1
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Elucidating the importance and regulation of key enhancers for human MEIS1 expression. Leukemia 2022; 36:1980-1989. [PMID: 35624144 PMCID: PMC9343249 DOI: 10.1038/s41375-022-01602-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Revised: 05/05/2022] [Accepted: 05/12/2022] [Indexed: 11/20/2022]
Abstract
Myeloid ecotropic virus insertion site 1 (MEIS1) is essential for normal hematopoiesis and is a critical factor in the pathogenesis of a large subset of acute myeloid leukemia (AML). Despite the clinical relevance of MEIS1, its regulation is largely unknown. To understand the transcriptional regulatory mechanisms contributing to human MEIS1 expression, we created a knock-in green florescent protein (GFP) reporter system at the endogenous MEIS1 locus in a human AML cell line. Using this model, we have delineated and dissected a critical enhancer region of the MEIS1 locus for transcription factor (TF) binding through in silico prediction in combination with oligo pull-down, mass-spectrometry and knockout analysis leading to the identification of FLI1, an E-twenty-six (ETS) transcription factor, as an important regulator of MEIS1 transcription. We further show direct binding of FLI1 to the MEIS1 locus in human AML cell lines as well as enrichment of histone acetylation in MEIS1-high healthy and leukemic cells. We also observe a positive correlation between high FLI1 transcript levels and worse overall survival in AML patients. Our study expands the role of ETS factors in AML and our model constitutes a feasible tool for a more detailed understanding of transcriptional regulatory elements and their interactome.
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2
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Yu F, Li JL, Feng WR, Tang YK, Su SY, Xu P, Zhong H. Heat Shock Procedure Affects Cell Division-Associated Genes in Gynogenetic Manipulation. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2022; 24:354-365. [PMID: 35305189 DOI: 10.1007/s10126-022-10112-4] [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] [Received: 12/27/2021] [Accepted: 03/02/2022] [Indexed: 06/14/2023]
Abstract
Heat shock procedure is crucial for gynogenetic manipulation leading to diploidization of the maternal genomes; however, the underlying molecular mechanism especially the transcriptomic changes during this procedure has still not been unveiled yet. Here, the artificial gynogenesis of zebrafish (Danio rerio) using inactivated sperm from rare minnow (Gobiocypris rarus) was conducted. We found that artificial gynogenetic manipulation, including pseudo-fertilization and heat shock, decreased hatching rates, whereas heat shock treatment alone had medium hatching rates. The first cleavage changed the expression of genes associated with RNA transcription and protein synthesis. A co-expression network regulated by hub genes GIT1, Sepsecs, and FLNB was significantly correlated with heat shock procedure. The cyclin family and cyclin-dependent kinase-related genes were lowly expressed in embryos from gynogenetic zebrafish, and genes involved in controlling the cell cycle and genomic stability were significantly altered by the gynogenetic treatment. Our results show the effects of artificial gynogenesis on embryos and describe changes in gene expression that suggest drastic changes take place in cell division by heat shock procedure. These findings will contribute to an understanding of the molecular basis for germplasm improving, including the purifying effect and allogynogenetic biological effect by gynogenesis.
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Affiliation(s)
- Fan Yu
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, 214081, China
| | - Jian-Lin Li
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, 214081, China
| | - Wen-Rong Feng
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, 214081, China
| | - Yong-Kai Tang
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, 214081, China
| | - Sheng-Yan Su
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, 214081, China
| | - Pao Xu
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, 214081, China.
| | - Huan Zhong
- Hunan Research Center of Engineering Technology for Utilization of Distinctive Aquatic Resource, Hunan Agricultural University, Changsha, 410128, China.
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3
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Tang L, Hill MC, Wang J, Wang J, Martin JF, Li M. Predicting unrecognized enhancer-mediated genome topology by an ensemble machine learning model. Genome Res 2020; 30:1835-1845. [PMID: 33184104 PMCID: PMC7706734 DOI: 10.1101/gr.264606.120] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2020] [Accepted: 10/02/2020] [Indexed: 01/08/2023]
Abstract
Transcriptional enhancers commonly work over long genomic distances to precisely regulate spatiotemporal gene expression patterns. Dissecting the promoters physically contacted by these distal regulatory elements is essential for understanding developmental processes as well as the role of disease-associated risk variants. Modern proximity-ligation assays, like HiChIP and ChIA-PET, facilitate the accurate identification of long-range contacts between enhancers and promoters. However, these assays are technically challenging, expensive, and time-consuming, making it difficult to investigate enhancer topologies, especially in uncharacterized cell types. To overcome these shortcomings, we therefore designed LoopPredictor, an ensemble machine learning model, to predict genome topology for cell types which lack long-range contact maps. To enrich for functional enhancer-promoter loops over common structural genomic contacts, we trained LoopPredictor with both H3K27ac and YY1 HiChIP data. Moreover, the integration of several related multi-omics features facilitated identifying and annotating the predicted loops. LoopPredictor is able to efficiently identify cell type–specific enhancer-mediated loops, and promoter–promoter interactions, with a modest feature input requirement. Comparable to experimentally generated H3K27ac HiChIP data, we found that LoopPredictor was able to identify functional enhancer loops. Furthermore, to explore the cross-species prediction capability of LoopPredictor, we fed mouse multi-omics features into a model trained on human data and found that the predicted enhancer loops outputs were highly conserved. LoopPredictor enables the dissection of cell type–specific long-range gene regulation and can accelerate the identification of distal disease-associated risk variants.
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Affiliation(s)
- Li Tang
- Hunan Provincial Key Lab on Bioinformatics, School of Computer Science and Engineering, Central South University, Changsha 410083, China.,Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Matthew C Hill
- Program in Developmental Biology, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Jun Wang
- Department of Pediatrics, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, Texas 77030, USA
| | - Jianxin Wang
- Hunan Provincial Key Lab on Bioinformatics, School of Computer Science and Engineering, Central South University, Changsha 410083, China
| | - James F Martin
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, Texas 77030, USA.,Program in Developmental Biology, Baylor College of Medicine, Houston, Texas 77030, USA.,Cardiovascular Research Institute, Baylor College of Medicine, Houston, Texas 77030, USA.,Texas Heart Institute, Houston, Texas 77030, USA
| | - Min Li
- Hunan Provincial Key Lab on Bioinformatics, School of Computer Science and Engineering, Central South University, Changsha 410083, China
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4
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Cheng M, Zeng Y, Zhang T, Xu M, Li Z, Wu Y. Transcription Factor ELF1 Activates MEIS1 Transcription and Then Regulates the GFI1/FBW7 Axis to Promote the Development of Glioma. MOLECULAR THERAPY. NUCLEIC ACIDS 2020; 23:418-430. [PMID: 33473327 PMCID: PMC7787950 DOI: 10.1016/j.omtn.2020.10.015] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Accepted: 10/11/2020] [Indexed: 02/06/2023]
Abstract
Glioma is the most common malignancy in the central nervous system with no immediate prospect of a cure. Comprehensive understanding on the pathogenesis of the disorder contributes to a better outcome. Herein, we aimed to investigate whether transcription factors erythroblast transformation-specific (ETS) transcription factor (ELF1), myeloid ecotropic viral integration site 1 (MEIS1), and growth factor independence 1 (GFI1)/F-box/WD repeat-containing protein 7 (FBW7) mediate progression of glioma. ELF1, MEIS1, and GFI1 were upregulated in glioma cells and tissues, as ELF1 was correlated with poor prognosis. Bioinformatics analysis identified the binding between ELF1 and MEIS1 as well as between GFI1 and FBW7, confirmed by chromatin immunoprecipitation (ChIP) experiments. Functional experiment indicated that silencing of ELT1 decreased MEIS1 expression and that overexpression of MEIS1 increased GFI1 expression by activating GFI1 enhancer but decreased FBW7 expression. Importantly, silencing of ELF1 decreased the capacities of proliferation, migration, and invasion of glioma cells whereas it increased apoptosis, supported by increased capase-3 and decreased matrix metalloproteinase-9 (MMP-9) and proliferating cell nuclear antigen (PCNA) expression. Moreover, an in vivo experiment confirmed the inhibitory role of silenced ELF1 in tumor growth, with a decreased level of MEIS1 and GFI1. Taken together, our study elucidated a potential mechanism that ELF1 promoted cell progression by increasing GFI1 and METS1 as well as decreasing FBW7 expression in glioma.
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Affiliation(s)
- Meixiong Cheng
- Department of Neurosurgery, Sichuan Provincial People’s Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu 610072, P.R. China
| | - Yi Zeng
- Department of Neurosurgery Critical Care Medicine, Sichuan Provincial People’s Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu 610072, P.R. China
| | - Tian Zhang
- Department of Neurosurgery, Sichuan Provincial People’s Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu 610072, P.R. China
| | - Min Xu
- Department of Neurosurgery Critical Care Medicine, Sichuan Provincial People’s Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu 610072, P.R. China
| | - Zhili Li
- Department of Neurosurgery, Sichuan Provincial People’s Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu 610072, P.R. China
- Corresponding author Zhili Li, Department of Neurosurgery, Sichuan Provincial People's Hospital (School of Medicine, University of Electronic Science and Technology of China), No. 32, the 2nd Section of Yihuan Road, Qingyang District, Chengdu 610072, Sichuan Province, P. R. China.
| | - Yaqiu Wu
- Department of Neurosurgery Critical Care Medicine, Sichuan Provincial People’s Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu 610072, P.R. China
- Corresponding author Yaqiu Wu, Department of Neurosurgery Critical Care Medicine, Sichuan Provincial People's Hospital (School of Medicine, University of Electronic Science and Technology of China), No. 32, the 2nd Section of Yihuan Road, Qingyang District, Chengdu 610072, Sichuan Province, P. R. China
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5
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Pang Y, Zhao Y, Wang Y, Wang X, Wang R, Liu N, Li P, Ji M, Ye J, Sun T, Li J, Ma D, Lu F, Ji C. TNFAIP8 promotes AML chemoresistance by activating ERK signaling pathway through interaction with Rac1. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2020; 39:158. [PMID: 32795319 PMCID: PMC7427779 DOI: 10.1186/s13046-020-01658-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Accepted: 07/28/2020] [Indexed: 12/18/2022]
Abstract
Background Chemoresistance is emerging as a major barrier to successful treatment in acute myeloid leukemia (AML), and evasion of apoptosis is among the fundamental underlying mechanisms. Therefore, unraveling molecular networks that drive this process constitutes an urgent unmet need. Herein, we aim to characterize the role and molecular mechanism of the tumor necrosis factor ɑ-induced protein 8 (TNFAIP8), a novel anti-apoptotic molecule, in AML chemoresistance. Methods The expression levels of TNFAIP8 were assessed in AML patients and cell lines by RT-qPCR and western blots. The transcriptional regulation of TNFAIP8 was analyzed with luciferase reporter assay and ChIP followed by RT-qPCR. Functional experiments were conducted to evaluate the effects of TNFAIP8 on apoptosis, drug sensitivity and proliferation of AML cells. Potential effects of TNFAIP8 on the activation of extracellular signal-regulated kinase (ERK) pathway were detected by western blots. CoIP and P21-activated kinase (PAK) pull-down assay were performed to ascertain the upstream target. The overall effects of TNFAIP8 on AML were examined in murine models. Results Upregulated TNFAIP8 expression was first confirmed in human AML patients and cell lines. E74 like ETS transcription factor 1 (ELF1) was then identified to contribute to its aberrant expression. Through manipulating TNFAIP8 expression, we described its role in protecting AML cells from apoptosis induced by chemotherapeutic agents and in promoting drug resistance. Notably, the leukemia-promoting action of TNFAIP8 was mediated by sustaining activity of the ERK signaling pathway, through an interaction with Rac family small GTPase 1 (Rac1). In addition, in vivo experiments confirmed that TNFAIP8 suppression lowered leukemia infiltration and improved survival. Conclusion Our data provide a molecular basis for the role of TNFAIP8 in chemoresistance and progression of AML and highlight the unique function of TNFAIP8 as an attractive therapeutic target.
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Affiliation(s)
- Yihua Pang
- Department of Hematology, Qilu Hospital of Shandong University, Jinan, 250012, Shandong, China
| | - Yanan Zhao
- Department of Hematology, Qilu Hospital of Shandong University, Jinan, 250012, Shandong, China
| | - Yan Wang
- Department of Hematology, Taian central hospital, Taian, 271000, Shandong, China
| | - Xinlu Wang
- Department of Hematology, Qilu Hospital of Shandong University, Jinan, 250012, Shandong, China
| | - Ruiqing Wang
- Department of Hematology, Qilu Hospital of Shandong University, Jinan, 250012, Shandong, China
| | - Na Liu
- Department of Hematology, Qilu Hospital of Shandong University, Jinan, 250012, Shandong, China
| | - Peng Li
- Department of Hematology, Qilu Hospital of Shandong University, Jinan, 250012, Shandong, China
| | - Min Ji
- Department of Hematology, Qilu Hospital of Shandong University, Jinan, 250012, Shandong, China
| | - Jingjing Ye
- Department of Hematology, Qilu Hospital of Shandong University, Jinan, 250012, Shandong, China
| | - Tao Sun
- Department of Hematology, Qilu Hospital of Shandong University, Jinan, 250012, Shandong, China
| | - Jingxin Li
- Department of Physiology, School of Basic Medical Sciences, Shandong University, Jinan, 250012, Shandong, China
| | - Daoxin Ma
- Department of Hematology, Qilu Hospital of Shandong University, Jinan, 250012, Shandong, China
| | - Fei Lu
- Department of Hematology, Qilu Hospital of Shandong University, Jinan, 250012, Shandong, China.
| | - Chunyan Ji
- Department of Hematology, Qilu Hospital of Shandong University, Jinan, 250012, Shandong, China.
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6
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Wang L, Tang D, Wu T, Sun F. ELF1-mediated LUCAT1 promotes choroidal melanoma by modulating RBX1 expression. Cancer Med 2020; 9:2160-2170. [PMID: 31968402 PMCID: PMC7064025 DOI: 10.1002/cam4.2859] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Revised: 12/10/2019] [Accepted: 01/06/2020] [Indexed: 12/14/2022] Open
Abstract
Long noncoding RNAs (lncRNAs) are essential regulators of gene expression and biological behaviors. However, the contribution of lncRNA LUCAT1 to choroidal melanoma (CM) remains unexplored. Here, we examined the expression of LUCAT1 in CM cells by qRT‐PCR and investigated its biological effects by cell counting kit‐8, EdU, TUNEL, transwell assays, and Western blot. Bioinformatics tools were applied to find RNA candidates for further study. Moreover, mechanistic experiments including RNA immunoprecipitation assay, pull‐down assay, and luciferase reporter assay confirmed the relation or interaction among the indicated molecules. Here, we reported ELF1 as the transcription activator of LUCAT1. Functionally, elevated expression of LUCAT1 positively regulated CM cell proliferation, metastasis, and epithelial‐mesenchymal transition process. In addition, we verified the competing endogenous RNA (ceRNA) hypothesis of LUCAT1 and confirmed LUCAT1 modulates CM progression by modulating miR‐514a/b‐3p/RBX1 axis. Meanwhile, miR‐514a/b‐3p was suggested to repress CM progression, whereas RBX1 was unmasked to aggravate CM development. Of note, RBX1 overexpression rescued the inhibitory effect of LUCAT1 silence on the biological processes of CM cells. Altogether, this study unveiled the modulation axis ELF1/LUCAT1/miR‐514a/b‐3p/RBX1 and evidenced LUCAT1 as a promoter in CM for the first time, providing a novel insight into future treatment of CM.
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Affiliation(s)
- Lina Wang
- Tianjin Medical University Eye Hospital, Tianjin, China.,Tianjin First Central Hospital, Tianjin, China
| | - Dongrun Tang
- Tianjin Medical University Eye Hospital, Tianjin, China
| | - Tong Wu
- Tianjin Medical University Eye Hospital, Tianjin, China
| | - Fengyuan Sun
- Tianjin Medical University Eye Hospital, Tianjin, China
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7
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Housman G, Havill LM, Quillen EE, Comuzzie AG, Stone AC. Assessment of DNA Methylation Patterns in the Bone and Cartilage of a Nonhuman Primate Model of Osteoarthritis. Cartilage 2019; 10:335-345. [PMID: 29457464 PMCID: PMC6585300 DOI: 10.1177/1947603518759173] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
OBJECTIVE Osteoarthritis (OA) affects humans and several other animals. Thus, the mechanisms underlying this disorder, such as specific skeletal tissue DNA methylation patterns, may be evolutionary conserved. However, associations between methylation and OA have not been readily studied in nonhuman animals. Baboons serve as important models of disease and develop OA at rates similar to those in humans. Therefore, this study investigated the associations between methylation and OA in baboons to advance the evolutionary understanding of OA. DESIGN Trabecular bone and cartilage was collected from the medial condyles of adult female baboon femora, 5 with and 5 without knee OA. The Infinium HumanMethylation450 BeadChip (450K array) was used to identify DNA methylation patterns in these tissues. RESULTS Approximately 44% of the 450K array probes reliably align to the baboon genome, contain a CpG site of interest, and maintain a wide distribution throughout the genome. Of the 2 filtering methods tested, both identified significantly differentially methylated positions (DMPs) between healthy and OA individuals in cartilage tissues, and some of these patterns overlap with those previously identified in humans. Conversely, no DMPs were found between tissue types or between disease states in bone tissues. CONCLUSIONS Overall, the 450K array can be used to measure genome-wide DNA methylation in baboon tissues and identify significant associations with complex traits. The results of this study indicate that some DNA methylation patterns associated with OA are evolutionarily conserved, while others are not. This warrants further investigation in a larger and more phylogenetically diverse sample set.
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Affiliation(s)
- Genevieve Housman
- School of Human Evolution and Social
Change, Arizona State University, Tempe, AZ, USA,Center for Evolution and Medicine,
Arizona State University, Tempe, AZ, USA,Genevieve Housman, Section of Genetic
Medicine, University of Chicago, 920 East 58th Street, CLSC 317, Chicago, IL
60637, USA.
| | - Lorena M. Havill
- Southwest National Primate Research
Center, Texas Biomedical Research Institute, San Antonio, TX, USA
| | - Ellen E. Quillen
- Department of Genetics, Texas Biomedical
Research Institute, San Antonio, TX, USA
| | - Anthony G. Comuzzie
- Department of Genetics, Texas Biomedical
Research Institute, San Antonio, TX, USA
| | - Anne C. Stone
- School of Human Evolution and Social
Change, Arizona State University, Tempe, AZ, USA,Center for Evolution and Medicine,
Arizona State University, Tempe, AZ, USA
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8
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Chen CH, Su LJ, Tsai HT, Hwang CF. ELF-1 expression in nasopharyngeal carcinoma facilitates proliferation and metastasis of cancer cells via modulation of CCL2/CCR2 signaling. Cancer Manag Res 2019; 11:5243-5254. [PMID: 31289447 PMCID: PMC6560358 DOI: 10.2147/cmar.s196355] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Accepted: 04/16/2019] [Indexed: 01/28/2023] Open
Abstract
Background: Nasopharyngeal carcinoma (NPC) is a prevalent malignant tumor in Southeast Asia. The management of NPC has remained a challenge until now. ELF-1 is a member of the ETS family of transcription factors that regulate genes involved in cellular growth. ELF-1 expression has been reported in various cancers and is required for tumor growth and angiogenesis; however, its function in NPC remains unclear. In the present study, we characterized the role and underlying mechanism of ELF-1 in NPC. Methods: The biological functions of ELF-1 in NPC cells such as proliferation, migration, invasion, and drug resistance were investigated using MTT, BrdU incorporation, and Transwell assays. To gain more insight into the mechanism of ELF-1 in NPC, we analyzed CCL2/CCR2 signaling by Western blotting, ELISA, siRNAs, and CCR2 antagonist. Results: Gain-of-function of ELF-1 in TW01 and TW04 cells promoted NPC cell proliferation, BrdU incorporation, migration, invasion and cisplatin resistance. By contrast, knockdown of ELF-1 produced opposite results. Overexpression of ELF-1 enhanced the expression of CCL2 via binding to its promoter region and increased the level of the extracellular matrix protein CCL2 in cell culture medium. ELF-1 expression also modulated the downstream targets of CCL2/CCR2 signaling. Most importantly, ELF-1-induced NPC malignant phenotypes were abrogated by a CCR2 inhibitor, implying that the CCL2/CCR2 signaling axis was involved in ELF-1-mediated regulation in NPC. Conclusion: Our data suggest that ELF-1 plays an oncogenic role in NPC development associated with the CCL2/CCR2 signaling pathway and may therefore be a potential target for NPC therapy.
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Affiliation(s)
- Chang-Han Chen
- Guangdong Institute of Gastroenterology, Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Disease, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510020, People's Republic of China.,Department of Applied Chemistry, Graduate Institute of Biomedicine and Biomedical Technology, National Chi Nan University, Nantou, 54561, Taiwan
| | - Li-Jen Su
- Department of Biomedical Sciences and Engineering, College of Health Sciences and Technology, National Central University, Taoyuan City, Taiwan.,Education and Research Center for Technology Assisted Substance Abuse Prevention and Management, Taoyuan City, Taiwan.,IHMed Global, Taipei City, Taiwan
| | - Hsin-Ting Tsai
- Guangdong Institute of Gastroenterology, Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Disease, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510020, People's Republic of China
| | - Chung-Feng Hwang
- Department of Otolaryngology, Kaohsiung Chang Gung Memorial Hospital, Chang Gung University College of Medicine, Kaohsiung, 83301, Taiwan.,Kaohsiung Chang Gung Head and Neck Oncology Group, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung 83301, Taiwan
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9
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Lu X, Luan S, Dai P, Luo K, Chen B, Cao B, Sun L, Yan Y, Kong J. Insights into the molecular basis of immunosuppression and increasing pathogen infection severity of ammonia toxicity by transcriptome analysis in pacific white shrimp Litopenaeus vannamei. FISH & SHELLFISH IMMUNOLOGY 2019; 88:528-539. [PMID: 30885745 DOI: 10.1016/j.fsi.2019.03.026] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/01/2019] [Revised: 03/09/2019] [Accepted: 03/12/2019] [Indexed: 06/09/2023]
Abstract
The high concentration of ammonia resulting from intensive culture system and environmental pollution could cause disease occurrence in shrimp, but little information is available on its molecular mechanisms. In this study, we performed comparative transcriptome analysis among WSSV-infected shrimp under ammonia stress (LAV), WSSV-infected shrimp under normal water (LV), and normal shrimp under ammonia stress (LA) groups to identify the key genes and pathways involved in immunosuppression and increasing pathogen infection severity caused by ammonia toxicity in Litopenaeus vannamei. Totally, 526 significantly differential expressed genes (DEGs) were identified in LAV group compared to LV and LA groups, among which 270 genes were lost expressed and 67 genes uniquely expressed in the LAV group. According to the public functional reports for the annotated DEGs, they potentially involved in the following functions: (1) accelerating pathogen adhesion, invasion and multiplication; (2) reducing the ability for pathogen defense and immune response; (3) inhibiting positive regulation of apoptotic and antioxidant defense for host homeostasis; (4) inhibiting transcription and protein transport; (5) and increasing protein methylation and ubiquitination, etc. A total of 13 pathways were obtained mainly involving in this process, which mainly led to the following changes: (1) increasing the immunosuppression, anemia, endocrine dysfunction, neurotoxic effect and neuroinvasion, atherosclerosis and thrombogenesis, blood-brain barrier penetration, thyroid disorder, necrosis, inflammation, and circadian disturbance; (2) reducing the ability of vascular remodeling, angiogenesis, cell survival, migration, apoptosis, and lymph transferred to blood stream; (3) leading to cell hypertrophy, cellular shape changes, and mesangial matrix expansion. The present results firstly supplied molecular mechanisms for the ammonia toxicity inhibiting the immune system and increasing pathogen infection severity in shrimp, which is a prerequisite for better understanding the pathogenesis caused by ammonia toxicity.
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Affiliation(s)
- Xia Lu
- Key Laboratory of Sustainable Utilization of Marine Fisheries Resources, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China
| | - Sheng Luan
- Key Laboratory of Sustainable Utilization of Marine Fisheries Resources, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China
| | - Ping Dai
- Key Laboratory of Sustainable Utilization of Marine Fisheries Resources, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China
| | - Kun Luo
- Key Laboratory of Sustainable Utilization of Marine Fisheries Resources, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China
| | - Baolong Chen
- Key Laboratory of Sustainable Utilization of Marine Fisheries Resources, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China
| | - Baoxiang Cao
- Key Laboratory of Sustainable Utilization of Marine Fisheries Resources, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China
| | - Li Sun
- Key Laboratory of Sustainable Utilization of Marine Fisheries Resources, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, China; College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, 201306, China
| | - Yunjun Yan
- Key Laboratory of Sustainable Utilization of Marine Fisheries Resources, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, China; Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, 214081, China
| | - Jie Kong
- Key Laboratory of Sustainable Utilization of Marine Fisheries Resources, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China.
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10
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Bolouri H, Farrar JE, Triche T, Ries RE, Lim EL, Alonzo TA, Ma Y, Moore R, Mungall AJ, Marra MA, Zhang J, Ma X, Liu Y, Liu Y, Auvil JMG, Davidsen TM, Gesuwan P, Hermida LC, Salhia B, Capone S, Ramsingh G, Zwaan CM, Noort S, Piccolo SR, Kolb EA, Gamis AS, Smith MA, Gerhard DS, Meshinchi S. The molecular landscape of pediatric acute myeloid leukemia reveals recurrent structural alterations and age-specific mutational interactions. Nat Med 2018; 24:103-112. [PMID: 29227476 PMCID: PMC5907936 DOI: 10.1038/nm.4439] [Citation(s) in RCA: 506] [Impact Index Per Article: 84.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Accepted: 10/12/2017] [Indexed: 02/07/2023]
Abstract
We present the molecular landscape of pediatric acute myeloid leukemia (AML) and characterize nearly 1,000 participants in Children's Oncology Group (COG) AML trials. The COG-National Cancer Institute (NCI) TARGET AML initiative assessed cases by whole-genome, targeted DNA, mRNA and microRNA sequencing and CpG methylation profiling. Validated DNA variants corresponded to diverse, infrequent mutations, with fewer than 40 genes mutated in >2% of cases. In contrast, somatic structural variants, including new gene fusions and focal deletions of MBNL1, ZEB2 and ELF1, were disproportionately prevalent in young individuals as compared to adults. Conversely, mutations in DNMT3A and TP53, which were common in adults, were conspicuously absent from virtually all pediatric cases. New mutations in GATA2, FLT3 and CBL and recurrent mutations in MYC-ITD, NRAS, KRAS and WT1 were frequent in pediatric AML. Deletions, mutations and promoter DNA hypermethylation convergently impacted Wnt signaling, Polycomb repression, innate immune cell interactions and a cluster of zinc finger-encoding genes associated with KMT2A rearrangements. These results highlight the need for and facilitate the development of age-tailored targeted therapies for the treatment of pediatric AML.
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Affiliation(s)
- Hamid Bolouri
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Jason E Farrar
- Winthrop P. Rockefeller Cancer Institute, University of Arkansas for Medical Sciences and Arkansas Children's Research Institute, Little Rock, Arkansas, USA
| | - Timothy Triche
- Jane Anne Nohl Division of Hematology, University of Southern California Norris Comprehensive Cancer Center, Los Angeles, California, USA
| | - Rhonda E Ries
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Emilia L Lim
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia, Canada
| | - Todd A Alonzo
- Keck School of Medicine, University of Southern California, Los Angeles, California, USA
- Children's Oncology Group, Monrovia, California, USA
| | - Yussanne Ma
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia, Canada
| | - Richard Moore
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia, Canada
| | - Andrew J Mungall
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia, Canada
| | - Marco A Marra
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia, Canada
| | - Jinghui Zhang
- Division of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Xiaotu Ma
- Division of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Yu Liu
- Division of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Yanling Liu
- Division of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | | | - Tanja M Davidsen
- Office of Cancer Genomics, National Cancer Institute, Bethesda, Maryland, USA
| | - Patee Gesuwan
- Office of Cancer Genomics, National Cancer Institute, Bethesda, Maryland, USA
| | - Leandro C Hermida
- Office of Cancer Genomics, National Cancer Institute, Bethesda, Maryland, USA
| | - Bodour Salhia
- Department of Translational Genomics, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | - Stephen Capone
- Jane Anne Nohl Division of Hematology, University of Southern California Norris Comprehensive Cancer Center, Los Angeles, California, USA
| | - Giridharan Ramsingh
- Jane Anne Nohl Division of Hematology, University of Southern California Norris Comprehensive Cancer Center, Los Angeles, California, USA
| | - Christian Michel Zwaan
- Department of Pediatric Oncology, Erasmus MC-Sophia Children's Hospital, Rotterdam, the Netherlands
| | - Sanne Noort
- Department of Pediatric Oncology, Erasmus MC-Sophia Children's Hospital, Rotterdam, the Netherlands
| | - Stephen R Piccolo
- Department of Biology, Brigham Young University, Provo, Utah, USA
- Department of Biomedical Informatics, University of Utah, Salt Lake City, Utah, USA
| | - E Anders Kolb
- Nemours Center for Cancer and Blood Disorders, Alfred I. DuPont Hospital for Children, Wilmington, Delaware, USA
| | - Alan S Gamis
- Division of Hematology, Oncology and Bone Marrow Transplantation, Children's Mercy Hospitals and Clinics, Kansas City, Missouri, USA
| | - Malcolm A Smith
- Cancer Therapy Evaluation Program, National Cancer Institute, Bethesda, Maryland, USA
| | - Daniela S Gerhard
- Office of Cancer Genomics, National Cancer Institute, Bethesda, Maryland, USA
| | - Soheil Meshinchi
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
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11
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Developmental Control of NRAMP1 (SLC11A1) Expression in Professional Phagocytes. BIOLOGY 2017; 6:biology6020028. [PMID: 28467369 PMCID: PMC5485475 DOI: 10.3390/biology6020028] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Revised: 04/25/2017] [Accepted: 04/25/2017] [Indexed: 12/11/2022]
Abstract
NRAMP1 (SLC11A1) is a professional phagocyte membrane importer of divalent metals that contributes to iron recycling at homeostasis and to nutritional immunity against infection. Analyses of data generated by several consortia and additional studies were integrated to hypothesize mechanisms restricting NRAMP1 expression to mature phagocytes. Results from various epigenetic and transcriptomic approaches were collected for mesodermal and hematopoietic cell types and compiled for combined analysis with results of genetic studies associating single nucleotide polymorphisms (SNPs) with variations in NRAMP1 expression (eQTLs). Analyses establish that NRAMP1 is part of an autonomous topologically associated domain delimited by ubiquitous CCCTC-binding factor (CTCF) sites. NRAMP1 locus contains five regulatory regions: a predicted super-enhancer (S-E) key to phagocyte-specific expression; the proximal promoter; two intronic areas, including 3' inhibitory elements that restrict expression during development; and a block of upstream sites possibly extending the S-E domain. Also the downstream region adjacent to the 3' CTCF locus boundary may regulate expression during hematopoiesis. Mobilization of the locus 14 predicted transcriptional regulatory elements occurs in three steps, beginning with hematopoiesis; at the onset of myelopoiesis and through myelo-monocytic differentiation. Basal expression level in mature phagocytes is further influenced by genetic variation, tissue environment, and in response to infections that induce various epigenetic memories depending on microorganism nature. Constitutively associated transcription factors (TFs) include CCAAT enhancer binding protein beta (C/EBPb), purine rich DNA binding protein (PU.1), early growth response 2 (EGR2) and signal transducer and activator of transcription 1 (STAT1) while hypoxia-inducible factors (HIFs) and interferon regulatory factor 1 (IRF1) may stimulate iron acquisition in pro-inflammatory conditions. Mouse orthologous locus is generally conserved; chromatin patterns typify a de novo myelo-monocytic gene whose expression is tightly controlled by TFs Pu.1, C/ebps and Irf8; Irf3 and nuclear factor NF-kappa-B p 65 subunit (RelA) regulate expression in inflammatory conditions. Functional differences in the determinants identified at these orthologous loci imply that species-specific mechanisms control gene expression.
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12
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Patel AV, Chaney KE, Choi K, Largaespada DA, Kumar AR, Ratner N. An ShRNA Screen Identifies MEIS1 as a Driver of Malignant Peripheral Nerve Sheath Tumors. EBioMedicine 2016; 9:110-119. [PMID: 27333032 PMCID: PMC4972548 DOI: 10.1016/j.ebiom.2016.06.007] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2016] [Revised: 05/27/2016] [Accepted: 06/03/2016] [Indexed: 01/25/2023] Open
Abstract
Malignant peripheral nerve sheath tumors (MPNST) are rare soft tissue sarcomas that are a major source of mortality in neurofibromatosis type 1 (NF1) patients. To identify MPNST driver genes, we performed a lentiviral short hairpin (sh) RNA screen, targeting all 130 genes up-regulated in neurofibroma and MPNSTs versus normal human nerve Schwann cells. NF1 mutant cells show activation of RAS/MAPK signaling, so a counter-screen in RAS mutant carcinoma cells was performed to exclude common RAS-pathway driven genes. We identified 7 genes specific for survival of MPSNT cells, including MEIS1. MEIS1 was frequently amplified or hypomethylated in human MPSNTs, correlating with elevated MEIS1 gene expression. In MPNST cells and in a genetically engineered mouse model, MEIS1 expression in developing nerve glial cells was necessary for MPNST growth. Mechanistically, MEIS1 drives MPNST cell growth via the transcription factor ID1, thereby suppressing expression of the cell cycle inhibitor p27Kip and maintaining cell survival. Targeting over-expressed genes facilitates identification of sarcoma driver genes. We identify MEIS1 as a MPNST oncogene. MEIS1 suppresses p27Kip enabling MPNST survival.
We identify MEIS1 as a sarcoma oncogene, and identify an additional 7 genes specific for survival of malignant peripheral nerve sheath cells. MEIS1 was frequently amplified or hypomethylated in human tumors, correlating with elevated MEIS1 gene and protein expression. MEIS1 enables cell cycle progression in these tumor cells through downregulation of expression of a pro-cell death protein p27Kip. Thus, inhibitors targeting cell cycle checkpoints and/or upregulating p27Kip may have therapeutic value for these patients, and perhaps for other tumor types in which MEIS1 is an oncogene.
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Affiliation(s)
- Ami V Patel
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital, Department of Pediatrics, University of Cincinnati, Cincinnati, OH 45229-0713, United States
| | - Katherine E Chaney
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital, Department of Pediatrics, University of Cincinnati, Cincinnati, OH 45229-0713, United States
| | - Kwangmin Choi
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital, Department of Pediatrics, University of Cincinnati, Cincinnati, OH 45229-0713, United States
| | - David A Largaespada
- Department of Pediatrics, Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, United States
| | - Ashish R Kumar
- Division of Bone Marrow Transplantation & Immune Deficiency, Cincinnati Children's Hospital, Department of Pediatrics, University of Cincinnati, Cincinnati, OH 45229-0713, United States
| | - Nancy Ratner
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital, Department of Pediatrics, University of Cincinnati, Cincinnati, OH 45229-0713, United States.
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13
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Predicting the molecular role of MEIS1 in esophageal squamous cell carcinoma. Tumour Biol 2015; 37:1715-25. [PMID: 26314854 DOI: 10.1007/s13277-015-3780-9] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2015] [Accepted: 07/07/2015] [Indexed: 12/30/2022] Open
Abstract
The three amino acid loop extension (TALE) class myeloid ecotropic viral integration site 1 (MEIS1) homeobox gene is known to play a crucial role in normal and tumor development. In contrast with its well-described cancer stemness properties in hematopoietic cancers, little is known about its role in solid tumors like esophageal squamous cell carcinoma (ESCC). Here, we analyzed MEIS1 expression and its clinical relevance in ESCC patients and also investigated its correlation with the SOX2 self-renewal master transcription factor in the ESCC samples and in the KYSE-30 ESCC cell line. MEIS1 mRNA and protein expression were significantly decreased in ESCC disease (P < 0.05). The inverse correlation between MEIS1 mRNA expression and tumor cell metastasis to the lymph nodes (P = 0.004) was significant. Also, MEIS1 protein levels inversely correlated to lymph node involvement (P = 0.048) and high tumor stage (stages III/IV, P = 0.030). The low levels of DNA methylation in the MEIS1 promoter showed that this suppression does not depend on methylation. We showed that downregulation of EZH2 restored MEIS1 expression significantly. Also, we investigated that MEIS1 downregulation is concomitant with increased SOX2 expression. To the best of our knowledge, this is the first report on the MEIS1 gene in ESCC. The inverse correlation of MEIS1 with metastasis, tumor staging, and the role of EZH2 in methylation, together with its correlation with stemness factor SOX2 expression, led us to predict cancer stemness properties for MEIS1 in ESCC.
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14
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Zhou J, Zhang X, Wang Y, Guan Y. PU.1 affects proliferation of the human acute myeloid leukemia U937 cell line by directly regulating MEIS1. Oncol Lett 2015; 10:1912-1918. [PMID: 26622774 DOI: 10.3892/ol.2015.3404] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2014] [Accepted: 05/29/2015] [Indexed: 02/06/2023] Open
Abstract
The transcription factor PU.1 is a member of the ETS family, which is expressed in a wide variety of hematopoietic lineages. Accumulating evidence has indicated that PU.1 plays a key role in hematopoiesis, and reduced expression of PU.1 leads to the pathogenesis of human myeloid leukemia. As a multi-functional factor, PU.1 is also required for mixed lineage leukemia (MLL) stem cell potential and the development of MLL. However, the function of PU.1 in human non-MLL leukemia and its molecular mechanism remains poorly understood. In the present study, PU.1 siRNA was demonstrated to efficiently inhibit the transcription level of oncogene MEIS1 in the human acute myeloid non-MLL leukemia U937 cell line. In addition, PU.1, as a positive regulator of MEIS1, performed a crucial role in maintaining cell proliferation. Using electrophoretic mobility shift assay, chromatin immunoprecipitation analysis and luciferase reporter assay, previously unexplored evidence that PU.1 activated the MEIS1 promoter through a conserved binding motif in vitro and in vivo was further defined. Overall, the present study provides insight into the molecular mechanism of the contribution of PU.1 to the pathogenesis of non-MLL U937 cells, which is mediated by direct regulation of MEIS1 transcription. The present data reveal the possibility of developing an alternative therapy for non-MLL leukemia by targeting PU.1-mediated MEIS1 gene activation.
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Affiliation(s)
- Jing Zhou
- Laboratory of Genome Variations and Precision Bio-Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, P.R. China ; Department of Immunology and Infectious Diseases, The Forsyth Institute, Cambridge, MA 02142, USA
| | - Xiaofeng Zhang
- Department of Chemistry, University of Massachusetts Boston, Boston, MA 02125, USA
| | - Yuhua Wang
- Department of Immunology and Infectious Diseases, The Forsyth Institute, Cambridge, MA 02142, USA ; Department of Prosthodontics, Ninth People's Hospital, College of Stomatology, School of Medicine, Shanghai Jiao Tong University, Shanghai Key Laboratory of Stomatology, Shanghai 200011, P.R. China
| | - Yinghui Guan
- Respiratory Department, 2nd Branch of First Hospital of Jilin University, Changchun, Jilin 130021, P.R. China
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15
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Puig-Oliveras A, Ballester M, Corominas J, Revilla M, Estellé J, Fernández AI, Ramayo-Caldas Y, Folch JM. A co-association network analysis of the genetic determination of pig conformation, growth and fatness. PLoS One 2014; 9:e114862. [PMID: 25503799 PMCID: PMC4263716 DOI: 10.1371/journal.pone.0114862] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2014] [Accepted: 11/14/2014] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Several QTLs have been identified for major economically relevant traits in livestock, such as growth and meat quality, revealing the complex genetic architecture of these traits. The use of network approaches considering the interactions of multiple molecules and traits provides useful insights into the molecular underpinnings of complex traits. Here, a network based methodology, named Association Weight Matrix, was applied to study gene interactions and pathways affecting pig conformation, growth and fatness traits. RESULTS The co-association network analysis underpinned three transcription factors, PPARγ, ELF1, and PRDM16 involved in mesoderm tissue differentiation. Fifty-four genes in the network belonged to growth-related ontologies and 46 of them were common with a similar study for growth in cattle supporting our results. The functional analysis uncovered the lipid metabolism and the corticotrophin and gonadotrophin release hormone pathways among the most important pathways influencing these traits. Our results suggest that the genes and pathways here identified are important determining either the total body weight of the animal and the fat content. For instance, a switch in the mesoderm tissue differentiation may determinate the age-related preferred pathways being in the puberty stage those related with the miogenic and osteogenic lineages; on the contrary, in the maturity stage cells may be more prone to the adipocyte fate. Hence, our results demonstrate that an integrative genomic co-association analysis is a powerful approach for identifying new connections and interactions among genes. CONCLUSIONS This work provides insights about pathways and key regulators which may be important determining the animal growth, conformation and body proportions and fatness traits. Molecular information concerning genes and pathways here described may be crucial for the improvement of genetic breeding programs applied to pork meat production.
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Affiliation(s)
- Anna Puig-Oliveras
- Departament de Ciència Animal i dels Aliments, Universitat Autònoma de Barcelona (UAB), 08193, Bellaterra, Spain
- Plant and Animal Genomics, Centre de Recerca en Agrigenòmica (CRAG), 08193, Bellaterra, Spain
| | - Maria Ballester
- Departament de Ciència Animal i dels Aliments, Universitat Autònoma de Barcelona (UAB), 08193, Bellaterra, Spain
- Plant and Animal Genomics, Centre de Recerca en Agrigenòmica (CRAG), 08193, Bellaterra, Spain
| | - Jordi Corominas
- Departament de Ciència Animal i dels Aliments, Universitat Autònoma de Barcelona (UAB), 08193, Bellaterra, Spain
- Plant and Animal Genomics, Centre de Recerca en Agrigenòmica (CRAG), 08193, Bellaterra, Spain
| | - Manuel Revilla
- Departament de Ciència Animal i dels Aliments, Universitat Autònoma de Barcelona (UAB), 08193, Bellaterra, Spain
- Plant and Animal Genomics, Centre de Recerca en Agrigenòmica (CRAG), 08193, Bellaterra, Spain
| | - Jordi Estellé
- Génétique Animale et Biologie Intégrative UMR1313 (GABI), Institut National de la Recherche Agronomique (INRA), 78350, Jouy-en-Josas, France
- Génétique Animale et Biologie Intégrative UMR1313 (GABI), AgroParisTech, 78350, Jouy-en-Josas, France
- Laboratoire de Radiobiologie et Etude du Génome (LREG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA), 78350, Jouy-en-Josas, France
| | - Ana I. Fernández
- Departamento de Genética Animal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), 28040, Madrid, Spain
| | - Yuliaxis Ramayo-Caldas
- Departament de Ciència Animal i dels Aliments, Universitat Autònoma de Barcelona (UAB), 08193, Bellaterra, Spain
- Plant and Animal Genomics, Centre de Recerca en Agrigenòmica (CRAG), 08193, Bellaterra, Spain
- Génétique Animale et Biologie Intégrative UMR1313 (GABI), Institut National de la Recherche Agronomique (INRA), 78350, Jouy-en-Josas, France
- Génétique Animale et Biologie Intégrative UMR1313 (GABI), AgroParisTech, 78350, Jouy-en-Josas, France
- Laboratoire de Radiobiologie et Etude du Génome (LREG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA), 78350, Jouy-en-Josas, France
| | - Josep M. Folch
- Departament de Ciència Animal i dels Aliments, Universitat Autònoma de Barcelona (UAB), 08193, Bellaterra, Spain
- Plant and Animal Genomics, Centre de Recerca en Agrigenòmica (CRAG), 08193, Bellaterra, Spain
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16
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Hou J, Wei W, Saund RS, Xiang P, Cunningham TJ, Yi Y, Alder O, Lu DYD, Savory JGA, Krentz NAJ, Montpetit R, Cullum R, Hofs N, Lohnes D, Humphries RK, Yamanaka Y, Duester G, Saijoh Y, Hoodless PA. A regulatory network controls nephrocan expression and midgut patterning. Development 2014; 141:3772-81. [PMID: 25209250 DOI: 10.1242/dev.108274] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Although many regulatory networks involved in defining definitive endoderm have been identified, the mechanisms through which these networks interact to pattern the endoderm are less well understood. To explore the mechanisms involved in midgut patterning, we dissected the transcriptional regulatory elements of nephrocan (Nepn), the earliest known midgut specific gene in mice. We observed that Nepn expression is dramatically reduced in Sox17(-/-) and Raldh2(-/-) embryos compared with wild-type embryos. We further show that Nepn is directly regulated by Sox17 and the retinoic acid (RA) receptor via two enhancer elements located upstream of the gene. Moreover, Nepn expression is modulated by Activin signaling, with high levels inhibiting and low levels enhancing RA-dependent expression. In Foxh1(-/-) embryos in which Nodal signaling is reduced, the Nepn expression domain is expanded into the anterior gut region, confirming that Nodal signaling can modulate its expression in vivo. Together, Sox17 is required for Nepn expression in the definitive endoderm, while RA signaling restricts expression to the midgut region. A balance of Nodal/Activin signaling regulates the anterior boundary of the midgut expression domain.
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Affiliation(s)
- Juan Hou
- Terry Fox Laboratory, BC Cancer Agency, Vancouver, British Columbia, V5Z 1L3, Canada
| | - Wei Wei
- Terry Fox Laboratory, BC Cancer Agency, Vancouver, British Columbia, V5Z 1L3, Canada
| | - Ranajeet S Saund
- Department of Neurobiology and Anatomy, University of Utah, Salt Lake City, UT 84132-3401, USA
| | - Ping Xiang
- Terry Fox Laboratory, BC Cancer Agency, Vancouver, British Columbia, V5Z 1L3, Canada
| | - Thomas J Cunningham
- Development, Aging and Regeneration Program, Sanford-Burnham Medical Research Institute, La Jolla, CA 92037, USA
| | - Yuyin Yi
- Terry Fox Laboratory, BC Cancer Agency, Vancouver, British Columbia, V5Z 1L3, Canada Cell and Developmental Biology Program, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
| | - Olivia Alder
- Terry Fox Laboratory, BC Cancer Agency, Vancouver, British Columbia, V5Z 1L3, Canada
| | - Daphne Y D Lu
- Terry Fox Laboratory, BC Cancer Agency, Vancouver, British Columbia, V5Z 1L3, Canada
| | - Joanne G A Savory
- Cellular and Molecular Medicine, University of Ottawa, Ottawa K1H 8M5, Canada
| | - Nicole A J Krentz
- Terry Fox Laboratory, BC Cancer Agency, Vancouver, British Columbia, V5Z 1L3, Canada
| | - Rachel Montpetit
- Terry Fox Laboratory, BC Cancer Agency, Vancouver, British Columbia, V5Z 1L3, Canada
| | - Rebecca Cullum
- Terry Fox Laboratory, BC Cancer Agency, Vancouver, British Columbia, V5Z 1L3, Canada
| | - Nicole Hofs
- Terry Fox Laboratory, BC Cancer Agency, Vancouver, British Columbia, V5Z 1L3, Canada
| | - David Lohnes
- Cellular and Molecular Medicine, University of Ottawa, Ottawa K1H 8M5, Canada
| | - R Keith Humphries
- Terry Fox Laboratory, BC Cancer Agency, Vancouver, British Columbia, V5Z 1L3, Canada Experimental Medicine, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
| | - Yojiro Yamanaka
- Goodman Cancer Research Centre, Department of Human Genetics, McGill University, Montreal, Quebec H2W 1S6, Canada
| | - Gregg Duester
- Development, Aging and Regeneration Program, Sanford-Burnham Medical Research Institute, La Jolla, CA 92037, USA
| | - Yukio Saijoh
- Department of Neurobiology and Anatomy, University of Utah, Salt Lake City, UT 84132-3401, USA
| | - Pamela A Hoodless
- Terry Fox Laboratory, BC Cancer Agency, Vancouver, British Columbia, V5Z 1L3, Canada Cell and Developmental Biology Program, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
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17
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Xiang P, Wei W, Lo C, Rosten P, Hou J, Hoodless PA, Bilenky M, Bonifer C, Cockerill PN, Kirkpatrick A, Gottgens B, Hirst M, Humphries KR. Delineating MEIS1 cis-regulatory elements active in hematopoietic cells. Leukemia 2013; 28:433-6. [PMID: 24097337 DOI: 10.1038/leu.2013.287] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- P Xiang
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, British Columbia, Canada
| | - W Wei
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, British Columbia, Canada
| | - C Lo
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, British Columbia, Canada
| | - P Rosten
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, British Columbia, Canada
| | - J Hou
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, British Columbia, Canada
| | - P A Hoodless
- 1] Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, British Columbia, Canada [2] University of British Columbia, Medical Genetics, Vancouver, British Columbia, Canada
| | - M Bilenky
- BC Cancer Agency, Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia, Canada
| | - C Bonifer
- School of Cancer Sciences, College of Medical and Dental Sciences, Institute of Biomedical Research, University of Birmingham, Birmingham, UK
| | - P N Cockerill
- School of Immunity and Infection, College of Medical and Dental Sciences, Institute of Biomedical Research, University of Birmingham, Birmingham, UK
| | - A Kirkpatrick
- Department of Haematology, Cambridge Institute for Medical Research and Wellcome Trust and MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - B Gottgens
- Department of Haematology, Cambridge Institute for Medical Research and Wellcome Trust and MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - M Hirst
- BC Cancer Agency, Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia, Canada
| | - K R Humphries
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, British Columbia, Canada
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18
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Regulation of MEIS1 by distal enhancer elements in acute leukemia. Leukemia 2013; 28:138-46. [PMID: 24022755 PMCID: PMC5774621 DOI: 10.1038/leu.2013.260] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2013] [Revised: 08/22/2013] [Accepted: 08/29/2013] [Indexed: 11/15/2022]
Abstract
Aberrant activation of the three-amino-acid-loop extension (TALE) homeobox gene MEIS1 shortens the latency and accelerates the onset and progression of acute leukemia, yet the molecular mechanism underlying persistent activation of the MEIS1 gene in leukemia remains poorly understood. Here we used a combined comparative genomics analysis and an in vivo transgenic zebrafish assay to identify 6 regulatory DNA elements that are able to direct GFP expression in a spatiotemporal manner during zebrafish embryonic hematopoiesis. Analysis of chromatin characteristics and regulatory signatures suggest that many of these predicted elements are potential enhancers in mammalian hematopoiesis. Strikingly, one of the enhancer elements (E9) is a frequent integration site in retroviral induced mouse acute leukemia. The genomic region corresponding to enhancer E9 is differentially marked by H3K4 mono-methylation and H3K27 acetylation, hallmarks of active enhancers, in multiple leukemia cell lines. Decreased enrichment of these histone marks is associated with downregulation of MEIS1 expression during hematopoietic differentiation. Furthermore, MEIS1/HOXA9 transactivate this enhancer via a conserved binding motif in vitro, and participate in an autoregulatory loop that modulates MEIS1 expression in vivo. Our results suggest that an intronic enhancer regulates the expression of MEIS1 in hematopoiesis and contributes to its aberrant expression in acute leukemia.
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19
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Royo JL, Bessa J, Hidalgo C, Fernández-Miñán A, Tena JJ, Roncero Y, Gómez-Skarmeta JL, Casares F. Identification and analysis of conserved cis-regulatory regions of the MEIS1 gene. PLoS One 2012; 7:e33617. [PMID: 22448256 PMCID: PMC3308983 DOI: 10.1371/journal.pone.0033617] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2011] [Accepted: 02/13/2012] [Indexed: 11/22/2022] Open
Abstract
Meis1, a conserved transcription factor of the TALE-homeodomain class, is expressed in a wide variety of tissues during development. Its complex expression pattern is likely to be controlled by an equally complex regulatory landscape. Here we have scanned the Meis1 locus for regulatory elements and found 13 non-coding regions, highly conserved between humans and teleost fishes, that have enhancer activity in stable transgenic zebrafish lines. All these regions are syntenic in most vertebrates. The composite expression of all these enhancer elements recapitulate most of Meis1 expression during early embryogenesis, indicating they comprise a basic set of regulatory elements of the Meis1 gene. Using bioinformatic tools, we identify a number of potential binding sites for transcription factors that are compatible with the regulation of these enhancers. Specifically, HHc2:066650, which is expressed in the developing retina and optic tectum, harbors several predicted Pax6 sites. Biochemical, functional and transgenic assays indicate that pax6 genes directly regulate HHc2:066650 activity.
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Affiliation(s)
| | | | | | | | | | | | - José Luis Gómez-Skarmeta
- Centro Andaluz de Biología del Desarrollo (CABD) CSIC-UPO-Junta de Anadalucía, Sevilla, Spain
- * E-mail: (JLGS); (FC)
| | - Fernando Casares
- Centro Andaluz de Biología del Desarrollo (CABD) CSIC-UPO-Junta de Anadalucía, Sevilla, Spain
- * E-mail: (JLGS); (FC)
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