Here, we show that the erythroid transcription factor GATA-1 — that typically binds T/AGATA sites — can also recognise CGATA elements, but only if the CpG dinucleotide is unmethylated. We focus on a single CGATA site in the c-Kit gene which progressively becomes unmethylated during haematopoiesis. We observe that methylation attenuates GATA-1 binding and gene regulation in cell lines. In mice, converting the CGATA element to a TGATA site that cannot be methylated leads to accumulation of megakaryocyte-erythroid progenitors. Thus, the CpG dinucleotide is essential for normal erythropoiesis and this study illustrates how a single methylated CpG can directly affect transcription factor binding and cellular regulation. While DNA methylation is thought to play a regulatory role, there are few examples where modification of a single CpG dinucleotide directly affects transcription factor binding. Here the authors show that methylation of a single CGATA element within the c-Kit gene inhibits binding and regulation by erythroid transcription factor GATA-1, both in cells and in mice, suggesting that methylation at this site plays an essential role in erythropoiesis.
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Affiliation(s)
- Lu Yang
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, NSW, 2052, Australia
| | - Zhiliang Chen
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, NSW, 2052, Australia
| | - Elizabeth S Stout
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, NSW, 2052, Australia
| | - Fabien Delerue
- Dementia Research Centre and Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, NSW, 2109, Australia.,Mark Wainwright Analytical Centre, Transgenic Animal Unit, UNSW Sydney, Sydney, NSW, 2052, Australia
| | - Lars M Ittner
- Dementia Research Centre and Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, NSW, 2109, Australia.,Mark Wainwright Analytical Centre, Transgenic Animal Unit, UNSW Sydney, Sydney, NSW, 2052, Australia
| | - Marc R Wilkins
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, NSW, 2052, Australia
| | - Kate G R Quinlan
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, NSW, 2052, Australia
| | - Merlin Crossley
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, NSW, 2052, Australia.
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9
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Knights AJ, Yang L, Shah M, Norton LJ, Green GS, Stout ES, Vohralik EJ, Crossley M, Quinlan KGR. Krüppel-like factor 3 (KLF3) suppresses NF-κB-driven inflammation in mice. J Biol Chem 2020; 295:6080-6091. [PMID: 32213596 DOI: 10.1074/jbc.ra120.013114] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Revised: 03/18/2020] [Indexed: 12/14/2022] Open
Abstract
Bacterial products such as lipopolysaccharides (or endotoxin) cause systemic inflammation, resulting in a substantial global health burden. The onset, progression, and resolution of the inflammatory response to endotoxin are usually tightly controlled to avoid chronic inflammation. Members of the NF-κB family of transcription factors are key drivers of inflammation that activate sets of genes in response to inflammatory signals. Such responses are typically short-lived and can be suppressed by proteins that act post-translationally, such as the SOCS (suppressor of cytokine signaling) family. Less is known about direct transcriptional regulation of these responses, however. Here, using a combination of in vitro approaches and in vivo animal models, we show that endotoxin treatment induced expression of the well-characterized transcriptional repressor Krüppel-like factor 3 (KLF3), which, in turn, directly repressed the expression of the NF-κB family member RELA/p65. We also observed that KLF3-deficient mice were hypersensitive to endotoxin and exhibited elevated levels of circulating Ly6C+ monocytes and macrophage-derived inflammatory cytokines. These findings reveal that KLF3 is a fundamental suppressor that operates as a feedback inhibitor of RELA/p65 and may be important in facilitating the resolution of inflammation.
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Affiliation(s)
- Alexander J Knights
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales 2052, Australia
| | - Lu Yang
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales 2052, Australia
| | - Manan Shah
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales 2052, Australia
| | - Laura J Norton
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales 2052, Australia
| | - Gamran S Green
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales 2052, Australia
| | - Elizabeth S Stout
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales 2052, Australia
| | - Emily J Vohralik
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales 2052, Australia
| | - Merlin Crossley
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales 2052, Australia
| | - Kate G R Quinlan
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales 2052, Australia.
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10
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Yan M, Liu H, Xu J, Cen X, Wang Q, Xu W, Wang W, Qiu Z, Ou J, Dong Y, Zhu P, Ren H, He F, Wang M. Expression of human Krüppel-like factor 3 in peripheral blood as a promising biomarker for acute leukemia. Cancer Med 2020; 9:2803-2811. [PMID: 32101374 PMCID: PMC7163096 DOI: 10.1002/cam4.2911] [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: 11/27/2019] [Revised: 01/10/2020] [Accepted: 01/27/2020] [Indexed: 02/06/2023] Open
Abstract
Background Universal gene targets are in persistent demand by real‐time quantitative polymerase chain reaction (RT‐qPCR)‐based methods in acute leukemia (AL) diagnosis and monitoring. Human Krüppel‐like factor 3 (hKLF3), a newly cloned human transcription factor, has proved to be a regulator of hematopoiesis. Methods Sanger sequencing was performed in bone marrow (BM) samples from 17 AL patients for mutations in hKLF3 coding exons. hKLF3 expression in peripheral blood (PB) and BM samples from 45 AL patients was dynamically detected by RT‐qPCR. PB samples from 31 healthy donors were tested as normal controls. Results No mutation was sequenced in hKLF3 coding exons. hKLF3 expression in PB of AL was significantly lower than that in healthy donors [0.30 (0.02‐1.07) vs 1.18 (0.62‐3.37), P < .0001]. Primary acute myeloid leukemia (AML) exhibited the least expression values compared with secondary AML and acute lymphoblastic leukemia. Receiver operating characteristic (ROC) analyses suggested that hKLF3 expression in PB was a good marker for AML diagnosis with an AUC of 0.99 (95% CI 0.98‐1.00) and an optimum cutoff value of 0.67 (sensitivity 93.94% and specificity 93.55%). hKLF3 expression was upregulated significantly when AML patients acquired morphological complete remission (CR), and the level of hKLF3 seemed to be higher in patients with deeper CR than in patients with minimal residual disease (MRD). Paired PB and BM samples showed highly consistent alteration in hKLF3 expression (r = .6533, P = .001). Besides, a significantly converse correlation between decreased hKLF3 expression in PB and markers for leukemic load was observed. Conclusions hKLF3 expression in PB may act as a potential marker for AL diagnosis and monitoring.
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Affiliation(s)
- Miao Yan
- Department of Hematology, Peking University First Hospital, Beijing, China
| | - Huihui Liu
- Department of Hematology, Peking University First Hospital, Beijing, China
| | - Junhui Xu
- Department of Hematology, Peking University First Hospital, Beijing, China
| | - Xinan Cen
- Department of Hematology, Peking University First Hospital, Beijing, China
| | - Qian Wang
- Department of Hematology, Peking University First Hospital, Beijing, China
| | - Weilin Xu
- Department of Hematology, Peking University First Hospital, Beijing, China
| | - Wensheng Wang
- Department of Hematology, Peking University First Hospital, Beijing, China
| | - Zhixiang Qiu
- Department of Hematology, Peking University First Hospital, Beijing, China
| | - Jinping Ou
- Department of Hematology, Peking University First Hospital, Beijing, China
| | - Yujun Dong
- Department of Hematology, Peking University First Hospital, Beijing, China
| | - Ping Zhu
- Department of Hematology, Peking University First Hospital, Beijing, China
| | - Hanyun Ren
- Department of Hematology, Peking University First Hospital, Beijing, China
| | - Fuchu He
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, Institute of Radiation Medicine, Academy of Military Medical Sciences, Beijing, China
| | - Mangju Wang
- Department of Hematology, Peking University First Hospital, Beijing, China
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11
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Sun Y, Zhang B, Luo L, Shi DL, Wang H, Cui Z, Huang H, Cao Y, Shu X, Zhang W, Zhou J, Li Y, Du J, Zhao Q, Chen J, Zhong H, Zhong TP, Li L, Xiong JW, Peng J, Xiao W, Zhang J, Yao J, Yin Z, Mo X, Peng G, Zhu J, Chen Y, Zhou Y, Liu D, Pan W, Zhang Y, Ruan H, Liu F, Zhu Z, Meng A. Systematic genome editing of the genes on zebrafish Chromosome 1 by CRISPR/Cas9. Genome Res 2019; 30:gr.248559.119. [PMID: 31831591 PMCID: PMC6961580 DOI: 10.1101/gr.248559.119] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Accepted: 11/06/2019] [Indexed: 02/05/2023]
Abstract
Genome editing by the well-established CRISPR/Cas9 technology has greatly facilitated our understanding of many biological processes. However, a complete whole-genome knockout for any species or model organism has rarely been achieved. Here, we performed a systematic knockout of all the genes (1333) on Chromosome 1 in zebrafish, successfully mutated 1029 genes, and generated 1039 germline-transmissible alleles corresponding to 636 genes. Meanwhile, by high-throughput bioinformatics analysis, we found that sequence features play pivotal roles in effective gRNA targeting at specific genes of interest, while the success rate of gene targeting positively correlates with GC content of the target sites. Moreover, we found that nearly one-fourth of all mutants are related to human diseases, and several representative CRISPR/Cas9-generated mutants are described here. Furthermore, we tried to identify the underlying mechanisms leading to distinct phenotypes between genetic mutants and antisense morpholino-mediated knockdown embryos. Altogether, this work has generated the first chromosome-wide collection of zebrafish genetic mutants by the CRISPR/Cas9 technology, which will serve as a valuable resource for the community, and our bioinformatics analysis also provides some useful guidance to design gene-specific gRNAs for successful gene editing.
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Affiliation(s)
- Yonghua Sun
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Wuhan, Hubei, 430072, China
| | - Bo Zhang
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, Peking University Genome Editing Research Center, College of Life Sciences, Peking University, Beijing, 100871, China
| | - Lingfei Luo
- School of Life Sciences, Southwest University, Chongqing, 400715, China
| | - De-Li Shi
- Guangdong Medical University, Zhanjiang, Guangdong, 524023, China
| | - Han Wang
- Center for Circadian Clocks, Soochow University, Suzhou, Jiangsu, 215123, China
| | - Zongbin Cui
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Wuhan, Hubei, 430072, China
| | - Honghui Huang
- School of Life Sciences, Southwest University, Chongqing, 400715, China
| | - Ying Cao
- School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China
| | - Xiaodong Shu
- Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, Guangdong, 510530, China
| | - Wenqing Zhang
- Division of Cell, Developmental and Integrative Biology, School of Medicine, South China University of Technology, Guangzhou, Guangdong, 510006, China
| | - Jianfeng Zhou
- School of Medicine and Pharmacy, Ocean University of China, Qingdao, Shandong, 266100, China
| | - Yun Li
- School of Medicine and Pharmacy, Ocean University of China, Qingdao, Shandong, 266100, China
| | - Jiulin Du
- State Key Laboratory of Neuroscience, Institute of Neuroscience, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Qingshun Zhao
- Model Animal Research Center, Nanjing University, Nanjing, Jiangsu, 210093, China
| | - Jun Chen
- College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Hanbing Zhong
- Department of Biology, South University of Science and Technology of China, Shenzhen, Guangdong, 518055, China
| | - Tao P Zhong
- Institute of Biomedical Sciences, East China Normal University, Shanghai, 200062, China
| | - Li Li
- School of Life Sciences, Southwest University, Chongqing, 400715, China
| | - Jing-Wei Xiong
- College of Life Sciences, Institute of Molecular Medicine, Peking University, Beijing, 100871, China
| | - Jinrong Peng
- College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Wuhan Xiao
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Wuhan, Hubei, 430072, China
| | - Jian Zhang
- School of Life Sciences, Yunnan University, Kunming, Yunnan, 650091, China
| | - Jihua Yao
- School of Life Sciences, Fudan University, Shanghai, 200433, China
| | - Zhan Yin
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Wuhan, Hubei, 430072, China
| | - Xianming Mo
- State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Gang Peng
- Institutes of Brain Science, Fudan University, Shanghai, 200433, China
| | - Jun Zhu
- Sino-French Research Center for Life Sciences and Genomics, Rui-Jin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Yan Chen
- Institute of Health Sciences, Chinese Academy of Sciences & Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Yong Zhou
- CAS Key Laboratory of Nutrition, Metabolism and Food Safety, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Dong Liu
- Department of Biology, South University of Science and Technology of China, Shenzhen, Guangdong, 518055, China
| | - Weijun Pan
- CAS Key Laboratory of Nutrition, Metabolism and Food Safety, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Yiyue Zhang
- Division of Cell, Developmental and Integrative Biology, School of Medicine, South China University of Technology, Guangzhou, Guangdong, 510006, China
| | - Hua Ruan
- School of Life Sciences, Southwest University, Chongqing, 400715, China
| | - Feng Liu
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Zuoyan Zhu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Wuhan, Hubei, 430072, China
| | - Anming Meng
- School of Life Sciences, Tsinghua University, Beijing, 100084, China
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12
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Kohara H, Utsugisawa T, Sakamoto C, Hirose L, Ogawa Y, Ogura H, Sugawara A, Liao J, Aoki T, Iwasaki T, Asai T, Doisaki S, Okuno Y, Muramatsu H, Abe T, Kurita R, Miyamoto S, Sakuma T, Shiba M, Yamamoto T, Ohga S, Yoshida K, Ogawa S, Ito E, Kojima S, Kanno H, Tani K. KLF1 mutation E325K induces cell cycle arrest in erythroid cells differentiated from congenital dyserythropoietic anemia patient-specific induced pluripotent stem cells. Exp Hematol 2019; 73:25-37.e8. [PMID: 30876823 DOI: 10.1016/j.exphem.2019.03.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Revised: 03/05/2019] [Accepted: 03/06/2019] [Indexed: 02/06/2023]
Abstract
Krüppel-like factor 1 (KLF1), a transcription factor controlling definitive erythropoiesis, is involved in sequential control of terminal cell division and enucleation via fine regulation of key cell cycle regulator gene expression in erythroid lineage cells. Type IV congenital dyserythropoietic anemia (CDA) is caused by a monoallelic mutation at the second zinc finger of KLF1 (c.973G>A, p.E325K). We recently diagnosed a female patient with type IV CDA with the identical missense mutation. To understand the mechanism underlying the dyserythropoiesis caused by the mutation, we generated induced pluripotent stem cells (iPSCs) from the CDA patient (CDA-iPSCs). The erythroid cells that differentiated from CDA-iPSCs (CDA-erythroid cells) displayed multinucleated morphology, absence of CD44, and dysregulation of the KLF1 target gene expression. In addition, uptake of bromodeoxyuridine by CDA-erythroid cells was significantly decreased at the CD235a+/CD71+ stage, and microarray analysis revealed that cell cycle regulator genes were dysregulated, with increased expression of negative regulators such as CDKN2C and CDKN2A. Furthermore, inducible expression of the KLF1 E325K, but not the wild-type KLF1, caused a cell cycle arrest at the G1 phase in CDA-erythroid cells. Microarray analysis of CDA-erythroid cells and real-time polymerase chain reaction analysis of the KLF1 E325K inducible expression system also revealed altered expression of several KLF1 target genes including erythrocyte membrane protein band 4.1 (EPB41), EPB42, glutathione disulfide reductase (GSR), glucose phosphate isomerase (GPI), and ATPase phospholipid transporting 8A1 (ATP8A1). Our data indicate that the E325K mutation in KLF1 is associated with disruption of transcriptional control of cell cycle regulators in association with erythroid membrane or enzyme abnormalities, leading to dyserythropoiesis.
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Affiliation(s)
- Hiroshi Kohara
- Project Division of ALA Advanced Medical Research, The Institute of Medical Science, University of Tokyo, Tokyo, Japan
| | - Taiju Utsugisawa
- Department of Transfusion Medicine and Cell Processing, Tokyo Women's Medical University, Tokyo, Japan
| | - Chika Sakamoto
- Division of Molecular and Clinical Genetics, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Lisa Hirose
- Project Division of ALA Advanced Medical Research, The Institute of Medical Science, University of Tokyo, Tokyo, Japan
| | - Yoshie Ogawa
- Project Division of ALA Advanced Medical Research, The Institute of Medical Science, University of Tokyo, Tokyo, Japan
| | - Hiromi Ogura
- Department of Transfusion Medicine and Cell Processing, Tokyo Women's Medical University, Tokyo, Japan
| | - Ai Sugawara
- Project Division of ALA Advanced Medical Research, The Institute of Medical Science, University of Tokyo, Tokyo, Japan
| | - Jiyuan Liao
- Project Division of ALA Advanced Medical Research, The Institute of Medical Science, University of Tokyo, Tokyo, Japan
| | - Takako Aoki
- Department of Transfusion Medicine and Cell Processing, Tokyo Women's Medical University, Tokyo, Japan
| | - Takuya Iwasaki
- Department of Transfusion Medicine and Cell Processing, Tokyo Women's Medical University, Tokyo, Japan
| | | | - Sayoko Doisaki
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yusuke Okuno
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Hideki Muramatsu
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Takaaki Abe
- Department of Research and Development, Central Blood Institute, Japanese Red Cross Society, Tokyo, Japan
| | - Ryo Kurita
- Department of Research and Development, Central Blood Institute, Japanese Red Cross Society, Tokyo, Japan
| | - Shohei Miyamoto
- Project Division of ALA Advanced Medical Research, The Institute of Medical Science, University of Tokyo, Tokyo, Japan
| | - Tetsushi Sakuma
- Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University, Hiroshima, Japan
| | - Masayuki Shiba
- Department of Research and Development, Central Blood Institute, Japanese Red Cross Society, Tokyo, Japan
| | - Takashi Yamamoto
- Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University, Hiroshima, Japan
| | - Shouichi Ohga
- Department of Pediatrics, Yamaguchi University Graduate School of Medicine, Ube, Japan
| | - Kenichi Yoshida
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Seishi Ogawa
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Etsuro Ito
- Department of Pediatrics, Hirosaki University Graduate School of Medicine, Hirosaki, Japan
| | - Seiji Kojima
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Hitoshi Kanno
- Department of Transfusion Medicine and Cell Processing, Tokyo Women's Medical University, Tokyo, Japan.
| | - Kenzaburo Tani
- Project Division of ALA Advanced Medical Research, The Institute of Medical Science, University of Tokyo, Tokyo, Japan; Division of Molecular and Clinical Genetics, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan; Department of Advanced Molecular and Cell Therapy, Kyushu University Hospital, Fukuoka, Japan.
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13
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Wang R, Xu J, Xu J, Zhu W, Qiu T, Li J, Zhang M, Wang Q, Xu T, Guo R, Lu K, Yin Y, Gu Y, Zhu L, Huang P, Liu P, Liu L, De W, Shu Y. MiR-326/Sp1/KLF3: A novel regulatory axis in lung cancer progression. Cell Prolif 2019; 52:e12551. [PMID: 30485570 PMCID: PMC6495967 DOI: 10.1111/cpr.12551] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Revised: 09/27/2018] [Accepted: 10/17/2018] [Indexed: 12/11/2022] Open
Abstract
OBJECTIVES To investigate the function and regulatory mechanism of Krüppel-like factor 3 (KLF3) in lung cancer. MATERIALS AND METHODS KLF3 expression was analysed by qRT-PCR and Western blot assays. The proliferation, migration, invasion, cycle and apoptosis were measured by CCK-8 and EdU, wound-healing and Transwell, and flow cytometry assays. The tumour growth was detected by nude mouse tumorigenesis assay. In addition, the interaction between KLF3 and Sp1 was accessed by luciferase reporter, EMSA and ChIP assay. JAK2, STAT3, PI3K and p-AKT levels were evaluated by Western blot and IHC assays. RESULTS The results indicated that KLF3 expression was elevated in lung cancer tissues. Knockdown of KLF3 inhibited lung cancer cell proliferation, migration and invasion, and induced cell cycle arrest and apoptosis. In addition, the downregulation of KLF3 suppressed tumour growth in vivo. KLF3 was transcriptionally activated by Sp1. miR-326 could bind to 3'UTR of Sp1 but not KLF3 and decreased the accumulation of Sp1, which further indirectly reduced KLF3 expression and inactivated JAK2/STAT3 and PI3K/AKT signaling pathways in vitro and in vivo. CONCLUSIONS Our data demonstrate that miR-326/Sp1/KLF3 regulatory axis is involved in the development of lung cancer, which hints the potential target for the further therapeutic strategy against lung cancer.
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Affiliation(s)
- Rong Wang
- Department of Oncologythe First Affiliated Hospital of Nanjing Medical University, Jiangsu Province HospitalNanjingChina
| | - Jiali Xu
- Department of Oncologythe First Affiliated Hospital of Nanjing Medical University, Jiangsu Province HospitalNanjingChina
| | - Jing Xu
- Department of Oncologythe First Affiliated Hospital of Nanjing Medical University, Jiangsu Province HospitalNanjingChina
| | - Wei Zhu
- Department of Oncologythe First Affiliated Hospital of Nanjing Medical University, Jiangsu Province HospitalNanjingChina
| | - Tianzhu Qiu
- Department of Oncologythe First Affiliated Hospital of Nanjing Medical University, Jiangsu Province HospitalNanjingChina
| | - Jun Li
- Department of Oncologythe First Affiliated Hospital of Nanjing Medical University, Jiangsu Province HospitalNanjingChina
| | - Meiling Zhang
- Department of Oncologythe First Affiliated Hospital of Nanjing Medical University, Jiangsu Province HospitalNanjingChina
| | - Qianqian Wang
- Department of Oncologythe First Affiliated Hospital of Nanjing Medical University, Jiangsu Province HospitalNanjingChina
| | - Tongpeng Xu
- Department of Oncologythe First Affiliated Hospital of Nanjing Medical University, Jiangsu Province HospitalNanjingChina
| | - Renhua Guo
- Department of Oncologythe First Affiliated Hospital of Nanjing Medical University, Jiangsu Province HospitalNanjingChina
| | - Kaihua Lu
- Department of Oncologythe First Affiliated Hospital of Nanjing Medical University, Jiangsu Province HospitalNanjingChina
| | - Yongmei Yin
- Department of Oncologythe First Affiliated Hospital of Nanjing Medical University, Jiangsu Province HospitalNanjingChina
| | - Yanhong Gu
- Department of Oncologythe First Affiliated Hospital of Nanjing Medical University, Jiangsu Province HospitalNanjingChina
| | - Lingjun Zhu
- Department of Oncologythe First Affiliated Hospital of Nanjing Medical University, Jiangsu Province HospitalNanjingChina
| | - Puwen Huang
- Department of OncologyLiyang people's Hospital of Jiangsu ProvinceLiyangChina
| | - Ping Liu
- Department of Oncologythe First Affiliated Hospital of Nanjing Medical University, Jiangsu Province HospitalNanjingChina
| | - Lianke Liu
- Department of Oncologythe First Affiliated Hospital of Nanjing Medical University, Jiangsu Province HospitalNanjingChina
| | - Wei De
- Department of Biochemistry and Molecular BiologyNanjing Medical UniversityNanjingChina
| | - Yongqian Shu
- Department of Oncologythe First Affiliated Hospital of Nanjing Medical University, Jiangsu Province HospitalNanjingChina
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14
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Collins PL, Cella M, Porter SI, Li S, Gurewitz GL, Hong HS, Johnson RP, Oltz EM, Colonna M. Gene Regulatory Programs Conferring Phenotypic Identities to Human NK Cells. Cell 2019; 176:348-360.e12. [PMID: 30595449 PMCID: PMC6329660 DOI: 10.1016/j.cell.2018.11.045] [Citation(s) in RCA: 99] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Revised: 09/09/2018] [Accepted: 11/28/2018] [Indexed: 01/03/2023]
Abstract
Natural killer (NK) cells develop from common progenitors but diverge into distinct subsets, which differ in cytokine production, cytotoxicity, homing, and memory traits. Given their promise in adoptive cell therapies for cancer, a deeper understanding of regulatory modules controlling clinically beneficial NK phenotypes is of high priority. We report integrated "-omics" analysis of human NK subsets, which revealed super-enhancers associated with gene cohorts that may coordinate NK functions and localization. A transcription factor-based regulatory scheme also emerged, which is evolutionarily conserved and shared by innate and adaptive lymphocytes. For both NK and T lineages, a TCF1-LEF1-MYC axis dominated the regulatory landscape of long-lived, proliferative subsets that traffic to lymph nodes. In contrast, effector populations circulating between blood and peripheral tissues shared a PRDM1-dominant landscape. This resource defines transcriptional modules, regulated by feedback loops, which may be leveraged to enhance phenotypes for NK cell-based therapies.
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Affiliation(s)
- Patrick L Collins
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Marina Cella
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Sofia I Porter
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Shasha Li
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Greer L Gurewitz
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | | | - R Paul Johnson
- Yerkes National Primate Research Center, Atlanta, GA 30329, USA
| | - Eugene M Oltz
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63110, USA.
| | - Marco Colonna
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63110, USA.
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15
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A natural regulatory mutation in the proximal promoter elevates fetal globin expression by creating a de novo GATA1 site. Blood 2019; 133:852-856. [PMID: 30617196 DOI: 10.1182/blood-2018-07-863951] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2018] [Accepted: 12/18/2018] [Indexed: 12/21/2022] Open
Abstract
β-hemoglobinopathies, such as sickle cell disease and β-thalassemia, result from mutations in the adult β-globin gene. Reactivating the developmentally silenced fetal γ-globin gene elevates fetal hemoglobin levels and ameliorates symptoms of β-hemoglobinopathies. The continued expression of fetal γ-globin into adulthood occurs naturally in a genetic condition termed hereditary persistence of fetal hemoglobin (HPFH). Point mutations in the fetal γ-globin proximal promoter can cause HPFH. The -113A>G HPFH mutation falls within the -115 cluster of HPFH mutations, a binding site for the fetal globin repressor BCL11A. We demonstrate that the -113A>G HPFH mutation, unlike other mutations in the cluster, does not disrupt BCL11A binding but rather creates a de novo binding site for the transcriptional activator GATA1. Introduction of the -113A>G HPFH mutation into erythroid cells using the clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR-associated protein 9 (Cas9) system increases GATA1 binding and elevates fetal globin levels. These results reveal the mechanism by which the -113A>G HPFH mutation elevates fetal globin and demonstrate the sensitivity of the fetal globin promoter to point mutations that often disrupt repressor binding sites but here create a de novo site for an erythroid activator.
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16
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Memon A, Lee WK. KLF10 as a Tumor Suppressor Gene and Its TGF-β Signaling. Cancers (Basel) 2018; 10:E161. [PMID: 29799499 PMCID: PMC6025274 DOI: 10.3390/cancers10060161] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Revised: 05/15/2018] [Accepted: 05/23/2018] [Indexed: 12/17/2022] Open
Abstract
Krüppel-like factor 10 (KLF10), originally named TGF-β (Transforming growth factor beta) inducible early gene 1 (TIEG1), is a DNA-binding transcriptional regulator containing a triple C2H2 zinc finger domain. By binding to Sp1 (specificity protein 1) sites on the DNA and interactions with other regulatory transcription factors, KLF10 encourages and suppresses the expression of multiple genes in many cell types. Many studies have investigated its signaling cascade, but other than the TGF-β/Smad signaling pathway, these are still not clear. KLF10 plays a role in proliferation, differentiation as well as apoptosis, just like other members of the SP (specificity proteins)/KLF (Krüppel-like Factors). Recently, several studies reported that KLF10 KO (Knock out) is associated with defects in cell and organs such as osteopenia, abnormal tendon or cardiac hypertrophy. Since KLF10 was first discovered, several studies have defined its role in cancer as a tumor suppressor. KLF10 demonstrate anti-proliferative effects and induce apoptosis in various carcinoma cells including pancreatic cancer, leukemia, and osteoporosis. Collectively, these data indicate that KLF10 plays a significant role in various biological processes and diseases, but its role in cancer is still unclear. Therefore, this review was conducted to describe and discuss the role and function of KLF10 in diseases, including cancer, with a special emphasis on its signaling with TGF-β.
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Affiliation(s)
- Azra Memon
- Laboratory of Developmental Genetics, Department of Biomedical Sciences, School of Medicine, Inha University, Incheon 22212, Korea.
| | - Woon Kyu Lee
- Laboratory of Developmental Genetics, Department of Biomedical Sciences, School of Medicine, Inha University, Incheon 22212, Korea.
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17
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Martyn GE, Wienert B, Yang L, Shah M, Norton LJ, Burdach J, Kurita R, Nakamura Y, Pearson RCM, Funnell APW, Quinlan KGR, Crossley M. Natural regulatory mutations elevate the fetal globin gene via disruption of BCL11A or ZBTB7A binding. Nat Genet 2018; 50:498-503. [PMID: 29610478 DOI: 10.1038/s41588-018-0085-0] [Citation(s) in RCA: 194] [Impact Index Per Article: 32.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Accepted: 02/02/2018] [Indexed: 01/26/2023]
Abstract
β-hemoglobinopathies such as sickle cell disease (SCD) and β-thalassemia result from mutations in the adult HBB (β-globin) gene. Reactivating the developmentally silenced fetal HBG1 and HBG2 (γ-globin) genes is a therapeutic goal for treating SCD and β-thalassemia 1 . Some forms of hereditary persistence of fetal hemoglobin (HPFH), a rare benign condition in which individuals express the γ-globin gene throughout adulthood, are caused by point mutations in the γ-globin gene promoter at regions residing ~115 and 200 bp upstream of the transcription start site. We found that the major fetal globin gene repressors BCL11A and ZBTB7A (also known as LRF) directly bound to the sites at -115 and -200 bp, respectively. Furthermore, introduction of naturally occurring HPFH-associated mutations into erythroid cells by CRISPR-Cas9 disrupted repressor binding and raised γ-globin gene expression. These findings clarify how these HPFH-associated mutations operate and demonstrate that BCL11A and ZBTB7A are major direct repressors of the fetal globin gene.
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Affiliation(s)
- Gabriella E Martyn
- School of Biotechnology and Biomolecular Sciences, University of New South Wales (UNSW) Sydney, Sydney, New South Wales, Australia
| | - Beeke Wienert
- School of Biotechnology and Biomolecular Sciences, University of New South Wales (UNSW) Sydney, Sydney, New South Wales, Australia
| | - Lu Yang
- School of Biotechnology and Biomolecular Sciences, University of New South Wales (UNSW) Sydney, Sydney, New South Wales, Australia
| | - Manan Shah
- School of Biotechnology and Biomolecular Sciences, University of New South Wales (UNSW) Sydney, Sydney, New South Wales, Australia
| | - Laura J Norton
- School of Biotechnology and Biomolecular Sciences, University of New South Wales (UNSW) Sydney, Sydney, New South Wales, Australia
| | - Jon Burdach
- School of Biotechnology and Biomolecular Sciences, University of New South Wales (UNSW) Sydney, Sydney, New South Wales, Australia
| | - Ryo Kurita
- Research and Development Department, Central Blood Institute, Blood Service Headquarters, Japanese Red Cross Society, Tokyo, Japan
| | - Yukio Nakamura
- Cell Engineering Division, RIKEN BioResource Center, Ibaraki, Japan
| | - Richard C M Pearson
- School of Biotechnology and Biomolecular Sciences, University of New South Wales (UNSW) Sydney, Sydney, New South Wales, Australia
| | - Alister P W Funnell
- School of Biotechnology and Biomolecular Sciences, University of New South Wales (UNSW) Sydney, Sydney, New South Wales, Australia
| | - Kate G R Quinlan
- School of Biotechnology and Biomolecular Sciences, University of New South Wales (UNSW) Sydney, Sydney, New South Wales, Australia
| | - Merlin Crossley
- School of Biotechnology and Biomolecular Sciences, University of New South Wales (UNSW) Sydney, Sydney, New South Wales, Australia.
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18
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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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19
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Wang X, Jiang Z, Zhang Y, Wang X, Liu L, Fan Z. RNA sequencing analysis reveals protective role of kruppel-like factor 3 in colorectal cancer. Oncotarget 2017; 8:21984-21993. [PMID: 28423541 PMCID: PMC5400639 DOI: 10.18632/oncotarget.15766] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Accepted: 01/27/2017] [Indexed: 01/03/2023] Open
Abstract
The Kruppel-like factor (KLF) family of transcription factors plays an important role in embryonic formation and cancer progression. This study was performed to determine the clinical importance of the KLF family in colorectal cancer (CRC). In total, 361 patients with CRC from The Cancer Genome Atlas (TCGA) cohort were used to comprehensively study the role of the KLF family in CRC. The results were then further validated using an in-house cohort (n=194). Univariate and multivariate Cox proportional hazards models were used to assess the risk factors for survival. In the TCGA cohort, KLF3 (hazard ratio [HR], 0.501; 95% confidence interval [CI], 0.272-0.920; P=0.025), KLF14 (HR, 1.454; 95% CI, 1.059-1.995; P=0.020), and KLF17 (HR, 1.241; 95% CI, 1.030-1.494, P=0.023) were identified as potential biomarkers in the univariate analysis, but after Cox proportional hazards analysis, only KLF3 (HR, 0.473; 95% CI, 0.230-0.831; P=0.012) was shown to be independently predictive of overall survival in patients with CRC. This finding was validated in our in-house cohort, which demonstrated that KLF3 expression was an independent predictor of both overall survival (HR, 0.628; 95% CI, 0.342-0.922; P=0.035) and disease-free survival (HR, 0.421; 95% CI, 0.317-0.697, P=0.016). KLF3 expression was inversely correlated with the N stage (P=0.015) and lymphovascular invasion (P=0.020). Collectively, loss of KLF3 was correlated with aggressive phenotypes and poor survival outcomes. KLF3 might be a potential new predictor and therapeutic target for CRC. Further study is needed for a more detailed understanding of the role of KLF3 in CRC.
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Affiliation(s)
- Xiaohong Wang
- Department of Digestive Endoscopy Center, Second Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu Province, China.,Department of Gastroenterology, Second Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu Province, China
| | - Zhonghua Jiang
- Department of Gastroenterology, First People's Hospital of Yancheng, Yancheng, Jiangsu Province, China
| | - Yu Zhang
- Department of Gastroenterology, Second Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu Province, China
| | - Xiang Wang
- Department of Digestive Endoscopy Center, First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu Province, China
| | - Li Liu
- Department of Digestive Endoscopy Center, First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu Province, China
| | - Zhining Fan
- Department of Digestive Endoscopy Center, First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu Province, China
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20
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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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21
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KLF1 drives the expression of fetal hemoglobin in British HPFH. Blood 2017; 130:803-807. [PMID: 28659276 DOI: 10.1182/blood-2017-02-767400] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2017] [Accepted: 06/19/2017] [Indexed: 01/13/2023] Open
Abstract
β-Hemoglobinopathies are among the most common single-locus inherited diseases. In this condition, high fetal hemoglobin (HbF) levels have been found to be beneficial, and boosting HbF expression is seen as an attractive therapy. Naturally occurring mutations in the fetal globin promoter can result in high HbF persisting into adulthood in a benign condition known as hereditary persistence of fetal hemoglobin (HPFH). Individuals with one form of HPFH, British HPFH, carry a T to C substitution at position -198 of the fetal globin gene promoter. These individuals exhibit HbF levels of up to 20%, enough to ameliorate the symptoms of β-hemoglobinopathies. Here, we use clustered regularly interspaced short palindromic repeat-mediated genome editing to introduce the -198 substitution into human erythroid HUDEP-2 cells and show that this mutation is sufficient to substantially elevate expression of HbF. We also examined the molecular mechanism underlying the increase in fetal globin expression. Through a combination of in vitro and in vivo studies, we demonstrate that the mutation creates a de novo binding site for the important erythroid gene activator Krüppel-like factor 1 (KLF1/erythroid KLF). Our results indicate that introducing this single naturally occurring mutation leads to significantly boosted HbF levels.
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22
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Ilsley MD, Gillinder KR, Magor GW, Huang S, Bailey TL, Crossley M, Perkins AC. Krüppel-like factors compete for promoters and enhancers to fine-tune transcription. Nucleic Acids Res 2017; 45:6572-6588. [PMID: 28541545 PMCID: PMC5499887 DOI: 10.1093/nar/gkx441] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Accepted: 05/22/2017] [Indexed: 12/16/2022] Open
Abstract
Krüppel-like factors (KLFs) are a family of 17 transcription factors characterized by a conserved DNA-binding domain of three zinc fingers and a variable N-terminal domain responsible for recruiting cofactors. KLFs have diverse functions in stem cell biology, embryo patterning, and tissue homoeostasis. KLF1 and related family members function as transcriptional activators via recruitment of co-activators such as EP300, whereas KLF3 and related members act as transcriptional repressors via recruitment of C-terminal Binding Proteins. KLF1 directly activates the Klf3 gene via an erythroid-specific promoter. Herein, we show KLF1 and KLF3 bind common as well as unique sites within the erythroid cell genome by ChIP-seq. We show KLF3 can displace KLF1 from key erythroid gene promoters and enhancers in vivo. Using 4sU RNA labelling and RNA-seq, we show this competition results in reciprocal transcriptional outputs for >50 important genes. Furthermore, Klf3-/- mice displayed exaggerated recovery from anemic stress and persistent cell cycling consistent with a role for KLF3 in dampening KLF1-driven proliferation. We suggest this study provides a paradigm for how KLFs work in incoherent feed-forward loops or networks to fine-tune transcription and thereby control diverse biological processes such as cell proliferation.
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Affiliation(s)
- Melissa D. Ilsley
- Mater Research Institute, Translational Research Institute, University of Queensland, Brisbane 4102, Australia
- School of Biomedical Sciences, University of Queensland, Brisbane 4072, Australia
| | - Kevin R. Gillinder
- Mater Research Institute, Translational Research Institute, University of Queensland, Brisbane 4102, Australia
| | - Graham W. Magor
- Mater Research Institute, Translational Research Institute, University of Queensland, Brisbane 4102, Australia
| | - Stephen Huang
- Mater Research Institute, Translational Research Institute, University of Queensland, Brisbane 4102, Australia
- School of Biomedical Sciences, University of Queensland, Brisbane 4072, Australia
| | | | | | - Andrew C. Perkins
- Mater Research Institute, Translational Research Institute, University of Queensland, Brisbane 4102, Australia
- School of Biomedical Sciences, University of Queensland, Brisbane 4072, Australia
- The Princess Alexandra Hospital, Brisbane 4102, Australia
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23
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Norton LJ, Hallal S, Stout ES, Funnell APW, Pearson RCM, Crossley M, Quinlan KGR. Direct competition between DNA binding factors highlights the role of Krüppel-like Factor 1 in the erythroid/megakaryocyte switch. Sci Rep 2017; 7:3137. [PMID: 28600522 PMCID: PMC5466599 DOI: 10.1038/s41598-017-03289-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Accepted: 04/26/2017] [Indexed: 11/15/2022] Open
Abstract
The Krüppel-like factor (KLF) family of transcription factors play critical roles in haematopoiesis. KLF1, the founding member of the family, has been implicated in the control of both erythropoiesis and megakaryopoiesis. Here we describe a novel system using an artificial dominant negative isoform of KLF1 to investigate the role of KLF1 in the erythroid/megakaryocytic switch in vivo. We developed murine cell lines stably overexpressing a GST-KLF1 DNA binding domain fusion protein (GST-KLF1 DBD), as well as lines expressing GST only as a control. Interestingly, overexpression of GST-KLF1 DBD led to an overall reduction in erythroid features and an increase in megakaryocytic features indicative of a reduced function of endogenous KLF1. We simultaneously compared in vivo DNA occupancy of both endogenous KLF1 and GST-KLF1 DBD by ChIP qPCR. Here we found that GST-KLF1 DBD physically displaces endogenous KLF1 at a number of loci, providing novel in vivo evidence of direct competition between DNA binding proteins. These results highlight the role of KLF1 in the erythroid/megakaryocyte switch and suggest that direct competition between transcription factors with similar consensus sequences is an important mechanism in transcriptional regulation.
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Affiliation(s)
- Laura J Norton
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, 2052, Australia
| | - Samantha Hallal
- School of Molecular Bioscience, University of Sydney, Sydney, NSW, 2006, Australia
| | - Elizabeth S Stout
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, 2052, Australia
| | - Alister P W Funnell
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, 2052, Australia.,School of Molecular Bioscience, University of Sydney, Sydney, NSW, 2006, Australia
| | - Richard C M Pearson
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, 2052, Australia.,School of Molecular Bioscience, University of Sydney, Sydney, NSW, 2006, Australia
| | - Merlin Crossley
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, 2052, Australia.,School of Molecular Bioscience, University of Sydney, Sydney, NSW, 2006, Australia
| | - Kate G R Quinlan
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, 2052, Australia.
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24
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KLF1 directly activates expression of the novel fetal globin repressor ZBTB7A/LRF in erythroid cells. Blood Adv 2017; 1:685-692. [PMID: 29296711 DOI: 10.1182/bloodadvances.2016002303] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Accepted: 02/24/2017] [Indexed: 12/29/2022] Open
Abstract
Genes encoding the human β-like hemoglobin proteins undergo a developmental switch from fetal γ-globin to adult β-globin expression around the time of birth. β-hemoglobinopathies, such as sickle-cell disease and β-thalassemia, result from mutations affecting the adult β-globin gene. The only treatment options currently available carry significant adverse effects. Analyses of heritable variations in fetal hemoglobin (HbF) levels have provided evidence that reactivation of the silenced fetal γ-globin genes in adult erythroid cells is a promising therapy. The γ-globin repressor BCL11A has become the major focus, with several studies investigating its regulation and function as a first step to inhibiting its expression or activity. However, a second repression mechanism was recently shown to be mediated by the transcription factor ZBTB7A/LRF, suggesting that understanding the regulation of ZBTB7A may also be useful. Here we show that Krüppel-like factor 1 (KLF1) directly drives expression of ZBTB7A in erythroid cells by binding to its proximal promoter. We have also uncovered an erythroid-specific regulation mechanism, leading to the upregulation of a novel ZBTB7A transcript in the erythroid compartment. The demonstration that ZBTB7A, like BCL11A, is a KLF1 target gene also fits with the observation that reduced KLF1 expression or activity is associated with HbF derepression.
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25
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Alawad AO, Alharbi SN, Alhazzaa OA, Alagrafi FS, Alkhrayef MN, Alhamdan ZA, Alenazi AD, Hammad M, Alyahya SA, AlJohi HA, Alanazi IO. Molecular Modeling and Phylogeny of the Krüppel-like Factor 4 (cKLF4) Protein from the Arabian Camel, Camelus dromedarius. Bioinform Biol Insights 2017; 10:291-300. [PMID: 28050127 PMCID: PMC5179146 DOI: 10.4137/bbi.s40782] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Revised: 10/13/2016] [Accepted: 10/20/2016] [Indexed: 11/30/2022] Open
Abstract
Krüppel-like factor 4 (KLF4) is a pluripotency transcription factor that helps in generating induced pluripotent stem cells (iPSCs). We sequenced for the first time the full coding sequence of Camelus dromedarius KLF4 (cKLF4), which is also known as the Arabian camel. Bioinformatics analysis revealed the molecular weight and the isoelectric point of cKLF4 protein to be 53.043 kDa and 8.74, respectively. The predicted cKLF4 protein sequence shows high identity with some other species as follows: 98% with Bactrian camel and 89% with alpaca KLF4 proteins. A three-dimensional (3D) structure was built based on the available crystal structure of the Mus musculus KLF4 (mKLF4) of 82 residues (PDB: 2 WBS) and by predicting 400 residues using bioinformatics software. The comparison confirms the presence of the zinc finger domains in cKLF4 protein. Phylogenetic analysis showed that KLF4 from the Arabian camel is grouped with the Bactrian camel, alpaca, cattle, and pig. This study will help in the annotation of KLF4 protein and in generating camel-induced pluripotent stem cells (CiPSCs).
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Affiliation(s)
- Abdullah O Alawad
- National Center for Stem Cell Technology, King Abdulaziz City for Science and Technology (KACST), Riyadh, Kingdom of Saudi Arabia
| | - Sultan N Alharbi
- National Center for Stem Cell Technology, King Abdulaziz City for Science and Technology (KACST), Riyadh, Kingdom of Saudi Arabia
| | - Othman A Alhazzaa
- National Center for Stem Cell Technology, King Abdulaziz City for Science and Technology (KACST), Riyadh, Kingdom of Saudi Arabia
| | - Faisal S Alagrafi
- National Center for Stem Cell Technology, King Abdulaziz City for Science and Technology (KACST), Riyadh, Kingdom of Saudi Arabia
| | - Mohammad N Alkhrayef
- National Center for Stem Cell Technology, King Abdulaziz City for Science and Technology (KACST), Riyadh, Kingdom of Saudi Arabia
| | - Ziyad A Alhamdan
- National Center for Stem Cell Technology, King Abdulaziz City for Science and Technology (KACST), Riyadh, Kingdom of Saudi Arabia
| | - Abdullah D Alenazi
- National Center for Stem Cell Technology, King Abdulaziz City for Science and Technology (KACST), Riyadh, Kingdom of Saudi Arabia
| | - Mohamed Hammad
- National Center for Stem Cell Technology, King Abdulaziz City for Science and Technology (KACST), Riyadh, Kingdom of Saudi Arabia.; SAAD Research and Development Center, Clinical Research Laboratory and Radiation Oncology, SAAD Specialist Hospital, Al Khobar, Kingdom of Saudi Arabia
| | - Sami A Alyahya
- National Center for biotechnology, King Abdulaziz City for Science and Technology (KACST), Riyadh, Kingdom of Saudi Arabia
| | - Hasan A AlJohi
- National Center for Genomic Technology, King Abdulaziz City for Science and Technology, Riyadh, Kingdom of Saudi Arabia
| | - Ibrahim O Alanazi
- National Center for Genomic Technology, King Abdulaziz City for Science and Technology, Riyadh, Kingdom of Saudi Arabia
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26
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Knights AJ, Yik JJ, Mat Jusoh H, Norton LJ, Funnell APW, Pearson RCM, Bell-Anderson KS, Crossley M, Quinlan KGR. Krüppel-like Factor 3 (KLF3/BKLF) Is Required for Widespread Repression of the Inflammatory Modulator Galectin-3 (Lgals3). J Biol Chem 2016; 291:16048-58. [PMID: 27226561 PMCID: PMC4965555 DOI: 10.1074/jbc.m116.715748] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2016] [Revised: 05/22/2016] [Indexed: 01/13/2023] Open
Abstract
The Lgals3 gene encodes a multifunctional β-galactoside-binding protein, galectin-3. Galectin-3 has been implicated in a broad range of biological processes from chemotaxis and inflammation to fibrosis and apoptosis. The role of galectin-3 as a modulator of inflammation has been studied intensively, and recent evidence suggests that it may serve as a protective factor in obesity and other metabolic disorders. Despite considerable interest in galectin-3, little is known about its physiological regulation at the transcriptional level. Here, using knockout mice, chromatin immunoprecipitations, and cellular and molecular analyses, we show that the zinc finger transcription factor Krüppel-like factor 3 (KLF3) directly represses galectin-3 transcription. We find that galectin-3 is broadly up-regulated in KLF3-deficient mouse tissues, that KLF3 occupies regulatory regions of the Lgals3 gene, and that KLF3 directly binds its cognate elements (CACCC boxes) in the galectin-3 promoter and represses its activation in cellular assays. We also provide mechanistic insights into the regulation of Lgals3, demonstrating that C-terminal binding protein (CtBP) is required to drive optimal KLF3-mediated silencing. These findings help to enhance our understanding of how expression of the inflammatory modulator galectin-3 is controlled, opening up avenues for potential therapeutic interventions in the future.
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Affiliation(s)
- Alexander J Knights
- From the School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales 2052 and
| | - Jinfen J Yik
- From the School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales 2052 and
| | | | - Laura J Norton
- From the School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales 2052 and
| | - Alister P W Funnell
- From the School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales 2052 and
| | - Richard C M Pearson
- From the School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales 2052 and
| | - Kim S Bell-Anderson
- Charles Perkins Centre, School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales 2006, Australia
| | - Merlin Crossley
- From the School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales 2052 and
| | - Kate G R Quinlan
- From the School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales 2052 and
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27
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Bhattarai S, Sochacka-Marlowe A, Crutchfield G, Khan R, Londraville R, Liu Q. Krüpple-like factors 7 and 6a mRNA expression in adult zebrafish central nervous system. Gene Expr Patterns 2016; 21:41-53. [PMID: 27364471 DOI: 10.1016/j.gep.2016.06.004] [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: 02/16/2016] [Revised: 06/15/2016] [Accepted: 06/18/2016] [Indexed: 11/25/2022]
Abstract
Krüpple-like factors (KLFs) are transcription factors with zinc finger DNA binding domains known to play important roles in brain development and central nervous system (CNS) regeneration. There is little information on KLFs expression in adult vertebrate CNS. In this study, we used in situ hybridization to examine Klf7 mRNA (klf7) and Klf6a mRNA (klf6a) expression in adult zebrafish CNS. Both klfs exhibit wide and similar expression in the zebrafish CNS. Brain areas containing strongly labeled cells include the ventricular regions of the dorsomedial telencephalon, the ventromedial telencephalon, periventricular regions of the thalamus and hypothalamus, torus longitudinalis, stratum periventriculare of the optic tectum, granular regions of the cerebellar body and valvula, and superficial layers of the facial and vagal lobes. In the spinal cord, klf7- and klf6a-expressing cells are found in both the dorsal and ventral horns. Numerous sensory structures (e.g. auditory, lateral line, olfactory and visual) and several motor nuclei (e.g. oculomotor, trigeminal, and vagal motor nuclei) contain klf7- and/or klf6a-expressing cells. Our results may provide useful information for determining these Klfs in maintenance and/or function in adult CNS.
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Affiliation(s)
- Sunil Bhattarai
- Department of Biology and Integrated Bioscience Program, University of Akron, Akron, OH 44325, United States
| | - Alicja Sochacka-Marlowe
- Department of Biology and Integrated Bioscience Program, University of Akron, Akron, OH 44325, United States
| | - Gerald Crutchfield
- Department of Biology and Integrated Bioscience Program, University of Akron, Akron, OH 44325, United States
| | - Ramisha Khan
- Department of Biology and Integrated Bioscience Program, University of Akron, Akron, OH 44325, United States
| | - Richard Londraville
- Department of Biology and Integrated Bioscience Program, University of Akron, Akron, OH 44325, United States
| | - Qin Liu
- Department of Biology and Integrated Bioscience Program, University of Akron, Akron, OH 44325, United States.
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28
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Lim WF, Burdach J, Funnell APW, Pearson RCM, Quinlan KGR, Crossley M. Directing an artificial zinc finger protein to new targets by fusion to a non-DNA-binding domain. Nucleic Acids Res 2015; 44:3118-30. [PMID: 26673701 PMCID: PMC4838343 DOI: 10.1093/nar/gkv1380] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Accepted: 11/27/2015] [Indexed: 01/05/2023] Open
Abstract
Transcription factors are often regarded as having two separable components: a DNA-binding domain (DBD) and a functional domain (FD), with the DBD thought to determine target gene recognition. While this holds true for DNA binding in vitro, it appears that in vivo FDs can also influence genomic targeting. We fused the FD from the well-characterized transcription factor Krüppel-like Factor 3 (KLF3) to an artificial zinc finger (AZF) protein originally designed to target the Vascular Endothelial Growth Factor-A (VEGF-A) gene promoter. We compared genome-wide occupancy of the KLF3FD-AZF fusion to that observed with AZF. AZF bound to the VEGF-A promoter as predicted, but was also found to occupy approximately 25 000 other sites, a large number of which contained the expected AZF recognition sequence, GCTGGGGGC. Interestingly, addition of the KLF3 FD re-distributes the fusion protein to new sites, with total DNA occupancy detected at around 50 000 sites. A portion of these sites correspond to known KLF3-bound regions, while others contained sequences similar but not identical to the expected AZF recognition sequence. These results show that FDs can influence and may be useful in directing AZF DNA-binding proteins to specific targets and provide insights into how natural transcription factors operate.
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Affiliation(s)
- Wooi F Lim
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, NSW 2052, Australia
| | - Jon Burdach
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, NSW 2052, Australia
| | - Alister P W Funnell
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, NSW 2052, Australia
| | - Richard C M Pearson
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, NSW 2052, Australia
| | - Kate G R Quinlan
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, NSW 2052, Australia
| | - Merlin Crossley
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, NSW 2052, Australia
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29
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Khalil MI, Ruyechan WT, Hay J, Arvin A. Differential effects of Sp cellular transcription factors on viral promoter activation by varicella-zoster virus (VZV) IE62 protein. Virology 2015; 485:47-57. [PMID: 26207799 PMCID: PMC4619144 DOI: 10.1016/j.virol.2015.06.031] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2015] [Revised: 05/08/2015] [Accepted: 06/25/2015] [Indexed: 12/12/2022]
Abstract
The immediate early (IE) 62 protein is the major varicella-zoster virus (VZV) regulatory factor. Analysis of the VZV genome revealed 40 predicted GC-rich boxes within 36 promoters. We examined effects of ectopic expression of Sp1-Sp4 on IE62- mediated transactivation of three viral promoters. Ectopic expression of Sp3 and Sp4 enhanced IE62 activation of ORF3 and gI promoters while Sp3 reduced IE62 activation of ORF28/29 promoter and VZV DNA replication. Sp2 reduced IE62 transactivation of gI while Sp1 had no significant influence on IE62 activation with any of these viral promoters. Electrophoretic mobility shift assays (EMSA) confirmed binding of Sp1 and Sp3 but not Sp2 and Sp4 to the gI promoter. Sp1-4 bound to IE62 and amino acids 238-258 of IE62 were important for the interaction with Sp3 and Sp4 as well as Sp1. This work shows that Sp family members have differential effects on IE62-mediated transactivation in a promoter-dependent manner.
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Affiliation(s)
- Mohamed I Khalil
- Departments of Pediatrics and Microbiology & Immunology, Stanford University School of Medicine, Stanford, CA, United States; Department of Molecular Biology, National Research Center EL-Buhouth St., Dokki, Cairo, Egypt.
| | - William T Ruyechan
- Department of Microbiology and Immunology and the Witebsky Center for Microbial Pathogenesis and Immunology, University at Buffalo, Buffalo, NY, United States
| | - John Hay
- Department of Microbiology and Immunology and the Witebsky Center for Microbial Pathogenesis and Immunology, University at Buffalo, Buffalo, NY, United States
| | - Ann Arvin
- Departments of Pediatrics and Microbiology & Immunology, Stanford University School of Medicine, Stanford, CA, United States
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30
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Presnell JS, Schnitzler CE, Browne WE. KLF/SP Transcription Factor Family Evolution: Expansion, Diversification, and Innovation in Eukaryotes. Genome Biol Evol 2015; 7:2289-309. [PMID: 26232396 PMCID: PMC4558859 DOI: 10.1093/gbe/evv141] [Citation(s) in RCA: 72] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/22/2015] [Indexed: 11/13/2022] Open
Abstract
The Krüppel-like factor and specificity protein (KLF/SP) genes play key roles in critical biological processes including stem cell maintenance, cell proliferation, embryonic development, tissue differentiation, and metabolism and their dysregulation has been implicated in a number of human diseases and cancers. Although many KLF/SP genes have been characterized in a handful of bilaterian lineages, little is known about the KLF/SP gene family in nonbilaterians and virtually nothing is known outside the metazoans. Here, we analyze and discuss the origins and evolutionary history of the KLF/SP transcription factor family and associated transactivation/repression domains. We have identified and characterized the complete KLF/SP gene complement from the genomes of 48 species spanning the Eukarya. We have also examined the phylogenetic distribution of transactivation/repression domains associated with this gene family. We report that the origin of the KLF/SP gene family predates the divergence of the Metazoa. Furthermore, the expansion of the KLF/SP gene family is paralleled by diversification of transactivation domains via both acquisitions of pre-existing ancient domains as well as by the appearance of novel domains exclusive to this gene family and is strongly associated with the expansion of cell type complexity.
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Affiliation(s)
| | - Christine E Schnitzler
- Genome Technology Branch, National Human Genome Research Institute, National Institutes of Health
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Genome-wide analysis of the zebrafish Klf family identifies two genes important for erythroid maturation. Dev Biol 2015; 403:115-27. [PMID: 26015096 DOI: 10.1016/j.ydbio.2015.05.015] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2015] [Revised: 05/17/2015] [Accepted: 05/18/2015] [Indexed: 01/01/2023]
Abstract
Krüppel-like transcription factors (Klfs), each of which contains a CACCC-box binding domain, have been investigated in a variety of developmental processes, such as angiogenesis, neurogenesis and somatic-cell reprogramming. However, the function and molecular mechanism by which the Klf family acts during developmental hematopoiesis remain elusive. Here, we report identification of 24 Klf family genes in zebrafish using bioinformatics. Gene expression profiling shows that 6 of these genes are expressed in blood and/or vascular endothelial cells during embryogenesis. Loss of function of 2 factors (klf3 or klf6a) leads to a decreased number of mature erythrocytes. Molecular studies indicate that both Klf3 and Klf6a are essential for erythroid cell differentiation and maturation but that these two proteins function in distinct manners. We find that Klf3 inhibits the expression of ferric-chelate reductase 1b (frrs1b), thereby promoting the maturation of erythroid cells, whereas Klf6a controls the erythroid cell cycle by negatively regulating cdkn1a expression to determine the rate of red blood cell proliferation. Taken together, our study provides a global view of the Klf family members that contribute to hematopoiesis in zebrafish and sheds new light on the function and molecular mechanism by which Klf3 and Klf6a act during erythropoiesis in vertebrates.
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Dewi V, Kwok A, Lee S, Lee MM, Tan YM, Nicholas HR, Isono KI, Wienert B, Mak KS, Knights AJ, Quinlan KGR, Cordwell SJ, Funnell APW, Pearson RCM, Crossley M. Phosphorylation of Krüppel-like factor 3 (KLF3/BKLF) and C-terminal binding protein 2 (CtBP2) by homeodomain-interacting protein kinase 2 (HIPK2) modulates KLF3 DNA binding and activity. J Biol Chem 2015; 290:8591-605. [PMID: 25659434 DOI: 10.1074/jbc.m115.638338] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Krüppel-like factor 3 (KLF3/BKLF), a member of the Krüppel-like factor (KLF) family of transcription factors, is a widely expressed transcriptional repressor with diverse biological roles. Although there is considerable understanding of the molecular mechanisms that allow KLF3 to silence the activity of its target genes, less is known about the signal transduction pathways and post-translational modifications that modulate KLF3 activity in response to physiological stimuli. We observed that KLF3 is modified in a range of different tissues and found that the serine/threonine kinase homeodomain-interacting protein kinase 2 (HIPK2) can both bind and phosphorylate KLF3. Mass spectrometry identified serine 249 as the primary phosphorylation site. Mutation of this site reduces the ability of KLF3 to bind DNA and repress transcription. Furthermore, we also determined that HIPK2 can phosphorylate the KLF3 co-repressor C-terminal binding protein 2 (CtBP2) at serine 428. Finally, we found that phosphorylation of KLF3 and CtBP2 by HIPK2 strengthens the interaction between these two factors and increases transcriptional repression by KLF3. Taken together, our results indicate that HIPK2 potentiates the activity of KLF3.
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Affiliation(s)
- Vitri Dewi
- From the School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales 2052, Australia
| | - Alister Kwok
- the School of Molecular Bioscience, University of Sydney, Sydney, New South Wales, 2006, Australia, and
| | - Stella Lee
- the School of Molecular Bioscience, University of Sydney, Sydney, New South Wales, 2006, Australia, and
| | - Ming Min Lee
- the School of Molecular Bioscience, University of Sydney, Sydney, New South Wales, 2006, Australia, and
| | - Yee Mun Tan
- the School of Molecular Bioscience, University of Sydney, Sydney, New South Wales, 2006, Australia, and
| | - Hannah R Nicholas
- the School of Molecular Bioscience, University of Sydney, Sydney, New South Wales, 2006, Australia, and
| | - Kyo-ichi Isono
- the RIKEN Research Center for Allergy and Immunology, Tsurumi-ku, Yokohama City, Kanagawa 230-0045, Japan
| | - Beeke Wienert
- From the School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales 2052, Australia
| | - Ka Sin Mak
- From the School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales 2052, Australia
| | - Alexander J Knights
- From the School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales 2052, Australia
| | - Kate G R Quinlan
- From the School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales 2052, Australia
| | - Stuart J Cordwell
- the School of Molecular Bioscience, University of Sydney, Sydney, New South Wales, 2006, Australia, and
| | - Alister P W Funnell
- From the School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales 2052, Australia
| | - Richard C M Pearson
- From the School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales 2052, Australia
| | - Merlin Crossley
- From the School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales 2052, Australia, the School of Molecular Bioscience, University of Sydney, Sydney, New South Wales, 2006, Australia, and
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Beishline K, Azizkhan-Clifford J. Sp1 and the 'hallmarks of cancer'. FEBS J 2015; 282:224-58. [PMID: 25393971 DOI: 10.1111/febs.13148] [Citation(s) in RCA: 365] [Impact Index Per Article: 40.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2014] [Revised: 09/26/2014] [Accepted: 11/10/2014] [Indexed: 12/19/2022]
Abstract
For many years, transcription factor Sp1 was viewed as a basal transcription factor and relegated to a role in the regulation of so-called housekeeping genes. Identification of Sp1's role in recruiting the general transcription machinery in the absence of a TATA box increased its importance in gene regulation, particularly in light of recent estimates that the majority of mammalian genes lack a TATA box. In this review, we briefly consider the history of Sp1, the founding member of the Sp family of transcription factors. We review the evidence suggesting that Sp1 is highly regulated by post-translational modifications that positively and negatively affect the activity of Sp1 on a wide array of genes. Sp1 is over-expressed in many cancers and is associated with poor prognosis. Targeting Sp1 in cancer treatment has been suggested; however, our review of the literature on the role of Sp1 in the regulation of genes that contribute to the 'hallmarks of cancer' illustrates the extreme complexity of Sp1 functions. Sp1 both activates and suppresses the expression of a number of essential oncogenes and tumor suppressors, as well as genes involved in essential cellular functions, including proliferation, differentiation, the DNA damage response, apoptosis, senescence and angiogenesis. Sp1 is also implicated in inflammation and genomic instability, as well as epigenetic silencing. Given the apparently opposing effects of Sp1, a more complete understanding of the function of Sp1 in cancer is required to validate its potential as a therapeutic target.
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Affiliation(s)
- Kate Beishline
- Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, Philadelphia, PA, USA
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Alles M, Turchinovich G, Zhang P, Schuh W, Agenès F, Kirberg J. Leukocyte β7 integrin targeted by Krüppel-like factors. THE JOURNAL OF IMMUNOLOGY 2014; 193:1737-46. [PMID: 25015818 DOI: 10.4049/jimmunol.1302613] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Constitutive expression of Krüppel-like factor 3 (KLF3, BKLF) increases marginal zone (MZ) B cell numbers, a phenotype shared with mice lacking KLF2. Ablation of KLF3, known to interact with serum response factor (SRF), or SRF itself, results in fewer MZ B cells. It is unknown how these functional equivalences result. In this study, it is shown that KLF3 acts as transcriptional repressor for the leukocyte-specific integrin β7 (Itgb7, Ly69) by binding to the β7 promoter, as revealed by chromatin immunoprecipitation. KLF2 overexpression antagonizes this repression and also binds the β7 promoter, indicating that these factors may compete for target sequence(s). Whereas β7 is identified as direct KLF target, its repression by KLF3 is not connected to the MZ B cell increase because β7-deficient mice have a normal complement of these and the KLF3-driven increase still occurs when β7 is deleted. Despite this, KLF3 overexpression abolishes lymphocyte homing to Peyer's patches, much like β7 deficiency does. Furthermore, KLF3 expression alone overcomes the MZ B cell deficiency when SRF is absent. SRF is also dispensable for the KLF3-mediated repression of β7. Thus, despite the shared phenotype of KLF3 and SRF-deficient mice, cooperation of these factors appears neither relevant for the formation of MZ B cells nor for the regulation of β7. Finally, a potent negative regulatory feedback loop limiting KLF3 expression is shown in this study, mediated by KLF3 directly repressing its own gene promoter. In summary, KLFs use regulatory circuits to steer lymphocyte maturation and homing and directly control leukocyte integrin expression.
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Affiliation(s)
- Melanie Alles
- Division of Immunology (3/3), Paul-Ehrlich-Institut, 63225 Langen, Germany
| | - Gleb Turchinovich
- Department of Biomedicine, Laboratory of Developmental Immunology, 4058 Basel, Switzerland; Basel University Children's Hospital, 4031 Basel, Switzerland
| | - Pumin Zhang
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX 77030
| | - Wolfgang Schuh
- Division of Molecular Immunology, Department of Internal Medicine III, Nikolaus-Fiebiger-Center, University of Erlangen-Nürnberg, 91054 Erlangen, Germany
| | - Fabien Agenès
- INSERM U743, Montreal, Quebec H2X 1P1, Canada; and INSERM ADR Paris V Saint Anne, 75014 Paris, France
| | - Jörg Kirberg
- Division of Immunology (3/3), Paul-Ehrlich-Institut, 63225 Langen, Germany;
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Funnell APW, Vernimmen D, Lim WF, Mak KS, Wienert B, Martyn GE, Artuz CM, Burdach J, Quinlan KGR, Higgs DR, Whitelaw E, Pearson RCM, Crossley M. Differential regulation of the α-globin locus by Krüppel-like Factor 3 in erythroid and non-erythroid cells. BMC Mol Biol 2014; 15:8. [PMID: 24885809 PMCID: PMC4033687 DOI: 10.1186/1471-2199-15-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2013] [Accepted: 05/06/2014] [Indexed: 12/17/2022] Open
Abstract
Background Krüppel-like Factor 3 (KLF3) is a broadly expressed zinc-finger transcriptional repressor with diverse biological roles. During erythropoiesis, KLF3 acts as a feedback repressor of a set of genes that are activated by Krüppel-like Factor 1 (KLF1). Noting that KLF1 binds α-globin gene regulatory sequences during erythroid maturation, we sought to determine whether KLF3 also interacts with the α-globin locus to regulate transcription. Results We found that expression of a human transgenic α-globin reporter gene is markedly up-regulated in fetal and adult erythroid cells of Klf3−/− mice. Inspection of the mouse and human α-globin promoters revealed a number of canonical KLF-binding sites, and indeed, KLF3 was shown to bind to these regions both in vitro and in vivo. Despite these observations, we did not detect an increase in endogenous murine α-globin expression in Klf3−/− erythroid tissue. However, examination of murine embryonic fibroblasts lacking KLF3 revealed significant de-repression of α-globin gene expression. This suggests that KLF3 may contribute to the silencing of the α-globin locus in non-erythroid tissue. Moreover, ChIP-Seq analysis of murine fibroblasts demonstrated that across the locus, KLF3 does not occupy the promoter regions of the α-globin genes in these cells, but rather, binds to upstream, DNase hypersensitive regulatory regions. Conclusions These findings reveal that the occupancy profile of KLF3 at the α-globin locus differs in erythroid and non-erythroid cells. In erythroid cells, KLF3 primarily binds to the promoters of the adult α-globin genes, but appears dispensable for normal transcriptional regulation. In non-erythroid cells, KLF3 distinctly binds to the HS-12 and HS-26 elements and plays a non-redundant, albeit modest, role in the silencing of α-globin expression.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | - Merlin Crossley
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia.
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Mak KS, Burdach J, Norton LJ, Pearson RCM, Crossley M, Funnell APW. Repression of chimeric transcripts emanating from endogenous retrotransposons by a sequence-specific transcription factor. Genome Biol 2014; 15:R58. [PMID: 24946810 PMCID: PMC4056533 DOI: 10.1186/gb-2014-15-4-r58] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2013] [Accepted: 04/30/2014] [Indexed: 11/10/2022] Open
Abstract
Background Retroviral elements are pervasively transcribed and dynamically regulated during development. While multiple histone- and DNA-modifying enzymes have broadly been associated with their global silencing, little is known about how the many diverse retroviral families are each selectively recognized. Results Here we show that the zinc finger protein Krüppel-like Factor 3 (KLF3) specifically silences transcription from the ORR1A0 long terminal repeat in murine fetal and adult erythroid cells. In the absence of KLF3, we detect widespread transcription from ORR1A0 elements driven by the master erythroid regulator KLF1. In several instances these aberrant transcripts are spliced to downstream genic exons. One such chimeric transcript produces a novel, dominant negative isoform of PU.1 that can induce erythroid differentiation. Conclusions We propose that KLF3 ensures the integrity of the murine erythroid transcriptome through the selective repression of a particular retroelement and is likely one of multiple sequence-specific factors that cooperate to achieve global silencing.
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37
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Zhang ZW, Wu CY, Li H, Wang N. Expression and functional analyses of Krüppel-like factor 3 in chicken adipose tissue. Biosci Biotechnol Biochem 2014; 78:614-23. [DOI: 10.1080/09168451.2014.896735] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Abstract
Studies in mammalian species showed that Krüppel-like factor 3 (KLF3) regulated adipose tissue development. However, it was not reported in chicken. In the current study, we found that during the growth and development of abdominal fat tissue, chicken KLF3 (Gallus gallus KLF3, gKLF3) was consecutively expressed, and its transcripts were higher at 7 weeks of age and lower at 10 weeks of age in lean broilers than in fat broilers. In addition, gKLF3 overexpression suppressed chicken CCAAT/enhancer binding protein alpha (C/EBPα), fatty acid binding protein 4 (FABP4), fatty acid synthase (FASN), and lipoprotein lipase (LPL) promoter activities, but increased chicken peroxisome proliferator-activated receptor gamma (PPARγ) promoter activity. Additionally, point mutagenesis analysis showed that the substitution of Asp by Gly within the Pro-Val-Asp-Leu-Thr (PVDLT) motif of gKLF3 significantly reduced the ability of gKLF3 to regulate the promoter activities of FABP4, FASN, LPL, C/EBPα, and PPARγ.
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Affiliation(s)
- Zhi-Wei Zhang
- Key Laboratory of Chicken Genetics and Breeding of Agriculture Ministry, Key Laboratory of Animal Genetics, Breeding and Reproduction of Education Department of Heilongjiang Province, College of Animal Science and Technology, Northeast Agricultural University, Harbin, China
- School of Medicine, Shihezi University, Shihezi, China
| | - Chun-Yan Wu
- Key Laboratory of Chicken Genetics and Breeding of Agriculture Ministry, Key Laboratory of Animal Genetics, Breeding and Reproduction of Education Department of Heilongjiang Province, College of Animal Science and Technology, Northeast Agricultural University, Harbin, China
| | - Hui Li
- Key Laboratory of Chicken Genetics and Breeding of Agriculture Ministry, Key Laboratory of Animal Genetics, Breeding and Reproduction of Education Department of Heilongjiang Province, College of Animal Science and Technology, Northeast Agricultural University, Harbin, China
| | - Ning Wang
- Key Laboratory of Chicken Genetics and Breeding of Agriculture Ministry, Key Laboratory of Animal Genetics, Breeding and Reproduction of Education Department of Heilongjiang Province, College of Animal Science and Technology, Northeast Agricultural University, Harbin, China
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Burdach J, Funnell APW, Mak KS, Artuz CM, Wienert B, Lim WF, Tan LY, Pearson RCM, Crossley M. Regions outside the DNA-binding domain are critical for proper in vivo specificity of an archetypal zinc finger transcription factor. Nucleic Acids Res 2013; 42:276-89. [PMID: 24106088 PMCID: PMC3874204 DOI: 10.1093/nar/gkt895] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Transcription factors (TFs) are often regarded as being composed of a DNA-binding domain (DBD) and a functional domain. The two domains are considered separable and autonomous, with the DBD directing the factor to its target genes and the functional domain imparting transcriptional regulation. We examined an archetypal zinc finger (ZF) TF, Krüppel-like factor 3 with an N-terminal domain that binds the corepressor CtBP and a DBD composed of three ZFs at its C-terminus. We established a system to compare the genomic occupancy profile of wild-type Krüppel-like factor 3 with two mutants affecting the N-terminal functional domain: a mutant unable to contact the cofactor CtBP and a mutant lacking the entire N-terminal domain, but retaining the ZFs intact. Chromatin immunoprecipitation followed by sequencing was used to assess binding across the genome in murine embryonic fibroblasts. Unexpectedly, we observe that mutations in the N-terminal domain generally reduced binding, but there were also instances where binding was retained or even increased. These results provide a clear demonstration that the correct localization of TFs to their target genes is not solely dependent on their DNA-contact domains. This informs our understanding of how TFs operate and is of relevance to the design of artificial ZF proteins.
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Affiliation(s)
- Jon Burdach
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, NSW 2052, Australia and School of Molecular Bioscience, University of Sydney, NSW 2006, Australia
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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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Three fingers on the switch: Krüppel-like factor 1 regulation of γ-globin to β-globin gene switching. Curr Opin Hematol 2013; 20:193-200. [PMID: 23474875 DOI: 10.1097/moh.0b013e32835f59ba] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
PURPOSE OF REVIEW Krüppel-like factor 1 (KLF1) regulates most aspects of erythropoiesis. Many years ago, transgenic mouse studies implicated KLF1 in the control of the human γ-globin to β-globin switch. In this review, we will integrate these initial studies with recent developments in human genetics to discuss our present understanding of how KLF1 and its target genes direct the switch. RECENT FINDINGS Recent studies have shown that human mutations in KLF1 are common and mostly asymptomatic, but lead to significant increases in levels of fetal hemoglobin (HbF) (α2γ2) and adult HbA2 (α2δ2). Genome-wide association studies (GWAS) have demonstrated that three primary loci are associated with increased HbF levels in the population: the β-globin locus itself, the BCL11A locus, and a site between MYB and HBS1L. We discuss evidence that KLF1 directly regulates BCL11A, MYB and other genes, which are involved directly or indirectly in γ-globin silencing, thus providing a link between GWAS and KLF1 in hemoglobin switching. SUMMARY KLF1 regulates the γ-globin to β-globin genetic switch by many mechanisms. Firstly, it facilitates formation of an active chromatin hub (ACH) at the β-globin gene cluster. Specifically, KLF1 conscripts the adult-stage β-globin gene to replace the γ-globin gene within the ACH in a stage-specific manner. Secondly, KLF1 acts as a direct activator of genes that encode repressors of γ-globin gene expression. Finally, KLF1 is a regulator of many components of the cell cycle machinery. We suggest that dysregulation of these genes leads to cell cycle perturbation and 'erythropoietic stress' leading to indirect upregulation of HbF.
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A feedback loop consisting of microRNA 23a/27a and the β-like globin suppressors KLF3 and SP1 regulates globin gene expression. Mol Cell Biol 2013; 33:3994-4007. [PMID: 23918807 DOI: 10.1128/mcb.00623-13] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
The developmental stage-specific expression of the human β-like globin genes has been studied for decades, and many transcriptional factors as well as other important cis elements have been identified. However, little is known about the microRNAs that potentially regulate β-like globin gene expression directly or indirectly during erythropoiesis. In this study, we show that microRNA 23a (miR-23a) and miR-27a promote β-like globin gene expression in K562 cells and primary erythroid cells through targeting of the transcription factors KLF3 and SP1. Intriguingly, miR-23a and miR-27a further enhance the transcription of β-like globin genes through repression of KLF3 and SP1 binding to the β-like globin gene locus during erythroid differentiation. Moreover, KLF3 can bind to the promoter of the miR-23a∼27a∼24-2 cluster and suppress this microRNA cluster expression. Hence, a positive feedback loop comprised of KLF3 and miR-23a promotes the expression of β-like globin genes and the miR-23a∼27a∼24-2 cluster during erythropoiesis.
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Bell-Anderson KS, Funnell AP, Williams H, Mat Jusoh H, Scully T, Lim WF, Burdach JG, Mak KS, Knights AJ, Hoy AJ, Nicholas HR, Sainsbury A, Turner N, Pearson RC, Crossley M. Loss of Krüppel-like factor 3 (KLF3/BKLF) leads to upregulation of the insulin-sensitizing factor adipolin (FAM132A/CTRP12/C1qdc2). Diabetes 2013; 62:2728-37. [PMID: 23633521 PMCID: PMC3717849 DOI: 10.2337/db12-1745] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Krüppel-like factor 3 (KLF3) is a transcriptional regulator that we have shown to be involved in the regulation of adipogenesis in vitro. Here, we report that KLF3-null mice are lean and protected from diet-induced obesity and glucose intolerance. On a chow diet, plasma levels of leptin are decreased, and adiponectin is increased. Despite significant reductions in body weight and adiposity, wild-type and knockout animals show equivalent energy intake, expenditure, and excretion. To investigate the molecular events underlying these observations, we used microarray analysis to compare gene expression in Klf3(+/+) and Klf3(-/-) tissues. We found that mRNA expression of Fam132a, which encodes a newly identified insulin-sensitizing adipokine, adipolin, is significantly upregulated in the absence of KLF3. We confirmed that KLF3 binds the Fam132a promoter in vitro and in vivo and that this leads to repression of promoter activity. Further, plasma adipolin levels were significantly increased in Klf3(-/-) mice compared with wild-type littermates. Boosting levels of adipolin via targeting of KLF3 offers a novel potential therapeutic strategy for the treatment of insulin resistance.
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Affiliation(s)
- Kim S Bell-Anderson
- School of Molecular Bioscience, University of Sydney, Sydney, New South Wales, Australia.
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Kelsey L, Flenniken AM, Qu D, Funnell APW, Pearson R, Zhou YQ, Voronina I, Berberovic Z, Wood G, Newbigging S, Weiss ES, Wong M, Quach I, Yeh SYS, Deshwar AR, Scott IC, McKerlie C, Henkelman M, Backx P, Simpson J, Osborne L, Rossant J, Crossley M, Bruneau B, Adamson SL. ENU-induced mutation in the DNA-binding domain of KLF3 reveals important roles for KLF3 in cardiovascular development and function in mice. PLoS Genet 2013; 9:e1003612. [PMID: 23874215 PMCID: PMC3708807 DOI: 10.1371/journal.pgen.1003612] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2012] [Accepted: 05/22/2013] [Indexed: 12/23/2022] Open
Abstract
KLF3 is a Krüppel family zinc finger transcription factor with widespread tissue expression and no previously known role in heart development. In a screen for dominant mutations affecting cardiovascular function in N-ethyl-N-nitrosourea (ENU) mutagenized mice, we identified a missense mutation in the Klf3 gene that caused aortic valvular stenosis and partially penetrant perinatal lethality in heterozygotes. All homozygotes died as embryos. In the first of three zinc fingers, a point mutation changed a highly conserved histidine at amino acid 275 to arginine (Klf3H275R). This change impaired binding of the mutant protein to KLF3's canonical DNA binding sequence. Heterozygous Klf3H275R mutants that died as neonates had marked biventricular cardiac hypertrophy with diminished cardiac chambers. Adult survivors exhibited hypotension, cardiac hypertrophy with enlarged cardiac chambers, and aortic valvular stenosis. A dominant negative effect on protein function was inferred by the similarity in phenotype between heterozygous Klf3H275R mutants and homozygous Klf3 null mice. However, the existence of divergent traits suggested the involvement of additional interactions. We conclude that KLF3 plays diverse and important roles in cardiovascular development and function in mice, and that amino acid 275 is critical for normal KLF3 protein function. Future exploration of the KLF3 pathway provides a new avenue for investigating causative factors contributing to cardiovascular disorders in humans. Cardiac defects are among the most common malformations in humans. Most causative genetic mutations remain unknown. To discover new causative genes important in cardiovascular development and function, we examined 1770 mice with randomly mutated genes and found a mutant with aortic valvular stenosis, and increased risk of fetal and neonatal death. Using linkage analysis and sequencing, we identified a protein-altering point mutation in the gene regulatory protein KLF3. Mice that survived into adulthood with one mutant copy of the Klf3 gene had low arterial blood pressure, enlarged hearts, and increased mortality due to heart failure. When both copies of the Klf3 gene was mutant, then embryos had heart defects, and all died before birth. KLF3 had no previously known role in heart development so to confirm these findings, we (1) knocked down klf3 expression in zebrafish embryos and (2) examined mice with a mutation that effectively eliminated the KLF3 protein. In both cases, cardiovascular dysfunction was observed. In conclusion, we have discovered that KLF3 plays diverse and important roles in cardiovascular development and function in mice. Future exploration of the KLF3 pathway provides a new avenue for investigating causative factors contributing to cardiovascular disorders in humans.
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Affiliation(s)
- Lois Kelsey
- Samuel Lunenfeld Research Institute of Mount Sinai Hospital, Toronto, Ontario, Canada
- Centre for Modeling Human Disease, Toronto Centre for Phenogenomics, Toronto, Ontario, Canada
| | - Ann M. Flenniken
- Samuel Lunenfeld Research Institute of Mount Sinai Hospital, Toronto, Ontario, Canada
- Centre for Modeling Human Disease, Toronto Centre for Phenogenomics, Toronto, Ontario, Canada
| | - Dawei Qu
- Samuel Lunenfeld Research Institute of Mount Sinai Hospital, Toronto, Ontario, Canada
- Centre for Modeling Human Disease, Toronto Centre for Phenogenomics, Toronto, Ontario, Canada
| | - Alister P. W. Funnell
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Richard Pearson
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Yu-Qing Zhou
- Mouse Imaging Centre, Toronto Centre for Phenogenomics, Toronto, Ontario, Canada
- The Hospital for Sick Children Research Institute, Toronto, Ontario, Canada
| | - Irina Voronina
- Samuel Lunenfeld Research Institute of Mount Sinai Hospital, Toronto, Ontario, Canada
- Centre for Modeling Human Disease, Toronto Centre for Phenogenomics, Toronto, Ontario, Canada
| | - Zorana Berberovic
- Samuel Lunenfeld Research Institute of Mount Sinai Hospital, Toronto, Ontario, Canada
- Centre for Modeling Human Disease, Toronto Centre for Phenogenomics, Toronto, Ontario, Canada
| | - Geoffrey Wood
- Centre for Modeling Human Disease, Toronto Centre for Phenogenomics, Toronto, Ontario, Canada
- The Hospital for Sick Children Research Institute, Toronto, Ontario, Canada
| | - Susan Newbigging
- Centre for Modeling Human Disease, Toronto Centre for Phenogenomics, Toronto, Ontario, Canada
- The Hospital for Sick Children Research Institute, Toronto, Ontario, Canada
| | - Edward S. Weiss
- Centre for Modeling Human Disease, Toronto Centre for Phenogenomics, Toronto, Ontario, Canada
| | - Michael Wong
- Mouse Imaging Centre, Toronto Centre for Phenogenomics, Toronto, Ontario, Canada
- The Hospital for Sick Children Research Institute, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Ivan Quach
- Samuel Lunenfeld Research Institute of Mount Sinai Hospital, Toronto, Ontario, Canada
| | - S. Y. Sandy Yeh
- Samuel Lunenfeld Research Institute of Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Ashish R. Deshwar
- The Hospital for Sick Children Research Institute, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Ian C. Scott
- The Hospital for Sick Children Research Institute, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- Heart and Stroke Richard Lewar Centre of Excellence, Toronto, Ontario, Canada
| | - Colin McKerlie
- Centre for Modeling Human Disease, Toronto Centre for Phenogenomics, Toronto, Ontario, Canada
- The Hospital for Sick Children Research Institute, Toronto, Ontario, Canada
| | - Mark Henkelman
- Mouse Imaging Centre, Toronto Centre for Phenogenomics, Toronto, Ontario, Canada
- The Hospital for Sick Children Research Institute, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Peter Backx
- Heart and Stroke Richard Lewar Centre of Excellence, Toronto, Ontario, Canada
- Department of Physiology, University of Toronto, Toronto, Ontario, Canada
| | - Jeremy Simpson
- Heart and Stroke Richard Lewar Centre of Excellence, Toronto, Ontario, Canada
- Department of Physiology, University of Toronto, Toronto, Ontario, Canada
| | - Lucy Osborne
- Centre for Modeling Human Disease, Toronto Centre for Phenogenomics, Toronto, Ontario, Canada
- Department of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Janet Rossant
- Centre for Modeling Human Disease, Toronto Centre for Phenogenomics, Toronto, Ontario, Canada
- The Hospital for Sick Children Research Institute, Toronto, Ontario, Canada
| | - Merlin Crossley
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Benoit Bruneau
- Gladstone Institute of Cardiovascular Disease, Department of Pediatrics, and Cardiovascular Research Institute, University of California, San Francisco, California, United States of America
| | - S. Lee Adamson
- Samuel Lunenfeld Research Institute of Mount Sinai Hospital, Toronto, Ontario, Canada
- Centre for Modeling Human Disease, Toronto Centre for Phenogenomics, Toronto, Ontario, Canada
- Heart and Stroke Richard Lewar Centre of Excellence, Toronto, Ontario, Canada
- Department of Physiology, University of Toronto, Toronto, Ontario, Canada
- Department of Obstetrics and Gynaecology, University of Toronto, Toronto, Ontario, Canada
- * E-mail:
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Lower KM, De Gobbi M, Hughes JR, Derry CJ, Ayyub H, Sloane-Stanley JA, Vernimmen D, Garrick D, Gibbons RJ, Higgs DR. Analysis of sequence variation underlying tissue-specific transcription factor binding and gene expression. Hum Mutat 2013; 34:1140-8. [PMID: 23616472 DOI: 10.1002/humu.22343] [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] [Received: 01/18/2013] [Accepted: 04/12/2013] [Indexed: 11/09/2022]
Abstract
Although mutations causing monogenic disorders most frequently lie within the affected gene, sequence variation in complex disorders is more commonly found in noncoding regions. Furthermore, recent genome- wide studies have shown that common DNA sequence variants in noncoding regions are associated with "normal" variation in gene expression resulting in cell-specific and/or allele-specific differences. The mechanism by which such sequence variation causes changes in gene expression is largely unknown. We have addressed this by studying natural variation in the binding of key transcription factors (TFs) in the well-defined, purified cell system of erythropoiesis. We have shown that common polymorphisms frequently directly perturb the binding sites of key TFs, and detailed analysis shows how this causes considerable (~10-fold) changes in expression from a single allele in a tissue-specific manner. We also show how a SNP, located at some distance from the recognized TF binding site, may affect the recruitment of a large multiprotein complex and alter the associated chromatin modification of the variant regulatory element. This study illustrates the principles by which common sequence variation may cause changes in tissue-specific gene expression, and suggests that such variation may underlie an individual's propensity to develop complex human genetic diseases.
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Affiliation(s)
- Karen M Lower
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, Oxford, UK
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Generation of mice deficient in both KLF3/BKLF and KLF8 reveals a genetic interaction and a role for these factors in embryonic globin gene silencing. Mol Cell Biol 2013; 33:2976-87. [PMID: 23716600 DOI: 10.1128/mcb.00074-13] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Krüppel-like factors 3 and 8 (KLF3 and KLF8) are highly related transcriptional regulators that bind to similar sequences of DNA. We have previously shown that in erythroid cells there is a regulatory hierarchy within the KLF family, whereby KLF1 drives the expression of both the Klf3 and Klf8 genes and KLF3 in turn represses Klf8 expression. While the erythroid roles of KLF1 and KLF3 have been explored, the contribution of KLF8 to this regulatory network has been unknown. To investigate this, we have generated a mouse model with disrupted KLF8 expression. While these mice are viable, albeit with a reduced life span, mice lacking both KLF3 and KLF8 die at around embryonic day 14.5 (E14.5), indicative of a genetic interaction between these two factors. In the fetal liver, Klf3 Klf8 double mutant embryos exhibit greater dysregulation of gene expression than either of the two single mutants. In particular, we observe derepression of embryonic, but not adult, globin expression. Taken together, these results suggest that KLF3 and KLF8 have overlapping roles in vivo and participate in the silencing of embryonic globin expression during development.
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46
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A CpG mutational hotspot in a ONECUT binding site accounts for the prevalent variant of hemophilia B Leyden. Am J Hum Genet 2013; 92:460-7. [PMID: 23472758 DOI: 10.1016/j.ajhg.2013.02.003] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2012] [Revised: 01/30/2013] [Accepted: 02/07/2013] [Indexed: 11/23/2022] Open
Abstract
Hemophilia B, or the "royal disease," arises from mutations in coagulation factor IX (F9). Mutations within the F9 promoter are associated with a remarkable hemophilia B subtype, termed hemophilia B Leyden, in which symptoms ameliorate after puberty. Mutations at the -5/-6 site (nucleotides -5 and -6 relative to the transcription start site, designated +1) account for the majority of Leyden cases and have been postulated to disrupt the binding of a transcriptional activator, the identity of which has remained elusive for more than 20 years. Here, we show that ONECUT transcription factors (ONECUT1 and ONECUT2) bind to the -5/-6 site. The various hemophilia B Leyden mutations that have been reported in this site inhibit ONECUT binding to varying degrees, which correlate well with their associated clinical severities. In addition, expression of F9 is crucially dependent on ONECUT factors in vivo, and as such, mice deficient in ONECUT1, ONECUT2, or both exhibit depleted levels of F9. Taken together, our findings establish ONECUT transcription factors as the missing hemophilia B Leyden regulators that operate through the -5/-6 site.
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47
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Lee H, Kim HJ, Lee YJ, Lee MY, Choi H, Lee H, Kim JW. Krüppel-like factor KLF8 plays a critical role in adipocyte differentiation. PLoS One 2012; 7:e52474. [PMID: 23285057 PMCID: PMC3528641 DOI: 10.1371/journal.pone.0052474] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2012] [Accepted: 11/13/2012] [Indexed: 11/18/2022] Open
Abstract
KLF8 (Krüppel-like factor 8) is a zinc-finger transcription factor known to play an essential role in the regulation of the cell cycle, apoptosis, and differentiation. However, its physiological roles and functions in adipogenesis remain unclear. In the present study, we show that KLF8 acts as a key regulator controlling adipocyte differentiation. In 3T3-L1 preadipocytes, we found that KLF8 expression was induced during differentiation, which was followed by expression of peroxisome proliferator-activated receptor γ (PPARγ) and CCAAT/enhancer-binding protein α (C/EBPα). Adipocyte differentiation was significantly attenuated by the addition of siRNA against KLF8, whereas overexpression of KLF8 resulted in enhanced differentiation. Furthermore, luciferase reporter assays demonstrated that overexpression of KLF8 induced PPARγ2 and C/EBPα promoter activity, suggesting that KLF8 is an upstream regulator of PPARγ and C/EBPα. The KLF8 binding sites were localized by site mutation analysis to −191 region in C/EBPα promoter and −303 region in PPARγ promoter, respectively. Taken together, these data reveal that KLF8 is a key component of the transcription factor network that controls terminal differentiation during adipogenesis.
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Affiliation(s)
- Haemi Lee
- Department of Biochemistry and Molecular Biology, Integrated Genomic Research Center for Metabolic Regulation, Institute of Genetic Science, Yonsei University College of Medicine, Seoul, Korea
- Brain Korea 21 Project for Medical Science, Yonsei University, Seoul, Korea
| | - Hyo Jung Kim
- Department of Biochemistry and Molecular Biology, Integrated Genomic Research Center for Metabolic Regulation, Institute of Genetic Science, Yonsei University College of Medicine, Seoul, Korea
| | - Yoo Jeong Lee
- Department of Biochemistry and Molecular Biology, Integrated Genomic Research Center for Metabolic Regulation, Institute of Genetic Science, Yonsei University College of Medicine, Seoul, Korea
- Brain Korea 21 Project for Medical Science, Yonsei University, Seoul, Korea
| | - Min-Young Lee
- Department of Biochemistry and Molecular Biology, Integrated Genomic Research Center for Metabolic Regulation, Institute of Genetic Science, Yonsei University College of Medicine, Seoul, Korea
- Brain Korea 21 Project for Medical Science, Yonsei University, Seoul, Korea
| | - Hyeonjin Choi
- Department of Biochemistry and Molecular Biology, Integrated Genomic Research Center for Metabolic Regulation, Institute of Genetic Science, Yonsei University College of Medicine, Seoul, Korea
- Brain Korea 21 Project for Medical Science, Yonsei University, Seoul, Korea
| | - Hyemin Lee
- Department of Biochemistry and Molecular Biology, Integrated Genomic Research Center for Metabolic Regulation, Institute of Genetic Science, Yonsei University College of Medicine, Seoul, Korea
- Department of Integrated OMICS for Biomedical Sciences, WCU Program of Graduate School, Yonsei University, Seoul, Korea
| | - Jae-woo Kim
- Department of Biochemistry and Molecular Biology, Integrated Genomic Research Center for Metabolic Regulation, Institute of Genetic Science, Yonsei University College of Medicine, Seoul, Korea
- Brain Korea 21 Project for Medical Science, Yonsei University, Seoul, Korea
- Department of Integrated OMICS for Biomedical Sciences, WCU Program of Graduate School, Yonsei University, Seoul, Korea
- * E-mail:
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48
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Wu Z, Wang S. Role of kruppel-like transcription factors in adipogenesis. Dev Biol 2012; 373:235-43. [PMID: 23142072 DOI: 10.1016/j.ydbio.2012.10.031] [Citation(s) in RCA: 107] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2012] [Revised: 10/31/2012] [Accepted: 10/31/2012] [Indexed: 01/27/2023]
Abstract
The zinc-finger transcription factors of the kruppel-like factor family (KLF) are critical in many physiological and pathological processes including cell proliferation, differentiation, inflammation, and apoptosis. Recently, there is increasing evidence that suggests these KLFs have an important role in fat biology. This review summarizes the role of KLFs in lipid metabolism, especially in adipogenesis, and reveals the relationship networks among members of KLF family in differentiation.
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Affiliation(s)
- Zeni Wu
- School of Public Health, Wuhan University, Wuhan, China
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49
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Krupp DR, Xu PT, Thomas S, Dellinger A, Etchevers HC, Vekemans M, Gilbert JR, Speer MC, Ashley-Koch AE, Gregory SG. Transcriptome profiling of genes involved in neural tube closure during human embryonic development using long serial analysis of gene expression (long-SAGE). ACTA ACUST UNITED AC 2012; 94:683-92. [PMID: 22806986 DOI: 10.1002/bdra.23040] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2012] [Revised: 05/01/2012] [Accepted: 05/04/2012] [Indexed: 12/14/2022]
Abstract
BACKGROUND Neural tube defects (NTDs) are common human birth defects with a complex etiology. To develop a comprehensive knowledge of the genes expressed during normal neurulation, we established transcriptomes from human neural tube fragments during and after neurulation using long Serial Analysis of Gene Expression (long-SAGE). METHODS Rostral and caudal neural tubes were dissected from normal human embryos aged between 26 and 32 days of gestation. Tissues from the same region and Carnegie stage were pooled (n ≥ 4) and total RNA extracted to construct four long-SAGE libraries. Tags were mapped using the UniGene Homo sapiens 17 bp tag-to-gene best mapping set. Differentially expressed genes were identified by chi-square or Fisher's exact test, and validation was performed for a subset of those transcripts using in situ hybridization. In silico analyses were performed with BinGO and EXPANDER. RESULTS We observed most genes to be similarly regulated in rostral and caudal regions, but expression profiles differed during and after closure. In silico analysis found similar enrichments in both regions for biologic process terms, transcription factor binding and miRNA target motifs. Twelve genes potentially expressing alternate isoforms by region or developmental stage, and the microRNAs miR-339-5p, miR-141/200a, miR-23ab, and miR-129/129-5p are among several potential candidates identified here for future research. CONCLUSIONS Time appears to influence gene expression in the developing central nervous system more than location. These data provide a novel complement to traditional strategies of identifying genes associated with human NTDs and offer unique insight into the genes associated with normal human neurulation.
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Affiliation(s)
- Deidre R Krupp
- Center for Human Genetics, Department of Medicine, Duke University Medical Center, Durham, North Carolina 27710, USA
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50
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The CACCC-binding protein KLF3/BKLF represses a subset of KLF1/EKLF target genes and is required for proper erythroid maturation in vivo. Mol Cell Biol 2012; 32:3281-92. [PMID: 22711990 DOI: 10.1128/mcb.00173-12] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The CACCC-box binding protein erythroid Krüppel-like factor (EKLF/KLF1) is a master regulator that directs the expression of many important erythroid genes. We have previously shown that EKLF drives transcription of the gene for a second KLF, basic Krüppel-like factor, or KLF3. We have now tested the in vivo role of KLF3 in erythroid cells by examining Klf3 knockout mice. KLF3-deficient adults exhibit a mild compensated anemia, including enlarged spleens, increased red pulp, and a higher percentage of erythroid progenitors, together with elevated reticulocytes and abnormal erythrocytes in the peripheral blood. Impaired erythroid maturation is also observed in the fetal liver. We have found that KLF3 levels rise as erythroid cells mature to become TER119(+). Consistent with this, microarray analysis of both TER119(-) and TER119(+) erythroid populations revealed that KLF3 is most critical at the later stages of erythroid maturation and is indeed primarily a transcriptional repressor. Notably, many of the genes repressed by KLF3 are also known to be activated by EKLF. However, the majority of these are not currently recognized as erythroid-cell-specific genes. These results reveal the molecular and physiological function of KLF3, defining it as a feedback repressor that counters the activity of EKLF at selected target genes to achieve normal erythropoiesis.
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