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Liao Y, Li R, Pei J, Zhang J, Chen B, Dong H, Feng X, Zhang H, Shang Y, Sui L, Kong Y. Melatonin suppresses tumor proliferation and metastasis by targeting GATA2 in endometrial cancer. J Pineal Res 2024; 76:e12918. [PMID: 37814536 DOI: 10.1111/jpi.12918] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 08/30/2023] [Accepted: 09/12/2023] [Indexed: 10/11/2023]
Abstract
Endometrial cancer (EC) is a reproductive system disease that occurs in perimenopausal and postmenopausal women. However, its etiology is unclear. Melatonin (MT) has been identified as a therapeutic agent for EC; however, its exact mechanism remains unclear. In the present study, we determined that GATA-binding protein 2 (GATA2) is expressed at low levels in EC and regulated by MT. MT upregulates the expression of GATA2 through MT receptor 1A (MTNR1A), whereas GATA2 can promote the expression of MTNR1A by binding to its promoter region. In addition, in vivo and in vitro experiments showed that MT inhibited the proliferation and metastasis of EC cells by upregulating GATA2 expression. The protein kinase B (AKT) pathway was also affected. In conclusion, these findings suggest that MT and GATA2 play significant roles in EC development.
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Affiliation(s)
- Yangyou Liao
- Core Laboratory of Glycobiology and Glycoengineering, College of Basic Medical Sciences, Dalian Medical University, Dalian, China
| | - Ruiling Li
- Core Laboratory of Glycobiology and Glycoengineering, College of Basic Medical Sciences, Dalian Medical University, Dalian, China
| | - Jingyuan Pei
- Core Laboratory of Glycobiology and Glycoengineering, College of Basic Medical Sciences, Dalian Medical University, Dalian, China
| | - Juan Zhang
- Core Laboratory of Glycobiology and Glycoengineering, College of Basic Medical Sciences, Dalian Medical University, Dalian, China
| | - Bo Chen
- Core Laboratory of Glycobiology and Glycoengineering, College of Basic Medical Sciences, Dalian Medical University, Dalian, China
| | - Haojie Dong
- Core Laboratory of Glycobiology and Glycoengineering, College of Basic Medical Sciences, Dalian Medical University, Dalian, China
| | - Xiaoyu Feng
- Core Laboratory of Glycobiology and Glycoengineering, College of Basic Medical Sciences, Dalian Medical University, Dalian, China
| | - Hongshuo Zhang
- Core Laboratory of Glycobiology and Glycoengineering, College of Basic Medical Sciences, Dalian Medical University, Dalian, China
| | - Yuhong Shang
- Department of Gynecology, First Affiliated Hospital, Dalian Medical University, Dalian, Liaoning, China
| | - Linlin Sui
- Core Laboratory of Glycobiology and Glycoengineering, College of Basic Medical Sciences, Dalian Medical University, Dalian, China
| | - Ying Kong
- Core Laboratory of Glycobiology and Glycoengineering, College of Basic Medical Sciences, Dalian Medical University, Dalian, China
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2
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Aktar A, Heit B. Role of the pioneer transcription factor GATA2 in health and disease. J Mol Med (Berl) 2023; 101:1191-1208. [PMID: 37624387 DOI: 10.1007/s00109-023-02359-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 08/04/2023] [Accepted: 08/14/2023] [Indexed: 08/26/2023]
Abstract
The transcription factor GATA2 is involved in human diseases ranging from hematopoietic disorders, to cancer, to infectious diseases. GATA2 is one of six GATA-family transcription factors that act as pioneering transcription factors which facilitate the opening of heterochromatin and the subsequent binding of other transcription factors to induce gene expression from previously inaccessible regions of the genome. Although GATA2 is essential for hematopoiesis and lymphangiogenesis, it is also expressed in other tissues such as the lung, prostate gland, gastrointestinal tract, central nervous system, placenta, fetal liver, and fetal heart. Gene or transcriptional abnormalities of GATA2 causes or predisposes patients to several diseases including the hematological cancers acute myeloid leukemia and acute lymphoblastic leukemia, the primary immunodeficiency MonoMAC syndrome, and to cancers of the lung, prostate, uterus, kidney, breast, gastric tract, and ovaries. Recent data has also linked GATA2 expression and mutations to responses to infectious diseases including SARS-CoV-2 and Pneumocystis carinii pneumonia, and to inflammatory disorders such as atherosclerosis. In this article we review the role of GATA2 in the etiology and progression of these various diseases.
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Affiliation(s)
- Amena Aktar
- Department of Microbiology and Immunology; the Western Infection, Immunity and Inflammation Centre, The University of Western Ontario, London, ON, N6A 5C1, Canada
| | - Bryan Heit
- Department of Microbiology and Immunology; the Western Infection, Immunity and Inflammation Centre, The University of Western Ontario, London, ON, N6A 5C1, Canada.
- Robarts Research Institute, London, ON, N6A 3K7, Canada.
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3
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Brown JS. Comparison of Oncogenes, Tumor Suppressors, and MicroRNAs Between Schizophrenia and Glioma: The Balance of Power. Neurosci Biobehav Rev 2023; 151:105206. [PMID: 37178944 DOI: 10.1016/j.neubiorev.2023.105206] [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: 11/29/2022] [Revised: 04/25/2023] [Accepted: 04/30/2023] [Indexed: 05/15/2023]
Abstract
The risk of cancer in schizophrenia has been controversial. Confounders of the issue are cigarette smoking in schizophrenia, and antiproliferative effects of antipsychotic medications. The author has previously suggested comparison of a specific cancer like glioma to schizophrenia might help determine a more accurate relationship between cancer and schizophrenia. To accomplish this goal, the author performed three comparisons of data; the first a comparison of conventional tumor suppressors and oncogenes between schizophrenia and cancer including glioma. This comparison determined schizophrenia has both tumor-suppressive and tumor-promoting characteristics. A second, larger comparison between brain-expressed microRNAs in schizophrenia with their expression in glioma was then performed. This identified a core carcinogenic group of miRNAs in schizophrenia offset by a larger group of tumor-suppressive miRNAs. This proposed "balance of power" between oncogenes and tumor suppressors could cause neuroinflammation. This was assessed by a third comparison between schizophrenia, glioma and inflammation in asbestos-related lung cancer and mesothelioma (ALRCM). This revealed that schizophrenia shares more oncogenic similarity to ALRCM than glioma.
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Giannopoulou AI, Kanakoglou DS, Papavassiliou AG, Piperi C. Insights into the multi-faceted role of Pioneer transcription factors in glioma formation and progression with targeting options. Biochim Biophys Acta Rev Cancer 2022; 1877:188801. [PMID: 36113627 DOI: 10.1016/j.bbcan.2022.188801] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2022] [Revised: 08/30/2022] [Accepted: 09/07/2022] [Indexed: 11/16/2022]
Abstract
Pioneer transcription factors (TFs) present an important subtype of transcription factors which are vital for cell programming during embryonic development and cellular memory during mitotic growth, as well as cell fate reprogramming. Pioneer TFs can engage specific target binding sites on nucleosomal DNA to attract chromatin remodeling complexes, cofactors, and other transcription factors, ultimately controlling gene expression by shaping locally the epigenome. The priority of binding that they exhibit in contrast to other transcription factors and their involvement in crucial events regarding cell fate, has implicated their aberrant function in the pathogenesis of several disorders including carcinogenesis. Emerging experimental data indicate that certain Pioneer TFs are highly implicated in gliomas development, in neoplastic cell proliferation, angiogenic processes, resistance to therapy, and patient survival. Herein, we describe the main structural characteristics and functional mechanisms of pioneer TFs, focusing on their central role in the pathogenesis and progression of gliomas. We further highlight the current treatment options ranging from natural agents (oleanolic acid) to a variety of chemical compounds (APR-246, COTI-2) and discuss potential delivery systems, including nanoparticles, viral vectors, and intracellular protein delivery techniques.
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Affiliation(s)
- Angeliki-Ioanna Giannopoulou
- Department of Biological Chemistry, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece,.
| | - Dimitrios S Kanakoglou
- Department of Biological Chemistry, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece,.
| | - Athanasios G Papavassiliou
- Department of Biological Chemistry, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece,.
| | - Christina Piperi
- Department of Biological Chemistry, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece,.
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5
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Uthamacumaran A. Dissecting cell fate dynamics in pediatric glioblastoma through the lens of complex systems and cellular cybernetics. BIOLOGICAL CYBERNETICS 2022; 116:407-445. [PMID: 35678918 DOI: 10.1007/s00422-022-00935-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Accepted: 05/04/2022] [Indexed: 06/15/2023]
Abstract
Cancers are complex dynamic ecosystems. Reductionist approaches to science are inadequate in characterizing their self-organized patterns and collective emergent behaviors. Since current approaches to single-cell analysis in cancer systems rely primarily on single time-point multiomics, many of the temporal features and causal adaptive behaviors in cancer dynamics are vastly ignored. As such, tools and concepts from the interdisciplinary paradigm of complex systems theory are introduced herein to decode the cellular cybernetics of cancer differentiation dynamics and behavioral patterns. An intuition for the attractors and complex networks underlying cancer processes such as cell fate decision-making, multiscale pattern formation systems, and epigenetic state-transitions is developed. The applications of complex systems physics in paving targeted therapies and causal pattern discovery in precision oncology are discussed. Pediatric high-grade gliomas are discussed as a model-system to demonstrate that cancers are complex adaptive systems, in which the emergence and selection of heterogeneous cellular states and phenotypic plasticity are driven by complex multiscale network dynamics. In specific, pediatric glioblastoma (GBM) is used as a proof-of-concept model to illustrate the applications of the complex systems framework in understanding GBM cell fate decisions and decoding their adaptive cellular dynamics. The scope of these tools in forecasting cancer cell fate dynamics in the emerging field of computational oncology and patient-centered systems medicine is highlighted.
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6
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Algorithmic reconstruction of glioblastoma network complexity. iScience 2022; 25:104179. [PMID: 35479408 PMCID: PMC9036113 DOI: 10.1016/j.isci.2022.104179] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 03/16/2022] [Accepted: 03/24/2022] [Indexed: 12/16/2022] Open
Abstract
Glioblastoma is a complex disease that is difficult to treat. Network and data science offer alternative approaches to classical bioinformatics pipelines to study gene expression patterns from single-cell datasets, helping to distinguish genes associated with the control of differentiation and aggression. To identify the key molecular regulators of the networks driving glioblastoma/GSC and predict their cell fate dynamics, we applied a host of data theoretic techniques to gene expression patterns from pediatric and adult glioblastoma, and adult glioma-derived stem cells (GSCs). We identified eight transcription factors (OLIG1/2, TAZ, GATA2, FOXG1, SOX6, SATB2, and YY1) and four signaling genes (ATL3, MTSS1, EMP1, and TPT1) as coordinators of cell state transitions and, thus, clinically targetable putative factors differentiating pediatric and adult glioblastomas from adult GSCs. Our study provides strong evidence of complex systems approaches for inferring complex dynamics from reverse-engineering gene networks, bolstering the search for new clinically relevant targets in glioblastoma. Complex cell fate attractors capture glioblastoma differentiation dynamics Graph theoretic approaches decode master regulators of GBM glioblastoma cell fate decisions Network dynamics of pediatric glioblastoma resemble adult GSCs Transcriptional networks may help reprogram glioblastoma behavioral patterns
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7
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Gene Regulatory Network of ETS Domain Transcription Factors in Different Stages of Glioma. J Pers Med 2021; 11:jpm11020138. [PMID: 33671331 PMCID: PMC7922321 DOI: 10.3390/jpm11020138] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 02/07/2021] [Accepted: 02/13/2021] [Indexed: 12/30/2022] Open
Abstract
The ETS domain family of transcription factors is involved in a number of biological processes, and is commonly misregulated in various forms of cancer. Using microarray datasets from patients with different grades of glioma, we have analyzed the expression profiles of various ETS genes, and have identified ETV1, ELK3, ETV4, ELF4, and ETV6 as novel biomarkers for the identification of different glioma grades. We have further analyzed the gene regulatory networks of ETS transcription factors and compared them to previous microarray studies, where Elk-1-VP16 or PEA3-VP16 were overexpressed in neuroblastoma cell lines, and we identify unique and common regulatory networks for these ETS proteins.
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8
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Xu D, Zhou D, Bum-Erdene K, Bailey BJ, Sishtla K, Liu S, Wan J, Aryal UK, Lee JA, Wells CD, Fishel ML, Corson TW, Pollok KE, Meroueh SO. Phenotypic Screening of Chemical Libraries Enriched by Molecular Docking to Multiple Targets Selected from Glioblastoma Genomic Data. ACS Chem Biol 2020; 15:1424-1444. [PMID: 32243127 PMCID: PMC7919753 DOI: 10.1021/acschembio.0c00078] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Like most solid tumors, glioblastoma multiforme (GBM) harbors multiple overexpressed and mutated genes that affect several signaling pathways. Suppressing tumor growth of solid tumors like GBM without toxicity may be achieved by small molecules that selectively modulate a collection of targets across different signaling pathways, also known as selective polypharmacology. Phenotypic screening can be an effective method to uncover such compounds, but the lack of approaches to create focused libraries tailored to tumor targets has limited its impact. Here, we create rational libraries for phenotypic screening by structure-based molecular docking chemical libraries to GBM-specific targets identified using the tumor's RNA sequence and mutation data along with cellular protein-protein interaction data. Screening this enriched library of 47 candidates led to several active compounds, including 1 (IPR-2025), which (i) inhibited cell viability of low-passage patient-derived GBM spheroids with single-digit micromolar IC50 values that are substantially better than standard-of-care temozolomide, (ii) blocked tube-formation of endothelial cells in Matrigel with submicromolar IC50 values, and (iii) had no effect on primary hematopoietic CD34+ progenitor spheroids or astrocyte cell viability. RNA sequencing provided the potential mechanism of action for 1, and mass spectrometry-based thermal proteome profiling confirmed that the compound engages multiple targets. The ability of 1 to inhibit GBM phenotypes without affecting normal cell viability suggests that our screening approach may hold promise for generating lead compounds with selective polypharmacology for the development of treatments of incurable diseases like GBM.
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Affiliation(s)
- David Xu
- Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, Indiana 46202, United States
- Department of BioHealth Informatics, Indiana University School of Informatics and Computing, Indianapolis, Indiana 46202, United States
| | - Donghui Zhou
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana 46202, United States
| | - Khuchtumur Bum-Erdene
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana 46202, United States
| | - Barbara J Bailey
- Department of Pediatrics, Herman B. Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, Indiana 46202, United States
- Department of Pharmacology and Toxicology, Indiana University School of Medicine, Indianapolis, Indiana 46202, United States
- Indiana University Melvin and Bren Simon Cancer Center, Indiana University School of Medicine, Indianapolis, Indiana 46202, United States
| | - Kamakshi Sishtla
- Eugene and Marilyn Glick Eye Institute, Department of Ophthalmology, Indiana University School of Medicine, Indianapolis, Indiana 46202, United States
| | - Sheng Liu
- Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, Indiana 46202, United States
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana 46202, United States
| | - Jun Wan
- Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, Indiana 46202, United States
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana 46202, United States
| | - Uma K Aryal
- Purdue Proteomics Facility, Bindley Bioscience Center, Purdue University, West Lafayette, Indiana 47907, United States
| | - Jonathan A Lee
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana 46202, United States
| | - Clark D Wells
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana 46202, United States
| | - Melissa L Fishel
- Department of Pediatrics, Herman B. Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, Indiana 46202, United States
- Department of Pharmacology and Toxicology, Indiana University School of Medicine, Indianapolis, Indiana 46202, United States
- Indiana University Melvin and Bren Simon Cancer Center, Indiana University School of Medicine, Indianapolis, Indiana 46202, United States
| | - Timothy W Corson
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana 46202, United States
- Department of Pharmacology and Toxicology, Indiana University School of Medicine, Indianapolis, Indiana 46202, United States
- Indiana University Melvin and Bren Simon Cancer Center, Indiana University School of Medicine, Indianapolis, Indiana 46202, United States
- Eugene and Marilyn Glick Eye Institute, Department of Ophthalmology, Indiana University School of Medicine, Indianapolis, Indiana 46202, United States
| | - Karen E Pollok
- Department of Pediatrics, Herman B. Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, Indiana 46202, United States
- Department of Pharmacology and Toxicology, Indiana University School of Medicine, Indianapolis, Indiana 46202, United States
- Indiana University Melvin and Bren Simon Cancer Center, Indiana University School of Medicine, Indianapolis, Indiana 46202, United States
| | - Samy O Meroueh
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana 46202, United States
- Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, Indiana 46202, United States
- Indiana University Melvin and Bren Simon Cancer Center, Indiana University School of Medicine, Indianapolis, Indiana 46202, United States
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9
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Sakthikumar S, Roy A, Haseeb L, Pettersson ME, Sundström E, Marinescu VD, Lindblad-Toh K, Forsberg-Nilsson K. Whole-genome sequencing of glioblastoma reveals enrichment of non-coding constraint mutations in known and novel genes. Genome Biol 2020; 21:127. [PMID: 32513296 PMCID: PMC7281935 DOI: 10.1186/s13059-020-02035-x] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Accepted: 04/30/2020] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Glioblastoma (GBM) has one of the worst 5-year survival rates of all cancers. While genomic studies of the disease have been performed, alterations in the non-coding regulatory regions of GBM have largely remained unexplored. We apply whole-genome sequencing (WGS) to identify non-coding mutations, with regulatory potential in GBM, under the hypothesis that regions of evolutionary constraint are likely to be functional, and somatic mutations are likely more damaging than in unconstrained regions. RESULTS We validate our GBM cohort, finding similar copy number aberrations and mutated genes based on coding mutations as previous studies. Performing analysis on non-coding constraint mutations and their position relative to nearby genes, we find a significant enrichment of non-coding constraint mutations in the neighborhood of 78 genes that have previously been implicated in GBM. Among them, SEMA3C and DYNC1I1 show the highest frequencies of alterations, with multiple mutations overlapping transcription factor binding sites. We find that a non-coding constraint mutation in the SEMA3C promoter reduces the DNA binding capacity of the region. We also identify 1776 other genes enriched for non-coding constraint mutations with likely regulatory potential, providing additional candidate GBM genes. The mutations in the top four genes, DLX5, DLX6, FOXA1, and ISL1, are distributed over promoters, UTRs, and multiple transcription factor binding sites. CONCLUSIONS These results suggest that non-coding constraint mutations could play an essential role in GBM, underscoring the need to connect non-coding genomic variation to biological function and disease pathology.
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Affiliation(s)
- Sharadha Sakthikumar
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, SE-751 23, Uppsala, Sweden
- Broad Institute, Cambridge, MA, 02142, USA
| | - Ananya Roy
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, SE-751 85, Uppsala, Sweden
| | - Lulu Haseeb
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, SE-751 85, Uppsala, Sweden
| | - Mats E Pettersson
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, SE-751 23, Uppsala, Sweden
| | - Elisabeth Sundström
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, SE-751 23, Uppsala, Sweden
| | - Voichita D Marinescu
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, SE-751 23, Uppsala, Sweden
| | - Kerstin Lindblad-Toh
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, SE-751 23, Uppsala, Sweden
- Broad Institute, Cambridge, MA, 02142, USA
| | - Karin Forsberg-Nilsson
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, SE-751 85, Uppsala, Sweden.
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10
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Jiang L, Yang H, Chen T, Zhu X, Ye J, Lv K. Identification of HMG-box family establishes the significance of SOX6 in the malignant progression of glioblastoma. Aging (Albany NY) 2020; 12:8084-8106. [PMID: 32388501 PMCID: PMC7244032 DOI: 10.18632/aging.103127] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2019] [Accepted: 03/30/2020] [Indexed: 12/20/2022]
Abstract
Glioblastoma multiforme (GBM) is the most malignant neuroepithelial primary brain tumor and its mean survival time is 15 months after diagnosis. This study undertook to investigate the genome-wide and transcriptome-wide analyses of human high mobility group box (HMG-box) TF (transcript factor) families / HOX, TOX, FOX, HMG and SOX gene families, and their relationships to GBM. According to the TCGA-GBM profile analysis, differentially expressed HOX, FOX, HMG and SOX gene families (62 DEmRNA) were found in this study. We also analyzed DEmRNA (HMG-box related genes) co-expressed eight DElncRNA in GBM, and constructed a ceRNA network analysis as well. We constructed 50 DElncRNA-DEmiRNA-DEmRNA (HMG-box related genes) pairs between GBM and normal tissues. Then, risk genes SOX6 and SOX21 expression were correlated with immune infiltration levels in GBM. SOX6 also had a strong association with MAPT, GSK3B, FYN and DPYSL4, suggesting that they might be functional members in GBM.
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Affiliation(s)
- Lan Jiang
- Central Laboratory, Yijishan Hospital of Wannan Medical College, Wuhu 241001, China
- Key Laboratory of Non-coding RNA Transformation Research of Anhui Higher Education Institution, Wannan Medical College, Wuhu 241001, China
| | - Hui Yang
- Central Laboratory, Yijishan Hospital of Wannan Medical College, Wuhu 241001, China
- Key Laboratory of Non-coding RNA Transformation Research of Anhui Higher Education Institution, Wannan Medical College, Wuhu 241001, China
| | - Tianbing Chen
- Central Laboratory, Yijishan Hospital of Wannan Medical College, Wuhu 241001, China
- Key Laboratory of Non-coding RNA Transformation Research of Anhui Higher Education Institution, Wannan Medical College, Wuhu 241001, China
| | - Xiaolong Zhu
- Central Laboratory, Yijishan Hospital of Wannan Medical College, Wuhu 241001, China
- Key Laboratory of Non-coding RNA Transformation Research of Anhui Higher Education Institution, Wannan Medical College, Wuhu 241001, China
| | - Jingjing Ye
- Central Laboratory, Yijishan Hospital of Wannan Medical College, Wuhu 241001, China
- Key Laboratory of Non-coding RNA Transformation Research of Anhui Higher Education Institution, Wannan Medical College, Wuhu 241001, China
| | - Kun Lv
- Central Laboratory, Yijishan Hospital of Wannan Medical College, Wuhu 241001, China
- Key Laboratory of Non-coding RNA Transformation Research of Anhui Higher Education Institution, Wannan Medical College, Wuhu 241001, China
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11
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Cheng M, Zhang ZW, Ji XH, Xu Y, Bian E, Zhao B. Super-enhancers: A new frontier for glioma treatment. Biochim Biophys Acta Rev Cancer 2020; 1873:188353. [PMID: 32112817 DOI: 10.1016/j.bbcan.2020.188353] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Revised: 02/21/2020] [Accepted: 02/21/2020] [Indexed: 01/17/2023]
Abstract
Glioma is the most common primary malignant tumor in the human brain. Although there are a variety of treatments, such as surgery, radiation and chemotherapy, glioma is still an incurable disease. Super-enhancers (SEs) are implicated in the control of tumor cell identity, and they promote oncogenic transcription, which supports tumor cells. Inhibition of the SE complex, which is required for the assembly and maintenance of SEs, may repress oncogenic transcription and impede tumor growth. In this review, we discuss the unique characteristics of SEs compared to typical enhancers, and we summarize the recent advances in the understanding of their properties and biological role in gene regulation. Additionally, we highlight that SE-driven lncRNAs, miRNAs and genes are involved in the malignant phenotype of glioma. Most importantly, the application of SE inhibitors in different cancer subtypes has introduced new directions in glioma treatment.
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Affiliation(s)
- Meng Cheng
- Department of Neurosurgery, The Second Affiliated Hospital of Anhui Medical University, Hefei 230601, China; Cerebral Vascular Disease Research Center, Anhui Medical University, Hefei 230601, China
| | - Zheng Wei Zhang
- Department of Neurosurgery, The Second Affiliated Hospital of Anhui Medical University, Hefei 230601, China; Cerebral Vascular Disease Research Center, Anhui Medical University, Hefei 230601, China
| | - Xing Hu Ji
- Department of Neurosurgery, The Second Affiliated Hospital of Anhui Medical University, Hefei 230601, China; Cerebral Vascular Disease Research Center, Anhui Medical University, Hefei 230601, China
| | - Yadi Xu
- Department of Neurosurgery, The Second Affiliated Hospital of Anhui Medical University, Hefei 230601, China; Cerebral Vascular Disease Research Center, Anhui Medical University, Hefei 230601, China
| | - Erbao Bian
- Department of Neurosurgery, The Second Affiliated Hospital of Anhui Medical University, Hefei 230601, China; Cerebral Vascular Disease Research Center, Anhui Medical University, Hefei 230601, China.
| | - Bing Zhao
- Department of Neurosurgery, The Second Affiliated Hospital of Anhui Medical University, Hefei 230601, China; Cerebral Vascular Disease Research Center, Anhui Medical University, Hefei 230601, China.
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12
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Zhang J, Guan M, Wang Q, Zhang J, Zhou T, Sun X. Single-cell transcriptome-based multilayer network biomarker for predicting prognosis and therapeutic response of gliomas. Brief Bioinform 2019; 21:1080-1097. [DOI: 10.1093/bib/bbz040] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 02/22/2019] [Accepted: 03/12/2019] [Indexed: 12/23/2022] Open
Abstract
Abstract
Occurrence and development of cancers are governed by complex networks of interacting intercellular and intracellular signals. The technology of single-cell RNA sequencing (scRNA-seq) provides an unprecedented opportunity for dissecting the interplay between the cancer cells and the associated microenvironment. Here we combined scRNA-seq data with clinical bulk gene expression data to develop a computational pipeline for identifying the prognostic and predictive signature that connects cancer cells and microenvironmental cells. The pipeline was applied to glioma scRNA-seq data and revealed a tumor-associated microglia/macrophage-mediated EGFR/ERBB2 feedback-crosstalk signaling module, which was defined as a multilayer network biomarker (MNB) to predict survival outcome and therapeutic response of glioma patients. We used publicly available clinical data sets from large cohorts of glioma patients to examine the prognostic significance and predictive accuracy of the MNB, which outperformed conventional gene biomarkers and other methods. Additionally, the MNB was found to be predictive of the sensitivity or resistance of glioma patients to molecularly targeted therapeutics. Moreover, the MNB was an independent and the strongest prognostic factor when adjusted for clinicopathologic risk factors and other existing gene signatures. The robustness of the MNB was further tested on additional data sets. Our study presents a promising scRNA-seq transcriptome-based multilayer network approach to elucidate the interactions between tumor cell and tumor-associated microenvironment and to identify prognostic and predictive signatures of cancer patients. The proposed MNB method may facilitate the design of more effective biomarkers for predicting prognosis and therapeutic resistance of cancer patients.
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Affiliation(s)
- Ji Zhang
- Department of Neurosurgery, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-Sen University Cancer Center, Guangzhou, China
| | - Meige Guan
- School of Mathematics, Sun Yat-Sen University, Guangzhou, China
| | - Qianliang Wang
- School of Life Science, Sun Yat-Sen University, Guangzhou, China
| | - Jiajun Zhang
- School of Mathematics, Sun Yat-Sen University, Guangzhou, China
| | - Tianshou Zhou
- School of Mathematics, Sun Yat-Sen University, Guangzhou, China
| | - Xiaoqiang Sun
- Department of Medical Informatics, Zhong-shan School of Medicine, Sun Yat-Sen University, Guangzhou 510080, China; Key Laboratory of Tropical Disease Control (Sun Yat-Sen University), Chinese Ministry of Education, Guangzhou, Guangdong, China
- School of Mathematics, Sun Yat-Sen University, Guangzhou, China
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13
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Liu CY, Hu MH, Hsu CJ, Huang CT, Wang DS, Tsai WC, Chen YT, Lee CH, Chu PY, Hsu CC, Chen MH, Shiau CW, Tseng LM, Chen KF. Lapatinib inhibits CIP2A/PP2A/p-Akt signaling and induces apoptosis in triple negative breast cancer cells. Oncotarget 2016; 7:9135-49. [PMID: 26824320 PMCID: PMC4891031 DOI: 10.18632/oncotarget.7035] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Accepted: 01/19/2016] [Indexed: 12/14/2022] Open
Abstract
We tested the efficacy of lapatinib, a dual tyrosine kinase inhibitor which interrupts the HER2 and epidermal growth factor receptor (EGFR) pathways, in a panel of triple-negative breast cancer (TNBC) cells, and examined the drug mechanism. Lapatinib showed an anti-proliferative effect in HCC 1937, MDA-MB-468, and MDA-MB-231 cell lines. Lapatinib induced significant apoptosis and inhibited CIP2A and p-Akt in a dose and time-dependent manner in the three TNBC cell lines. Overexpression of CIP2A reduced lapatinib-induced apoptosis in MDA-MB-468 cells. In addition, lapatinib increased PP2A activity (in relation to CIP2A inhibition). Moreover, lapatinib-induced apoptosis and p-Akt downregulation was attenuated by PP2A antagonist okadaic acid. Furthermore, lapatinib indirectly decreased CIP2A transcription by disturbing the binding of Elk1 to the CIP2A promoter. Importantly, lapatinib showed anti-tumor activity in mice bearing MDA-MB-468 xenograft tumors, and suppressed CIP2A as well as p-Akt in these xenografted tumors. In summary, inhibition of CIP2A determines the effects of lapatinib-induced apoptosis in TNBC cells. In addition to being a dual tyrosine kinase inhibitor of HER2 and EGFR, lapatinib also inhibits CIP2A/PP2A/p-Akt signaling in TNBC cells.
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Affiliation(s)
- Chun-Yu Liu
- Division of Medical Oncology, Department of Oncology, Taipei Veterans General Hospital, Taipei, Taiwan.,School of Medicine, National Yang-Ming University, Taipei, Taiwan
| | - Ming-Hung Hu
- Division of Hematology and Oncology, Department of Medicine, Cardinal Tien Hospital, New Taipei City, Taiwan.,School of Medicine, Fu Jen Catholic University, New Taipei City, Taiwan
| | - Chia-Jung Hsu
- Division of Medical Oncology, Department of Oncology, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Chun-Teng Huang
- School of Medicine, National Yang-Ming University, Taipei, Taiwan.,Division of Hematology & Oncology, Department of Medicine, Yang-Ming Branch of Taipei City Hospital, Taipei, Taiwan
| | - Duen-Shian Wang
- Division of Medical Oncology, Department of Oncology, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Wen-Chun Tsai
- Division of Medical Oncology, Department of Oncology, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Yi-Ting Chen
- Division of Medical Oncology, Department of Oncology, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Chia-Han Lee
- Division of Medical Oncology, Department of Oncology, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Pei-Yi Chu
- Department of Pathology, Show Chwan Memorial Hospital, Changhua City, Taiwan
| | - Chia-Chi Hsu
- Institute of Pharmacology, National Yang-Ming University, Taipei, Taiwan
| | - Ming-Huang Chen
- Division of Medical Oncology, Department of Oncology, Taipei Veterans General Hospital, Taipei, Taiwan.,School of Medicine, National Yang-Ming University, Taipei, Taiwan
| | - Chung-Wai Shiau
- Institute of Biopharmaceutical Sciences, National Yang-Ming University, Taipei, Taiwan
| | - Ling-Ming Tseng
- School of Medicine, National Yang-Ming University, Taipei, Taiwan.,Department of Surgery, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Kuen-Feng Chen
- Department of Medical Research, National Taiwan University Hospital, Taipei, Taiwan.,National Taiwan University College of Medicine, Taipei, Taiwan
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14
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Katsumura KR, Ong IM, DeVilbiss AW, Sanalkumar R, Bresnick EH. GATA Factor-Dependent Positive-Feedback Circuit in Acute Myeloid Leukemia Cells. Cell Rep 2016; 16:2428-41. [PMID: 27545880 DOI: 10.1016/j.celrep.2016.07.058] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2016] [Revised: 06/17/2016] [Accepted: 07/21/2016] [Indexed: 01/09/2023] Open
Abstract
The master regulatory transcription factor GATA-2 triggers hematopoietic stem and progenitor cell generation. GATA2 haploinsufficiency is implicated in myelodysplastic syndrome (MDS) and acute myeloid leukemia (AML), and GATA2 overexpression portends a poor prognosis for AML. However, the constituents of the GATA-2-dependent genetic network mediating pathogenesis are unknown. We described a p38-dependent mechanism that phosphorylates GATA-2 and increases GATA-2 target gene activation. We demonstrate that this mechanism establishes a growth-promoting chemokine/cytokine circuit in AML cells. p38/ERK-dependent GATA-2 phosphorylation facilitated positive autoregulation of GATA2 transcription and expression of target genes, including IL1B and CXCL2. IL-1β and CXCL2 enhanced GATA-2 phosphorylation, which increased GATA-2-mediated transcriptional activation. p38/ERK-GATA-2 stimulated AML cell proliferation via CXCL2 induction. As GATA2 mRNA correlated with IL1B and CXCL2 mRNAs in AML-M5 and high expression of these genes predicted poor prognosis of cytogenetically normal AML, we propose that the circuit is functionally important in specific AML contexts.
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Affiliation(s)
- Koichi R Katsumura
- UW-Madison Blood Research Program, Department of Cell and Regenerative Biology, Wisconsin Institutes for Medical Research, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, USA; UW Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, USA
| | - Irene M Ong
- Department of Biostatistics and Medical Informatics, University of Wisconsin, Madison, WI 53705, USA; UW Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, USA
| | - Andrew W DeVilbiss
- UW-Madison Blood Research Program, Department of Cell and Regenerative Biology, Wisconsin Institutes for Medical Research, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, USA; UW Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, USA
| | - Rajendran Sanalkumar
- UW-Madison Blood Research Program, Department of Cell and Regenerative Biology, Wisconsin Institutes for Medical Research, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, USA; UW Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, USA
| | - Emery H Bresnick
- UW-Madison Blood Research Program, Department of Cell and Regenerative Biology, Wisconsin Institutes for Medical Research, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, USA; UW Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, USA.
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15
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Yan Y, Xu Z, Dai S, Qian L, Sun L, Gong Z. Targeting autophagy to sensitive glioma to temozolomide treatment. J Exp Clin Cancer Res 2016; 35:23. [PMID: 26830677 PMCID: PMC4736617 DOI: 10.1186/s13046-016-0303-5] [Citation(s) in RCA: 219] [Impact Index Per Article: 27.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2015] [Accepted: 01/28/2016] [Indexed: 02/08/2023] Open
Abstract
Temozolomide (TMZ), an alkylating agent, is widely used for treating primary and recurrent high-grade gliomas. However, the efficacy of TMZ is often limited by the development of resistance. Recently, studies have found that TMZ treatment could induce autophagy, which contributes to therapy resistance in glioma. To enhance the benefit of TMZ in the treatment of glioblastomas, effective combination strategies are needed to sensitize glioblastoma cells to TMZ. In this regard, as autophagy could promote cell survival or autophagic cell death, modulating autophagy using a pharmacological inhibitor, such as chloroquine, or an inducer, such as rapamycin, has received considerably more attention. To understand the effectiveness of regulating autophagy in glioblastoma treatment, this review summarizes reports on glioblastoma treatments with TMZ and autophagic modulators from in vitro and in vivo studies, as well as clinical trials. Additionally, we discuss the possibility of using autophagy regulatory compounds that can sensitive TMZ treatment as a chemotherapy for glioma treatment.
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Affiliation(s)
- Yuanliang Yan
- Department of Pharmacy, Xiangya Hospital, Central South University, Changsha, 410008, China.
- Institute of Hospital Pharmacy, Central South University, Changsha, 410008, China.
| | - Zhijie Xu
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, 410008, China.
| | - Shuang Dai
- Department of Pharmacy, Xiangya Hospital, Central South University, Changsha, 410008, China.
- Institute of Hospital Pharmacy, Central South University, Changsha, 410008, China.
| | - Long Qian
- Department of Pharmacy, Xiangya Hospital, Central South University, Changsha, 410008, China.
- Institute of Hospital Pharmacy, Central South University, Changsha, 410008, China.
| | - Lunquan Sun
- Center for Molecular Medicine, Xiangya Hospital, Key Laboratory of Molecular Radiation Oncology of Hunan Province, Central South University, Changsha, 410008, China.
| | - Zhicheng Gong
- Department of Pharmacy, Xiangya Hospital, Central South University, Changsha, 410008, China.
- Institute of Hospital Pharmacy, Central South University, Changsha, 410008, China.
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