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Yu Y, Yang H, Wang H, Xiao F. Zinc finger protein 217 contributes to natural killer cell dysfunction in murine colorectal cancer. Cell Immunol 2025; 413:104971. [PMID: 40381549 DOI: 10.1016/j.cellimm.2025.104971] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2025] [Revised: 04/30/2025] [Accepted: 05/09/2025] [Indexed: 05/20/2025]
Abstract
Immune cells play active roles in the surveillance and control of colorectal cancer (CRC) progression. Natural killer (NK) cells are powerful anti-tumor effector cells but their regulatory mechanisms in the CRC tissues have not been thoroughly elucidated. In this research using a murine inflammatory colorectal cancer model, we characterized the phenotype and function of NK cells. We found signs of NK cell dysfunction in CRC tissues, including up-regulation of exhaustion markers, down-regulation of activating receptors, deficiencies in degranulation and cytokine expression, and weak cytolytic effect. Interestingly, zinc finger protein 217 (ZNF217), a transcription repressor, was significantly up-regulated in CRC-associated NK cells. In vitro assays revealed that ZNF217 knockdown promoted NK cell cytolytic activity, implying that ZNF217 is an inhibitory factor of NK cell function. Adoptive transfer assays indicated that ZNF217 knockdown also resulted in enhancement of NK cell function in vivo and subsequently suppressed CRC development. Furthermore, hypoxia rather than exhaustion up-regulated ZNF217 expression in NK cells. ZNF217 knockdown promoted NK cell resistance to hypoxia-mediated NK cell dysfunction. Therefore, we discovered a novel regulatory factor of NK cell dysfunction during CRC development.
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Affiliation(s)
- Yibing Yu
- The Department of Neurosurgery and Cardiothoracic Surgery, Wuhan Fourth Hospital Gutian Section, 76 Jiefang Street, Qiaokou District, Wuhan, Hubei Province 430033, China
| | - Huanbin Yang
- The Division of Gastrointestinal Surgery, Wuhan Fourth Hospital, 473 Hanzheng Street, Qiaokou District, Wuhan, Hubei Province 430033, China
| | - Hao Wang
- The Division of Gastrointestinal Surgery, Wuhan Fourth Hospital, 473 Hanzheng Street, Qiaokou District, Wuhan, Hubei Province 430033, China
| | - Fei Xiao
- The Division of Gastrointestinal Surgery, Wuhan Fourth Hospital, 473 Hanzheng Street, Qiaokou District, Wuhan, Hubei Province 430033, China.
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2
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Melnik BC, Weiskirchen R, John SM, Stremmel W, Leitzmann C, Weiskirchen S, Schmitz G. White Adipocyte Stem Cell Expansion Through Infant Formula Feeding: New Insights into Epigenetic Programming Explaining the Early Protein Hypothesis of Obesity. Int J Mol Sci 2025; 26:4493. [PMID: 40429638 PMCID: PMC12110815 DOI: 10.3390/ijms26104493] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2025] [Revised: 05/03/2025] [Accepted: 05/06/2025] [Indexed: 05/29/2025] Open
Abstract
Prolonged breastfeeding (BF), as opposed to artificial infant formula feeding (FF), has been shown to prevent the development of obesity later in life. The aim of our narrative review is to investigate the missing molecular link between postnatal protein overfeeding-often referred to as the "early protein hypothesis"-and the subsequent transcriptional and epigenetic changes that accelerate the expansion of adipocyte stem cells (ASCs) in the adipose vascular niche during postnatal white adipose tissue (WAT) development. To achieve this, we conducted a search on the Web of Science, Google Scholar, and PubMed databases from 2000 to 2025 and reviewed 750 papers. Our findings revealed that the overactivation of mechanistic target of rapamycin complex 1 (mTORC1) and S6 kinase 1 (S6K1), which inhibits wingless (Wnt) signaling due to protein overfeeding, serves as the primary pathway promoting ASC commitment and increasing preadipocyte numbers. Moreover, excessive protein intake, combined with the upregulation of the fat mass and obesity-associated gene (FTO) and a deficiency of breast milk-derived microRNAs from lactation, disrupts the proper regulation of FTO and Wnt pathway components. This disruption enhances ASC expansion in WAT while inhibiting brown adipose tissue development. While BF has been shown to have protective effects against obesity, the postnatal transcriptional and epigenetic changes induced by excessive protein intake from FF may predispose infants to early and excessive ASC commitment in WAT, thereby increasing the risk of obesity later in life.
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Affiliation(s)
- Bodo C. Melnik
- Department of Dermatology, Environmental Medicine and Health Theory, University of Osnabrück, D-49076 Osnabrück, Germany;
| | - Ralf Weiskirchen
- Institute of Molecular Pathobiochemistry, Experimental Gene Therapy and Clinical Chemistry (IFMPEGKC), RWTH University Hospital Aachen, D-52074 Aachen, Germany;
| | - Swen Malte John
- Department of Dermatology, Environmental Medicine and Health Theory, University of Osnabrück, D-49076 Osnabrück, Germany;
- Institute for Interdisciplinary Dermatological Prevention and Rehabilitation (iDerm), University of Osnabrück, D-49076 Osnabrück, Germany
| | | | - Claus Leitzmann
- Institut für Ernährungswissenschaft, Universität Gießen, D-35392 Gießen, Germany;
| | - Sabine Weiskirchen
- Institute of Molecular Pathobiochemistry, Experimental Gene Therapy and Clinical Chemistry (IFMPEGKC), RWTH University Hospital Aachen, D-52074 Aachen, Germany;
| | - Gerd Schmitz
- Institute of Clinical Chemistry and Laboratory Medicine, University Hospital of Regensburg, D-93053 Regensburg, Germany;
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Qin X, Zhou K, Dong L, Yang L, Li W, Chen Z, Shen C, Han L, Li Y, Chan AK, Pokharel SP, Qing Y, Chen M, Wang K, Leung K, Sau L, Chen CW, Deng X, Su R, Chen J. CRISPR screening reveals ZNF217 as a vulnerability in high-risk B-cell acute lymphoblastic leukemia. Theranostics 2025; 15:3234-3256. [PMID: 40093906 PMCID: PMC11905140 DOI: 10.7150/thno.100295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2024] [Accepted: 01/08/2025] [Indexed: 03/19/2025] Open
Abstract
Rationale: Despite substantial advancement in the treatment of B-cell acute lymphoblastic leukemia (B-ALL), it remains a leading cause of cancer mortality in children due to the high relapse rate. Moreover, the long-term survival rates for adult B-ALL patients are still less than 40%. The B-ALL patients carrying MLL rearrangements or BCR-ABL fusion represent high-risk B-ALL subtypes that face particularly dismal prognoses. This study aims to identify innovative therapeutic vulnerability for high-risk B-ALL. Methods: The CRISPR-Cas9 screen was conducted to pinpoint genes essential for high-risk B-ALL cell survival/growth. Both in vitro and in vivo models were then employed to investigate the pathological role of ZNF217 in high-risk B-ALL. To characterize the downstream functionally essential targets of ZNF217, we performed RNA-seq and CUT&RUN-seq, followed by integrative bioinformatics analysis and experimental validation. Results: Through the focused CRISPR-Cas9 screening, ZNF217 emerged as the most essential gene for the cell survival/growth of B-ALL driven by MLL rearrangement or BCR-ABL. Through in vitro gain- and loss-of-function assays, we demonstrated that ZNF217 is indeed required for B-ALL cell survival/growth. Moreover, we established the B-ALL xenograft model and patient-derived xenograft (PDX) model and demonstrated that ZNF217 depletion significantly suppressed B-ALL progression and substantially extended the survival of recipient mice. Through integrative multiple-omics analysis, we elucidated that ZNF217 exerts its oncogenic role in B-ALL through both CoREST-dependent and CoREST-independent mechanisms. Furthermore, we characterized FOS as a functionally essential downstream target of ZNF217, and ZNF217 inhibited FOS expression in a CoREST-independent manner. Conclusions: Our findings highlight ZNF217 as a promising therapeutic target for the treatment of high-risk B-ALL, such as those carrying MLL-rearrangements or BCR-ABL fusion.
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Affiliation(s)
- Xi Qin
- Department of Systems Biology, Beckman Research Institute of City of Hope, Duarte, CA 91010, USA
- Center for RNA Biology and Therapeutics, Beckman Research Institute of City of Hope, Duarte, CA 91010, USA
- Irell and Manella Graduate School of Biological Sciences, Beckman Research Institute of City of Hope, Duarte, CA 91010, USA
| | - Keren Zhou
- Department of Systems Biology, Beckman Research Institute of City of Hope, Duarte, CA 91010, USA
| | - Lei Dong
- Department of Systems Biology, Beckman Research Institute of City of Hope, Duarte, CA 91010, USA
| | - Lu Yang
- Department of Systems Biology, Beckman Research Institute of City of Hope, Duarte, CA 91010, USA
- Center for RNA Biology and Therapeutics, Beckman Research Institute of City of Hope, Duarte, CA 91010, USA
- Division of Epigenetic and Transcriptional Engineering, Beckman Research Institute, City of Hope, Duarte, CA 91010, USA
| | - Wei Li
- Department of Systems Biology, Beckman Research Institute of City of Hope, Duarte, CA 91010, USA
- Center for RNA Biology and Therapeutics, Beckman Research Institute of City of Hope, Duarte, CA 91010, USA
| | - Zhenhua Chen
- Department of Systems Biology, Beckman Research Institute of City of Hope, Duarte, CA 91010, USA
- Center for RNA Biology and Therapeutics, Beckman Research Institute of City of Hope, Duarte, CA 91010, USA
| | - Chao Shen
- Department of Systems Biology, Beckman Research Institute of City of Hope, Duarte, CA 91010, USA
- Center for RNA Biology and Therapeutics, Beckman Research Institute of City of Hope, Duarte, CA 91010, USA
| | - Li Han
- Department of Systems Biology, Beckman Research Institute of City of Hope, Duarte, CA 91010, USA
| | - Yangchan Li
- Department of Systems Biology, Beckman Research Institute of City of Hope, Duarte, CA 91010, USA
| | - Anthony K.N. Chan
- Department of Systems Biology, Beckman Research Institute of City of Hope, Duarte, CA 91010, USA
- Division of Epigenetic and Transcriptional Engineering, Beckman Research Institute, City of Hope, Duarte, CA 91010, USA
| | - Sheela Pangeni Pokharel
- Department of Systems Biology, Beckman Research Institute of City of Hope, Duarte, CA 91010, USA
- Division of Epigenetic and Transcriptional Engineering, Beckman Research Institute, City of Hope, Duarte, CA 91010, USA
| | - Ying Qing
- Department of Systems Biology, Beckman Research Institute of City of Hope, Duarte, CA 91010, USA
- Center for RNA Biology and Therapeutics, Beckman Research Institute of City of Hope, Duarte, CA 91010, USA
| | - Meiling Chen
- Department of Systems Biology, Beckman Research Institute of City of Hope, Duarte, CA 91010, USA
| | - Kitty Wang
- Department of Systems Biology, Beckman Research Institute of City of Hope, Duarte, CA 91010, USA
- Center for RNA Biology and Therapeutics, Beckman Research Institute of City of Hope, Duarte, CA 91010, USA
| | - Keith Leung
- Department of Systems Biology, Beckman Research Institute of City of Hope, Duarte, CA 91010, USA
- Center for RNA Biology and Therapeutics, Beckman Research Institute of City of Hope, Duarte, CA 91010, USA
| | - Lillian Sau
- Department of Systems Biology, Beckman Research Institute of City of Hope, Duarte, CA 91010, USA
- Center for RNA Biology and Therapeutics, Beckman Research Institute of City of Hope, Duarte, CA 91010, USA
| | - Chun-Wei Chen
- Department of Systems Biology, Beckman Research Institute of City of Hope, Duarte, CA 91010, USA
- Irell and Manella Graduate School of Biological Sciences, Beckman Research Institute of City of Hope, Duarte, CA 91010, USA
- City of Hope Comprehensive Cancer Center, City of Hope, Duarte, CA 91010, USA
- Division of Epigenetic and Transcriptional Engineering, Beckman Research Institute, City of Hope, Duarte, CA 91010, USA
| | - Xiaolan Deng
- Department of Systems Biology, Beckman Research Institute of City of Hope, Duarte, CA 91010, USA
- Center for RNA Biology and Therapeutics, Beckman Research Institute of City of Hope, Duarte, CA 91010, USA
- City of Hope Comprehensive Cancer Center, City of Hope, Duarte, CA 91010, USA
| | - Rui Su
- Department of Systems Biology, Beckman Research Institute of City of Hope, Duarte, CA 91010, USA
- Center for RNA Biology and Therapeutics, Beckman Research Institute of City of Hope, Duarte, CA 91010, USA
- Irell and Manella Graduate School of Biological Sciences, Beckman Research Institute of City of Hope, Duarte, CA 91010, USA
- City of Hope Comprehensive Cancer Center, City of Hope, Duarte, CA 91010, USA
| | - Jianjun Chen
- Department of Systems Biology, Beckman Research Institute of City of Hope, Duarte, CA 91010, USA
- Center for RNA Biology and Therapeutics, Beckman Research Institute of City of Hope, Duarte, CA 91010, USA
- Irell and Manella Graduate School of Biological Sciences, Beckman Research Institute of City of Hope, Duarte, CA 91010, USA
- City of Hope Comprehensive Cancer Center, City of Hope, Duarte, CA 91010, USA
- Gehr Family Center for Leukemia Research, City of Hope, Duarte, CA 91010, USA
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Li M, Dai M, Cheng B, Li S, Guo E, Fu J, Ma T, Yu B. Strategies that regulate LSD1 for novel therapeutics. Acta Pharm Sin B 2024; 14:1494-1507. [PMID: 38572094 PMCID: PMC10985039 DOI: 10.1016/j.apsb.2024.01.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2023] [Revised: 12/05/2023] [Accepted: 12/06/2023] [Indexed: 04/05/2024] Open
Abstract
Histone methylation plays crucial roles in regulating chromatin structure and gene transcription in epigenetic modifications. Lysine-specific demethylase 1 (LSD1), the first identified histone demethylase, is universally overexpressed in various diseases. LSD1 dysregulation is closely associated with cancer, viral infections, and neurodegenerative diseases, etc., making it a promising therapeutic target. Several LSD1 inhibitors and two small-molecule degraders (UM171 and BEA-17) have entered the clinical stage. LSD1 can remove methyl groups from histone 3 at lysine 4 or lysine 9 (H3K4 or H3K9), resulting in either transcription repression or activation. While the roles of LSD1 in transcriptional regulation are well-established, studies have revealed that LSD1 can also be dynamically regulated by other factors. For example, the expression or activity of LSD1 can be regulated by many proteins that form transcriptional corepressor complexes with LSD1. Moreover, some post-transcriptional modifications and cellular metabolites can also regulate LSD1 expression or its demethylase activity. Therefore, in this review, we will systematically summarize how proteins involved in the transcriptional corepressor complex, various post-translational modifications, and metabolites act as regulatory factors for LSD1 activity.
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Affiliation(s)
- Meng Li
- School of Pharmaceutical Sciences & Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, Zhengzhou University, Zhengzhou 450001, China
| | - Mengge Dai
- School of Pharmaceutical Sciences & Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, Zhengzhou University, Zhengzhou 450001, China
| | - Bing Cheng
- School of Pharmaceutical Sciences & Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, Zhengzhou University, Zhengzhou 450001, China
| | - Shaotong Li
- School of Pharmaceutical Sciences & Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, Zhengzhou University, Zhengzhou 450001, China
| | - Enhui Guo
- School of Pharmaceutical Sciences & Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, Zhengzhou University, Zhengzhou 450001, China
| | - Junwei Fu
- School of Pharmaceutical Sciences & Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, Zhengzhou University, Zhengzhou 450001, China
| | - Ting Ma
- School of Pharmaceutical Sciences & Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, Zhengzhou University, Zhengzhou 450001, China
- Pingyuan Laboratory, State Key Laboratory of Antiviral Drugs, Henan Normal University, Xinxiang 453007, China
| | - Bin Yu
- School of Pharmaceutical Sciences & Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, Zhengzhou University, Zhengzhou 450001, China
- College of Chemistry, Zhengzhou University, Zhengzhou 450001, China
- Tianjian Laboratory of Advanced Biomedical Sciences, Institute of Advanced Biomedical Sciences, Zhengzhou University, Zhengzhou 450000, China
- Pingyuan Laboratory, State Key Laboratory of Antiviral Drugs, Henan Normal University, Xinxiang 453007, China
- State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing 210023, China
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5
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Rangel N, Sánchez IL, Valbuena DS, Rondón-Lagos M. ZNF217 Gene Copy Number as a Marker of Response to Standard Therapy Drugs According to ERα Status in Breast Cancer. BREAST CANCER (DOVE MEDICAL PRESS) 2024; 16:127-139. [PMID: 38505863 PMCID: PMC10950081 DOI: 10.2147/bctt.s445753] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Accepted: 01/24/2024] [Indexed: 03/21/2024]
Abstract
Purpose The therapeutic decision for the management of breast cancer (BC) patients is based on the evaluation of prognostic factors alongside clinical and pathological parameters. Despite the use of standard biomarkers, response and resistance to therapy represent a challenge for clinicians. Among the new potential biomarkers for BC the ZNF217 gene have gained importance in recent years. However, while associations between ZNF217 gene copy number and clinicopathological characteristics have been established, its correlation with treatment response remains unclear. Patients and Methods This study aimed to evaluate the ZNF217 gene copy number and establish its associations with treatment response in estrogen receptor positive (ERα+) and ERα negative (ERα-) BC cell lines. In addition, a validation of the relationship between ZNF217 gene copy number and its prognostic value was performed using datasets of BC patients retrieved from the cBioPortal public database. Results Our data show that in ERα+ cells, ZNF217 gene copy number increase (amplification), while cell proliferation decreases in response to standard drug treatments. In contrast, both ZNF217 gene copy number (gain) and cell proliferation increases in response to standard drug treatments in ERα- cells. The results obtained align with findings from the cBioPortal database analysis, demonstrating that ERα+/HER2- low proliferation patients, exhibiting ZNF217 gene amplification or gain, have a significantly higher survival probability after treatment, compared to ERα-/HER2- and HER2+ patients. Conclusion Our results suggest that in ERα+ BC cells, ZNF217 gene amplification could be indicative of a favorable response, while in ERα- BC cells, ZNF217 gene gain could be postulated as a potential predictor of treatment resistance. A broader understanding of the role of ZNF217 gene in treatment response, together with prospective studies in BC patients, could contribute to confirming our data, as well as optimizing existing treatments and exploring novel approaches to improve overall cancer treatment outcomes.
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Affiliation(s)
- Nelson Rangel
- Departamento de Nutrición y Bioquímica, Facultad de Ciencias, Pontificia Universidad Javeriana, Bogotá, 110231, Colombia
| | - Iris Lorena Sánchez
- School of Biological Sciences, Universidad Pedagógica Y Tecnológica de Colombia, Tunja, 150003, Colombia
| | - Duván Sebastián Valbuena
- School of Biological Sciences, Universidad Pedagógica Y Tecnológica de Colombia, Tunja, 150003, Colombia
| | - Milena Rondón-Lagos
- School of Biological Sciences, Universidad Pedagógica Y Tecnológica de Colombia, Tunja, 150003, Colombia
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Briest F, Noerenberg D, Hennch C, Yoshida K, Hablesreiter R, Nimo J, Sasca D, Kirchner M, Mansouri L, Inoue Y, Wiegand L, Staiger AM, Casadei B, Korkolopoulou P, Weiner J, Lopez-Guillermo A, Warth A, Schneider T, Nagy Á, Klapper W, Hummel M, Kanellis G, Anagnostopoulos I, Mertins P, Bullinger L, Rosenquist R, Vassilakopoulos TP, Ott G, Ogawa S, Damm F. Frequent ZNF217 mutations lead to transcriptional deregulation of interferon signal transduction via altered chromatin accessibility in B cell lymphoma. Leukemia 2023; 37:2237-2249. [PMID: 37648814 PMCID: PMC10624633 DOI: 10.1038/s41375-023-02013-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 08/15/2023] [Accepted: 08/22/2023] [Indexed: 09/01/2023]
Abstract
Recent exome-wide studies discovered frequent somatic mutations in the epigenetic modifier ZNF217 in primary mediastinal B cell lymphoma (PMBCL) and related disorders. As functional consequences of ZNF217 alterations remain unknown, we comprehensively evaluated their impact in PMBCL. Targeted sequencing identified genetic lesions affecting ZNF217 in 33% of 157 PMBCL patients. Subsequent gene expression profiling (n = 120) revealed changes in cytokine and interferon signal transduction in ZNF217-aberrant PMBCL cases. In vitro, knockout of ZNF217 led to changes in chromatin accessibility interfering with binding motifs for crucial lymphoma-associated transcription factors. This led to disturbed expression of interferon-responsive and inflammation-associated genes, altered cell behavior, and aberrant differentiation. Mass spectrometry demonstrates that ZNF217 acts within a histone modifier complex containing LSD1, CoREST and HDAC and interferes with H3K4 methylation and H3K27 acetylation. Concluding, our data suggest non-catalytic activity of ZNF217, which directs histone modifier complex function and controls B cell differentiation-associated patterns of chromatin structure.
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Affiliation(s)
- Franziska Briest
- Department of Hematology, Oncology and Cancer Immunology, Campus Virchow, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Daniel Noerenberg
- Department of Hematology, Oncology and Cancer Immunology, Campus Virchow, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Cornelius Hennch
- Department of Hematology, Oncology and Cancer Immunology, Campus Virchow, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Kenichi Yoshida
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
- Cancer Genome Project Wellcome Trust Sanger Institute, Hinxton, United Kingdom
| | - Raphael Hablesreiter
- Department of Hematology, Oncology and Cancer Immunology, Campus Virchow, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Jose Nimo
- Department of Hematology, Oncology and Cancer Immunology, Campus Virchow, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Daniel Sasca
- Department of Hematology, Oncology, and Pulmonary Medicine, University Medical Center, Johannes Gutenberg-University, Mainz, Germany
| | - Marieluise Kirchner
- Core Unit Proteomics, Berlin Institute of Health at Charité - Universitätsmedizin Berlin and Max-Delbrück-Center for Molecular Medicine, Berlin, Germany
| | - Larry Mansouri
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Yoshikage Inoue
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Laura Wiegand
- Department of Hematology, Oncology and Cancer Immunology, Campus Virchow, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Annette M Staiger
- Department of Clinical Pathology, Robert-Bosch-Krankenhaus, Stuttgart, Germany
- Dr Margarete Fischer-Bosch Institute of Clinical Pharmacology Stuttgart, and University of Tuebingen, Stuttgart, Germany
| | - Beatrice Casadei
- IRCCS Azienda Ospedaliero-Universitaria di Bologna, Istituto di Ematologia "Seràgnoli", Bologna, Italy
| | - Penelope Korkolopoulou
- First Department of Pathology, National and Kapodistrian University of Athens, Laikon General Hospital, Athens, Greece
| | - January Weiner
- Core Unit Bioinformatics Berlin, Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany
| | | | - Arne Warth
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
| | | | - Ákos Nagy
- HCEMM-SE Molecular Oncohematology Research Group, Department of Pathology and Experimental Cancer Research, Semmelweis University, Budapest, Hungary
| | - Wolfram Klapper
- Department of Pathology, Hematopathology Section and Lymph Node Registry, Universitätsklinikum Schleswig-Holstein, Kiel, Germany
| | - Michael Hummel
- Department of Pathology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - George Kanellis
- Department of Hematopathology, Evangelismos General Hospital, Athens, Greece
| | - Ioannis Anagnostopoulos
- Department of Pathology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- Institute of Pathology, University of Würzburg and Comprehensive Cancer Center (CCC) Mainfranken, Würzburg, Germany
| | - Philipp Mertins
- Core Unit Proteomics, Berlin Institute of Health at Charité - Universitätsmedizin Berlin and Max-Delbrück-Center for Molecular Medicine, Berlin, Germany
| | - Lars Bullinger
- Department of Hematology, Oncology and Cancer Immunology, Campus Virchow, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Richard Rosenquist
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Theodoros P Vassilakopoulos
- Department of Hematology and Bone Marrow Transplantation, National and Kapodistrian University of Athens, Laikon General Hospital, Athens, Greece
| | - German Ott
- Department of Clinical Pathology, Robert-Bosch-Krankenhaus, Stuttgart, Germany
| | - Seishi Ogawa
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
- Institute for the Advanced Study of Human Biology (WPI-ASHBi), Kyoto University, Kyoto, Japan
- Department of Medicine, Centre for Haematology and Regenerative Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Frederik Damm
- Department of Hematology, Oncology and Cancer Immunology, Campus Virchow, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany.
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Heidelberg, Germany.
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7
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Mao F, Shi YG. Targeting the LSD1/KDM1 Family of Lysine Demethylases in Cancer and Other Human Diseases. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2023; 1433:15-49. [PMID: 37751134 DOI: 10.1007/978-3-031-38176-8_2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/27/2023]
Abstract
Lysine-specific demethylase 1 (LSD1) was the first histone demethylase discovered and the founding member of the flavin-dependent lysine demethylase family (KDM1). The human KDM1 family includes KDM1A and KDM1B, which primarily catalyze demethylation of histone H3K4me1/2. The KDM1 family is involved in epigenetic gene regulation and plays important roles in various biological and disease pathogenesis processes, including cell differentiation, embryonic development, hormone signaling, and carcinogenesis. Malfunction of many epigenetic regulators results in complex human diseases, including cancers. Regulators such as KDM1 have become potential therapeutic targets because of the reversibility of epigenetic control of genome function. Indeed, several classes of KDM1-selective small molecule inhibitors have been developed, some of which are currently in clinical trials to treat various cancers. In this chapter, we review the discovery, biochemical, and molecular mechanisms, atomic structure, genetics, biology, and pathology of the KDM1 family of lysine demethylases. Focusing on cancer, we also provide a comprehensive summary of recently developed KDM1 inhibitors and related preclinical and clinical studies to provide a better understanding of the mechanisms of action and applications of these KDM1-specific inhibitors in therapeutic treatment.
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Affiliation(s)
- Fei Mao
- Longevity and Aging Institute (LAI), IBS and Department of Endocrinology and Metabolism, Zhongshan Hospital, Fudan University, Shanghai, 200032, P.R. China
- Division of Endocrinology, Diabetes and Hypertension, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Yujiang Geno Shi
- Longevity and Aging Institute (LAI), IBS and Department of Endocrinology and Metabolism, Zhongshan Hospital, Fudan University, Shanghai, 200032, P.R. China.
- Division of Endocrinology, Diabetes and Hypertension, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
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The Intricate Interplay between the ZNF217 Oncogene and Epigenetic Processes Shapes Tumor Progression. Cancers (Basel) 2022; 14:cancers14246043. [PMID: 36551531 PMCID: PMC9776013 DOI: 10.3390/cancers14246043] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 12/02/2022] [Accepted: 12/05/2022] [Indexed: 12/14/2022] Open
Abstract
The oncogenic transcription factor ZNF217 orchestrates several molecular signaling networks to reprogram integrated circuits governing hallmark capabilities within cancer cells. High levels of ZNF217 expression provide advantages to a specific subset of cancer cells to reprogram tumor progression, drug resistance and cancer cell plasticity. ZNF217 expression level, thus, provides a powerful biomarker of poor prognosis and a predictive biomarker for anticancer therapies. Cancer epigenetic mechanisms are well known to support the acquisition of hallmark characteristics during oncogenesis. However, the complex interactions between ZNF217 and epigenetic processes have been poorly appreciated. Deregulated DNA methylation status at ZNF217 locus or an intricate cross-talk between ZNF217 and noncoding RNA networks could explain aberrant ZNF217 expression levels in a cancer cell context. On the other hand, the ZNF217 protein controls gene expression signatures and molecular signaling for tumor progression by tuning DNA methylation status at key promoters by interfering with noncoding RNAs or by refining the epitranscriptome. Altogether, this review focuses on the recent advances in the understanding of ZNF217 collaboration with epigenetics processes to orchestrate oncogenesis. We also discuss the exciting burgeoning translational medicine and candidate therapeutic strategies emerging from those recent findings connecting ZNF217 to epigenetic deregulation in cancer.
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Ou H, Li J, Lv Q, Feng D. Hsa_circ_0069094 positively regulates the expression of oncogenic ZNF217 by competitively targeting miR-758–3p to promote the development of breast cancer. Reprod Biol 2022; 22:100708. [DOI: 10.1016/j.repbio.2022.100708] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 10/08/2022] [Accepted: 10/26/2022] [Indexed: 11/09/2022]
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He K, Zhang S, Pang J, Yin JC, Mu D, Wang J, Ge H, Ma J, Yang Z, Zheng X, Dong L, Zhang J, Chang P, Li L, Tang S, Bao H, Wu X, Wang X, Shao Y, Yu J, Yuan S. Genomic Profiling Reveals Novel Predictive Biomarkers for Chemo-Radiotherapy Efficacy and Thoracic Toxicity in Non-Small-Cell Lung Cancer. Front Oncol 2022; 12:928605. [PMID: 35912186 PMCID: PMC9329611 DOI: 10.3389/fonc.2022.928605] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 05/23/2022] [Indexed: 11/23/2022] Open
Abstract
Chemo-radiotherapy (CRT) remains the main treatment modality for non-small-cell lung cancer (NSCLC). However, its clinical efficacy is largely limited by individual variations in radio-sensitivity and radiotherapy-associated toxicity. There is an urgent need to identify genetic determinants that can explain patients’ likelihood to develop recurrence and radiotherapy-associated toxicity following CRT. In this study, we performed comprehensive genomic profiling, using a 474-cancer- and radiotherapy-related gene panel, on pretreatment biopsy samples from patients with unresectable stage III NSCLCs who underwent definitive CRT. Patients’ baseline clinical characteristics and genomic features, including tumor genetic, genomic and molecular pathway alterations, as well as single nucleotide polymorphisms (SNPs), were correlated with progression-free survival (PFS), overall survival (OS), and radiotherapy-associated pneumonitis and/or esophagitis development after CRT. A total of 122 patients were enrolled between 2014 and 2019, with 84 (69%) squamous cell carcinomas and 38 (31%) adenocarcinomas. Genetic analysis confirmed the association between the KEAP1-NRF2 pathway gene alterations and unfavorable survival outcome, and revealed alterations in FGFR family genes, MET, PTEN, and NOTCH2 as potential novel and independent risk factors of poor post-CRT survival. Combined analysis of such alterations led to improved stratification of the risk populations. In addition, patients with EGFR activating mutations or any oncogenic driver mutations exhibited improved OS. On the other hand, we also identified genetic markers in relation to radiotherapy-associated thoracic toxicity. SNPs in the DNA repair-associated XRCC5 (rs3835) and XRCC1 (rs25487) were associated with an increased risk of high-grade esophagitis and pneumonitis respectively. MTHFR (rs1801133) and NQO1 (rs1800566) were additional risk alleles related to higher susceptibility to pneumonitis and esophagitis overall. Moreover, through their roles in genome integrity and replicative fidelity, somatic alterations in ZNF217 and POLD1 might also serve as risk predictors of high-grade pneumonitis and esophagitis. Taken together, leveraging targeted next-generating sequencing, we identified a set of novel clinically applicable biomarkers that might enable prediction of survival outcomes and risk of radiotherapy-associated thoracic toxicities. Our findings highlight the value of pre-treatment genetic testing to better inform CRT outcomes and clinical actions in stage III unresectable NSCLCs.
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Affiliation(s)
- Kewen He
- Department of Radiation Oncology, Shandong University Cancer Center, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, China
| | - Shaotong Zhang
- Department of Ultrasound, Jinan Central Hospital Affiliated to Shandong First Medical University, Jinan, China
| | - Jiaohui Pang
- Geneseeq Research Institute, Nanjing Geneseeq Technology Inc., Nanjing, China
| | - Jiani C. Yin
- Geneseeq Research Institute, Nanjing Geneseeq Technology Inc., Nanjing, China
| | - Dianbin Mu
- Department of Pathology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, China
| | - Jun Wang
- Department of Radiation Oncology, Fourth Hospital of Hebei Medical University, Shijiazhuang, China
| | - Hong Ge
- Department of Radiation Oncology, The Affiliated Cancer Hospital of Zhengzhou University, Zhengzhou, China
| | - Jie Ma
- Department of Pathology, The Affiliated Cancer Hospital of Zhengzhou University, Zhengzhou, China
| | - Zhe Yang
- Department of Radiation Oncology, Shandong Provincial Hospital, Jinan, China
| | - Xiaoli Zheng
- Department of Radiation Oncology, The Affiliated Cancer Hospital of Zhengzhou University, Zhengzhou, China
| | - Lihua Dong
- Department of Radiation Oncology & Therapy, Jilin Provincial Key Laboratory of Radiation Oncology & Therapy, The First Hospital of Jilin University, Jilin, China
| | - Junli Zhang
- Geneseeq Research Institute, Nanjing Geneseeq Technology Inc., Nanjing, China
| | - Pengyu Chang
- Department of Radiation Oncology & Therapy, Jilin Provincial Key Laboratory of Radiation Oncology & Therapy, The First Hospital of Jilin University, Jilin, China
| | - Li Li
- Department of Radiation Oncology, Shandong University Cancer Center, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, China
| | - Shanshan Tang
- Department of Radiation Oncology, Shandong University Cancer Center, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, China
| | - Hua Bao
- Geneseeq Research Institute, Nanjing Geneseeq Technology Inc., Nanjing, China
| | - Xue Wu
- Geneseeq Research Institute, Nanjing Geneseeq Technology Inc., Nanjing, China
| | - Xiaonan Wang
- Geneseeq Research Institute, Nanjing Geneseeq Technology Inc., Nanjing, China
| | - Yang Shao
- Geneseeq Research Institute, Nanjing Geneseeq Technology Inc., Nanjing, China
- School of Public Health, Nanjing Medical University, Nanjing, China
- *Correspondence: Shuanghu Yuan, ; Jinming Yu, ; Yang Shao,
| | - Jinming Yu
- Department of Radiation Oncology, Shandong University Cancer Center, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, China
- *Correspondence: Shuanghu Yuan, ; Jinming Yu, ; Yang Shao,
| | - Shuanghu Yuan
- Department of Radiation Oncology, Shandong University Cancer Center, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, China
- *Correspondence: Shuanghu Yuan, ; Jinming Yu, ; Yang Shao,
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Sukocheva OA, Lukina E, Friedemann M, Menschikowski M, Hagelgans A, Aliev G. The crucial role of epigenetic regulation in breast cancer anti-estrogen resistance: Current findings and future perspectives. Semin Cancer Biol 2022; 82:35-59. [PMID: 33301860 DOI: 10.1016/j.semcancer.2020.12.004] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 10/22/2020] [Accepted: 12/03/2020] [Indexed: 02/07/2023]
Abstract
Breast cancer (BC) cell de-sensitization to Tamoxifen (TAM) or other selective estrogen receptor (ER) modulators (SERM) is a complex process associated with BC heterogeneity and the transformation of ER signalling. The most influential resistance-related mechanisms include modifications in ER expression and gene regulation patterns. During TAM/SERM treatment, epigenetic mechanisms can effectively silence ER expression and facilitate the development of endocrine resistance. ER status is efficiently regulated by specific epigenetic tools including hypermethylation of CpG islands within ER promoters, increased histone deacetylase activity in the ER promoter, and/or translational repression by miRNAs. Over-methylation of the ER α gene (ESR1) promoter by DNA methyltransferases was associated with poor prognosis and indicated the development of resistance. Moreover, BC progression and spreading were marked by transformed chromatin remodelling, post-translational histone modifications, and expression of specific miRNAs and/or long non-coding RNAs. Therefore, targeted inhibition of histone acetyltransferases (e.g. MYST3), deacetylases (e.g. HDAC1), and/or demethylases (e.g. lysine-specific demethylase LSD1) was shown to recover and increase BC sensitivity to anti-estrogens. Indicated as a powerful molecular instrument, the administration of epigenetic drugs can regain ER expression along with the activation of tumour suppressor genes, which can in turn prevent selection of resistant cells and cancer stem cell survival. This review examines recent advances in the epigenetic regulation of endocrine drug resistance and evaluates novel anti-resistance strategies. Underlying molecular mechanisms of epigenetic regulation will be discussed, emphasising the utilization of epigenetic enzymes and their inhibitors to re-program irresponsive BCs.
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Affiliation(s)
- Olga A Sukocheva
- Discipline of Health Sciences, College of Nursing and Health Sciences, Flinders University, Bedford Park, South Australia, 5042, Australia.
| | - Elena Lukina
- Discipline of Biology, College of Sciences, Flinders University, Bedford Park, South Australia, 5042, Australia
| | - Markus Friedemann
- Institute of Clinical Chemistry and Laboratory Medicine, University Hospital `Carl Gustav Carus`, Technical University of Dresden, Dresden 01307, Germany
| | - Mario Menschikowski
- Institute of Clinical Chemistry and Laboratory Medicine, University Hospital `Carl Gustav Carus`, Technical University of Dresden, Dresden 01307, Germany
| | - Albert Hagelgans
- Institute of Clinical Chemistry and Laboratory Medicine, University Hospital `Carl Gustav Carus`, Technical University of Dresden, Dresden 01307, Germany
| | - Gjumrakch Aliev
- Sechenov First Moscow State Medical University (Sechenov University), Moscow, 119991, Russia; Institute of Physiologically Active Compounds, Russian Academy of Sciences, Chernogolovka, 142432, Russia; Federal State Budgetary Institution «Research Institute of Human Morphology», 3, Tsyurupy Str., Moscow, 117418, Russian Federation; GALLY International Research Institute, San Antonio, TX, 78229, USA.
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12
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An G, Feng L, Hou L, Li X, Bai J, He L, Gu S, Zhao X. A bioinformatics analysis of zinc finger protein family reveals potential oncogenic biomarkers in breast cancer. Gene 2022; 828:146471. [PMID: 35378249 DOI: 10.1016/j.gene.2022.146471] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 03/02/2022] [Accepted: 03/31/2022] [Indexed: 11/29/2022]
Abstract
BACKGROUND Zinc finger protein family is the largest transcription factor family in the human genome. Studies have shown that the aberrant expression of zinc finger protein (ZNF) had a potential role in tumorigenesis. However, due to the high complexity of the ZNF family genes, the role of the ZNF family genes in breast cancer (BRCA) is still lacking in systematic understanding. AIM In the study, we aim to understand the expression profile, prognostic value, immune invasion pattern, tumor microenvironment, epigenetic and pathway relationships, and drug sensitivity of ZNFs using multi-omics data from public databases. RESULTS We focused on six members of ZNFs, which were upregulated in a variety of cancers. Notably, ZNF750 and ZNF224 were lower expressed in BRCA, and their expressions were significantly associated with BRCA prognosis. We confirmed the observations obtained by analyzing the clinic-pathological data. Otherwise, the expressions of ZNFs were significantly related to stromal and immune scores, and was significantly different among different immune subtypes in BRCA. Here, we found down-regulated methylation of ZNF217 and ZNF750. The relationship between methylation and survival showed the survival was worse for hypo-methylation of ZNF750 in BRCA, which is consistent with the correlation of high expression of ZNF750 in BRCA with worse survival. CONCLUSIONS Collectively, our results provide clues for a better understanding of the characterization of ZNF family genes in BRCA from a multi-omics perspective and show their potential for use as new tumor markers and therapeutic targets.
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Affiliation(s)
- Gaili An
- Department of Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, Shaanxi, China; Department of Oncology, Shaanxi Provincial People's Hospital, Xi'an 710068, Shaanxi, China
| | - Lu Feng
- Department of Radiotherapy, Shaanxi Provincial People's Hospital, Xi'an 710068, Shaanxi, China
| | - Lei Hou
- Department of Oncology, Shaanxi Provincial People's Hospital, Xi'an 710068, Shaanxi, China
| | - Xu Li
- Department of Oncology, Shaanxi Provincial Cancer Hospital, Xi'an 712000, Shaanxi, China
| | - Jun Bai
- Department of Oncology, Shaanxi Provincial People's Hospital, Xi'an 710068, Shaanxi, China
| | - Li He
- Department of Oncology, Shaanxi Provincial People's Hospital, Xi'an 710068, Shaanxi, China
| | - Shanzhi Gu
- Department of College of Forensic Medicine, Xi'an Jiaotong University Health Science Center, Xi'an 710061, China.
| | - Xinhan Zhao
- Department of Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, Shaanxi, China.
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Taylor-Papadimitriou J, Burchell JM. Histone Methylases and Demethylases Regulating Antagonistic Methyl Marks: Changes Occurring in Cancer. Cells 2022; 11:1113. [PMID: 35406676 PMCID: PMC8997813 DOI: 10.3390/cells11071113] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 03/17/2022] [Accepted: 03/22/2022] [Indexed: 02/06/2023] Open
Abstract
Epigenetic regulation of gene expression is crucial to the determination of cell fate in development and differentiation, and the Polycomb (PcG) and Trithorax (TrxG) groups of proteins, acting antagonistically as complexes, play a major role in this regulation. Although originally identified in Drosophila, these complexes are conserved in evolution and the components are well defined in mammals. Each complex contains a protein with methylase activity (KMT), which can add methyl groups to a specific lysine in histone tails, histone 3 lysine 27 (H3K27), by PcG complexes, and H3K4 and H3K36 by TrxG complexes, creating transcriptionally repressive or active marks, respectively. Histone demethylases (KDMs), identified later, added a new dimension to histone methylation, and mutations or changes in levels of expression are seen in both methylases and demethylases and in components of the PcG and TrX complexes across a range of cancers. In this review, we focus on both methylases and demethylases governing the methylation state of the suppressive and active marks and consider their action and interaction in normal tissues and in cancer. A picture is emerging which indicates that the changes which occur in cancer during methylation of histone lysines can lead to repression of genes, including tumour suppressor genes, or to the activation of oncogenes. Methylases or demethylases, which are themselves tumour suppressors, are highly mutated. Novel targets for cancer therapy have been identified and a methylase (KMT6A/EZH2), which produces the repressive H3K27me3 mark, and a demethylase (KDM1A/LSD1), which demethylates the active H3K4me2 mark, are now under clinical evaluation.
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14
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Circ_0087960 stabilizes KDM5B by reducing SKP2 mediated ubiquitination degradation and promotes osteogenic differentiation in periodontal ligament stem cells. Regen Ther 2022; 19:122-130. [PMID: 35229010 PMCID: PMC8844145 DOI: 10.1016/j.reth.2022.01.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Revised: 12/28/2021] [Accepted: 01/12/2022] [Indexed: 12/19/2022] Open
Abstract
Background Periodontitis is a common chronic oral disease among the world. Periodontal ligament stem cells (PDLSCs) has been proved to be a promising tool for the treatment of periodontitis due to their capability of generating periodontal tissues. Circ_0087960 and KDM5B have been shown to participate in the process of osteogenic differentiation with unclear function and mechanism. Methods Circ_0087960 and KDM5B expressions were detected during the osteogenic induction of PDLSCs. The functions of circ_0087960 and KDM5B were validated by manipulating their expression with shRNA. ChIP and luciferase reporter assays were used to prove the KDM5B-based osteogenic gene regulation. Co-IP assay was used to determine the interaction between SKP2 and KDM5B. In vivo ubiquitination assay was used to test the modification of KDM5B by SKP2. RNA pull-down was used to demonstrate the interaction between circ_0087960 and KDM5B. Results Circ_0087960 and KDM5B were found to be upregulated in the osteogenic differentiation of PDLSCs and promote the expression of related genes. KDM5B could directly bind and promote the expression of Runx2, ALP and OCN. KDM5B protein level in PDLSCs was controlled by SKP2-mediated protein ubiquitination and degradation. Circ_0087960 was identified to bind to KDM5B protein and protect it against SKP2-induced protein degradation, leading to the upregulation of osteogenic genes. Conclusion Circ_0087960 and KDM5B could be applied as promising therapeutic methods to stimulate the osteogenic differentiation of PDLSCs, expanding their capability in the treatment of periodontitis.
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Li Y, Wu H, Wang Q, Xu S. ZNF217: the cerberus who fails to guard the gateway to lethal malignancy. Am J Cancer Res 2021; 11:3378-3405. [PMID: 34354851 PMCID: PMC8332857] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Accepted: 05/14/2021] [Indexed: 06/13/2023] Open
Abstract
The aberrant expression of the zinc finger protein 217 (ZNF217) promotes multiple malignant phenotypes, such as replicative immortality, maintenance of proliferation, malignant heterogeneity, metastasis, and cell death resistance, via diverse mechanisms, including transcriptional activation, mRNA N6-methyladenosine (m6A) regulation, and protein interactions. The induction of these cellular processes by ZNF217 leads to therapeutic resistance and patients' poor outcomes. However, few ZNF217 related clinical applications or trials, have been reported. Moreover, looming observations about ZNF217 roles in m6A regulation and cancer immune response triggered significant attention while lacking critical evidence. Thus, in this review, we revisit the literature about ZNF217 and emphasize its importance as a prognostic biomarker for early prevention and as a therapeutic target.
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Affiliation(s)
- Yingpu Li
- Department of Breast Surgery, Harbin Medical University Cancer HospitalHarbin, China
| | - Hao Wu
- Sino-Russian Medical Research Center, Harbin Medical University Cancer HospitalHarbin, China
- Heilongjiang Academy of Medical SciencesHarbin, China
| | - Qin Wang
- Department of Breast Surgery, Harbin Medical University Cancer HospitalHarbin, China
- Sino-Russian Medical Research Center, Harbin Medical University Cancer HospitalHarbin, China
- Heilongjiang Academy of Medical SciencesHarbin, China
| | - Shouping Xu
- Department of Breast Surgery, Harbin Medical University Cancer HospitalHarbin, China
- Sino-Russian Medical Research Center, Harbin Medical University Cancer HospitalHarbin, China
- Heilongjiang Academy of Medical SciencesHarbin, China
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Bukova I, Szczerkowska KI, Prochazkova M, Beck IM, Prochazka J, Sedlacek R. Loss of Wiz Function Affects Methylation Pattern in Palate Development and Leads to Cleft Palate. Front Cell Dev Biol 2021; 9:620692. [PMID: 34150743 PMCID: PMC8206640 DOI: 10.3389/fcell.2021.620692] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Accepted: 04/26/2021] [Indexed: 11/13/2022] Open
Abstract
WIZ (Widely Interspaced Zinc Finger) is associated with the G9a-GLP protein complex, a key H3K9 methyltransferase suggesting a role in transcriptional repression. However, its role in embryonic development is poorly described. In order to assess the loss of function of WIZ, we generated CRISPR/Cas9 WIZ knockout mouse model with 32 nucleotide deletion. Observing the lethality status, we identified the WIZ knockouts to be subviable during embryonic development and non-viable after birth. Morphology of developing embryo was analyzed at E14.5 and E18.5 and our findings were supported by microCT scans. Wiz KO showed improper development in multiple aspects, specifically in the craniofacial area. In particular, shorter snout, cleft palate, and cleft eyelids were present in mutant embryos. Palatal shelves were hypomorphic and though elevated to a horizontal position on top of the tongue, they failed to make contact and fuse. By comparison of proliferation pattern and histone methylation in developing palatal shelves we brought new evidence of importance WIZ dependent G9a-GLP methylation complex in craniofacial development, especially in palate shelf fusion.
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Affiliation(s)
- Ivana Bukova
- Laboratory of Transgenic Models of Diseases and the Czech Centre of Phenogenomics, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czechia
| | - Katarzyna Izabela Szczerkowska
- Laboratory of Transgenic Models of Diseases and the Czech Centre of Phenogenomics, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czechia
| | - Michaela Prochazkova
- Laboratory of Transgenic Models of Diseases and the Czech Centre of Phenogenomics, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czechia
| | - Inken M. Beck
- Laboratory of Transgenic Models of Diseases and the Czech Centre of Phenogenomics, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czechia
- Animal Research Centre, Ulm University, Ulm, Germany
| | - Jan Prochazka
- Laboratory of Transgenic Models of Diseases and the Czech Centre of Phenogenomics, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czechia
| | - Radislav Sedlacek
- Laboratory of Transgenic Models of Diseases and the Czech Centre of Phenogenomics, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czechia
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LSD1 as a Biomarker and the Outcome of Its Inhibitors in the Clinical Trial: The Therapy Opportunity in Tumor. JOURNAL OF ONCOLOGY 2021; 2021:5512524. [PMID: 33833800 PMCID: PMC8018836 DOI: 10.1155/2021/5512524] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 03/04/2021] [Accepted: 03/10/2021] [Indexed: 01/06/2023]
Abstract
Tumors are the foremost cause of death worldwide. As a result of that, there has been a significant enhancement in the investigation, treatment methods, and good maintenance practices on cancer. However, the sensitivity and specificity of a lot of tumor biomarkers are not adequate. Hence, it is of inordinate significance to ascertain novel biomarkers to forecast the prognosis and therapy targets for tumors. This review characterized LSD1 as a biomarker in different tumors. LSD1 inhibitors in clinical trials were also discussed. The recent pattern advocates that LSD1 is engaged at sauce chromatin zones linking with complexes of multi-protein having an exact DNA-binding transcription factor, establishing LSD1 as a favorable epigenetic target, and also gives a large selection of therapeutic targets to treat different tumors. This review sturdily backing the oncogenic probable of LSD1 in different tumors indicated that LSD1 levels can be used to monitor and identify different tumors and can be a useful biomarker of progression and fair diagnosis in tumor patients. The clinical trials showed that inhibitors of LSD1 have growing evidence of clinical efficacy which is very encouraging and promising. However, for some of the inhibitors such as GSK2879552, though selective, potent, and effective, its disease control was poor as the rate of adverse events (AEs) was high in tumor patients causing clinical trial termination, and continuation could not be supported by the risk-benefit profile. Therefore, we propose that, to attain excellent clinical results of inhibitors of LSD1, much attention is required in designing appropriate dosing regimens, developing in-depth in vitro/in vivo mechanistic works of LSD1 inhibitors, and developing inhibitors of LSD1 that are reversible, safe, potent, and selective which may offer safer profiles.
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Wang X, Zhang Z, Qin W, Liu S, Liu C, Genchev GZ, Hui L, Zhao H, Lu H. RePhine: An Integrative Method for Identification of Drug Response-related Transcriptional Regulators. GENOMICS PROTEOMICS & BIOINFORMATICS 2021; 19:534-548. [PMID: 33713851 PMCID: PMC9040019 DOI: 10.1016/j.gpb.2019.09.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Revised: 08/04/2019] [Accepted: 10/23/2019] [Indexed: 11/25/2022]
Abstract
Transcriptional regulators (TRs) participate in essential processes in cancer pathogenesis and are critical therapeutic targets. Identification of drug response-related TRs from cell line-based compound screening data is often challenging due to low mRNA abundance of TRs, protein modifications, and other confounders (CFs). In this study, we developed a regression-based pharmacogenomic and ChIP-seq data integration method (RePhine) to infer the impact of TRs on drug response through integrative analyses of pharmacogenomic and ChIP-seq data. RePhine was evaluated in simulation and pharmacogenomic data and was applied to pan-cancer datasets with the goal of biological discovery. In simulation data with added noises or CFs and in pharmacogenomic data, RePhine demonstrated an improved performance in comparison with three commonly used methods (including Pearson correlation analysis, logistic regression model, and gene set enrichment analysis). Utilizing RePhine and Cancer Cell Line Encyclopedia data, we observed that RePhine-derived TR signatures could effectively cluster drugs with different mechanisms of action. RePhine predicted that loss-of-function of EZH2/PRC2 reduces cancer cell sensitivity toward the BRAF inhibitor PLX4720. Experimental validation confirmed that pharmacological EZH2 inhibition increases the resistance of cancer cells to PLX4720 treatment. Our results support that RePhine is a useful tool for inferring drug response-related TRs and for potential therapeutic applications. The source code for RePhine is freely available at https://github.com/coexps/RePhine.
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Affiliation(s)
- Xujun Wang
- SJTU-Yale Joint Center for Biostatistics and Data Science, Department of Bioinformatics and Biostatistics, School of Life Science and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Zhengtao Zhang
- State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Shanghai 200031, China
| | - Wenyi Qin
- Department of Bioengineering, University of Illinois at Chicago, Chicago, IL, USA; Department of Genetics, School of Medicine, Yale University, New Haven, CT 06511, USA
| | - Shiyi Liu
- SJTU-Yale Joint Center for Biostatistics and Data Science, Department of Bioinformatics and Biostatistics, School of Life Science and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Cong Liu
- Department of Bioengineering, University of Illinois at Chicago, Chicago, IL, USA; Department of Medical Informatics, Columbia University, New York, NY 10032, USA
| | - Georgi Z Genchev
- SJTU-Yale Joint Center for Biostatistics and Data Science, Department of Bioinformatics and Biostatistics, School of Life Science and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China; Bulgarian Institute for Genomics and Precision Medicine, Sofia 1000, Bulgaria
| | - Lijian Hui
- State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Shanghai 200031, China
| | - Hongyu Zhao
- SJTU-Yale Joint Center for Biostatistics and Data Science, Department of Bioinformatics and Biostatistics, School of Life Science and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China; Department of Biostatistics, Yale School of Public Health, New Haven, CT 06511, USA.
| | - Hui Lu
- SJTU-Yale Joint Center for Biostatistics and Data Science, Department of Bioinformatics and Biostatistics, School of Life Science and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China; Department of Bioengineering, University of Illinois at Chicago, Chicago, IL, USA; Department of Biostatistics, Yale School of Public Health, New Haven, CT 06511, USA; Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai 200433, China; Center for Biomedical informatics, Shanghai Children's Hospital, Shanghai 200040, China.
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Song T, Yang Y, Wei H, Xie X, Lu J, Zeng Q, Peng J, Zhou Y, Jiang S, Peng J. Zfp217 mediates m6A mRNA methylation to orchestrate transcriptional and post-transcriptional regulation to promote adipogenic differentiation. Nucleic Acids Res 2020; 47:6130-6144. [PMID: 31037292 PMCID: PMC6614822 DOI: 10.1093/nar/gkz312] [Citation(s) in RCA: 123] [Impact Index Per Article: 24.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Revised: 04/14/2019] [Accepted: 04/28/2019] [Indexed: 02/06/2023] Open
Abstract
A complex and highly orchestrated gene expression program chiefly establishes the properties that define the adipocyte phenotype, in which the vast majority of factors are involved in transcriptional regulation. However, the mechanisms by post-transcriptional modulation are poorly understood. Here, we showed that zinc finger protein (Zfp217) couples gene transcription to m6A mRNA modification to facilitate adipogenesis. Zfp217 modulates m6A mRNA methylation by activating the transcription of m6A demethylase FTO. Consistently, depletion of Zfp217 compromises adipogenic differentiation of 3T3L1 cells and results in a global increase of m6A modification. Moreover, the interaction of Zfp217 with YTHDF2 is critical for allowing FTO to maintain its interaction with m6A sites on various mRNAs, as loss of Zfp217 leads to FTO decrease and augmented m6A levels. These findings highlight a role for Zfp217-dependent m6A modification to coordinate transcriptional and post-transcriptional regulation and thus promote adipogenic differentiation.
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Affiliation(s)
- Tongxing Song
- Department of Animal Nutrition and Feed Science, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, China.,The Cooperative Innovation Center for Sustainable Pig Production, Wuhan 430070, China
| | - Yang Yang
- Department of Animal Nutrition and Feed Science, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, China.,The Cooperative Innovation Center for Sustainable Pig Production, Wuhan 430070, China
| | - Hongkui Wei
- Department of Animal Nutrition and Feed Science, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, China.,The Cooperative Innovation Center for Sustainable Pig Production, Wuhan 430070, China
| | - Xiaowei Xie
- Department of Animal Nutrition and Feed Science, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, China.,The Cooperative Innovation Center for Sustainable Pig Production, Wuhan 430070, China
| | - Jinxin Lu
- Department of Animal Nutrition and Feed Science, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, China.,The Cooperative Innovation Center for Sustainable Pig Production, Wuhan 430070, China
| | - Qianhui Zeng
- The Cooperative Innovation Center for Sustainable Pig Production, Wuhan 430070, China.,Key Laboratory of Animal Genetics, Breeding and Reproduction Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Jie Peng
- Department of Animal Nutrition and Feed Science, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, China.,The Cooperative Innovation Center for Sustainable Pig Production, Wuhan 430070, China
| | - Yuanfei Zhou
- Department of Animal Nutrition and Feed Science, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, China.,The Cooperative Innovation Center for Sustainable Pig Production, Wuhan 430070, China
| | - Siwen Jiang
- The Cooperative Innovation Center for Sustainable Pig Production, Wuhan 430070, China.,Key Laboratory of Animal Genetics, Breeding and Reproduction Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Jian Peng
- Department of Animal Nutrition and Feed Science, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, China.,The Cooperative Innovation Center for Sustainable Pig Production, Wuhan 430070, China
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20
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Yue B, Song C, Yang L, Cui R, Cheng X, Zhang Z, Zhao G. METTL3-mediated N6-methyladenosine modification is critical for epithelial-mesenchymal transition and metastasis of gastric cancer. Mol Cancer 2019; 18:142. [PMID: 31607270 PMCID: PMC6790244 DOI: 10.1186/s12943-019-1065-4] [Citation(s) in RCA: 431] [Impact Index Per Article: 71.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Accepted: 08/28/2019] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND As one of the most frequent chemical modifications in eukaryotic mRNAs, N6-methyladenosine (m6A) modification exerts important effects on mRNA stability, splicing, and translation. Recently, the regulatory role of m6A in tumorigenesis has been increasingly recognized. However, dysregulation of m6A and its functions in tumor epithelial-mesenchymal transition (EMT) and metastasis remain obscure. METHODS qRT-PCR and immunohistochemistry were used to evaluate the expression of methyltransferase-like 3 (METTL3) in gastric cancer (GC). The effects of METTL3 on GC metastasis were investigated through in vitro and in vivo assays. The mechanism of METTL3 action was explored through transcriptome-sequencing, m6A-sequencing, m6A methylated RNA immunoprecipitation quantitative reverse transcription polymerase chain reaction (MeRIP qRT-PCR), confocal immunofluorescent assay, luciferase reporter assay, co-immunoprecipitation, RNA immunoprecipitation and chromatin immunoprecipitation assay. RESULTS Here, we show that METTL3, a major RNA N6-adenosine methyltransferase, was upregulated in GC. Clinically, elevated METTL3 level was predictive of poor prognosis. Functionally, we found that METTL3 was required for the EMT process in vitro and for metastasis in vivo. Mechanistically, we unveiled the METTL3-mediated m6A modification profile in GC cells for the first time and identified zinc finger MYM-type containing 1 (ZMYM1) as a bona fide m6A target of METTL3. The m6A modification of ZMYM1 mRNA by METTL3 enhanced its stability relying on the "reader" protein HuR (also known as ELAVL1) dependent pathway. In addition, ZMYM1 bound to and mediated the repression of E-cadherin promoter by recruiting the CtBP/LSD1/CoREST complex, thus facilitating the EMT program and metastasis. CONCLUSIONS Collectively, our findings indicate the critical role of m6A modification in GC and uncover METTL3/ZMYM1/E-cadherin signaling as a potential therapeutic target in anti-metastatic strategy against GC.
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Affiliation(s)
- Ben Yue
- Department of Gastrointestinal Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, 160 Pujian Road, Shanghai, 200127 China
| | - Chenlong Song
- Department of General Surgery, Shanghai General Hospital, School of Medicine, Shanghai Jiao Tong University, 85 Wujin Road, Shanghai, 200080 China
| | - Linxi Yang
- Department of Gastrointestinal Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, 160 Pujian Road, Shanghai, 200127 China
| | - Ran Cui
- Department of Gastrointestinal Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, 160 Pujian Road, Shanghai, 200127 China
| | - Xingwang Cheng
- Department of General Surgery, Shanghai Public Health Clinical Center, 2901 Caolang Road, Shanghai, 201508 China
| | - Zizhen Zhang
- Department of Gastrointestinal Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, 160 Pujian Road, Shanghai, 200127 China
| | - Gang Zhao
- Department of Gastrointestinal Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, 160 Pujian Road, Shanghai, 200127 China
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21
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Ramírez-Ramírez R, Gutiérrez-Angulo M, Peregrina-Sandoval J, Moreno-Ortiz JM, Franco-Topete RA, Cerda-Camacho FDJ, Ayala-Madrigal MDLL. Somatic deletion of KDM1A/LSD1 gene is associated to advanced colorectal cancer stages. J Clin Pathol 2019; 73:107-111. [PMID: 31471467 PMCID: PMC7027028 DOI: 10.1136/jclinpath-2019-206128] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 08/20/2019] [Accepted: 08/20/2019] [Indexed: 01/08/2023]
Abstract
Aims KDM1A/LSD1 and ZNF217 are involved in a protein complex that participates in transcriptional regulation. ZNF217 has been analysed in numerous cancers and its amplification has been associated with advanced stages of disease; however, a similar role for KDM1A/LSD1 has not been uncovered. In this study, we estimated the number of KDM1A/LSD1 and ZNF217 gene copies in tissue samples from patients diagnosed with colorectal cancer (CRC), as well as its association with clinicopathological features in patients with CRC. Methods Paraffin-embedded tumour samples from 50 patients with CRC with a histopathological diagnosis of CRC were included. The number of copies of KDM1A/LSD1 and ZNF217 genes was determined by fluorescence in situ hybridisation (FISH). We also analysed the association between copy numbers of selected genes and clinicopathological data based on multivariate analysis. Results Deletion of the KDM1A/LSD1 gene occurred in 19 samples (38%), whereas ZNF217 gene amplification was identified in 11 samples (22%). We found a significant association between lymph node metastasis or advanced tumour stage and KDM1A/LSD1 gene deletion (p value=0.0003 and p value=0.011, respectively). Conclusions KDM1A/LSD1 gene deletion could be considered a novel prognostic biomarker of late-stage CRC.
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Affiliation(s)
- Ruth Ramírez-Ramírez
- Laboratorio de Inmunología, Centro Universitario de Ciencias Biológicas y Agropecuarias, Universidad de Guadalajara, Zapopan, México
| | - Melva Gutiérrez-Angulo
- Departamento de Clínicas, Centro Universitario de los Altos, Universidad de Guadalajara, Tepatitlán de Morelos, México.,Programa de Doctorado en Genética Humana, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara, México
| | - Jorge Peregrina-Sandoval
- Laboratorio de Inmunología, Centro Universitario de Ciencias Biológicas y Agropecuarias, Universidad de Guadalajara, Zapopan, México.,Laboratorio de Patología Clínica, Hospital Civil de Guadalajara "Fray Antonio Alcalde", Guadalajara, México
| | - José Miguel Moreno-Ortiz
- Programa de Doctorado en Genética Humana, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara, México.,Instituto de Genética Humana "Dr. Enrique Corona Rivera", Departamento de Biología Molecular y Genómica, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara, México
| | - Ramon Antonio Franco-Topete
- Servicio de Anatomía Patológica, Hospital Civil de Guadalajara "Dr. Juan I Menchaca", Guadalajara, México.,Departamento de Microbiología y Patología, Universidad de Guadalajara, Guadalajara, México
| | | | - Maria de la Luz Ayala-Madrigal
- Programa de Doctorado en Genética Humana, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara, México .,Instituto de Genética Humana "Dr. Enrique Corona Rivera", Departamento de Biología Molecular y Genómica, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara, México
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22
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Kwak S, Kim TW, Kang BH, Kim JH, Lee JS, Lee HT, Hwang IY, Shin J, Lee JH, Cho EJ, Youn HD. Zinc finger proteins orchestrate active gene silencing during embryonic stem cell differentiation. Nucleic Acids Res 2019; 46:6592-6607. [PMID: 29846698 PMCID: PMC6061687 DOI: 10.1093/nar/gky454] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Accepted: 05/11/2018] [Indexed: 01/03/2023] Open
Abstract
Transcription factors and chromatin remodeling proteins control the transcriptional variability for ESC lineage commitment. During ESC differentiation, chromatin modifiers are recruited to the regulatory regions by transcription factors, thereby activating the lineage-specific genes or silencing the transcription of active ESC genes. However, the underlying mechanisms that link transcription factors to exit from pluripotency are yet to be identified. In this study, we show that the Ctbp2-interacting zinc finger proteins, Zfp217 and Zfp516, function as linkers for the chromatin regulators during ESC differentiation. CRISPR-Cas9-mediated knock-outs of both Zfp217 and Zfp516 in ESCs prevent the exit from pluripotency. Both zinc finger proteins regulate the Ctbp2-mediated recruitment of the NuRD complex and polycomb repressive complex 2 (PRC2) to active ESC genes, subsequently switching the H3K27ac to H3K27me3 during ESC differentiation for active gene silencing. We therefore suggest that some zinc finger proteins orchestrate to control the concise epigenetic states on active ESC genes during differentiation, resulting in natural lineage commitment.
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Affiliation(s)
- Sojung Kwak
- National Creative Research Center for Epigenome Reprogramming Network, Department of Biomedical Sciences, Ischemic/Hypoxic Disease Institute, Seoul National University College of Medicine, Seoul 03080, Republic of Korea
| | - Tae Wan Kim
- National Creative Research Center for Epigenome Reprogramming Network, Department of Biomedical Sciences, Ischemic/Hypoxic Disease Institute, Seoul National University College of Medicine, Seoul 03080, Republic of Korea
| | - Byung-Hee Kang
- National Creative Research Center for Epigenome Reprogramming Network, Department of Biomedical Sciences, Ischemic/Hypoxic Disease Institute, Seoul National University College of Medicine, Seoul 03080, Republic of Korea
| | - Jae-Hwan Kim
- National Creative Research Center for Epigenome Reprogramming Network, Department of Biomedical Sciences, Ischemic/Hypoxic Disease Institute, Seoul National University College of Medicine, Seoul 03080, Republic of Korea
| | - Jang-Seok Lee
- National Creative Research Center for Epigenome Reprogramming Network, Department of Biomedical Sciences, Ischemic/Hypoxic Disease Institute, Seoul National University College of Medicine, Seoul 03080, Republic of Korea
| | - Han-Teo Lee
- Department of Molecular Medicine & Biopharmaceutical Sciences, Graduate School of Convergence Science, Seoul National University, Seoul 03080, Republic of Korea
| | - In-Young Hwang
- National Creative Research Center for Epigenome Reprogramming Network, Department of Biomedical Sciences, Ischemic/Hypoxic Disease Institute, Seoul National University College of Medicine, Seoul 03080, Republic of Korea
| | - Jihoon Shin
- National Creative Research Center for Epigenome Reprogramming Network, Department of Biomedical Sciences, Ischemic/Hypoxic Disease Institute, Seoul National University College of Medicine, Seoul 03080, Republic of Korea
| | - Jong-Hyuk Lee
- National Creative Research Center for Epigenome Reprogramming Network, Department of Biomedical Sciences, Ischemic/Hypoxic Disease Institute, Seoul National University College of Medicine, Seoul 03080, Republic of Korea
| | - Eun-Jung Cho
- College of Pharmacy, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Hong-Duk Youn
- National Creative Research Center for Epigenome Reprogramming Network, Department of Biomedical Sciences, Ischemic/Hypoxic Disease Institute, Seoul National University College of Medicine, Seoul 03080, Republic of Korea.,Department of Molecular Medicine & Biopharmaceutical Sciences, Graduate School of Convergence Science, Seoul National University, Seoul 03080, Republic of Korea
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23
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Si W, Zhao Y, Zhou J, Zhang Q, Zhang Y. The coordination between ZNF217 and LSD1 contributes to hepatocellular carcinoma progress and is negatively regulated by miR-101. Exp Cell Res 2019; 379:1-10. [DOI: 10.1016/j.yexcr.2019.03.017] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 03/08/2019] [Accepted: 03/10/2019] [Indexed: 12/16/2022]
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24
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Hypoxia-inducible factors promote breast cancer stem cell specification and maintenance in response to hypoxia or cytotoxic chemotherapy. Adv Cancer Res 2019; 141:175-212. [PMID: 30691683 DOI: 10.1016/bs.acr.2018.11.001] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Clinical studies have revealed that breast cancers contain regions of intratumoral hypoxia (reduced oxygen availability), which activates hypoxia-inducible factors (HIFs). The relationship between intratumoral hypoxia, distant metastasis and cancer mortality has been well established. A major mechanism by which intratumoral hypoxia contributes to disease progression is through induction of the breast cancer stem cell (BCSC) phenotype. BCSCs are a small subpopulation of cells with the capability for self-renewal. BCSCs have been implicated in resistance to chemotherapy, disease recurrence, and metastasis. In this review, we will discuss our current understanding of the molecular mechanisms underlying HIF-dependent induction of the BCSC phenotype in response to hypoxia or chemotherapy.
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25
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Rao RC, Chan MP, Andrews CA, Kahana A. Epigenetic markers in basal cell carcinoma: universal themes in oncogenesis and tumor stratification? - a short report. Cell Oncol (Dordr) 2018; 41:693-698. [PMID: 30215205 DOI: 10.1007/s13402-018-0402-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/16/2018] [Indexed: 11/26/2022] Open
Abstract
BACKGROUND Advanced basal cell carcinomas (BCCs) suffer from a scarcity of effective treatment options. Previously, we found that the targetable histone methyltransferase EZH2 was upregulated in aggressive BCC subtypes, suggesting that epigenetics may play a role in BCC progression. The purpose of this study was to determine whether EZH2-associated proteins and marks may be employed for the stratification of BCC histologic subtypes. METHODS Sixty-two specimens (from 61 patients), representing more or less aggressive BCC histologic subtypes and matching non-malignant epidermal cells, were included in this study. Immunohistochemistry of H3K27me3, 5hmC, NSD2, MOF and JARID1B was performed to assess their putative associations with BCC histologic subtypes, as well as with EZH2 and Ki67 expression levels. RESULTS We found that H3K27me3 and 5hmC upregulation was positively correlated with the occurrence of a less aggressive BCC histology. The modifications were also positively correlated with each other. Interestingly, we found that they were negatively correlated with the expression of EZH2, a marker for an aggressive BCC histology. The levels of NSD2, MOF, H3K27me3 and 5hmC were found to be universally upregulated in BCCs versus non-malignant epidermal cells. CONCLUSIONS Our data reveal an EZH2-associated epigenetic marker profile that correlates with histologic signs of BCC aggressiveness. Our findings may have diagnostic and therapeutic implications, and indicate that epigenetic markers may be shared even with relatively less aggressive tumor types, thereby suggesting universal themes.
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Affiliation(s)
- Rajesh C Rao
- Department of Ophthalmology and Visual Sciences, W.K. Kellogg Eye Center, University of Michigan, Brehm 8333, 1000 Wall Street, Ann Arbor, MI, 48105, USA.
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA.
- Comprehensive Cancer Center, University of Michigan, Ann Arbor, MI, USA.
- Section of Ophthalmology, Surgery Service, VA Ann Arbor Health System, Ann Arbor, MI, USA.
| | - May P Chan
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Dermatology, University of Michigan, Ann Arbor, MI, USA
| | - Chris A Andrews
- Department of Ophthalmology and Visual Sciences, W.K. Kellogg Eye Center, University of Michigan, Brehm 8333, 1000 Wall Street, Ann Arbor, MI, 48105, USA
| | - Alon Kahana
- Department of Ophthalmology and Visual Sciences, W.K. Kellogg Eye Center, University of Michigan, Brehm 8333, 1000 Wall Street, Ann Arbor, MI, 48105, USA.
- Comprehensive Cancer Center, University of Michigan, Ann Arbor, MI, USA.
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26
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Ismail T, Lee HK, Kim C, Kwon T, Park TJ, Lee HS. KDM1A microenvironment, its oncogenic potential, and therapeutic significance. Epigenetics Chromatin 2018; 11:33. [PMID: 29921310 PMCID: PMC6006565 DOI: 10.1186/s13072-018-0203-3] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 06/12/2018] [Indexed: 12/12/2022] Open
Abstract
The lysine-specific histone demethylase 1A (KDM1A) was the first demethylase to challenge the concept of the irreversible nature of methylation marks. KDM1A, containing a flavin adenine dinucleotide (FAD)-dependent amine oxidase domain, demethylates histone 3 lysine 4 and histone 3 lysine 9 (H3K4me1/2 and H3K9me1/2). It has emerged as an epigenetic developmental regulator and was shown to be involved in carcinogenesis. The functional diversity of KDM1A originates from its complex structure and interactions with transcription factors, promoters, enhancers, oncoproteins, and tumor-associated genes (tumor suppressors and activators). In this review, we discuss the microenvironment of KDM1A in cancer progression that enables this protein to activate or repress target gene expression, thus making it an important epigenetic modifier that regulates the growth and differentiation potential of cells. A detailed analysis of the mechanisms underlying the interactions between KDM1A and the associated complexes will help to improve our understanding of epigenetic regulation, which may enable the discovery of more effective anticancer drugs.
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Affiliation(s)
- Tayaba Ismail
- KNU-Center for Nonlinear Dynamics, CMRI, School of Life Sciences, BK21 Plus KNU Creative BioResearch Group, College of Natural Sciences, Kyungpook National University, Daegu, 41566, South Korea
| | - Hyun-Kyung Lee
- KNU-Center for Nonlinear Dynamics, CMRI, School of Life Sciences, BK21 Plus KNU Creative BioResearch Group, College of Natural Sciences, Kyungpook National University, Daegu, 41566, South Korea
| | - Chowon Kim
- KNU-Center for Nonlinear Dynamics, CMRI, School of Life Sciences, BK21 Plus KNU Creative BioResearch Group, College of Natural Sciences, Kyungpook National University, Daegu, 41566, South Korea
| | - Taejoon Kwon
- School of Life Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, South Korea
| | - Tae Joo Park
- School of Life Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, South Korea.
| | - Hyun-Shik Lee
- KNU-Center for Nonlinear Dynamics, CMRI, School of Life Sciences, BK21 Plus KNU Creative BioResearch Group, College of Natural Sciences, Kyungpook National University, Daegu, 41566, South Korea.
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27
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LSD1 activates a lethal prostate cancer gene network independently of its demethylase function. Proc Natl Acad Sci U S A 2018; 115:E4179-E4188. [PMID: 29581250 DOI: 10.1073/pnas.1719168115] [Citation(s) in RCA: 159] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Medical castration that interferes with androgen receptor (AR) function is the principal treatment for advanced prostate cancer. However, clinical progression is universal, and tumors with AR-independent resistance mechanisms appear to be increasing in frequency. Consequently, there is an urgent need to develop new treatments targeting molecular pathways enriched in lethal prostate cancer. Lysine-specific demethylase 1 (LSD1) is a histone demethylase and an important regulator of gene expression. Here, we show that LSD1 promotes the survival of prostate cancer cells, including those that are castration-resistant, independently of its demethylase function and of the AR. Importantly, this effect is explained in part by activation of a lethal prostate cancer gene network in collaboration with LSD1's binding protein, ZNF217. Finally, that a small-molecule LSD1 inhibitor-SP-2509-blocks important demethylase-independent functions and suppresses castration-resistant prostate cancer cell viability demonstrates the potential of LSD1 inhibition in this disease.
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28
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Maes T, Mascaró C, Tirapu I, Estiarte A, Ciceri F, Lunardi S, Guibourt N, Perdones A, Lufino MMP, Somervaille TCP, Wiseman DH, Duy C, Melnick A, Willekens C, Ortega A, Martinell M, Valls N, Kurz G, Fyfe M, Castro-Palomino JC, Buesa C. ORY-1001, a Potent and Selective Covalent KDM1A Inhibitor, for the Treatment of Acute Leukemia. Cancer Cell 2018; 33:495-511.e12. [PMID: 29502954 DOI: 10.1016/j.ccell.2018.02.002] [Citation(s) in RCA: 231] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Revised: 09/17/2017] [Accepted: 02/01/2018] [Indexed: 01/02/2023]
Abstract
The lysine-specific demethylase KDM1A is a key regulator of stem cell potential in acute myeloid leukemia (AML). ORY-1001 is a highly potent and selective KDM1A inhibitor that induces H3K4me2 accumulation on KDM1A target genes, blast differentiation, and reduction of leukemic stem cell capacity in AML. ORY-1001 exhibits potent synergy with standard-of-care drugs and selective epigenetic inhibitors, reduces growth of an AML xenograft model, and extends survival in a mouse PDX (patient-derived xenograft) model of T cell acute leukemia. Surrogate pharmacodynamic biomarkers developed based on expression changes in leukemia cell lines were translated to samples from patients treated with ORY-1001. ORY-1001 is a selective KDM1A inhibitor in clinical trials and is currently being evaluated in patients with leukemia and solid tumors.
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Affiliation(s)
- Tamara Maes
- Oryzon Genomics, S.A. Carrer Sant Ferran 74, 08940 Cornellà de Llobregat, Spain.
| | - Cristina Mascaró
- Oryzon Genomics, S.A. Carrer Sant Ferran 74, 08940 Cornellà de Llobregat, Spain
| | - Iñigo Tirapu
- Oryzon Genomics, S.A. Carrer Sant Ferran 74, 08940 Cornellà de Llobregat, Spain
| | - Angels Estiarte
- Oryzon Genomics, S.A. Carrer Sant Ferran 74, 08940 Cornellà de Llobregat, Spain
| | - Filippo Ciceri
- Oryzon Genomics, S.A. Carrer Sant Ferran 74, 08940 Cornellà de Llobregat, Spain
| | - Serena Lunardi
- Oryzon Genomics, S.A. Carrer Sant Ferran 74, 08940 Cornellà de Llobregat, Spain
| | - Nathalie Guibourt
- Oryzon Genomics, S.A. Carrer Sant Ferran 74, 08940 Cornellà de Llobregat, Spain
| | - Alvaro Perdones
- Oryzon Genomics, S.A. Carrer Sant Ferran 74, 08940 Cornellà de Llobregat, Spain
| | - Michele M P Lufino
- Oryzon Genomics, S.A. Carrer Sant Ferran 74, 08940 Cornellà de Llobregat, Spain
| | - Tim C P Somervaille
- Leukaemia Biology Laboratory, Cancer Research UK Manchester Institute, The University of Manchester, Manchester M20 4BX, UK
| | - Dan H Wiseman
- Leukaemia Biology Laboratory, Cancer Research UK Manchester Institute, The University of Manchester, Manchester M20 4BX, UK
| | - Cihangir Duy
- Department of Medicine, Division of Hematology & Medical Oncology, Weill Cornell Medicine, New York, 10065 NY, USA
| | - Ari Melnick
- Department of Medicine, Division of Hematology & Medical Oncology, Weill Cornell Medicine, New York, 10065 NY, USA; Department of Pharmacology, Weill Cornell Medicine, New York, 10065 NY, USA
| | - Christophe Willekens
- Drug Development Department (DITEP) and Hematology Department, Gustave Roussy, Université Paris-Saclay, 94805 Villejuif, France
| | - Alberto Ortega
- Oryzon Genomics, S.A. Carrer Sant Ferran 74, 08940 Cornellà de Llobregat, Spain
| | - Marc Martinell
- Oryzon Genomics, S.A. Carrer Sant Ferran 74, 08940 Cornellà de Llobregat, Spain
| | - Nuria Valls
- Oryzon Genomics, S.A. Carrer Sant Ferran 74, 08940 Cornellà de Llobregat, Spain
| | - Guido Kurz
- Oryzon Genomics, S.A. Carrer Sant Ferran 74, 08940 Cornellà de Llobregat, Spain
| | - Matthew Fyfe
- Oryzon Genomics, S.A. Carrer Sant Ferran 74, 08940 Cornellà de Llobregat, Spain
| | | | - Carlos Buesa
- Oryzon Genomics, S.A. Carrer Sant Ferran 74, 08940 Cornellà de Llobregat, Spain
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29
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Jiang X, Zhang C, Qi S, Guo S, Chen Y, Du E, Zhang H, Wang X, Liu R, Qiao B, Yang K, Zhang Z, Xu Y. Elevated expression of ZNF217 promotes prostate cancer growth by restraining ferroportin-conducted iron egress. Oncotarget 2018; 7:84893-84906. [PMID: 27768596 PMCID: PMC5356707 DOI: 10.18632/oncotarget.12753] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2016] [Accepted: 10/05/2016] [Indexed: 01/09/2023] Open
Abstract
Although we and other studies indicated ZNF217 expression was increased in prostate cancer (PCa), the factors mediating its misregulated expression and their oncogenic activity remain largely unexplored. Recent evidence demonstrated that ferroportin (FPN) reduction lead to decreased iron export and increased intercellular iron that consequently aggravates the oncogenic effects of iron. In the present study, ZNF217 was identified as a transcriptional repressor that inhibits FPN expression. Increased of ZNF217 expression led to decreased FPN concentration, coupled with resultant intracellular iron retention, increased iron-related cellular activities and enhanced tumor cell growth. In contrast, decreased of ZNF217 expression restrained tumor cell growth by promoting FPN-driven iron egress. Mechanistic investigation manifested that ZNF217 facilitated the H3K27me3 levels of FPN promoter by interacting with EZH2. Besides, we also found that MAZ increased the transcription level of ZNF217, and subsequently inhibited the FPN expression and their iron–related activities. Strikingly, the expression of MAZ, EZH2 and ZNF217 were concurrently upregulated in PCa, leading to decreased expression of FPN, which induce disordered iron metabolism. Collectively, this study underscored that elevated expression of ZNF217 promotes prostate cancer growth by restraining FPN-conducted iron egress.
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Affiliation(s)
- Xingkang Jiang
- Department of Urology, The Second Hospital of Tianjin Medical University, Tianjin Institute of Urology, Tianjin 300211, China
| | - Changwen Zhang
- Department of Urology, The Second Hospital of Tianjin Medical University, Tianjin Institute of Urology, Tianjin 300211, China
| | - Shiyong Qi
- Department of Urology, The Second Hospital of Tianjin Medical University, Tianjin Institute of Urology, Tianjin 300211, China
| | - Shanqi Guo
- Department of Oncology, First Teaching Hospital of Tianjin University of Traditional Chinese Medicine, Tianjin 300112, China
| | - Yue Chen
- Department of Urology, The Second Hospital of Tianjin Medical University, Tianjin Institute of Urology, Tianjin 300211, China
| | - E Du
- Department of Urology, The Second Hospital of Tianjin Medical University, Tianjin Institute of Urology, Tianjin 300211, China
| | - Hongtuan Zhang
- Department of Urology, The Second Hospital of Tianjin Medical University, Tianjin Institute of Urology, Tianjin 300211, China
| | - Xiaoming Wang
- Department of Urology, The Second Hospital of Tianjin Medical University, Tianjin Institute of Urology, Tianjin 300211, China
| | - Ranlu Liu
- Department of Urology, The Second Hospital of Tianjin Medical University, Tianjin Institute of Urology, Tianjin 300211, China
| | - Baomin Qiao
- Department of Urology, The Second Hospital of Tianjin Medical University, Tianjin Institute of Urology, Tianjin 300211, China
| | - Kuo Yang
- Department of Urology, The Second Hospital of Tianjin Medical University, Tianjin Institute of Urology, Tianjin 300211, China
| | - Zhihong Zhang
- Department of Urology, The Second Hospital of Tianjin Medical University, Tianjin Institute of Urology, Tianjin 300211, China
| | - Yong Xu
- Department of Urology, The Second Hospital of Tianjin Medical University, Tianjin Institute of Urology, Tianjin 300211, China
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30
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Ferrer-Torres D, Nancarrow DJ, Kuick R, Thomas DG, Nadal E, Lin J, Chang AC, Reddy RM, Orringer MB, Taylor JMG, Wang TD, Beer DG. Genomic similarity between gastroesophageal junction and esophageal Barrett's adenocarcinomas. Oncotarget 2018; 7:54867-54882. [PMID: 27363029 PMCID: PMC5342387 DOI: 10.18632/oncotarget.10253] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2015] [Accepted: 05/17/2016] [Indexed: 12/18/2022] Open
Abstract
The current high mortality rate of esophageal adenocarcinoma (EAC) reflects frequent presentation at an advanced stage. Recent efforts utilizing fluorescent peptides have identified overexpressed cell surface targets for endoscopic detection of early stage Barrett's-derived EAC. Unfortunately, 30% of EAC patients present with gastroesophageal junction adenocarcinomas (GEJAC) and lack premalignant Barrett's metaplasia, limiting this early detection strategy. We compared mRNA profiles from 52 EACs (tubular EAC; tEAC) collected above the gastroesophageal junction with 70 GEJACs, 8 normal esophageal and 5 normal gastric mucosa samples. We also analyzed our previously published whole-exome sequencing data in a large cohort of these tumors. Principal component analysis, hierarchical clustering and survival-based analyses demonstrated that GEJAC and tEAC were highly similar, with only modest differences in expression and mutation profiles. The combined expression cohort allowed identification of 49 genes coding cell surface targets overexpressed in both GEJAC and tEAC. We confirmed that three of these candidates (CDH11, ICAM1 and CLDN3) were overexpressed in tumors when compared to normal esophagus, normal gastric and non-dysplastic Barrett's, and localized to the surface of tumor cells. Molecular profiling of tEAC and GEJAC tumors indicated extensive similarity and related molecular processes. Identified genes that encode cell surface proteins overexpressed in both Barrett's-derived EAC and those that arise without Barrett's metaplasia will allow simultaneous detection strategies.
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Affiliation(s)
- Daysha Ferrer-Torres
- Cancer Biology, Program in Biomedical Science, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Derek J Nancarrow
- Section of Thoracic Surgery, Department of Surgery, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Rork Kuick
- Center for Cancer Biostatistics, Department of Biostatistics, School of Public Health, Ann Arbor, Michigan, USA
| | - Dafydd G Thomas
- Department of Pathology and Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Ernest Nadal
- Medical Oncology Department, Catalan Institute of Oncology, Barcelona, Spain
| | - Jules Lin
- Section of Thoracic Surgery, Department of Surgery, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Andrew C Chang
- Section of Thoracic Surgery, Department of Surgery, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Rishindra M Reddy
- Section of Thoracic Surgery, Department of Surgery, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Mark B Orringer
- Section of Thoracic Surgery, Department of Surgery, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Jeremy M G Taylor
- Center for Cancer Biostatistics, Department of Biostatistics, School of Public Health, Ann Arbor, Michigan, USA
| | - Thomas D Wang
- Department of Medicine and Department of Biomedical Engineering, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - David G Beer
- Section of Thoracic Surgery, Department of Surgery, University of Michigan Medical School, Ann Arbor, Michigan, USA
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31
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ZNF516 suppresses EGFR by targeting the CtBP/LSD1/CoREST complex to chromatin. Nat Commun 2017; 8:691. [PMID: 28947780 PMCID: PMC5612949 DOI: 10.1038/s41467-017-00702-5] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2016] [Accepted: 07/18/2017] [Indexed: 01/01/2023] Open
Abstract
EGFR is required for animal development, and dysregulation of EGFR is critically implicated in malignant transformation. However, the molecular mechanism underlying the regulation of EGFR expression remains poorly explored. Here we report that the zinc-finger protein ZNF516 is a transcription repressor. ZNF516 is physically associated with the CtBP/LSD1/CoREST complex and transcriptionally represses a cohort of genes including EGFR that are critically involved in cell proliferation and motility. We demonstrate that the ZNF516–CtBP/LSD1/CoREST complex inhibits the proliferation and invasion of breast cancer cells in vitro and suppresses breast cancer growth and metastasis in vivo. Significantly, low expression of ZNF516 is positively associated with advanced pathological staging and poor survival of breast carcinomas. Our data indicate that ZNF516 is a transcription repressor and a potential suppressor of EGFR, adding to the understanding of EGFR-related breast carcinogenesis and supporting the pursuit of ZNF516 as a potential therapeutic target for breast cancer. EGFR is a well-known oncogene; however, the mechanisms regulating its expression are still unclear. Here, analysing genome-wide chromatin associations, the authors show that in breast cancer cells ZNF516 represses EGFR transcription through the interaction with the CtBP/LSD1/CoREST complex.
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32
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Xiang H, Zhong ZX, Peng YD, Jiang SW. The Emerging Role of Zfp217 in Adipogenesis. Int J Mol Sci 2017; 18:ijms18071367. [PMID: 28653987 PMCID: PMC5535860 DOI: 10.3390/ijms18071367] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Revised: 06/12/2017] [Accepted: 06/21/2017] [Indexed: 12/16/2022] Open
Abstract
Zinc finger protein 217 (Zfp217), a member of the krüppel-type zinc finger protein family, plays diverse roles in cell differentiation and development of mammals. Despite extensive research on the functions of Zfp217 in cancer, pluripotency and reprogramming, its physiological roles in adipogenesis remain unknown. Our previous RNA sequencing data suggest the involvement of Zfp217 in adipogenesis. In this study, the potential function of Zfp217 in adipogenesis was investigated through bioinformatics analysis and a series of experiments. The expression of Zfp217 was found to be gradually upregulated during the adipogenic differentiation in C3H10T1/2 cells, which was consistent with that of the adipogenic marker gene Pparg2. Furthermore, there was a positive, significant relationship between Zfp217 expression and adipocyte differentiation. It was also observed that Zfp217 could not only trigger proliferative defect in C3H10T1/2 cells, but also interact with Ezh2 and suppress the downstream target genes of Ezh2. Besides, three microRNAs (miR-503-5p, miR-135a-5p and miR-19a-3p) which target Zfp217 were found to suppress the process of adipogenesis. This is the first report showing that Zfp217 has the capacity to regulate adipogenesis.
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Affiliation(s)
- Hong Xiang
- Key Laboratory of Swine Genetics and Breeding of Agricultural Ministry, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, China.
| | - Zhu-Xia Zhong
- Key Laboratory of Swine Genetics and Breeding of Agricultural Ministry, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, China.
| | - Yong-Dong Peng
- Key Laboratory of Swine Genetics and Breeding of Agricultural Ministry, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, China.
- Hebei Key Laboratory of Veterinary Preventive Medicine, College of Animal Science and Technology, Hebei Normal University of Science and Technology, Qinhuangdao 066004, China.
| | - Si-Wen Jiang
- Key Laboratory of Swine Genetics and Breeding of Agricultural Ministry, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, China.
- The Cooperative Innovation Center for Sustainable Pig Production, Wuhan 430070, China.
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33
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Cohen PA, Donini CF, Nguyen NT, Lincet H, Vendrell JA. The dark side of ZNF217, a key regulator of tumorigenesis with powerful biomarker value. Oncotarget 2016; 6:41566-81. [PMID: 26431164 PMCID: PMC4747174 DOI: 10.18632/oncotarget.5893] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2015] [Accepted: 09/18/2015] [Indexed: 12/31/2022] Open
Abstract
The recently described oncogene ZNF217 belongs to a chromosomal region that is frequently amplified in human cancers. Recent findings have revealed that alternative mechanisms such as epigenetic regulation also govern the expression of the encoded ZNF217 protein. Newly discovered molecular functions of ZNF217 indicate that it orchestrates complex intracellular circuits as a new key regulator of tumorigenesis. In this review, we focus on recent research on ZNF217-driven molecular functions in human cancers, revisiting major hallmarks of cancer and highlighting the downstream molecular targets and signaling pathways of ZNF217. We also discuss the exciting translational medicine investigating ZNF217 expression levels as a new powerful biomarker, and ZNF217 as a candidate target for future anti-cancer therapies.
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Affiliation(s)
- Pascale A Cohen
- ISPB, Faculté de Pharmacie, Lyon, France.,Université Lyon 1, Lyon, France.,INSERM U1052, CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, Lyon, France
| | - Caterina F Donini
- ISPB, Faculté de Pharmacie, Lyon, France.,Université Lyon 1, Lyon, France.,INSERM U1052, CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, Lyon, France
| | - Nhan T Nguyen
- ISPB, Faculté de Pharmacie, Lyon, France.,Université Lyon 1, Lyon, France.,INSERM U1052, CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, Lyon, France
| | - Hubert Lincet
- ISPB, Faculté de Pharmacie, Lyon, France.,Université Lyon 1, Lyon, France.,INSERM U1052, CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, Lyon, France
| | - Julie A Vendrell
- ISPB, Faculté de Pharmacie, Lyon, France.,Université Lyon 1, Lyon, France.,INSERM U1052, CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, Lyon, France
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34
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Lee DF, Walsh MJ, Aguiló F. ZNF217/ZFP217 Meets Chromatin and RNA. Trends Biochem Sci 2016; 41:986-988. [PMID: 27519282 DOI: 10.1016/j.tibs.2016.07.013] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Revised: 07/22/2016] [Accepted: 07/27/2016] [Indexed: 10/21/2022]
Abstract
The Kruppel-like transcription factor zinc finger protein (ZNF)217 (mouse homolog ZFP217) contributes to tumorigenesis by dysregulating gene expression programs. The newly discovered molecular function of ZFP217 in controlling N6-methyladenosine (m6A) deposition in embryonic stem cells (ESCs) sheds new light on the role of this transcription factor in tumor development.
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Affiliation(s)
- Dung-Fang Lee
- Department of Integrative Biology and Pharmacology, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA; Center for Stem Cell and Regenerative Medicine, The Brown Foundation Institute of Molecular Medicine for the Prevention of Human Diseases, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA; The University of Texas Graduate School of Biomedical Sciences at Houston, Houston, TX 77030, USA
| | - Martin J Walsh
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
| | - Francesca Aguiló
- Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Current address: Wallenberg Centre for Molecular Medicine, Department of Medical Biosciences, Umeå University, SE-901 85 Umeå, Sweden.
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35
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Abstract
Rhabdoid tumor is a rare, highly aggressive malignancy that primarily affects infants and young children. These tumors typically arise in the brain and kidney, although extrarenal, non-central nervous system tumors in almost all soft-tissue sites have been described. SMARCB1 is a member of the SWI/SNF chromatin-remodeling complex and functions as a tumor suppressor in the vast majority of rhabdoid tumors. Patients with germline mutations or deletions affecting SMARCB1 are predisposed to the development of rhabdoid tumors, as well as the genetic disorder schwannomatosis. The current hypothesis is that rhabdoid tumors are driven by epigenetic dysregulation, as opposed to the alteration of a specific biologic pathway. The strategies for novel therapeutic approaches based on what is currently known about rhabdoid tumor biology are presented.
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Affiliation(s)
- James I Geller
- Division of Oncology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Jacquelyn J Roth
- Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Jaclyn A Biegel
- Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania; Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles; Keck School of Medicine, University of Southern California, Los Angeles, Ca
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36
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Aguilo F, Zhang F, Sancho A, Fidalgo M, Di Cecilia S, Vashisht A, Lee DF, Chen CH, Rengasamy M, Andino B, Jahouh F, Roman A, Krig SR, Wang R, Zhang W, Wohlschlegel JA, Wang J, Walsh MJ. Coordination of m(6)A mRNA Methylation and Gene Transcription by ZFP217 Regulates Pluripotency and Reprogramming. Cell Stem Cell 2015; 17:689-704. [PMID: 26526723 DOI: 10.1016/j.stem.2015.09.005] [Citation(s) in RCA: 252] [Impact Index Per Article: 25.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2015] [Revised: 06/24/2015] [Accepted: 09/11/2015] [Indexed: 12/15/2022]
Abstract
Epigenetic and epitranscriptomic networks have important functions in maintaining the pluripotency of embryonic stem cells (ESCs) and somatic cell reprogramming. However, the mechanisms integrating the actions of these distinct networks are only partially understood. Here we show that the chromatin-associated zinc finger protein 217 (ZFP217) coordinates epigenetic and epitranscriptomic regulation. ZFP217 interacts with several epigenetic regulators, activates the transcription of key pluripotency genes, and modulates N6-methyladenosine (m(6)A) deposition on their transcripts by sequestering the enzyme m(6)A methyltransferase-like 3 (METTL3). Consistently, Zfp217 depletion compromises ESC self-renewal and somatic cell reprogramming, globally increases m(6)A RNA levels, and enhances m(6)A modification of the Nanog, Sox2, Klf4, and c-Myc mRNAs, promoting their degradation. ZFP217 binds its own target gene mRNAs, which are also METTL3 associated, and is enriched at promoters of m(6)A-modified transcripts. Collectively, these findings shed light on how a transcription factor can tightly couple gene transcription to m(6)A RNA modification to ensure ESC identity.
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Affiliation(s)
- Francesca Aguilo
- Department of Structural and Chemical Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
| | - Fan Zhang
- Bioinformatics Laboratory, Division of Nephrology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Ana Sancho
- Department of Structural and Chemical Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Miguel Fidalgo
- Department of Developmental and Regenerative Biology and The Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Serena Di Cecilia
- Department of Structural and Chemical Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Ajay Vashisht
- Department of Biological Chemistry and Institute of Genomics and Proteomics, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Dung-Fang Lee
- Department of Developmental and Regenerative Biology and The Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Chih-Hung Chen
- Department of Structural and Chemical Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Madhumitha Rengasamy
- Department of Structural and Chemical Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Blanca Andino
- Department of Structural and Chemical Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Farid Jahouh
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Angel Roman
- Instituto Cajal, Consejo Superior de Investigaciones Científicas, Madrid 28002, Spain
| | - Sheryl R Krig
- Department of Biochemistry and Molecular Medicine, University of California Davis School of Medicine, Sacramento, CA 95817, USA
| | - Rong Wang
- Department of Structural and Chemical Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Weijia Zhang
- Bioinformatics Laboratory, Division of Nephrology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - James A Wohlschlegel
- Department of Biological Chemistry and Institute of Genomics and Proteomics, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Jianlong Wang
- Department of Developmental and Regenerative Biology and The Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Martin J Walsh
- Department of Structural and Chemical Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
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37
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Rojas A, Aguilar R, Henriquez B, Lian JB, Stein JL, Stein GS, van Wijnen AJ, van Zundert B, Allende ML, Montecino M. Epigenetic Control of the Bone-master Runx2 Gene during Osteoblast-lineage Commitment by the Histone Demethylase JARID1B/KDM5B. J Biol Chem 2015; 290:28329-28342. [PMID: 26453309 DOI: 10.1074/jbc.m115.657825] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2015] [Indexed: 12/30/2022] Open
Abstract
Transcription factor Runx2 controls bone development and osteoblast differentiation by regulating expression of a significant number of bone-related target genes. Here, we report that transcriptional activation and repression of the Runx2 gene via its osteoblast-specific P1 promoter (encoding mRNA for the Runx2/p57 isoform) is accompanied by selective deposition and elimination of histone marks during differentiation of mesenchymal cells to the osteogenic and myoblastic lineages. These epigenetic profiles are mediated by key components of the Trithorax/COMPASS-like and Polycomb group complexes together with histone arginine methylases like PRMT5 and lysine demethylases like JARID1B/KDM5B. Importantly, knockdown of the H3K4me2/3 demethylase JARID1B, but not of the demethylases UTX and NO66, prevents repression of the Runx2 P1 promoter during myogenic differentiation of mesenchymal cells. The epigenetically forced expression of Runx2/p57 and osteocalcin, a classical bone-related target gene, under myoblastic-differentiation is accompanied by enrichment of the H3K4me3 and H3K27ac marks at the Runx2 P1 promoter region. Our results identify JARID1B as a key component of a potent epigenetic switch that controls mesenchymal cell fate into myogenic and osteogenic lineages.
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Affiliation(s)
- Adriana Rojas
- Center for Biomedical Research, Faculty of Biological Sciences and Faculty of Medicine, Universidad Andres Bello, Santiago, 8370146, Chile; Faculty of Sciences, Universidad de Chile, Santiago, 7800003, Chile; FONDAP Center for Genome Regulation, Santiago, Chile
| | - Rodrigo Aguilar
- Center for Biomedical Research, Faculty of Biological Sciences and Faculty of Medicine, Universidad Andres Bello, Santiago, 8370146, Chile; FONDAP Center for Genome Regulation, Santiago, Chile
| | - Berta Henriquez
- Center for Biomedical Research, Faculty of Biological Sciences and Faculty of Medicine, Universidad Andres Bello, Santiago, 8370146, Chile
| | - Jane B Lian
- University of Vermont Medical School, Burlington, Vermont 05405
| | - Janet L Stein
- University of Vermont Medical School, Burlington, Vermont 05405
| | - Gary S Stein
- University of Vermont Medical School, Burlington, Vermont 05405
| | | | - Brigitte van Zundert
- Center for Biomedical Research, Faculty of Biological Sciences and Faculty of Medicine, Universidad Andres Bello, Santiago, 8370146, Chile
| | - Miguel L Allende
- Faculty of Sciences, Universidad de Chile, Santiago, 7800003, Chile; FONDAP Center for Genome Regulation, Santiago, Chile
| | - Martin Montecino
- Center for Biomedical Research, Faculty of Biological Sciences and Faculty of Medicine, Universidad Andres Bello, Santiago, 8370146, Chile; FONDAP Center for Genome Regulation, Santiago, Chile.
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38
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Burg JM, Link JE, Morgan BS, Heller FJ, Hargrove AE, McCafferty DG. KDM1 class flavin-dependent protein lysine demethylases. Biopolymers 2015; 104:213-46. [PMID: 25787087 PMCID: PMC4747437 DOI: 10.1002/bip.22643] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2015] [Revised: 03/02/2015] [Accepted: 03/07/2015] [Indexed: 12/11/2022]
Abstract
Flavin-dependent, lysine-specific protein demethylases (KDM1s) are a subfamily of amine oxidases that catalyze the selective posttranslational oxidative demethylation of methyllysine side chains within protein and peptide substrates. KDM1s participate in the widespread epigenetic regulation of both normal and disease state transcriptional programs. Their activities are central to various cellular functions, such as hematopoietic and neuronal differentiation, cancer proliferation and metastasis, and viral lytic replication and establishment of latency. Interestingly, KDM1s function as catalytic subunits within complexes with coregulatory molecules that modulate enzymatic activity of the demethylases and coordinate their access to specific substrates at distinct sites within the cell and chromatin. Although several classes of KDM1-selective small molecule inhibitors have been recently developed, these pan-active site inhibition strategies lack the ability to selectively discriminate between KDM1 activity in specific, and occasionally opposing, functional contexts within these complexes. Here we review the discovery of this class of demethylases, their structures, chemical mechanisms, and specificity. Additionally, we review inhibition of this class of enzymes as well as emerging interactions with coregulatory molecules that regulate demethylase activity in highly specific functional contexts of biological and potential therapeutic importance.
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39
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Maier VK, Feeney CM, Taylor JE, Creech AL, Qiao JW, Szanto A, Das PP, Chevrier N, Cifuentes-Rojas C, Orkin SH, Carr SA, Jaffe JD, Mertins P, Lee JT. Functional Proteomic Analysis of Repressive Histone Methyltransferase Complexes Reveals ZNF518B as a G9A Regulator. Mol Cell Proteomics 2015; 14:1435-46. [PMID: 25680957 DOI: 10.1074/mcp.m114.044586] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2014] [Indexed: 01/17/2023] Open
Abstract
Cell-type specific gene silencing by histone H3 lysine 27 and lysine 9 methyltransferase complexes PRC2 and G9A-GLP is crucial both during development and to maintain cell identity. Although studying their interaction partners has yielded valuable insight into their functions, how these factors are regulated on a network level remains incompletely understood. Here, we present a new approach that combines quantitative interaction proteomics with global chromatin profiling to functionally characterize repressive chromatin modifying protein complexes in embryonic stem cells. We define binding stoichiometries of 9 new and 12 known interaction partners of PRC2 and 10 known and 29 new interaction partners of G9A-GLP, respectively. We demonstrate that PRC2 and G9A-GLP interact physically and share several interaction partners, including the zinc finger proteins ZNF518A and ZNF518B. Using global chromatin profiling by targeted mass spectrometry, we discover that even sub-stoichiometric binding partners such as ZNF518B can positively regulate global H3K9me2 levels. Biochemical analysis reveals that ZNF518B directly interacts with EZH2 and G9A. Our systematic analysis suggests that ZNF518B may mediate the structural association between PRC2 and G9A-GLP histone methyltransferases and additionally regulates the activity of G9A-GLP.
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Affiliation(s)
- Verena K Maier
- From the ‡Department of Molecular Biology, Massachusetts General Hospital, Department of Genetics, Harvard Medical School, 185 Cambridge Street, Boston, Massachusetts 02143
| | - Caitlin M Feeney
- §Proteomics Platform, The Broad Institute, 7 Cambridge Center, Cambridge, Massachusetts 02142
| | - Jordan E Taylor
- §Proteomics Platform, The Broad Institute, 7 Cambridge Center, Cambridge, Massachusetts 02142
| | - Amanda L Creech
- §Proteomics Platform, The Broad Institute, 7 Cambridge Center, Cambridge, Massachusetts 02142
| | - Jana W Qiao
- §Proteomics Platform, The Broad Institute, 7 Cambridge Center, Cambridge, Massachusetts 02142
| | - Attila Szanto
- From the ‡Department of Molecular Biology, Massachusetts General Hospital, Department of Genetics, Harvard Medical School, 185 Cambridge Street, Boston, Massachusetts 02143
| | - Partha P Das
- ¶Department of Pediatric Oncology, Dana-Farber Cancer Institute and Division of Hematology/Oncology, Boston Children's Hospital, Harvard Stem Cell Institute, Harvard Medical School, Boston, Massachusetts, 02115
| | - Nicholas Chevrier
- ‖FAS Center for Systems Biology, Harvard University, Cambridge, Massachusetts 02138
| | - Catherine Cifuentes-Rojas
- From the ‡Department of Molecular Biology, Massachusetts General Hospital, Department of Genetics, Harvard Medical School, 185 Cambridge Street, Boston, Massachusetts 02143
| | - Stuart H Orkin
- ¶Department of Pediatric Oncology, Dana-Farber Cancer Institute and Division of Hematology/Oncology, Boston Children's Hospital, Harvard Stem Cell Institute, Harvard Medical School, Boston, Massachusetts, 02115
| | - Steven A Carr
- §Proteomics Platform, The Broad Institute, 7 Cambridge Center, Cambridge, Massachusetts 02142
| | - Jacob D Jaffe
- §Proteomics Platform, The Broad Institute, 7 Cambridge Center, Cambridge, Massachusetts 02142
| | - Philipp Mertins
- §Proteomics Platform, The Broad Institute, 7 Cambridge Center, Cambridge, Massachusetts 02142;
| | - Jeannie T Lee
- From the ‡Department of Molecular Biology, Massachusetts General Hospital, Department of Genetics, Harvard Medical School, 185 Cambridge Street, Boston, Massachusetts 02143
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Sancho A, Li S, Paul T, Zhang F, Aguilo F, Vashisht A, Balasubramaniyan N, Leleiko NS, Suchy FJ, Wohlschlegel JA, Zhang W, Walsh MJ. CHD6 regulates the topological arrangement of the CFTR locus. Hum Mol Genet 2015; 24:2724-32. [PMID: 25631877 DOI: 10.1093/hmg/ddv032] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Accepted: 01/26/2015] [Indexed: 01/19/2023] Open
Abstract
The control of transcription is regulated through the well-coordinated spatial and temporal interactions between distal genomic regulatory elements required for specialized cell-type and developmental gene expression programs. With recent findings CFTR has served as a model to understand the principles that govern genome-wide and topological organization of distal intra-chromosomal contacts as it relates to transcriptional control. This is due to the extensive characterization of the DNase hypersensitivity sites, modification of chromatin, transcription factor binding sites and the arrangement of these sites in CFTR consistent with the restrictive expression in epithelial cell types. Here, we identified CHD6 from a screen among several chromatin-remodeling proteins as a putative epigenetic modulator of CFTR expression. Moreover, our findings of CTCF interactions with CHD6 are consistent with the role described previously for CTCF in CFTR regulation. Our results now reveal that the CHD6 protein lies within the infrastructure of multiple transcriptional complexes, such as the FACT, PBAF, PAF1C, Mediator, SMC/Cohesion and MLL complexes. This model underlies the fundamental role CHD6 facilitates by tethering cis-acting regulatory elements of CFTR in proximity to these multi-subunit transcriptional protein complexes. Finally, we indicate that CHD6 structurally coordinates a three-dimensional stricture between intragenic elements of CFTR bound by several cell-type specific transcription factors, such as CDX2, SOX18, HNF4α and HNF1α. Therefore, our results reveal new insights into the epigenetic regulation of CFTR expression, whereas the manipulation of CFTR gene topology could be considered for treating specific indications of cystic fibrosis and/or pancreatitis.
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Affiliation(s)
- Ana Sancho
- Departments of Pediatrics, Structural and Chemical Biology
| | | | - Thankam Paul
- Department of Paediatrics, St. George's Hospital, University of London, London SW17 0QT, UK
| | - Fan Zhang
- Laboratory of Bioinformatics, Division of Nephrology, Department of Medicine
| | | | - Ajay Vashisht
- Department of Biological Chemistry and the Institute of Genomics and Proteomics, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Natarajan Balasubramaniyan
- Children's Hospital Research Institute of Colorado, University of Colorado School of Medicine, Aurora, CO 80045, USA and
| | - Neal S Leleiko
- Department of Pediatrics, Division of Gastroenterology, Hasbro Children's Hospital, Brown University School of Medicine, Providence, NY, USA
| | - Frederick J Suchy
- Children's Hospital Research Institute of Colorado, University of Colorado School of Medicine, Aurora, CO 80045, USA and
| | - James A Wohlschlegel
- Department of Biological Chemistry and the Institute of Genomics and Proteomics, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Weijia Zhang
- Laboratory of Bioinformatics, Division of Nephrology, Department of Medicine
| | - Martin J Walsh
- Departments of Pediatrics, Structural and Chemical Biology, Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA,
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Su H, Ma X, Huang Y, Han H, Zou Y, Huang W. JARID1B deletion induced apoptosis in Jeko-1 and HL-60 cell lines. INTERNATIONAL JOURNAL OF CLINICAL AND EXPERIMENTAL PATHOLOGY 2015; 8:171-183. [PMID: 25755704 PMCID: PMC4348832] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 09/29/2014] [Accepted: 12/20/2014] [Indexed: 06/04/2023]
Abstract
AIMS To investigate the involvement of JARID1B histone methyltransferase in the epigenetic change of euchromatic promoter in mantle cell lymphoma (MCL) and acute leukemia. METHODS We retrospectively analyzed the protein of JARID1B and tri-methylated histone H3 lysine 4 (H3K4), histone H3 lysine 9 (H3K9), and cyclin D1 and Ki67 in 30 cases of MCL by immunohistochemistry. JARID1B was depleted by small interfering RNA (siRNA), and cell apoptosis and cell proliferation were detected by flow cytometry and MTT [3-(4,5-dimethylthiazol-2-yl)-2, 5-diphenyltetrazolium bromide], histone tri-methylated H3K4 and histone acetylated H3, H4, cyclin D1, Bcl-2, procaspase-3, C-myc were studied by Western blot. RESULTS We demonstrated that JARID1B was upregulated and histone tri-methylated H3K4 was downregulated in MCL compared to proliferative lymphadenitis, P < 0.05. The expression of histone methylated H3K9 was similar in both. Histone methylation of H3K4 was positively correlated with Ki67 in MCL (Kappa = 0.757, P < 0.05). This study showed that depletion of JARID1B cleavage apoptotic proteins of Bcl-2, procaspase-3, C-myc and resulted in loss cell viability and inducing apoptosis in Jeko-1 and HL-60 cell lines. JARID1B siRNA improved tri-methyl H3K4 and histone acetylated H3 and inhibited cyclin D1, but did not affect histone acetylated H4. CONCLUSIONS This study revealed hyper JARID1B expression and hypo histone H3K4 tri-methylation in MCL. We identify depletion JARID1B as a demethylase which is capable of removing three methyl groups from H3K4 and up-regulating histone acetylation of H3 in both cell lines. Interestingly, depletion of JARID1B inhibits Cyclin D1, which is one of the genes contributes to MCL pathogenesis. JARID1B might be one of therapeutic targets in acute leukemia and MCL.
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Affiliation(s)
- Haiyan Su
- Department of Pathology, Zhangzhou Affiliated Hospital of Fujian Medical UniversityZhangzhou, Fujian, China
| | - Xudong Ma
- Department of Hematology Zhangzhou Affiliated Hospital of Fujian Medical UniversityZhangzhou, Fujian, China
| | - Yiqun Huang
- Department of Hematology Zhangzhou Affiliated Hospital of Fujian Medical UniversityZhangzhou, Fujian, China
| | - Huidan Han
- Department of Hematology Zhangzhou Affiliated Hospital of Fujian Medical UniversityZhangzhou, Fujian, China
| | - Yong Zou
- Department of Hematology Zhangzhou Affiliated Hospital of Fujian Medical UniversityZhangzhou, Fujian, China
| | - Wenhua Huang
- School of Basic Medical Sciences, Southern Medical UniversityGuangzhou, China
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42
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Maes T, Mascaró C, Ortega A, Lunardi S, Ciceri F, Somervaille TCP, Buesa C. KDM1 histone lysine demethylases as targets for treatments of oncological and neurodegenerative disease. Epigenomics 2015; 7:609-26. [PMID: 26111032 DOI: 10.2217/epi.15.9] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Histone methylation and demethylation are important processes associated with the regulation of gene transcription, and alterations in histone methylation status have been linked to a large number of human diseases. Initially thought to be an irreversible process, histone methylation is now known to be reversed by two families of proteins containing over 30 members that act to remove methyl groups from specific lysine residues present in the tails of histone H3 and histone H4. A rapidly growing number of reports have implicated the FAD-dependent lysine specific demethylase (KDM1) family in cancer, and several small-molecule inhibitors are in development for the treatment of cancer. An additional role has emerged for KDM1 in brain function, offering additional opportunities for the development of novel therapeutic strategies in neurodegenerative disease. A decade after the identification of KDM1A as a histone demethylase, the first selective inhibitors have now reached the clinic.
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Affiliation(s)
- Tamara Maes
- Oryzon Genomics S.A., Carrer Sant Ferran 74, 08940 Cornella de Llobregat, Barcelona, España
| | - Cristina Mascaró
- Oryzon Genomics S.A., Carrer Sant Ferran 74, 08940 Cornella de Llobregat, Barcelona, España
| | - Alberto Ortega
- Oryzon Genomics S.A., Carrer Sant Ferran 74, 08940 Cornella de Llobregat, Barcelona, España
| | - Serena Lunardi
- Oryzon Genomics S.A., Carrer Sant Ferran 74, 08940 Cornella de Llobregat, Barcelona, España
| | - Filippo Ciceri
- Oryzon Genomics S.A., Carrer Sant Ferran 74, 08940 Cornella de Llobregat, Barcelona, España
| | - Tim C P Somervaille
- Leukaemia Biology Laboratory, Cancer Research UK Manchester Institute, Manchester, M20 4BX, UK
| | - Carlos Buesa
- Oryzon Genomics S.A., Carrer Sant Ferran 74, 08940 Cornella de Llobregat, Barcelona, España
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43
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The hypoxia-inducible epigenetic regulators Jmjd1a and G9a provide a mechanistic link between angiogenesis and tumor growth. Mol Cell Biol 2014; 34:3702-20. [PMID: 25071150 DOI: 10.1128/mcb.00099-14] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Hypoxia promotes stem cell maintenance and tumor progression, but it remains unclear how it regulates long-term adaptation toward these processes. We reveal a striking downregulation of the hypoxia-inducible histone H3 lysine 9 (H3K9) demethylase JMJD1A as a hallmark of clinical human germ cell-derived tumors, such as seminomas, yolk sac tumors, and embryonal carcinomas. Jmjd1a was not essential for stem cell self-renewal but played a crucial role as a tumor suppressor in opposition to the hypoxia-regulated oncogenic H3K9 methyltransferase G9a. Importantly, loss of Jmjd1a resulted in increased tumor growth, whereas loss of G9a produced smaller tumors. Pharmacological inhibition of G9a also resulted in attenuation of tumor growth, offering a novel therapeutic strategy for germ cell-derived tumors. Finally, Jmjd1a and G9a drive mutually opposing expression of the antiangiogenic factor genes Robo4, Igfbp4, Notch4, and Tfpi accompanied by changes in H3K9 methylation status. Thus, we demonstrate a novel mechanistic link whereby hypoxia-regulated epigenetic changes are instrumental for the control of tumor growth through coordinated dysregulation of antiangiogenic gene expression.
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Frietze S, O'Geen H, Littlepage LE, Simion C, Sweeney CA, Farnham PJ, Krig SR. Global analysis of ZNF217 chromatin occupancy in the breast cancer cell genome reveals an association with ERalpha. BMC Genomics 2014; 15:520. [PMID: 24962896 PMCID: PMC4082627 DOI: 10.1186/1471-2164-15-520] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2014] [Accepted: 06/18/2014] [Indexed: 02/03/2023] Open
Abstract
BACKGROUND The ZNF217 gene, encoding a C2H2 zinc finger protein, is located at 20q13 and found amplified and overexpressed in greater than 20% of breast tumors. Current studies indicate ZNF217 drives tumorigenesis, yet the regulatory mechanisms of ZNF217 are largely unknown. Because ZNF217 associates with chromatin modifying enzymes, we postulate that ZNF217 functions to regulate specific gene signaling networks. Here, we present a large-scale functional genomic analysis of ZNF217, which provides insights into the regulatory role of ZNF217 in MCF7 breast cancer cells. RESULTS ChIP-seq analysis reveals that the majority of ZNF217 binding sites are located at distal regulatory regions associated with the chromatin marks H3K27ac and H3K4me1. Analysis of ChIP-seq transcription factor binding sites shows clustering of ZNF217 with FOXA1, GATA3 and ERalpha binding sites, supported by the enrichment of corresponding motifs for the ERalpha-associated cis-regulatory sequences. ERalpha expression highly correlates with ZNF217 in lysates from breast tumors (n = 15), and ERalpha co-precipitates ZNF217 and its binding partner CtBP2 from nuclear extracts. Transcriptome profiling following ZNF217 depletion identifies differentially expressed genes co-bound by ZNF217 and ERalpha; gene ontology suggests a role for ZNF217-ERalpha in expression programs associated with ER+ breast cancer studies found in the Molecular Signature Database. Data-mining of expression data from breast cancer patients correlates ZNF217 with reduced overall survival. CONCLUSIONS Our genome-wide ZNF217 data suggests a functional role for ZNF217 at ERalpha target genes. Future studies will investigate whether ZNF217 expression contributes to aberrant ERalpha regulatory events in ER+ breast cancer and hormone resistance.
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Affiliation(s)
- Seth Frietze
- School of Biological Sciences, University of Northern Colorado, Greeley, CO 80639, USA.
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45
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A functional interplay between ZNF217 and estrogen receptor alpha exists in luminal breast cancers. Mol Oncol 2014; 8:1441-57. [PMID: 24973012 DOI: 10.1016/j.molonc.2014.05.013] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2014] [Revised: 05/26/2014] [Accepted: 05/26/2014] [Indexed: 01/15/2023] Open
Abstract
We aimed at highlighting the role of ZNF217, a Krüppel-like finger protein, in Estrogen Receptor-α (ERα)-positive (ER+) and luminal breast cancers. Here we report for the first time that ZNF217 and ERα proteins bind to each other in both breast cancer cells and breast tumour samples, via the ERα hinge domain and the ZNF217 C-terminal domain. ZNF217 enhances the recruitment of ERα to its estrogen response elements (ERE) and the ERα-dependent transcription of the GREB1 estrogen-regulated gene. The prognostic power of ZNF217 mRNA expression levels is most discriminatory in breast cancers classified with a "good prognosis", particularly the Luminal-A subclass. A new immunohistochemistry ZNF217 index, based on nuclear and cytoplasmic ZNF217 staining, also allowed the identification of intermediate/poor relapse-free survivors in the Luminal-A subgroup. ZNF217 confers tamoxifen resistance in ER+ breast cancer cells and is a predictor of relapse under endocrine therapy in patients with ER+ breast cancer. ZNF217 thus allows the re-stratification of patients with ER+ breast cancers considered as cancers with good prognosis where no other biomarkers are currently available and widely used. Here we propose a model in ER+ breast cancer where ZNF217-driven aggressiveness incorporates ZNF217 as a positive enhancer of ERα direct genomic activity and where ZNF217 possesses its highest discriminatory prognostic value.
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46
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Abstract
Clear cell carcinomas of the female genital tract are rare tumours with a fearsome reputation for having poor responses to conventional platinum-based chemotherapy and poor prognosis. However, it is now clear that early-stage ovarian clear cell carcinoma has an excellent prognosis and may not require any adjuvant therapy. In addition, radiotherapy may also have a key role to play in adjuvant management of clear cell tumours. Identification of patients who truly do not need adjuvant chemotherapy is important. The past 3 years has seen a significant improvement in our understanding of clear cell carcinoma biology-in particular, the role of mutations in the chromatin remodelling gene ARID1A as key drivers that are common to clear cell carcinomas of ovarian and endometrial origin. Moreover, gynaecological clear cell carcinomas appear to share many features with renal clear cell tumours, suggesting a common pathogenesis. This raises the possibility of clinical trials that include patients with clear cell tumours from different organs of origin. Dissecting the role of disordered chromatin organisation in clear cell carcinoma pathogenesis is a key priority. Finally, the role of endometriosis and the attendant chronic inflammation are recognised. The inflammatory cytokine interleukin-6 appears to play a key role in clear cell carcinoma biology and is an excellent potential therapeutic target.
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47
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The histone variant MacroH2A1 regulates target gene expression in part by recruiting the transcriptional coregulator PELP1. Mol Cell Biol 2014; 34:2437-49. [PMID: 24752897 DOI: 10.1128/mcb.01315-13] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
MacroH2A1 is a histone variant harboring an ∼25-kDa carboxyl-terminal macrodomain. Due to its enrichment on the inactive X chromosome, macroH2A1 was thought to play a role in transcriptional repression. However, recent studies have shown that macroH2A1 occupies autosomal chromatin and regulates genes in a context-specific manner. The macrodomain may play a role in the modulation of gene expression outcomes via physical interactions with effector proteins, which may depend on the ability of the macrodomain to bind NAD(+) metabolite ligands. Here, we identify proline, glutamic acid, and leucine-rich protein 1 (PELP1), a chromatin-associated factor and transcriptional coregulator, as a ligand-independent macrodomain-interacting factor. We used chromatin immunoprecipitation coupled with tiling microarrays (ChIP-chip) to determine the genomic localization of PELP1 in MCF-7 human breast cancer cells. We find that PELP1 genomic localization is highly correlated with that of macroH2A1. Additionally, PELP1 positively correlates with heterochromatic chromatin marks and negatively correlates with active transcription marks, much like macroH2A1. MacroH2A1 specifically recruits PELP1 to the promoters of macroH2A1 target genes, but macroH2A1 occupancy occurs independent of PELP1. This recruitment allows macroH2A1 and PELP1 to cooperatively regulate gene expression outcomes.
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48
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Prestat E, de Morais SR, Vendrell JA, Thollet A, Gautier C, Cohen PA, Aussem A. Learning the local Bayesian network structure around the ZNF217 oncogene in breast tumours. Comput Biol Med 2013; 43:334-41. [PMID: 23375235 DOI: 10.1016/j.compbiomed.2012.12.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2011] [Revised: 07/23/2012] [Accepted: 12/07/2012] [Indexed: 01/18/2023]
Abstract
In this study, we discuss and apply a novel and efficient algorithm for learning a local Bayesian network model in the vicinity of the ZNF217 oncogene from breast cancer microarray data without having to decide in advance which genes have to be included in the learning process. ZNF217 is a candidate oncogene located at 20q13, a chromosomal region frequently amplified in breast and ovarian cancer, and correlated with shorter patient survival in these cancers. To properly address the difficulties in managing complex gene interactions given our limited sample, statistical significance of edge strengths was evaluated using bootstrapping and the less reliable edges were pruned to increase the network robustness. We found that 13 out of the 35 genes associated with deregulated ZNF217 expression in breast tumours have been previously associated with survival and/or prognosis in cancers. Identifying genes involved in lipid metabolism opens new fields of investigation to decipher the molecular mechanisms driven by the ZNF217 oncogene. Moreover, nine of the 13 genes have already been identified as putative ZNF217 targets by independent biological studies. We therefore suggest that the algorithms for inferring local BNs are valuable data mining tools for unraveling complex mechanisms of biological pathways from expression data. The source code is available at http://www710.univ-lyon1.fr/∼aaussem/Software.html.
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49
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Nicholson TB, Singh AK, Su H, Hevi S, Wang J, Bajko J, Li M, Valdez R, Goetschkes M, Capodieci P, Loureiro J, Cheng X, Li E, Kinzel B, Labow M, Chen T. A hypomorphic lsd1 allele results in heart development defects in mice. PLoS One 2013; 8:e60913. [PMID: 23637775 PMCID: PMC3634827 DOI: 10.1371/journal.pone.0060913] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2012] [Accepted: 03/06/2013] [Indexed: 11/19/2022] Open
Abstract
Lysine-specific demethylase 1 (Lsd1/Aof2/Kdm1a), the first enzyme with specific lysine demethylase activity to be described, demethylates histone and non-histone proteins and is essential for mouse embryogenesis. Lsd1 interacts with numerous proteins through several different domains, most notably the tower domain, an extended helical structure that protrudes from the core of the protein. While there is evidence that Lsd1-interacting proteins regulate the activity and specificity of Lsd1, the significance and roles of such interactions in developmental processes remain largely unknown. Here we describe a hypomorphic Lsd1 allele that contains two point mutations in the tower domain, resulting in a protein with reduced interaction with known binding partners and decreased enzymatic activity. Mice homozygous for this allele die perinatally due to heart defects, with the majority of animals suffering from ventricular septal defects. Molecular analyses revealed hyperphosphorylation of E-cadherin in the hearts of mutant animals. These results identify a previously unknown role for Lsd1 in heart development, perhaps partly through the control of E-cadherin phosphorylation.
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MESH Headings
- Alleles
- Animals
- Cadherins/metabolism
- Disease Models, Animal
- Enzyme Activation
- Female
- Gene Expression Profiling
- Gene Expression Regulation, Developmental
- Heart Defects, Congenital/genetics
- Heart Defects, Congenital/metabolism
- Heart Defects, Congenital/pathology
- Heart Septal Defects, Ventricular/genetics
- Heart Septal Defects, Ventricular/metabolism
- Heart Septal Defects, Ventricular/pathology
- Histone Demethylases
- Homozygote
- Mice
- Mice, Knockout
- Oxidoreductases, N-Demethylating/genetics
- Oxidoreductases, N-Demethylating/metabolism
- Phosphorylation
- Point Mutation
- Pregnancy
- Protein Binding
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Affiliation(s)
- Thomas B. Nicholson
- Developmental and Molecular Pathways, Novartis Institutes for BioMedical Research, Cambridge, Massachusetts, United States of America
- Epigenetics Program, Novartis Institutes for BioMedical Research, Cambridge, Massachusetts, United States of America
| | - Anup K. Singh
- Department of Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, Texas, United States of America
| | - Hui Su
- Developmental and Molecular Pathways, Novartis Institutes for BioMedical Research, Cambridge, Massachusetts, United States of America
- Epigenetics Program, Novartis Institutes for BioMedical Research, Cambridge, Massachusetts, United States of America
| | - Sarah Hevi
- Developmental and Molecular Pathways, Novartis Institutes for BioMedical Research, Cambridge, Massachusetts, United States of America
- Epigenetics Program, Novartis Institutes for BioMedical Research, Cambridge, Massachusetts, United States of America
| | - Jing Wang
- Epigenetics Program, Novartis Institutes for BioMedical Research, Cambridge, Massachusetts, United States of America
| | - Jeff Bajko
- Epigenetics Program, Novartis Institutes for BioMedical Research, Cambridge, Massachusetts, United States of America
| | - Mei Li
- Developmental and Molecular Pathways, Novartis Institutes for BioMedical Research, Cambridge, Massachusetts, United States of America
| | - Reginald Valdez
- Developmental and Molecular Pathways, Novartis Institutes for BioMedical Research, Cambridge, Massachusetts, United States of America
| | - Margaret Goetschkes
- Developmental and Molecular Pathways, Novartis Institutes for BioMedical Research, Cambridge, Massachusetts, United States of America
| | - Paola Capodieci
- Developmental and Molecular Pathways, Novartis Institutes for BioMedical Research, Cambridge, Massachusetts, United States of America
| | - Joseph Loureiro
- Developmental and Molecular Pathways, Novartis Institutes for BioMedical Research, Cambridge, Massachusetts, United States of America
| | - Xiaodong Cheng
- Department of Biochemistry, Emory University, Atlanta, Georgia, United States of America
| | - En Li
- Epigenetics Program, Novartis Institutes for BioMedical Research, Cambridge, Massachusetts, United States of America
| | - Bernd Kinzel
- Developmental and Molecular Pathways, Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Mark Labow
- Developmental and Molecular Pathways, Novartis Institutes for BioMedical Research, Cambridge, Massachusetts, United States of America
| | - Taiping Chen
- Developmental and Molecular Pathways, Novartis Institutes for BioMedical Research, Cambridge, Massachusetts, United States of America
- Epigenetics Program, Novartis Institutes for BioMedical Research, Cambridge, Massachusetts, United States of America
- Department of Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, Texas, United States of America
- * E-mail:
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50
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Razin SV, Borunova VV, Maksimenko OG, Kantidze OL. Cys2His2 zinc finger protein family: classification, functions, and major members. BIOCHEMISTRY (MOSCOW) 2013; 77:217-26. [PMID: 22803940 DOI: 10.1134/s0006297912030017] [Citation(s) in RCA: 112] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Cys2His2 (C2H2)-type zinc fingers are widespread DNA binding motifs in eukaryotic transcription factors. Zinc fingers are short protein motifs composed of two or three β-layers and one α-helix. Two cysteine and two histidine residues located in certain positions bind zinc to stabilize the structure. Four other amino acid residues localized in specific positions in the N-terminal region of the α-helix participate in DNA binding by interacting with hydrogen donors and acceptors exposed in the DNA major groove. The number of zinc fingers in a single protein can vary over a wide range, thus enabling variability of target DNA sequences. Besides DNA binding, zinc fingers can also provide protein-protein and RNA-protein interactions. For the most part, proteins containing the C2H2-type zinc fingers are trans regulators of gene expression that play an important role in cellular processes such as development, differentiation, and suppression of malignant cell transformation (oncosuppression).
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Affiliation(s)
- S V Razin
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334, Russia.
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