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Yu M, Tang X, Li Z, Wang W, Wang S, Li M, Yu Q, Xie S, Zuo X, Chen C. High-throughput DNA synthesis for data storage. Chem Soc Rev 2024; 53:4463-4489. [PMID: 38498347 DOI: 10.1039/d3cs00469d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/20/2024]
Abstract
With the explosion of digital world, the dramatically increasing data volume is expected to reach 175 ZB (1 ZB = 1012 GB) in 2025. Storing such huge global data would consume tons of resources. Fortunately, it has been found that the deoxyribonucleic acid (DNA) molecule is the most compact and durable information storage medium in the world so far. Its high coding density and long-term preservation properties make itself one of the best data storage carriers for the future. High-throughput DNA synthesis is a key technology for "DNA data storage", which encodes binary data stream (0/1) into quaternary long DNA sequences consisting of four bases (A/G/C/T). In this review, the workflow of DNA data storage and the basic methods of artificial DNA synthesis technology are outlined first. Then, the technical characteristics of different synthesis methods and the state-of-the-art of representative commercial companies, with a primary focus on silicon chip microarray-based synthesis and novel enzymatic DNA synthesis are presented. Finally, the recent status of DNA storage and new opportunities for future development in the field of high-throughput, large-scale DNA synthesis technology are summarized.
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Affiliation(s)
- Meng Yu
- Institute of Medical Chips, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, 200025, Shanghai, China.
- School of Microelectronics, Shanghai University, 201800, Shanghai, China
- Shanghai Industrial μTechnology Research Institute, 201800, Shanghai, China
| | - Xiaohui Tang
- Institute of Medical Chips, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, 200025, Shanghai, China.
- Shanghai Industrial μTechnology Research Institute, 201800, Shanghai, China
| | - Zhenhua Li
- Institute of Medical Chips, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, 200025, Shanghai, China.
- Shanghai Industrial μTechnology Research Institute, 201800, Shanghai, China
| | - Weidong Wang
- Shanghai Industrial μTechnology Research Institute, 201800, Shanghai, China
| | - Shaopeng Wang
- Institute of Molecular Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, 200127, Shanghai, China.
| | - Min Li
- Institute of Molecular Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, 200127, Shanghai, China.
| | - Qiuliyang Yu
- Shenzhen Key Laboratory for the Intelligent Microbial Manufacturing of Medicines, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, 518055, Shenzhen, China
| | - Sijia Xie
- Institute of Medical Chips, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, 200025, Shanghai, China.
- School of Microelectronics, Shanghai University, 201800, Shanghai, China
- Shanghai Industrial μTechnology Research Institute, 201800, Shanghai, China
| | - Xiaolei Zuo
- Institute of Molecular Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, 200127, Shanghai, China.
| | - Chang Chen
- Institute of Medical Chips, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, 200025, Shanghai, China.
- School of Microelectronics, Shanghai University, 201800, Shanghai, China
- Shanghai Industrial μTechnology Research Institute, 201800, Shanghai, China
- State Key Laboratory of Transducer Technology, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, 200050, Shanghai, China
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2
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Yang R, Wang QQ, Feng Y, Li XH, Li GX, She FL, Zhu XJ, Li CL. Over-expression of miR-3584-5p Represses Nav1.8 Channel Aggravating Neuropathic Pain caused by Chronic Constriction Injury. Mol Neurobiol 2023; 60:5237-5255. [PMID: 37280408 DOI: 10.1007/s12035-023-03394-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Accepted: 05/18/2023] [Indexed: 06/08/2023]
Abstract
Nav1.8, a tetrodotoxin-resistant voltage-gated sodium channels (VGSCs) subtype encoded by SCN10A, which plays an important role in the production and transmission of peripheral neuropathic pain signals. Studies have shown that VGSCs may be key targets of MicroRNAs (miRNAs) in the regulation of neuropathic pain. In our study, bioinformatics analysis showed that the targeting relationship between miR-3584-5p and Nav1.8 was the most closely. The purpose of this study was to investigate the roles of miR-3584-5p and Nav1.8 in neuropathic pain. The effects of miR-3584-5p on chronic constriction injury (CCI)-induced neuropathic pain in rats was investigated by intrathecal injection of miR-3584-5p agomir (an agonist, 20 μM, 15 μL) or antagomir (an antagonist, 20 μM, 15 μL). The results showed that over-expression of miR-3584-5p aggravated neuronal injury by hematoxylin-eosin (H&E) staining and mechanical/thermal hypersensitivity in CCI rats. MiR-3584-5p indirectly inhibited the expression of Nav1.8 by up-regulating the expression of key proteins in the ERK5/CREB signaling pathway, and also inhibited the current density of the Nav1.8 channel, changed its channel dynamics characteristic, thereby accelerating the transmission of pain signals, and further aggravating pain. Similarly, in PC12 and SH-SY5Y cell cultures, miR-3584-5p increased the level of reactive oxygen species (ROS) and inhibited mitochondrial membrane potential (Δψm) in the mitochondrial pathway, decreased the ratio of apoptosis-related factor Bcl-2/Bax, and thus promoted neuronal apoptosis. In brief, over-expression of miR-3584-5p aggravates neuropathic pain by directly inhibiting the current density of Nav1.8 channel and altering its channel dynamics, or indirectly inhibiting Nav1.8 expression through ERK5/CREB pathway, and promoting apoptosis through mitochondrial pathway.
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Affiliation(s)
- Ran Yang
- Department of Pharmacology, Shenyang Pharmaceutical University, Shenyang, 110016, Liaoning, People's Republic of China
| | - Qian-Qian Wang
- Department of Pharmacology, Shenyang Pharmaceutical University, Shenyang, 110016, Liaoning, People's Republic of China
| | - Yuan Feng
- Department of Pharmacology, Shenyang Pharmaceutical University, Shenyang, 110016, Liaoning, People's Republic of China
| | - Xue-Hao Li
- Department of Pharmacology, Shenyang Pharmaceutical University, Shenyang, 110016, Liaoning, People's Republic of China
| | - Gui-Xia Li
- Department of Pharmacology, Shenyang Pharmaceutical University, Shenyang, 110016, Liaoning, People's Republic of China
| | - Feng-Lin She
- Department of Pharmacology, Shenyang Pharmaceutical University, Shenyang, 110016, Liaoning, People's Republic of China
| | - Xi-Jin Zhu
- Department of Pharmacology, Shenyang Pharmaceutical University, Shenyang, 110016, Liaoning, People's Republic of China
| | - Chun-Li Li
- Department of Pharmacology, Shenyang Pharmaceutical University, Shenyang, 110016, Liaoning, People's Republic of China.
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3
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Gunasekaran M, Mishra R, Saha P, Morales D, Cheng WC, Jayaraman AR, Hoffman JR, Davidson L, Chen L, Shah AM, Bittle G, Fu X, Tulshyan A, Abdullah M, Kingsbury T, Civin C, Yang P, Davis ME, Bolli R, Hare JM, Sharma S, Kaushal S. Comparative efficacy and mechanism of action of cardiac progenitor cells after cardiac injury. iScience 2022; 25:104656. [PMID: 35847554 PMCID: PMC9283895 DOI: 10.1016/j.isci.2022.104656] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 04/08/2022] [Accepted: 06/17/2022] [Indexed: 11/17/2022] Open
Affiliation(s)
- Muthukumar Gunasekaran
- Departments of Surgery and Pediatrics, Ann and Robert H. Lurie Children’s Hospital of Chicago, Feinberg School of Medicine, Northwestern University, 225 E. Chicago Avenue, Chicago, IL 60611, USA
| | - Rachana Mishra
- Departments of Surgery and Pediatrics, Ann and Robert H. Lurie Children’s Hospital of Chicago, Feinberg School of Medicine, Northwestern University, 225 E. Chicago Avenue, Chicago, IL 60611, USA
| | - Progyaparamita Saha
- Departments of Surgery and Pediatrics, Ann and Robert H. Lurie Children’s Hospital of Chicago, Feinberg School of Medicine, Northwestern University, 225 E. Chicago Avenue, Chicago, IL 60611, USA
| | - David Morales
- Departments of Surgery and Pediatrics, Ann and Robert H. Lurie Children’s Hospital of Chicago, Feinberg School of Medicine, Northwestern University, 225 E. Chicago Avenue, Chicago, IL 60611, USA
| | - Wen-Chih Cheng
- Center for Stem Cell Biology and Regenerative Medicine, Department of Pediatrics, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Arun R. Jayaraman
- Wallace H. Coulter Department of Biomedical Engineering, Emory University and Georgia Institute of Technology, 1760 Haygood Drive, W200, Atlanta, GA 30322, USA
| | - Jessica R. Hoffman
- Wallace H. Coulter Department of Biomedical Engineering, Emory University and Georgia Institute of Technology, 1760 Haygood Drive, W200, Atlanta, GA 30322, USA
| | - Lauran Davidson
- Departments of Surgery and Pediatrics, Ann and Robert H. Lurie Children’s Hospital of Chicago, Feinberg School of Medicine, Northwestern University, 225 E. Chicago Avenue, Chicago, IL 60611, USA
| | - Ling Chen
- Departments of Surgery and Pediatrics, Ann and Robert H. Lurie Children’s Hospital of Chicago, Feinberg School of Medicine, Northwestern University, 225 E. Chicago Avenue, Chicago, IL 60611, USA
| | - Aakash M. Shah
- Departments of Surgery and Pediatrics, Ann and Robert H. Lurie Children’s Hospital of Chicago, Feinberg School of Medicine, Northwestern University, 225 E. Chicago Avenue, Chicago, IL 60611, USA
| | - Gregory Bittle
- Departments of Surgery and Pediatrics, Ann and Robert H. Lurie Children’s Hospital of Chicago, Feinberg School of Medicine, Northwestern University, 225 E. Chicago Avenue, Chicago, IL 60611, USA
| | - Xuebin Fu
- Departments of Surgery and Pediatrics, Ann and Robert H. Lurie Children’s Hospital of Chicago, Feinberg School of Medicine, Northwestern University, 225 E. Chicago Avenue, Chicago, IL 60611, USA
| | - Antariksh Tulshyan
- Departments of Surgery and Pediatrics, Ann and Robert H. Lurie Children’s Hospital of Chicago, Feinberg School of Medicine, Northwestern University, 225 E. Chicago Avenue, Chicago, IL 60611, USA
| | - Mohamed Abdullah
- Departments of Surgery and Pediatrics, Ann and Robert H. Lurie Children’s Hospital of Chicago, Feinberg School of Medicine, Northwestern University, 225 E. Chicago Avenue, Chicago, IL 60611, USA
- Department of Cardiothoracic Surgery, Cairo University, Cairo 11553, Egypt
| | - Tami Kingsbury
- Center for Stem Cell Biology and Regenerative Medicine, Department of Physiology, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Curt Civin
- Center for Stem Cell Biology and Regenerative Medicine, Department of Pediatrics, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Peixin Yang
- Departments of Surgery and Pediatrics, Ann and Robert H. Lurie Children’s Hospital of Chicago, Feinberg School of Medicine, Northwestern University, 225 E. Chicago Avenue, Chicago, IL 60611, USA
| | - Michael E. Davis
- Wallace H. Coulter Department of Biomedical Engineering, Emory University and Georgia Institute of Technology, 1760 Haygood Drive, W200, Atlanta, GA 30322, USA
| | - Roberto Bolli
- Institute of Molecular Cardiology, University of Louisville, Louisville, KY 40202, USA
| | - Joshua M. Hare
- University of Miami, Miller School of Medicine, Miami, FL, USA
| | - Sudhish Sharma
- Departments of Surgery and Pediatrics, Ann and Robert H. Lurie Children’s Hospital of Chicago, Feinberg School of Medicine, Northwestern University, 225 E. Chicago Avenue, Chicago, IL 60611, USA
- Corresponding author
| | - Sunjay Kaushal
- Departments of Surgery and Pediatrics, Ann and Robert H. Lurie Children’s Hospital of Chicago, Feinberg School of Medicine, Northwestern University, 225 E. Chicago Avenue, Chicago, IL 60611, USA
- Corresponding author
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4
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Banerjee N, Wang H, Wang G, Boor PJ, Khan MF. Differential Expression of miRNAs in Trichloroethene-Mediated Inflammatory/Autoimmune Response and Its Modulation by Sulforaphane: Delineating the Role of miRNA-21 and miRNA-690. Front Immunol 2022; 13:868539. [PMID: 35422807 PMCID: PMC9001960 DOI: 10.3389/fimmu.2022.868539] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Accepted: 02/28/2022] [Indexed: 11/13/2022] Open
Abstract
Trichloroethene (TCE), an occupational and ubiquitous environmental contaminant, is associated with the induction of autoimmune diseases (ADs). Although oxidative stress plays a major role in TCE-mediated autoimmunity, the underlying molecular mechanisms still need to be delineated. Altered non-coding RNAs, including the expression of microRNAs (miRNAs), can influence target genes, especially related to apoptosis and inflammation, and contribute to ADs. Therefore, the objective of this study was to delineate the contribution of miRNAs in TCE-mediated inflammatory and autoimmune response. To achieve this, we treated female MRL+/+ mice with TCE (10 mmol/kg in corn oil, i.p., every fourth day) with/without antioxidant sulforaphane (SFN; 8 mg/kg in corn oil, i.p., every other day) for 6 weeks. With the use of miRNA microarray, 293 miRNAs were analyzed, which included 35 miRNAs that were relevant to inflammation and ADs. Among those 35 miRNAs, 8 were modulated by TCE and/or TCE+SFN exposure. TCE treatment led to increased expression of 3 miRNAs and also decreased expression of 3 miRNAs. Interestingly, among the 35 differentially expressed miRNAs, antioxidant SFN modulated the expression of 6 miRNAs. Based on the microarray findings, we subsequently focused on two miRNAs (miRNA-21 and miRNA-690), which are known to be involved in inflammation and autoimmune response. The increases in miRNA-21 and miR-690 (observed using miRNA microarray) were further validated by RT-PCR, and the TCE-mediated increases in miR-21 and miR-690 were ameliorated by SFN treatment. Modulating miR-21 and miR-690 by respective inhibitors or mimics suppressed the expression of NF-κB (p65) and IL-12 in RAW 264.7 cells. Our findings suggest a contributory role of miR-21 and miR-690 in TCE-mediated and its metabolite dichloroacetyl chloride (DCAC)-mediated inflammation and autoimmune response and support that antioxidant SFN could be a potential therapeutic candidate for inflammatory responses and ADs.
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Affiliation(s)
- Nivedita Banerjee
- Department of Pathology, University of Texas Medical Branch, Galveston, TX, United States
| | - Hui Wang
- Department of Pathology, University of Texas Medical Branch, Galveston, TX, United States
| | - Gangduo Wang
- Department of Pathology, University of Texas Medical Branch, Galveston, TX, United States
| | - Paul J Boor
- Department of Pathology, University of Texas Medical Branch, Galveston, TX, United States
| | - M Firoze Khan
- Department of Pathology, University of Texas Medical Branch, Galveston, TX, United States
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5
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Bao J, Chen J, Zhang X, Xu L, Fan Y, Dou X. Combined signatures of serum proteome and transcriptome in patients with recurrent aphthous ulcer. Oral Dis 2021; 28:691-702. [PMID: 33576097 DOI: 10.1111/odi.13800] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 02/02/2021] [Accepted: 02/05/2021] [Indexed: 12/11/2022]
Abstract
OBJECTIVES Recurrent aphthous ulcer (RAU) is a common oral disease with unclear mechanism. This study aimed to explore the serum signatures of RAU patients via proteomic and transcriptomic analysis. METHODS This study was based on clinical observation. Part of serum was used for clinical tests, while the rest was processed for isobaric tags for relative and absolute quantitation (ITRAQ) labeling coupled with two-dimensional liquid chromatography-tandem mass spectrometry (2D LC-MS/MS) combined with microRNA (miRNA) microarrays. Bioinformatic analysis was then used to obtain significant signatures, which was verified by ELISA, qRT-PCR, and dual-luciferase reporter gene assays. RESULTS Clinical data showed that triglyceride level, white blood cell count, and neutrophils percentage were increased in RAU group, while lymphocytes percentage was decreased. ITRAQ-2D LC-MS/MS identified 22 upregulated and 33 downregulated proteins in RAU group. Simultaneously, miRNA microarrays identified 64 upregulated and 31 downregulated miRNAs. After integrative bioinformatic analysis and verification, three miRNA-protein pairs, mainly involved in oxidative stress and inflammation responses, were obtained. Additionally, the interaction network indicated the crucial role of complement and coagulation cascade pathway in RAU. CONCLUSIONS Our study revealed that complement and coagulation cascade pathway, oxidative stress, and inflammation responses may act as vital factors in pathogenesis of RAU.
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Affiliation(s)
- Jie Bao
- School of Basic Medical Sciences, Zhejiang Chinese Medical University, Hangzhou, China
| | - Juan Chen
- School of Basic Medical Sciences, Zhejiang Chinese Medical University, Hangzhou, China
| | - XiZhao Zhang
- School of 1st Clinical Medical Sciences, Zhejiang Chinese Medical University, Hangzhou, China
| | - Li Xu
- School of Basic Medical Sciences, Zhejiang Chinese Medical University, Hangzhou, China
| | - YongSheng Fan
- School of Basic Medical Sciences, Zhejiang Chinese Medical University, Hangzhou, China
| | - XiaoBing Dou
- School of Life Sciences, Zhejiang Chinese Medical University, Hangzhou, China
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6
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Sun T, Li T, Yi K, Yan G, Gao X. Fluorescent Protein Variants Generated by Reassembly between Skeleton and Chromophore. ACS OMEGA 2021; 6:2925-2933. [PMID: 33553911 PMCID: PMC7860096 DOI: 10.1021/acsomega.0c05299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 01/06/2021] [Indexed: 06/12/2023]
Abstract
Fluorescent proteins (FPs) can be used as intrinsic molecular tags to track the dynamic activity in live cells. To obtain variants in an available and massive manner is always a challenge. Here, we adopted a computer-based microarray synthesis method to realize the reassembly between the chromophore and the skeleton. DNAWorks was used to segment the input FP templates into a set of overlapping oligonucleotides (20-43 mer) with a balanced annealing temperature, G + C content, and codon frequency. The constitution of the chromophore was kept in the same section by switching the divided sites during segmentation and the codon was optimized to further keep the balanced parameters. The designed oligonucleotides were synthesized on photo-programmable microfluidic arrays. Sequence analysis and the subsequent conditional induced expression of FPs revealed that oligonucleotides were highly reassembled. Spectra, photostability, and molecular size detection of randomly selected variants showed that they were distinct monomeric proteins that preserved photoactivity. Our study provides an effective means of obtaining FP variants based on a computer-designed parallel synthesis.
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Affiliation(s)
- Tingting Sun
- College
of Food Science and Pharmaceutical Engineering, Zaozhuang University, Zaozhuang, Shandong 277160, China
| | - Tianpeng Li
- College
of Civil and Architecture Engineering, Zaozhuang
University, Zaozhuang, Shandong 277160, China
- School
of the Environment, Henan Normal University, Xinxiang, Henan 453007, China
- Shandong
Key Laboratory of Water Pollution Control and Resource Reuse, Shandong University, Qingdao, Shandong 266237, China
| | - Ke Yi
- Laboratory
of Medical Genetics, Central South University, Changsha 410008, Hunan, China
| | - Guoquan Yan
- Bioengineering
Institute, Zhejiang University of Science
and Technology, Hangzhou, Zhejiang 310018, China
| | - Xiaolian Gao
- Department
of Biology and Biochemistry, University
of Houston, Houston, Texas 77004-5001, United States
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Huang W, Yang Y, Wu J, Niu Y, Yao Y, Zhang J, Huang X, Liang S, Chen R, Chen S, Guo L. Circular RNA cESRP1 sensitises small cell lung cancer cells to chemotherapy by sponging miR-93-5p to inhibit TGF-β signalling. Cell Death Differ 2020; 27:1709-1727. [PMID: 31728016 PMCID: PMC7206039 DOI: 10.1038/s41418-019-0455-x] [Citation(s) in RCA: 105] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Revised: 10/30/2019] [Accepted: 10/31/2019] [Indexed: 12/24/2022] Open
Abstract
Circular RNAs (circRNAs) are novel RNA molecules that play important roles in chemoresistance in different cancers, including breast and gastric cancers. However, whether circRNAs are involved in the response to chemotherapy in small cell lung cancer (SCLC) remains largely unknown. In this study, we observed that cESRP1 (circular RNA epithelial splicing regulatory protein-1) expression was significantly downregulated in the chemoresistant cells compared with the parental chemosensitive cells. cESRP1 enhanced drug sensitivity by repressing miR-93-5p in SCLC. Cytoplasmic cESRP1 could directly bind to miR-93-5p and inhibit the posttranscriptional repression mediated by miR-93-5p, thereby upregulating the expression of the miR-93-5p downstream targets Smad7/p21(CDKN1A) and forming a negative feedback loop to regulate transforming growth factor-β (TGF-β) mediated epithelial-mesenchymal transition. Furthermore, cESRP1 overexpression and TGF-β pathway inhibition both altered tumour responsiveness to chemotherapy in an acquired chemoresistant patient-derived xenograft model. Importantly, cESRP1 expression was downregulated in SCLC patient tissues and was associated with survival. Our findings reveal, for the first time, that cESRP1 plays crucial a role in SCLC chemosensitivity by sponging miR-93-5p to inhibit the TGF-β pathway, suggesting that cESRP1 may serve as a valuable prognostic biomarker and a potential therapeutic target in SCLC patients.
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Affiliation(s)
- Weimei Huang
- Department of Pathology, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Yunchu Yang
- Department of Pathology, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Jingfang Wu
- Department of Pathology, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Yuchun Niu
- Department of Pathology, Zhujiang Hospital, Southern Medical University, Guangzhou, China
- Department of Oncology, The First Affiliated Hospital of Hebei North University, Zhangjiakou, China
| | - Yao Yao
- Department of Pathology, Peking University Third Hospital, Beijing, China
| | - Jian Zhang
- Department of Oncology, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Xiaoxian Huang
- Clinical Laboratory, Gushang Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
| | - Shumei Liang
- Department of Pathology, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Rui Chen
- Department of Pathology, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Size Chen
- Department of Oncology, The First Affiliated Hospital of Guangdong Pharmaceutical University, Guangzhou, China.
| | - Linlang Guo
- Department of Pathology, Zhujiang Hospital, Southern Medical University, Guangzhou, China.
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8
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Hao M, Qiao J, Qi H. Current and Emerging Methods for the Synthesis of Single-Stranded DNA. Genes (Basel) 2020; 11:E116. [PMID: 31973021 PMCID: PMC7073533 DOI: 10.3390/genes11020116] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Revised: 01/16/2020] [Accepted: 01/18/2020] [Indexed: 12/21/2022] Open
Abstract
Methods for synthesizing arbitrary single-strand DNA (ssDNA) fragments are rapidly becoming fundamental tools for gene editing, DNA origami, DNA storage, and other applications. To meet the rising application requirements, numerous methods have been developed to produce ssDNA. Some approaches allow the synthesis of freely chosen user-defined ssDNA sequences to overcome the restrictions and limitations of different length, purity, and yield. In this perspective, we provide an overview of the representative ssDNA production strategies and their most significant challenges to enable the readers to make informed choices of synthesis methods and enhance the availability of increasingly inexpensive synthetic ssDNA. We also aim to stimulate a broader interest in the continued development of efficient ssDNA synthesis techniques and improve their applications in future research.
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Affiliation(s)
- Min Hao
- School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China; (M.H.); (J.Q.)
- Key Laboratory of Systems Bioengineering of Ministry of Education, Tianjin University, Tianjin 300072, China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering, Tianjin University, Tianjin 300072, China
| | - Jianjun Qiao
- School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China; (M.H.); (J.Q.)
- Key Laboratory of Systems Bioengineering of Ministry of Education, Tianjin University, Tianjin 300072, China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering, Tianjin University, Tianjin 300072, China
| | - Hao Qi
- School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China; (M.H.); (J.Q.)
- Key Laboratory of Systems Bioengineering of Ministry of Education, Tianjin University, Tianjin 300072, China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering, Tianjin University, Tianjin 300072, China
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9
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Gallo E. High-Throughput Generation of In Silico Derived Synthetic Antibodies via One-step Enzymatic DNA Assembly of Fragments. Mol Biotechnol 2020; 62:142-150. [PMID: 31894513 DOI: 10.1007/s12033-019-00232-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Phage-display technology offers robust methods for isolating antibody (Ab) molecules with specificity for different target antigens. Recent advancements couple Ab selections with in silico strategies, such as predictive computational models or next-generation sequencing metadata analysis of Ab selections. These advancements result in enhanced Ab clonal diversities with potential for enlarged epitope coverage of the target antigen. A current limitation however, is that de novo Ab sequences must undergo DNA gene synthesis, and subsequent expression as Ab proteins for downstream validations. Due to the high costs and time for commercially generating large sets of DNA genes, we report a high-throughput platform for the synthesis of in silico derived Ab clones. As a proof of concept we demonstrate the simultaneous synthesis of 96 unique Abs with varied lengths and complementary determining region compositions. Each of the 96 Ab clones undergoes a one-step enzymatic assembly of distinct DNA fragments that combine into a circularized Fab expression plasmid. This strategy allows for the rapid and efficient synthesis of 96 DNA constructs in a 3 day window, and exhibits high percentage fidelity-greater than 93%. Accordingly, the synthesis of Ab DNA constructs as Fab expression plasmids allow for rapid execution of downstream Ab protein validations, with potential for implementation into high-throughput Ab protein characterization pipelines. Altogether, the platform presented here proves rapid and also cost-effective, which is important for labs with limited resources, since it utilizes standard laboratory equipment and molecular reagents.
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Affiliation(s)
- Eugenio Gallo
- Department of Molecular Genetics, Charles Best Institute, University of Toronto, 112 College Street, 112 College Street, Room 70, Toronto, ON, M5G 1L6, Canada.
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10
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Jeyaraj A, Wang X, Wang S, Liu S, Zhang R, Wu A, Wei C. Identification of Regulatory Networks of MicroRNAs and Their Targets in Response to Colletotrichum gloeosporioides in Tea Plant ( Camellia sinensis L.). FRONTIERS IN PLANT SCIENCE 2019; 10:1096. [PMID: 31572415 PMCID: PMC6751461 DOI: 10.3389/fpls.2019.01096] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Accepted: 08/09/2019] [Indexed: 05/21/2023]
Abstract
Anthracnose disease is caused by Colletotrichum gloeosporioides, and is common in leaves of the tea plant (Camellia sinensis). MicroRNAs (miRNAs) have been known as key modulators of gene expression in response to environmental stresses, disease resistance, defense responses, and plant immunity. However, the role of miRNAs in responses to C. gloeosporioides remains unexplored in tea plant. Therefore, in the present study, six miRNA sequencing data sets and two degradome data sets were generated from C. gloeosporioides-inoculated and control tea leaves. A total of 485 conserved and 761 novel miRNAs were identified. Of those, 239 known and 369 novel miRNAs exhibited significantly differential expression under C. gloeosporioides stress. One thousand one hundred thirty-four and 596 mRNAs were identified as targets of 389 conserved and 299 novel miRNAs by degradome analysis, respectively. Based on degradome analysis, most of the predicted targets are negatively correlated with their corresponding conserved and novel miRNAs. The expression levels of 12 miRNAs and their targets were validated by quantitative real-time PCR. A negative correlation between expression profiles of five miRNAs (PC-5p-80764_22, csn-miR160c, csn-miR828a, csn-miR164a, and csn-miR169e) and their targets (WRKY, ARF, MYB75, NAC, and NFY transcription factor) was observed. The predicted targets of five interesting miRNAs were further validated through 5'RLM-RACE. Furthermore, Gene Ontology and metabolism pathway analysis revealed that most of the target genes were involved in the regulation of auxin pathway, ROS scavenging pathway, salicylic acid mediated pathway, receptor kinases, and transcription factors for plant growth and development as well as stress responses in tea plant against C. gloeosporioides stress. This study enriches the resources of stress-responsive miRNAs and their targets in C. sinensis and thus provides novel insights into the miRNA-mediated regulatory mechanisms, which could contribute to the enhanced susceptibility of C. gloeosporioides in tea plant.
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Affiliation(s)
- Anburaj Jeyaraj
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, China
- Department of Biotechnology, Karpagam Academy of Higher Education, Coimbatore, India
| | - Xuewen Wang
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, China
- Department of Genetics, University of Georgia, Athens, United States
| | - Shuangshuang Wang
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, China
| | - Shengrui Liu
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, China
| | - Ran Zhang
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, China
| | - Ailin Wu
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, China
| | - Chaoling Wei
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, China
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11
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Zhang S, Wang L, Cheng L. Aberrant ERG expression associates with downregulation of miR-4638-5p and selected genomic alterations in a subset of diffuse large B-cell lymphoma. Mol Carcinog 2019; 58:1846-1854. [PMID: 31237044 DOI: 10.1002/mc.23074] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Revised: 05/22/2019] [Accepted: 05/31/2019] [Indexed: 12/19/2022]
Abstract
ERG (avian v-ets erythroblastosis virus E26 oncogene homolog), an oncoprotein in prostate carcinoma and Ewing's sarcoma is associated with poor prognosis in patients with acute myeloid leukemia and T lymphoblastic leukemia. However little is known about ERG in lymphoma. Here we studied ERG in diffuse large B-cell lymphoma (DLBCL) by immunohistochemistry, fluorescence in situ hybridization (FISH), genome-wide microRNA (miRNA) expression profiling, real-time reverse-transcriptase polymerase chain reaction (RT-PCR) and whole exome sequencing (WES). Approximately 30% of de novo DLBCLs (37 of 118) expressed ERG (ERG+). ERG expression showed no significant correlation with DLBCL cell-of-origin classification, patient's age, sex, nodal, or extranodal disease status, tumor expression of p53 or p63. There was no ERG rearrangement in 10 randomly selected ERG+ DLBCLs by FISH. Forty-three miRNAs showed significant differential expression between ERG+ and ERG- DLBCLs. Downregulation of miR-4638-5p was confirmed by real-time RT-PCR. WES not only confirmed known gene mutations in DLBCLs but also revealed multiple novel gene mutations in POLA1, E2F1, PSMD8, AXIN1, GAB2, and GNB2L1, which occur more frequently in ERG+ DLBCLs. In conclusion, our studies demonstrated aberrant ERG expression in a subset of DLBCL, which is associated with downregulation of miR-4638-5p. In comparison with ERG-negative DLBCL, ERG+ DLBCL more likely harbors mutations in genes important in cell cycle control, B-cell receptor-mediated signaling and degradation of β-catenin. Further clinicopathological correlation and functional studies of ERG-related miRNAs and pathways may provide new insight into the pathogenesis of DLBCL and reveal novel targets for better management of patients with DLBCL.
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Affiliation(s)
- Shanxiang Zhang
- Department of Pathology & Laboratory Medicine, Indiana University School of Medicine, Indianapolis, Indiana
| | - Lin Wang
- Department of Pathology & Laboratory Medicine, Indiana University School of Medicine, Indianapolis, Indiana
| | - Liang Cheng
- Department of Pathology & Laboratory Medicine, Indiana University School of Medicine, Indianapolis, Indiana
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12
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A High-Throughput Platform for the Generation of Synthetic Ab Clones by Single-Strand Site-Directed Mutagenesis. Mol Biotechnol 2019; 61:410-420. [PMID: 30963479 DOI: 10.1007/s12033-019-00171-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Current developments in meta-data analysis and predictive computational models offer alternative routes for the identification of antibodies. In silico-based technologies and NGS data analysis from Ab phage-display selections offer expanded selections of Ab candidates. Accordingly, the identified de novo Abs with predicted selectivity for a target antigen must undergo rapid gene synthesis for downstream Ab characterizations. Here we describe a high-throughput strategy for the generation of synthetic Ab clones for expression as Fab proteins in Escherichia coli. Our approach utilizes simultaneous single-stranded site-directed mutagenesis of diversified Ab regions of a phagemid template with engineered complementary determining regions that contain multiple stop codon and restriction enzyme sites. Subsequently, we perform rapid screening of Ab DNA clones for correct gene assemblies by high-throughput Ab-phage protein expression screens. Identified sequences are corroborated by Sanger DNA sequencing analysis. In summary, our work describes a rapid and cost-effective platform for the high-throughput synthesis of synthetic Ab genes as Fab proteins for implementation into downstream protein validation pipelines.
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13
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Long-Term Effects of Myoinositol on Behavioural Seizures and Biochemical Changes Evoked by Kainic Acid Induced Epileptogenesis. BIOMED RESEARCH INTERNATIONAL 2019; 2019:4518160. [PMID: 30941363 PMCID: PMC6421025 DOI: 10.1155/2019/4518160] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Revised: 12/18/2018] [Accepted: 01/10/2019] [Indexed: 12/25/2022]
Abstract
Epilepsy is one of the most devastating neurological diseases and despite significant efforts there is no cure available. Occurrence of spontaneous seizures in epilepsy is preceded by numerous functional and structural pathophysiological reorganizations in the brain—a process called epileptogenesis. Treatment strategies targeting this process may be efficient for preventing spontaneous recurrent seizures (SRS) in epilepsy, or for modification of disease progression. We have previously shown that (i) myoinositol (MI) pretreatment significantly decreases severity of acute seizures (status epilepticus: SE) induced by kainic acid (KA) in experimental animals and (ii) that daily post-SE administration of MI for 4 weeks prevents certain biochemical changes triggered by SE. However it was not established whether such MI treatment also exerts long-term effects on the frequency of SRS. In the present study we have shown that, in KA-induced post-SE epilepsy model in rats, MI treatment for 28 days reduces frequency and duration of behavioural SRS not only during the treatment, but also after its termination for the following 4 weeks. Moreover, MI has significant effects on molecular changes in the hippocampus, including mi-RNA expression spectrum, as well as mRNA levels of sodium-MI transporter and LRRC8A subunit of the volume regulated anionic channel. Taken together, these data suggest that molecular changes induced by MI treatment may counteract epileptogenesis. Thus, here we provide data indicating antiepileptogenic properties of MI, which further supports the idea of developing new antiepileptogenic and disease modifying drug that targets MI system.
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14
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Huy Le B, Nguyen VT, Seo YJ. Site-specific incorporation of multiple units of functional nucleotides into DNA using a step-wise approach with polymerase and its application to monitoring DNA structural changes. Chem Commun (Camb) 2019; 55:2158-2161. [PMID: 30675606 DOI: 10.1039/c8cc09444f] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
We have developed a new method, a step-wise approach with polymerase, for site-specific incorporation of multiple units of functional nucleotides into DNA to form hairpin secondary structures. The fluorescence of the resulting DNA incorporating the functional nucleotides varied upon transitioning from single-strand to hairpin and duplex structures.
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Affiliation(s)
- Binh Huy Le
- Department of Bioactive Material Sciences, Chonbuk National University, South Korea
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15
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Mukherjee K, Dubovskiy I, Grizanova E, Lehmann R, Vilcinskas A. Epigenetic mechanisms mediate the experimental evolution of resistance against parasitic fungi in the greater wax moth Galleria mellonella. Sci Rep 2019; 9:1626. [PMID: 30733453 PMCID: PMC6367475 DOI: 10.1038/s41598-018-36829-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Accepted: 11/23/2018] [Indexed: 02/07/2023] Open
Abstract
Recent concepts in evolutionary biology suggest that epigenetic mechanisms can translate environmental selection pressures into heritable changes in phenotype. To determine whether experimental selection for a complex trait in insects involves epigenetic modifications, we carried out a generation-spanning experiment using larvae of the greater wax moth Galleria mellonella as a model host to investigate the role of epigenetics in the heritability of resistance against the parasitic fungus Metarhizium robertsii. We investigated differences in DNA methylation, histone acetylation and microRNA (miRNA) expression between an experimentally resistant population and an unselected, susceptible line, revealing that the survival of G. mellonella larvae infected with M. robertsii correlates with tissue-specific changes in DNA methylation and histone modification and the modulation of genes encoding the corresponding enzymes. We also identified miRNAs differentially expressed between resistant and susceptible larvae and showed that these regulatory molecules target genes encoding proteinases and proteinase inhibitors, as well as genes related to cuticle composition, innate immunity and metabolism. These results support our hypothesis that epigenetic mechanisms facilitate, at least in part, the heritable manifestation of parasite resistance in insects. The reciprocal adaptations underlying host–parasite coevolution therefore extend beyond the genetic level to encompass epigenetic modifications.
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Affiliation(s)
- Krishnendu Mukherjee
- Fraunhofer Institute for Molecular Biology and Applied Ecology, Department of Bioresources, Winchester Str. 2, 35394, Giessen, Germany
| | - Ivan Dubovskiy
- Novosibirsk State Agrarian University, Dobrolubova 160, 630039, Novosibirsk, Russia
| | - Ekaterina Grizanova
- Novosibirsk State Agrarian University, Dobrolubova 160, 630039, Novosibirsk, Russia
| | - Rüdiger Lehmann
- Fraunhofer Institute for Molecular Biology and Applied Ecology, Department of Bioresources, Winchester Str. 2, 35394, Giessen, Germany
| | - Andreas Vilcinskas
- Fraunhofer Institute for Molecular Biology and Applied Ecology, Department of Bioresources, Winchester Str. 2, 35394, Giessen, Germany. .,Institute for Insect Biotechnology, Justus-Liebig University of Giessen, Heinrich-Buff-Ring 26-32, 35392, Giessen, Germany.
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16
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Ampadu Boateng D, Word MD, Gutsev LG, Jena P, Tibbetts KM. Conserved Vibrational Coherence in the Ultrafast Rearrangement of 2-Nitrotoluene Radical Cation. J Phys Chem A 2019; 123:1140-1152. [DOI: 10.1021/acs.jpca.8b11723] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Derrick Ampadu Boateng
- Department of Chemistry, Virginia Commonwealth University, Richmond, Virginia 23284, United States
| | - Mi’Kayla D. Word
- Department of Chemistry, Virginia Commonwealth University, Richmond, Virginia 23284, United States
| | - Lavrenty G. Gutsev
- Department of Physics, Virginia Commonwealth University, Richmond, Virginia 23284, United States
| | - Puru Jena
- Department of Physics, Virginia Commonwealth University, Richmond, Virginia 23284, United States
| | - Katharine Moore Tibbetts
- Department of Chemistry, Virginia Commonwealth University, Richmond, Virginia 23284, United States
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17
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Margvelani G, Meparishvili M, Kiguradze T, McCabe BJ, Solomonia R. Micro-RNAs, their target proteins, predispositions and the memory of filial imprinting. Sci Rep 2018; 8:17444. [PMID: 30487553 PMCID: PMC6262022 DOI: 10.1038/s41598-018-35097-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Accepted: 10/28/2018] [Indexed: 12/18/2022] Open
Abstract
Visual imprinting is a learning process whereby young animals come to prefer a visual stimulus after exposure to it (training). The intermediate medial mesopallium (IMM) in the domestic chick forebrain is critical for visual imprinting and contributes to molecular regulation of memory formation. We investigated the role of micro-RNAs (miRNAs) in such regulation. Twenty-four hours after training, miRNA spectra in the left IMM were compared between chicks with high preference scores (strong memory for imprinting stimulus), and chicks with low preference scores (weak memory for imprinting stimulus). Using criteria of significance and expression level, we chose gga-miR-130b-3p for further study and found that down-regulation correlated with learning strength. No effect was detected in posterior nidopallium, a region not involved in imprinting. We studied two targets of gga-miR-130b-3p, cytoplasmic polyadenylation element binding proteins 1 (CPEB-1) and 3 (CPEB-3), in two subcellular fractions (P2 membrane-mitochondrial and cytoplasmic) of IMM and posterior nidopallium. Only in the left IMM was a learning-related effect observed, in membrane CPEB-3. Variances from the regression with preference score and untrained chicks suggest that, in the IMM, gga-miR-130b-3p level reflects a predisposition, i.e. capacity to learn, whereas P2 membrane-mitochondrial CPEB-3 is up-regulated in a learning-specific way.
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Affiliation(s)
- Giorgi Margvelani
- Institute of Chemical Biology, Ilia State University, Tbilisi, Georgia
| | - Maia Meparishvili
- Institute of Chemical Biology, Ilia State University, Tbilisi, Georgia.,I. Beritashvili Centre of Experimental Biomedicine, Tbilisi, Georgia
| | - Tamar Kiguradze
- I. Beritashvili Centre of Experimental Biomedicine, Tbilisi, Georgia
| | - Brian J McCabe
- Department of Zoology, University of Cambridge, Cambridge, UK.
| | - Revaz Solomonia
- Institute of Chemical Biology, Ilia State University, Tbilisi, Georgia. .,I. Beritashvili Centre of Experimental Biomedicine, Tbilisi, Georgia.
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18
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Luo L, Yu ZP, Qin H, Zhu ZX, Liao MH, Liao HT, Yuan KF, Zeng Y. Exosomal MicroRNA-10a Is Associated with Liver Regeneration in Rats through Downregulation of EphA4. Chin Med J (Engl) 2018; 131:454-460. [PMID: 29451151 PMCID: PMC5830831 DOI: 10.4103/0366-6999.225057] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Background: MicroRNAs (miRNAs) have been reported to play vital roles in liver regeneration. Previous studies mainly focused on the functions of intracellular miRNAs, while the functions of circulating exosomal miRNAs in liver regeneration remain largely unknown. The aim of this study was to identify the key exosomal miRNA that played vital roles in liver regeneration. Methods: The Sprague–Dawley male rats were assigned to 70% partially hepatectomized group (n = 6) and sham surgery group (n = 6). The peripheral blood of both groups was collected 24 h after surgery. The exosomal miRNAs were extracted, and microarray was used to find out the key miRNA implicated in liver regeneration. Adenovirus was used to overexpress the key miRNA in rats, and proliferating cell nuclear antigen (PCNA) staining was applied to study the effect of key miRNA overexpression on liver regeneration. Western blotting was used to validate the predicted target of the key miRNA. Results: Exosomal miR-10a was upregulated more than nine times in hepatectomized rats. The level of miR-10a was increased in the early phase of liver regeneration, reached the top at 72 h postsurgery, and decreased to perioperative level 168 h after surgery. Moreover, enforced expression of miR-10a by adenovirus facilitated the process of liver regeneration as evidenced by immunohistochemical staining of PCNA. Erythropoietin-producing hepatocellular receptor A4 (EphA4) has been predicted to be a target of miR-10a. The protein level of EphA4 was decreased in the early phase of liver regeneration, reached the bottom at 72 h postsurgery, and rose to perioperative level 168 h after surgery, which was negatively correlated with miR-10a, confirming that EphA4 served as a downstream target of miR-10a. Moreover, inhibition of EphA4 by rhynchophylline could promote the proliferation of hepatocytes by regulating the cell cycle. Conclusion: Exosomal miR-10a might accelerate liver regeneration through downregulation of EphA4.
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Affiliation(s)
- Lin Luo
- Department of Liver Surgery, Liver Transplantation Division, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Ze-Ping Yu
- Department of Orthopedics, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Han Qin
- Department of Liver Surgery, Liver Transplantation Division, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Ze-Xin Zhu
- Department of Orthopedics, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Ming-Heng Liao
- Department of Liver Surgery, Liver Transplantation Division, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Hao-Tian Liao
- Department of Liver Surgery, Liver Transplantation Division, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Ke-Fei Yuan
- Laboratory of Liver Surgery, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Yong Zeng
- Department of Liver Surgery, Liver Transplantation Division, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
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19
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Fay MJ, Alt LAC, Ryba D, Salamah R, Peach R, Papaeliou A, Zawadzka S, Weiss A, Patel N, Rahman A, Stubbs-Russell Z, Lamar PC, Edwards JR, Prozialeck WC. Cadmium Nephrotoxicity Is Associated with Altered MicroRNA Expression in the Rat Renal Cortex. TOXICS 2018; 6:E16. [PMID: 29543730 PMCID: PMC5874789 DOI: 10.3390/toxics6010016] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Revised: 03/08/2018] [Accepted: 03/09/2018] [Indexed: 11/25/2022]
Abstract
Cadmium (Cd) is a nephrotoxic environmental pollutant that causes a generalized dysfunction of the proximal tubule characterized by polyuria and proteinuria. Even though the effects of Cd on the kidney have been well-characterized, the molecular mechanisms underlying these effects have not been fully elucidated. MicroRNAs (miRNAs) are small non-coding RNAs that regulate cellular and physiologic function by modulating gene expression at the post-transcriptional level. The goal of the present study was to determine if Cd affects renal cortex miRNA expression in a well-established animal model of Cd-induced kidney injury. Male Sprague-Dawley rats were treated with subcutaneous injections of either isotonic saline or CdCl₂ (0.6 mg/kg) 5 days a week for 12 weeks. The 12-week Cd-treatment protocol resulted in kidney injury as determined by the development of polyuria and proteinuria, and a significant increase in the urinary biomarkers Kim-1, β₂ microglobulin and cystatin C. Total RNA was isolated from the renal cortex of the saline control and Cd treated animals, and differentially expressed miRNAs were identified using µParafloTM microRNA microarray analysis. The microarray results demonstrated that the expression of 44 miRNAs were significantly increased and 54 miRNAs were significantly decreased in the Cd treatment group versus the saline control (t-test, p ≤ 0.05, N = 6 per group). miR-21-5p, miR-34a-5p, miR-146b-5p, miR-149-3p, miR-224-5p, miR-451-5p, miR-1949, miR-3084a-3p, and miR-3084c-3p demonstrated more abundant expression and a significant two-fold or greater increased expression in the Cd-treatment group versus the saline control group. miR-193b-3p, miR-455-3p, and miR-342-3p demonstrated more abundant expression and a significant two-fold or greater decreased expression in the Cd-treatment group versus the saline control group. Real-time PCR validation demonstrated (1) a significant (t-test, p ≤ 0.05, N = 6 per group) increase in expression in the Cd-treated group for miR-21-5p (2.7-fold), miR-34a-5p (10.8-fold), miR-146b-5p (2-fold), miR-224-5p (10.2-fold), miR-3084a-3p (2.4-fold), and miR-3084c-3p (3.3-fold) and (2) a significant (t-test, p ≤ 0.05, N = 6 per group) 52% decrease in miR-455-3p expression in the Cd-treatment group. These findings demonstrate that Cd significantly alters the miRNA expression profile in the renal cortex and raises the possibility that dysregulated miRNA expression may play a role in the pathophysiology of Cd-induced kidney injury. In addition, these findings raise the possibility that Cd-dysregulated miRNAs might be used as urinary biomarkers of Cd exposure or Cd-induced kidney injury.
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Affiliation(s)
- Michael J Fay
- Department of Biomedical Sciences, Midwestern University, 555 31st Street, Downers Grove, IL 60515, USA.
- Department of Pharmacology, Midwestern University, 555 31st Street, Downers Grove, IL 60515, USA.
| | - Lauren A C Alt
- Department of Biomedical Sciences, Midwestern University, 555 31st Street, Downers Grove, IL 60515, USA.
| | - Dominika Ryba
- Department of Biomedical Sciences, Midwestern University, 555 31st Street, Downers Grove, IL 60515, USA.
| | - Ribhi Salamah
- Department of Biomedical Sciences, Midwestern University, 555 31st Street, Downers Grove, IL 60515, USA.
| | - Ryan Peach
- Department of Biomedical Sciences, Midwestern University, 555 31st Street, Downers Grove, IL 60515, USA.
| | - Alexander Papaeliou
- Department of Biomedical Sciences, Midwestern University, 555 31st Street, Downers Grove, IL 60515, USA.
| | - Sabina Zawadzka
- Department of Biomedical Sciences, Midwestern University, 555 31st Street, Downers Grove, IL 60515, USA.
| | - Andrew Weiss
- Department of Biomedical Sciences, Midwestern University, 555 31st Street, Downers Grove, IL 60515, USA.
| | - Nil Patel
- Department of Biomedical Sciences, Midwestern University, 555 31st Street, Downers Grove, IL 60515, USA.
| | - Asad Rahman
- Department of Biomedical Sciences, Midwestern University, 555 31st Street, Downers Grove, IL 60515, USA.
| | - Zyaria Stubbs-Russell
- Department of Biomedical Sciences, Midwestern University, 555 31st Street, Downers Grove, IL 60515, USA.
| | - Peter C Lamar
- Department of Pharmacology, Midwestern University, 555 31st Street, Downers Grove, IL 60515, USA.
| | - Joshua R Edwards
- Department of Pharmacology, Midwestern University, 555 31st Street, Downers Grove, IL 60515, USA.
| | - Walter C Prozialeck
- Department of Pharmacology, Midwestern University, 555 31st Street, Downers Grove, IL 60515, USA.
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20
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Ju Z, Jiang Q, Liu G, Wang X, Luo G, Zhang Y, Zhang J, Zhong J, Huang J. Solexa sequencing and custom microRNA chip reveal repertoire of microRNAs in mammary gland of bovine suffering from natural infectious mastitis. Anim Genet 2018; 49:3-18. [PMID: 29315680 DOI: 10.1111/age.12628] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/17/2017] [Indexed: 12/13/2022]
Abstract
Identification of microRNAs (miRNAs), target genes and regulatory networks associated with innate immune and inflammatory responses and tissue damage is essential to elucidate the molecular and genetic mechanisms for resistance to mastitis. In this study, a combination of Solexa sequencing and custom miRNA chip approaches was used to profile the expression of miRNAs in bovine mammary gland at the late stage of natural infection with Staphylococcus aureus, a widespread mastitis pathogen. We found 383 loci corresponding to 277 known and 49 putative novel miRNAs, two potential mitrons and 266 differentially expressed miRNAs in the healthy and mastitic cows' mammary glands. Several interaction networks and regulators involved in mastitis susceptibility, such as ALCAM, COL1A1, APOP4, ITIH4, CRP and fibrinogen alpha (FGA), were highlighted. Significant down-regulation and location of bta-miR-26a, which targets FGA in the mastitic mammary glands, were validated using quantitative real-time PCR, in situ hybridization and dual-luciferase reporter assays. We propose that the observed miRNA variations in mammary glands of mastitic cows are related to the maintenance of immune and defense responses, cell proliferation and apoptosis, and tissue injury and healing during the late stage of infection. Furthermore, the effect of bta-miR-26a in mastitis, mediated at least in part by enhancing FGA expression, involves host defense, inflammation and tissue damage.
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Affiliation(s)
- Zhihua Ju
- Dairy Cattle Research Center, Shandong Academy of Agricultural Sciences, No. 159 North of Industry Road, Jinan, Shandong, 250131, China
| | - Qiang Jiang
- Dairy Cattle Research Center, Shandong Academy of Agricultural Sciences, No. 159 North of Industry Road, Jinan, Shandong, 250131, China
| | - Gang Liu
- National Center for Preservation and Utilization of Genetic Resources of Domestic Animals, National Animal Husbandry Service, Beijing, 100193, China
| | - Xiuge Wang
- Dairy Cattle Research Center, Shandong Academy of Agricultural Sciences, No. 159 North of Industry Road, Jinan, Shandong, 250131, China
| | - Guojing Luo
- Dairy Cattle Research Center, Shandong Academy of Agricultural Sciences, No. 159 North of Industry Road, Jinan, Shandong, 250131, China
| | - Yan Zhang
- Dairy Cattle Research Center, Shandong Academy of Agricultural Sciences, No. 159 North of Industry Road, Jinan, Shandong, 250131, China
| | - Jibin Zhang
- Department of Animal Science, Iowa State University, 2361 Kildee Hall, 806 Stange Road, Ames, IA, 50010, USA
| | - Jifeng Zhong
- Engineering Center of Animal Breeding and Reproduction, Jinan, Shandong, 250100, China
| | - Jinming Huang
- Dairy Cattle Research Center, Shandong Academy of Agricultural Sciences, No. 159 North of Industry Road, Jinan, Shandong, 250131, China.,Engineering Center of Animal Breeding and Reproduction, Jinan, Shandong, 250100, China
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21
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Mannala GK, Izar B, Rupp O, Schultze T, Goesmann A, Chakraborty T, Hain T. Listeria monocytogenes Induces a Virulence-Dependent microRNA Signature That Regulates the Immune Response in Galleria mellonella. Front Microbiol 2017; 8:2463. [PMID: 29312175 PMCID: PMC5733040 DOI: 10.3389/fmicb.2017.02463] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Accepted: 11/27/2017] [Indexed: 12/11/2022] Open
Abstract
microRNAs (miRNAs) coordinate several physiological and pathological processes by regulating the fate of mRNAs. Studies conducted in vitro indicate a role of microRNAs in the control of host-microbe interactions. However, there is limited understanding of miRNA functions in in vivo models of bacterial infections. In this study, we systematically explored changes in miRNA expression levels of Galleria mellonella larvae (greater-wax moth), a model system that recapitulates the vertebrate innate immunity, following infection with L. monocytogenes. Using an insect-specific miRNA microarray with more than 2000 probes, we found differential expression of 90 miRNAs (39 upregulated and 51 downregulated) in response to infection with L. monocytogenes. We validated the expression of a subset of miRNAs which have mammalian homologs of known or predicted function. In contrast, non-pathogenic L. innocua failed to induce these miRNAs, indicating a virulence-dependent miRNA deregulation. To predict miRNA targets using established algorithms, we generated a publically available G. mellonella transcriptome database. We identified miRNA targets involved in innate immunity, signal transduction and autophagy, including spätzle, MAP kinase, and optineurin, respectively, which exhibited a virulence-specific differential expression. Finally, in silico estimation of minimum free energy of miRNA-mRNA duplexes of validated microRNAs and target transcripts revealed a regulatory network of the host immune response to L. monocytogenes. In conclusion, this study provides evidence for a role of miRNAs in the regulation of the innate immune response following bacterial infection in a simple, rapid and scalable in vivo model that may predict host-microbe interactions in higher vertebrates.
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Affiliation(s)
- Gopala K Mannala
- Institute of Medical Microbiology, Justus-Liebig University, Giessen, Germany
| | - Benjamin Izar
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, United States.,Broad Institute of MIT and Harvard University, Cambridge, MA, United States
| | - Oliver Rupp
- Department of Bioinformatics and Systems Biology, Justus-Liebig University, Giessen, Germany
| | - Tilman Schultze
- Institute of Medical Microbiology, Justus-Liebig University, Giessen, Germany
| | - Alexander Goesmann
- Department of Bioinformatics and Systems Biology, Justus-Liebig University, Giessen, Germany
| | - Trinad Chakraborty
- Institute of Medical Microbiology, Justus-Liebig University, Giessen, Germany
| | - Torsten Hain
- Institute of Medical Microbiology, Justus-Liebig University, Giessen, Germany
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He K, Sun Y, Xiao H, Ge C, Li F, Han Z. Multiple miRNAs jointly regulate the biosynthesis of ecdysteroid in the holometabolous insects, Chilo suppressalis. RNA (NEW YORK, N.Y.) 2017; 23:1817-1833. [PMID: 28860304 PMCID: PMC5689003 DOI: 10.1261/rna.061408.117] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Accepted: 08/18/2017] [Indexed: 05/30/2023]
Abstract
The accurate rise and fall of active hormones is important for insect development. The ecdysteroids must be cleared in a timely manner. However, the mechanism of suppressing the ecdysteroid biosynthesis at the right time remains unclear. Here, we sequenced a small RNA library of Chilo suppressalis and identified 300 miRNAs in this notorious rice insect pest. Microarray analysis yielded 54 differentially expressed miRNAs during metamorphosis development. Target prediction and in vitro dual-luciferase assays confirmed that seven miRNAs (two conserved and five novel miRNAs) jointly targeted three Halloween genes in the ecdysteroid biosynthesis pathway. Overexpression of these seven miRNAs reduced the titer of 20-hydroxyecdysone (20E), induced mortality, and retarded development, which could be rescued by treatment with 20E. Comparative analysis indicated that the miRNA regulation of metamorphosis development is a conserved process but that the miRNAs involved are highly divergent. In all, we present evidence that both conserved and lineage-specific miRNAs have crucial roles in regulating development in insects by controlling ecdysteroid biosynthesis, which is important for ensuring developmental convergence and evolutionary diversity.
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Affiliation(s)
- Kang He
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Yang Sun
- Department of Entomology, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
- Institute of Plant Protection, Jiangxi Academy of Agricultural Science, Nanchang 330200, China
| | - Huamei Xiao
- College of Life Sciences and Resource Environment, Yichun University, Yichun 336000, China
| | - Chang Ge
- Department of Entomology, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
| | - Fei Li
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Zhaojun Han
- Department of Entomology, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
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23
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Lu XG, Kang X, Zhan LB, Kang LM, Fan ZW, Bai LZ. Circulating miRNAs as biomarkers for severe acute pancreatitis associated with acute lung injury. World J Gastroenterol 2017; 23:7440-7449. [PMID: 29151698 PMCID: PMC5685850 DOI: 10.3748/wjg.v23.i41.7440] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/29/2017] [Revised: 08/23/2017] [Accepted: 09/19/2017] [Indexed: 02/06/2023] Open
Abstract
AIM To identify circulating micro (mi)RNAs as biological markers for prediction of severe acute pancreatitis (SAP) with acute lung injury (ALI).
METHODS Twenty-four serum samples were respectively collected and classified as SAP associated with ALI and SAP without ALI, and the miRNA expression profiles were determined by microarray analysis. These miRNAs were validated by quantitative reverse transcription-polymerase chain reaction, and their putative targets were predicted by the online software TargetScan, miRanda and PicTar database. Gene ontology (GO) and Kyoto encyclopedia of genes and genomes (commonly known as KEGG) were used to predict their possible functions and pathways involved.
RESULTS We investigated 287 miRNAs based on microarray data analysis. Twelve miRNAs were differentially expressed in the patients with SAP with ALI and those with SAP without ALI. Hsa-miR-1260b, 762, 22-3p, 23b and 23a were differently up-regulated and hsa-miR-550a*, 324-5p, 484, 331-3p, 140-3p, 342-3p and 150 were differently down-regulated in patients with SAP with ALI compared to those with SAP without ALI. In addition, 85 putative target genes of the significantly dysregulated miRNAs were found by TargetScan, miRanda and PicTar. Finally, GO and pathway network analysis showed that they were mainly enriched in signal transduction, metabolic processes, cytoplasm and cell membranes.
CONCLUSION This is the first study to identify 12 circulating miRNAs in patients with SAP with ALI, which may be biomarkers for prediction of ALI after SAP.
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Affiliation(s)
- Xiao-Guang Lu
- Department of Emergency, Zhongshan Hospital, Dalian University, Dalian 116001, Liaoning Province, China
| | - Xin Kang
- Department of Emergency, Zhongshan Hospital, Dalian University, Dalian 116001, Liaoning Province, China
| | - Li-Bin Zhan
- College of Basic Medicine, Nanjing University of Chinese Medicine, Nanjing 210000, Jiangsu Province, China
| | - Li-Min Kang
- Department of Hepatobiliary and Pancreatic Surgery, Puer People’s Hospital, Puer 665000, Yunnan Province, China
| | - Zhi-Wei Fan
- Department of Emergency, Zhongshan Hospital, Dalian University, Dalian 116001, Liaoning Province, China
| | - Li-Zhi Bai
- Department of Emergency, Zhongshan Hospital, Dalian University, Dalian 116001, Liaoning Province, China
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24
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Meng S, Wang H, Xue D, Zhang W. Screening and validation of differentially expressed extracellular miRNAs in acute pancreatitis. Mol Med Rep 2017; 16:6412-6418. [PMID: 28849189 DOI: 10.3892/mmr.2017.7374] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2016] [Accepted: 06/08/2017] [Indexed: 11/06/2022] Open
Abstract
The present study aimed to screen for differentially expressed extracellular microRNAs (miRNAs) during the development of acute pancreatitis (AP) and validate the miRNA expression in the plasma of patients with AP. The culture medium of taurolithocholic acid‑3 sulfate‑treated rat pancreatic acinar AR42J cells was collected to extract total RNA for miRNA microarray analysis. Compared with the miRNA test results of the AP rats in the GEO databases, the differentially expressed extracellular miRNAs were screened. The TargetScan, miRanda, and PicTar programs were used for target gene prediction of the identified miRNAs, and gene ontology‑biological processes (GO‑BP) functional annotation was performed. Finally, the results from the combined microarray analyses (in vitro cell line and in vivo rat samples) were validated using plasma samples from patients with mild and moderately severe AP by reverse transcription‑polymerase chain reaction. The results demonstrated that extracellular miR‑24 was differentially expressed by microarray and bioinformatics analysis in both the cell line and the animal model of AP. Bioinformatics prediction analysis revealed that downstream target genes of miR‑24 included Vav2, Syk, Lhcgr, Slc9a3r1, Cacnb1, Cacna1b, Bcl10, and Fgd3. Functional enrichment analysis revealed that the main GO‑BP predicted functional presentations were positive regulation of calcium‑mediated signaling, activation of c‑Jun N‑terminal kinase activity, calcium ion transport, regulation of Rho protein signal transduction, negative regulation of the protein kinase B signaling cascade, and the T cell receptor signaling pathway. Validation analysis for the plasma miR‑24 expression in humans revealed a significant upregulation of miR‑24 in the plasma samples of AP patients compared with the healthy controls, while no significant difference was observed in the miR‑24 expression between the mild and the moderately severe AP groups. The present study confirmed the high expression of miR‑24 in peripheral blood during AP, suggesting that miR‑24 might have an intercellular communication role contributing to the AP‑associated distant organ injury.
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Affiliation(s)
- Shishuai Meng
- Department of Critical Care Medicine, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang 150001, P.R. China
| | - Hao Wang
- Department of General Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang 150001, P.R. China
| | - Dongbo Xue
- Department of General Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang 150001, P.R. China
| | - Weihui Zhang
- Department of General Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang 150001, P.R. China
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25
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Chai H, Yan Z, Huang K, Jiang Y, Zhang L. MicroRNA expression, target genes, and signaling pathways in infants with a ventricular septal defect. Mol Cell Biochem 2017; 439:171-187. [PMID: 28822034 DOI: 10.1007/s11010-017-3146-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Accepted: 08/02/2017] [Indexed: 10/19/2022]
Abstract
This study aimed to systematically investigate the relationship between miRNA expression and the occurrence of ventricular septal defect (VSD), and characterize the miRNA target genes and pathways that can lead to VSD. The miRNAs that were differentially expressed in blood samples from VSD and normal infants were screened and validated by implementing miRNA microarrays and qRT-PCR. The target genes regulated by differentially expressed miRNAs were predicted using three target gene databases. The functions and signaling pathways of the target genes were enriched using the GO database and KEGG database, respectively. The transcription and protein expression of specific target genes in critical pathways were compared in the VSD and normal control groups using qRT-PCR and western blotting, respectively. Compared with the normal control group, the VSD group had 22 differentially expressed miRNAs; 19 were downregulated and three were upregulated. The 10,677 predicted target genes participated in many biological functions related to cardiac development and morphogenesis. Four target genes (mGLUR, Gq, PLC, and PKC) were involved in the PKC pathway and four (ECM, FAK, PI3 K, and PDK1) were involved in the PI3 K-Akt pathway. The transcription and protein expression of these eight target genes were significantly upregulated in the VSD group. The 22 miRNAs that were dysregulated in the VSD group were mainly downregulated, which may result in the dysregulation of several key genes and biological functions related to cardiac development. These effects could also be exerted via the upregulation of eight specific target genes, the subsequent over-activation of the PKC and PI3 K-Akt pathways, and the eventual abnormal cardiac development and VSD.
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Affiliation(s)
- Hui Chai
- College of Life Science, Zhejiang Chinese Medical University, Hangzhou, 310053, Zhejiang Province, China
| | - Zhaoyuan Yan
- College of Life Science, Zhejiang Chinese Medical University, Hangzhou, 310053, Zhejiang Province, China
| | - Ke Huang
- Zhejiang University School of Medicine, Hangzhou, 310058, Zhejiang Province, China
| | | | - Lin Zhang
- College of Life Science, Zhejiang Chinese Medical University, Hangzhou, 310053, Zhejiang Province, China.
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26
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Liao X, Yang L, Zhang Q, Chen J. microRNA expression changes after lipopolysaccharide treatment in gills of amphioxus Branchiostoma belcheri. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2017; 70:39-44. [PMID: 28069432 DOI: 10.1016/j.dci.2017.01.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2016] [Revised: 01/05/2017] [Accepted: 01/05/2017] [Indexed: 06/06/2023]
Abstract
Recently, amphioxus has served as a model for studying the origin and evolution of vertebrate immunity. However, little is known about how microRNAs (miRNAs) are involved in the immune defense in amphioxus. In this article, we identified the amphioxus miRNAs in the acute-phase response to lipopolysaccharide (LPS). We determined the time point for the peak of immune response in amphioxus after LPS challenge by evaluating the expression of Branchiostoma belcheri toll-like receptor 1, NF-κb (c-Rel), and big defensin which react with pathogen-associated molecular patterns(PAMPs). Then we chose 12 h as the point to perform miRNA microarray analysis to select the differentially expressed miRNAs. Furthermore, we used quantitative real-time PCR to detect the expression patterns of selected amphioxus miRNAs under effective LPS challenge during the time course. The microarray data revealed that the miRNA expression file was significantly changed after LPS stimulation. The changes of the 10 most upregulated and 7 most downregualted miRNAs in gills of the amphioxus following challenge with LPS revealed a temporal induction kinetic. Our current study will provide valuable information to take an insight into molecular mechanism of innate immune and the evolution of the miRNA family.
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Affiliation(s)
- Xin Liao
- School of Life Sciences, Nanjing University, China; Beihai Marine Station of Evo-devo Institute, Nanjing University, China
| | - Liu Yang
- Department of Biomedical Research Center, The First People's Hospital of Kunming, China
| | - Qilin Zhang
- School of Life Sciences, Nanjing University, China; Beihai Marine Station of Evo-devo Institute, Nanjing University, China
| | - Junyuan Chen
- Beihai Marine Station of Evo-devo Institute, Nanjing University, China; Nanjing Institute of Geology and Paleontology, Nanjing, China.
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27
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Guo D, Ye Y, Qi J, Tan X, Zhang Y, Ma Y, Li Y. Age and sex differences in microRNAs expression during the process of thymus aging. Acta Biochim Biophys Sin (Shanghai) 2017; 49:409-419. [PMID: 28369179 DOI: 10.1093/abbs/gmx029] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Indexed: 12/18/2022] Open
Abstract
The gender-biased thymus involution and the importance of microRNAs (miRNAs, miRs) expression in modulating the thymus development have been reported in many studies. However, how males and females differ in so many ways in thymus involution remains unclear. To address this question, we investigated the miRNA expression profiles in both untreated 3- and 12-month-old female and male mice thymuses. The results showed that 7 and 18 miRNAs were defined as the sex- and age-specific miRNAs, respectively. The expression of miR-181c-5p, miR-20b-5p, miR-98b-5p, miR-329-3p, miR-341-5p, and miR-2137 showed significant age-difference in mice thymus by quantitative polymerase chain reaction. High expression levels of miR-2137 were detected in mice thymic epithelial cells and gradually increased during the process of thymus aging. MiR-27b-3p and miR-378a-3p of the female-biased miRNAs were confirmed as the sex- and estrogen-responsive miRNAs in mice thymus in vivo. Their potential target genes and the pathway were identified by the online software. Possible regulation roles of sex- and age-specific miRNA expression during the process of thymus aging were discussed. Our results suggested that these miRNAs may be potential biomarkers for the study of sex- and age-specific thymus aging and involution.
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Affiliation(s)
- Dongguang Guo
- Department of Basic Veterinary Medicine, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
| | - Yaqiong Ye
- Department of Basic Veterinary Medicine, School of Life Science and Engineering, Foshan University, Foshan 528000, China
| | - Junjie Qi
- Department of Basic Veterinary Medicine, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
| | - Xiaotong Tan
- Department of Basic Veterinary Medicine, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
| | - Yuan Zhang
- Department of Basic Veterinary Medicine, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
| | - Yongjiang Ma
- Department of Basic Veterinary Medicine, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
| | - Yugu Li
- Department of Basic Veterinary Medicine, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
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28
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Srinivasan V, Stedtfeld RD, Tourlousse DM, Baushke SW, Xin Y, Miller SM, Pham T, Rouillard JM, Gulari E, Tiedje JM, Hashsham SA. Diagnostic microarray for 14 water and foodborne pathogens using a flatbed scanner. J Microbiol Methods 2017; 139:15-21. [PMID: 28438642 DOI: 10.1016/j.mimet.2017.04.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Revised: 04/20/2017] [Accepted: 04/20/2017] [Indexed: 02/06/2023]
Abstract
Parallel detection approaches are of interest to many researchers interested in identifying multiple water and foodborne pathogens simultaneously. Availability and cost-effectiveness are two key factors determining the usefulness of such approaches for laboratories with limited resources. In this study, we developed and validated a high-density microarray for simultaneous screening of 14 bacterial pathogens using an approach that employs gold labeling with silver enhancement (GLS) protocol. In total, 8887 probes (50-mer) were designed using an in-house database of virulence and marker genes (VMGs), and synthesized in quadruplicate on glass slides using an in-situ synthesis technology. Target VMG amplicons were obtained using multiplex polymerase chain reaction (PCR), labeled with biotin, and hybridized to the microarray. The signals generated after gold deposition and silver enhancement, were quantified using a flatbed scanner having 2-μm resolution. Data analysis indicated that reliable presence/absence calls could be made, if: i) over four probes were used per gene, ii) the signal-to-noise ratio (SNR) cutoff was greater than or equal to two, and iii) the positive fraction (PF), i.e., number of probes with SNR≥2 for a given VMG was greater than 0.75. Hybridization of the array with blind samples resulted in 100% correct calls, and no false positive. Because amplicons were obtained by multiplex PCR, sensitivity of this method is similar to PCR. This assay is an inexpensive and reliable technique for high throughput screening of multiple pathogens.
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Affiliation(s)
- Vidya Srinivasan
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, MI 48824, United States
| | - Robert D Stedtfeld
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, MI 48824, United States
| | - Dieter M Tourlousse
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, MI 48824, United States
| | - Samuel W Baushke
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, MI 48824, United States
| | - Yu Xin
- Department of Environmental Engineering, Nanjing University, China
| | - Sarah M Miller
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, MI 48824, United States
| | - Trinh Pham
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI 48109, United States
| | - Jean-Marie Rouillard
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI 48109, United States
| | - Erdogan Gulari
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI 48109, United States
| | - James M Tiedje
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, MI 48824, United States
| | - Syed A Hashsham
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, MI 48824, United States.
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29
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Miura S, Himaki T, Takahashi J, Iwahashi H. THE ROLE OF TRANSCRIPTOMICS: PHYSIOLOGICAL EQUIVALENCE BASED ON GENE EXPRESSION PROFILES. ACTA ACUST UNITED AC 2017. [DOI: 10.7831/ras.5.21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Shiori Miura
- The United Graduate School of Agricultural Science, Gifu University
| | - Takehiro Himaki
- The United Graduate School of Agricultural Science, Gifu University
| | - Junko Takahashi
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST)
| | - Hitoshi Iwahashi
- The United Graduate School of Agricultural Science, Gifu University
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30
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Yan L, Jiao D, Hu H, Wang J, Tang X, Chen J, Chen Q. Identification of lymph node metastasis-related microRNAs in lung adenocarcinoma and analysis of the underlying mechanisms using a bioinformatics approach. Exp Biol Med (Maywood) 2016; 242:709-717. [PMID: 28299977 DOI: 10.1177/1535370216677353] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
This study aimed to screen lymphatic metastasis-related microRNAs (miRNAs) in lung adenocarcinoma and explore their underlying mechanisms using bioinformatics. The miRNA expression in primary lung adenocarcinoma, matched adjacent non-tumorigenic and lymph node metastasis tissues of patients were profiled via microarray. The screened metastasis-related miRNAs were then validated using quantitative real-time PCR in a second cohort of lung adenocarcinoma patients with lymphatic metastasis. Significance was determined using a paired t-test. Target genes of the metastasis-related miRNAs were predicted using TargetScan, and transcription factors (TFs) were predicted based on the TRANSFAC and ENCODE databases. Furthermore, the related long non-coding RNAs (lncRNAs) were screened with starBase v2.0. The miRNA-TF-mRNA and lncRNA-miRNA-mRNA networks were constructed to determine the key interactions associated with lung adenocarcinoma metastasis. According to the miRNA microarray results, there were 10 miRNAs that were differentially expressed in metastatic tissues compared with primary tumor and adjacent non-tumorigenic tissues. Among them were increased levels of miR-146a-5p, miR-342-3p, and miR-150-5p, which were validated in the second cohort. Based on the miRNA-TF-mRNA network, vascular endothelial growth factor A and transcription factors (TFs) including TP53, SMAD4, and EP300 were recognized as critical targets of the three miRNAs. Interactions involving SNHG16-miR-146a-5p-SMAD4 and RP6-24A23.7-miR-342-3p/miR-150-5p-EP300 were highlighted according to the lncRNA-miRNA-mRNA network. miR-146a-5p, miR-342-3p, and miR-150-5p are lymphatic metastasis-related miRNAs in lung adenocarcinoma. Bioinformatics analyses demonstrated that SNHG16 might inhibit the interaction between miR-146a-5p and SMAD4, while RP6-24A23.7 might weaken miR-342-3p-EP300 and miR-150-5p-EP300 interactions in metastasis.
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Affiliation(s)
- Li Yan
- 1 Department of Oncology, The 117th Hospital of PLA, Hangzhou 310013, P.R. China
| | - Demin Jiao
- 2 Department of Respiratory Disease, The 117th Hospital of PLA, Hangzhou 310013, P.R. China
| | - Huizhen Hu
- 2 Department of Respiratory Disease, The 117th Hospital of PLA, Hangzhou 310013, P.R. China
| | - Jian Wang
- 2 Department of Respiratory Disease, The 117th Hospital of PLA, Hangzhou 310013, P.R. China
| | - Xiali Tang
- 2 Department of Respiratory Disease, The 117th Hospital of PLA, Hangzhou 310013, P.R. China
| | - Jun Chen
- 2 Department of Respiratory Disease, The 117th Hospital of PLA, Hangzhou 310013, P.R. China
| | - Qingyong Chen
- 2 Department of Respiratory Disease, The 117th Hospital of PLA, Hangzhou 310013, P.R. China
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31
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Sun J, Yan J, Yuan X, Yang R, Dan T, Wang X, Kong G, Gao S. A computationally constructed ceRNA interaction network based on a comparison of the SHEE and SHEEC cell lines. Cell Mol Biol Lett 2016; 21:21. [PMID: 28536623 PMCID: PMC5415789 DOI: 10.1186/s11658-016-0022-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2016] [Accepted: 09/10/2016] [Indexed: 12/16/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) play critical and complicated roles in the regulation of various biological processes, including chromatin modification, transcription and post-transcriptional processing. Interestingly, some lncRNAs serve as miRNA "sponges" that inhibit interaction with miRNA targets in post-transcriptional regulation. We constructed a putative competing endogenous RNA (ceRNA) network by integrating lncRNA, miRNA and mRNA expression based on high-throughput RNA sequencing and microarray data to enable a comparison of the SHEE and SHEEC cell lines. Using Targetscan and miRanda bioinformatics algorithms and miRTarbase microRNA-target interactions database, we established that 51 miRNAs sharing 13,623 MREs with 2260 genes and 82 lncRNAs were involved in this ceRNA network. Through a biological function analysis, the ceRNA network appeared to be primarily involved in cell proliferation, apoptosis, the cell cycle, invasion and metastasis. Functional pathway analyses demonstrated that the ceRNA network potentially modulated multiple signaling pathways, such as the MAPK, Ras, HIF-1, Rap1, and PI3K/Akt signaling pathways. These results might provide new clues to better understand the regulation of the ceRNA network in cancer.
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Affiliation(s)
- Jiachun Sun
- Department of Oncology, Cancer Institute, First Affiliated Hospital of Henan University of Science and Technology, Luoyang, People’s Republic of China
| | - Junqiang Yan
- Department of Neurology, Cancer Institute, First Affiliated Hospital of Henan University of Science and Technology, Luoyang, People’s Republic of China
| | - Xiaozhi Yuan
- Department of Oncology, Cancer Institute, First Affiliated Hospital of Henan University of Science and Technology, Luoyang, People’s Republic of China
| | - Ruina Yang
- Department of Oncology, Cancer Institute, First Affiliated Hospital of Henan University of Science and Technology, Luoyang, People’s Republic of China
| | - Tanyou Dan
- Department of Oncology, Cancer Institute, First Affiliated Hospital of Henan University of Science and Technology, Luoyang, People’s Republic of China
| | - Xinshuai Wang
- Department of Oncology, Cancer Institute, First Affiliated Hospital of Henan University of Science and Technology, Luoyang, People’s Republic of China
| | - Guoqiang Kong
- Department of Oncology, Cancer Institute, First Affiliated Hospital of Henan University of Science and Technology, Luoyang, People’s Republic of China
| | - Shegan Gao
- Department of Oncology, Cancer Institute, First Affiliated Hospital of Henan University of Science and Technology, Luoyang, People’s Republic of China
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32
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Li H, Wang Y, Wang Z, Guo X, Wang F, Xia XJ, Zhou J, Shi K, Yu JQ, Zhou YH. Microarray and genetic analysis reveals that csa-miR159b plays a critical role in abscisic acid-mediated heat tolerance in grafted cucumber plants. PLANT, CELL & ENVIRONMENT 2016; 39:1790-804. [PMID: 27037862 DOI: 10.1111/pce.12745] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2015] [Revised: 03/16/2016] [Accepted: 03/17/2016] [Indexed: 05/19/2023]
Abstract
Root-shoot communication plays a vital role in plant growth, development and adaptation to environmental stimuli. Grafting-induced stress tolerance is associated with the induction of plentiful stress-related genes and proteins; the mechanism involved, however, remains obscure. Here, we show that the enhanced tolerance against heat stress in cucumber plants with luffa as rootstock was accompanied with an increased accumulation of abscisic acid (ABA), down-regulation of a subset of microRNAs (miRNAs) but up-regulation of their target genes and CsHSP70 accumulation in the shoots. Significantly, luffa rootstock and foliar application of ABA both down-regulated csa-miR159b and up-regulated its target mRNAs CsGAMYB1 and CsMYB29-like and CsHSP70 accumulation in cucumber, while ectopic expression of csa-miR159b led to decreased heat tolerance, AtMYB33 transcript and AtHSP70 accumulation in Arabidopsis plants. Taken together, our results suggest that root-originated signals such as ABA could alter miRNAs in the shoots, which have a major role in the post-transcriptional regulation of the stress-responsive genes.
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Affiliation(s)
- Hao Li
- Department of Horticulture, Zijingang Campus, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, China
- College of Horticulture, Northwest A&F University, Yangling, 712100, China
| | - Yu Wang
- Department of Horticulture, Zijingang Campus, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, China
| | - Ze Wang
- Department of Horticulture, Zijingang Campus, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, China
| | - Xie Guo
- Department of Horticulture, Zijingang Campus, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, China
| | - Feng Wang
- Department of Horticulture, Zijingang Campus, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, China
| | - Xiao-Jian Xia
- Department of Horticulture, Zijingang Campus, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, China
| | - Jie Zhou
- Department of Horticulture, Zijingang Campus, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, China
| | - Kai Shi
- Department of Horticulture, Zijingang Campus, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, China
| | - Jing-Quan Yu
- Department of Horticulture, Zijingang Campus, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, China
| | - Yan-Hong Zhou
- Department of Horticulture, Zijingang Campus, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, China
- Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, 866 Yuhangtang Road, Hangzhou, 310058, China
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He SF, Zhu HJ, Han ZY, Wu H, Jin SY, Irwin MG, Zhang Y. MicroRNA-133b-5p Is Involved in Cardioprotection of Morphine Preconditioning in Rat Cardiomyocytes by Targeting Fas. Can J Cardiol 2016; 32:996-1007. [DOI: 10.1016/j.cjca.2015.10.019] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2015] [Revised: 10/20/2015] [Accepted: 10/22/2015] [Indexed: 12/11/2022] Open
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Pancreatic Acinar Cells Employ miRNAs as Mediators of Intercellular Communication to Participate in the Regulation of Pancreatitis-Associated Macrophage Activation. Mediators Inflamm 2016; 2016:6340457. [PMID: 27546996 PMCID: PMC4980583 DOI: 10.1155/2016/6340457] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2016] [Accepted: 06/22/2016] [Indexed: 12/27/2022] Open
Abstract
Macrophage activation plays an important role in the inflammatory response in acute pancreatitis. In the present study, the activation of AR42J pancreatic acinar cells was induced by taurolithocholate treatment. The results showed that the culture medium from the activated AR42J cells significantly enhanced NFκB activation in the macrophages compared to that without taurolithocholate treatment. Additionally, the precipitates obtained from ultracentrifugation of the culture media that were rich in exosomes were markedly more potent in activating macrophages compared with the supernatant fraction lacking exosomes. The results indicated that the mediators carried by the exosomes played important roles in macrophage activation. Exosomal miRNAs were extracted and examined using microarrays. A total of 115 differentially expressed miRNAs were identified, and 30 showed upregulated expression, while 85 displayed downregulated expression. Target genes of the differentially expressed miRNAs were predicted using TargetScan, MiRanda, and PicTar software programs. The putative target genes were subjected to KEGG functional analysis. The functions of the target genes were primarily enriched in MAPK pathways. Specifically, the target genes regulated macrophage activation through the TRAF6-TAB2-TAK1-NIK/IKK-NFκB pathway. As the mediators of signal transduction, miRNAs and their predicted target mRNAs regulate every step in the MAPK pathway.
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Chen Q, Hu H, Jiao D, Yan J, Xu W, Tang X, Chen J, Wang J. miR-126-3p and miR-451a correlate with clinicopathological features of lung adenocarcinoma: The underlying molecular mechanisms. Oncol Rep 2016; 36:909-17. [DOI: 10.3892/or.2016.4854] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Accepted: 02/18/2016] [Indexed: 11/06/2022] Open
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Ghosh SP, Pathak R, Kumar P, Biswas S, Bhattacharyya S, Kumar VP, Hauer-Jensen M, Biswas R. Gamma-Tocotrienol Modulates Radiation-Induced MicroRNA Expression in Mouse Spleen. Radiat Res 2016; 185:485-95. [PMID: 27128741 DOI: 10.1667/rr14248.1] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Ionizing radiation causes depletion of hematopoietic cells and enhances the risk of developing secondary hematopoietic malignancies. Vitamin E analog gamma-tocotrienol (GT3), which has anticancer properties, promotes postirradiation hematopoietic cell recovery by enhancing spleen colony-forming capacity, and provides protection against radiation-induced lethality in mice. However, the underlying molecular mechanism involved in GT3-mediated postirradiation survival is not clearly understood. Recent studies have shown that natural dietary products including vitamin E provide a benefit to biological systems by modulating microRNA (miR) expression. In this study, we show that GT3 differentially modulates the miR footprint in the spleen of irradiated mice compared to controls at early times (day 1), as well as later times (day 4 and 15) after total-body irradiation. We observed that miR expression was altered in a dose- and time-dependent manner in GT3-pretreated spleen tissues from total-body irradiated mice. GT3 appeared to affect the expression of a number of radiation-modulated miRs known to be involved in hematopoiesis and lymphogenesis. Moreover, GT3 pretreatment also suppressed the upregulation of radiation-induced p53, suggesting the function of GT3 in the prevention of radiation-induced damage to the spleen. In addition, we have shown that GT3 significantly reduced serum levels of Flt3L, a biomarker of radiation-induced bone marrow aplasia. Further in silico analyses of the effect of GT3 implied the association of p38 MAPK, ERK and insulin signaling pathways. Our study provides initial insight into the mechanism by which GT3 mediates protection of spleen after total-body irradiation.
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Affiliation(s)
- Sanchita P Ghosh
- a Armed Forces Radiobiology Research Institute, Uniformed Services University of the Health Sciences Scientific Research Department, Armed Forces Radiobiology Research Institute, Uniformed Services University of the Health Sciences, Bethesda, Maryland
| | - Rupak Pathak
- b Division of Radiation Health, University of Arkansas for Medical Sciences, Little Rock, Arkansas
| | - Parameet Kumar
- c Anatomy, Physiology and Genetics, School of Medicine, Uniformed Services University of the Health Sciences, Bethesda, Maryland; and
| | - Shukla Biswas
- a Armed Forces Radiobiology Research Institute, Uniformed Services University of the Health Sciences Scientific Research Department, Armed Forces Radiobiology Research Institute, Uniformed Services University of the Health Sciences, Bethesda, Maryland
| | | | - Vidya P Kumar
- a Armed Forces Radiobiology Research Institute, Uniformed Services University of the Health Sciences Scientific Research Department, Armed Forces Radiobiology Research Institute, Uniformed Services University of the Health Sciences, Bethesda, Maryland
| | - Martin Hauer-Jensen
- b Division of Radiation Health, University of Arkansas for Medical Sciences, Little Rock, Arkansas
| | - Roopa Biswas
- c Anatomy, Physiology and Genetics, School of Medicine, Uniformed Services University of the Health Sciences, Bethesda, Maryland; and
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Sun S, Fu H, Ge X, Zhu J, Gu Z, Xuan F. Identification and comparative analysis of the oriental river prawn ( Macrobrachium nipponense ) microRNA expression profile during hypoxia using a deep sequencing approach. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2016; 17:41-7. [DOI: 10.1016/j.cbd.2016.01.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2015] [Revised: 12/31/2015] [Accepted: 01/10/2016] [Indexed: 01/12/2023]
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Zheng HZ, Jiang W, Zhao XF, Du J, Liu PG, Chang LD, Li WB, Hu HT, Shi XM. Electroacupuncture induces acute changes in cerebral cortical miRNA profile, improves cerebral blood flow and alleviates neurological deficits in a rat model of stroke. Neural Regen Res 2016; 11:1940-1950. [PMID: 28197190 PMCID: PMC5270432 DOI: 10.4103/1673-5374.197135] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Electroacupuncture has been shown to improve cerebral blood flow in animal models of stroke. However, it is unclear whether electroacupuncture alters miRNA expression in the cortex. In this study, we examined changes in the cerebral cortical miRNA profile, cerebral blood flow and neurological function induced by electroacupuncture in a rat model of stroke. Electroacupuncture was performed at Renzhong (GV26) and Neiguan (PC6), with a frequency of 2 Hz, continuous wave, current intensity of 3.0 mA, and stimulation time of 1 minute. Electroacupuncture increased cerebral blood flow and alleviated neurological impairment in the rats. miRNA microarray profiling revealed that the vascular endothelial growth factor signaling pathway, which links cell proliferation with stroke, was most significantly affected by electroacupuncture. Electroacupuncture induced changes in expression of rno-miR-206-3p, rno-miR-3473, rno-miR-6216 and rno-miR-494-3p, and these changes were confirmed by quantitative real-time polymerase chain reaction. Our findings suggest that changes in cell proliferation-associated miRNA expression induced by electroacupuncture might be associated with the improved cerebral blood supply and functional recovery following stroke.
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Affiliation(s)
- Hai-Zhen Zheng
- VIP of Acupuncture Department, First Teaching Hospital of Tianjin University of Traditional Chinese Medicine, Tianjin, China; Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Wei Jiang
- Department of Acupuncture and Moxibustion, First Teaching Hospital of Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Xiao-Feng Zhao
- VIP of Acupuncture Department, First Teaching Hospital of Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Jing Du
- Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Pan-Gong Liu
- Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Li-Dan Chang
- Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Wen-Bo Li
- Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Han-Tong Hu
- Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Xue-Min Shi
- VIP of Acupuncture Department, First Teaching Hospital of Tianjin University of Traditional Chinese Medicine, Tianjin, China; Department of Acupuncture and Moxibustion, First Teaching Hospital of Tianjin University of Traditional Chinese Medicine, Tianjin, China
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Scalable amplification of strand subsets from chip-synthesized oligonucleotide libraries. Nat Commun 2015; 6:8634. [PMID: 26567534 PMCID: PMC4660042 DOI: 10.1038/ncomms9634] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2015] [Accepted: 09/14/2015] [Indexed: 02/01/2023] Open
Abstract
Synthetic oligonucleotides are the main cost factor for studies in DNA nanotechnology, genetics and synthetic biology, which all require thousands of these at high quality. Inexpensive chip-synthesized oligonucleotide libraries can contain hundreds of thousands of distinct sequences, however only at sub-femtomole quantities per strand. Here we present a selective oligonucleotide amplification method, based on three rounds of rolling-circle amplification, that produces nanomole amounts of single-stranded oligonucleotides per millilitre reaction. In a multistep one-pot procedure, subsets of hundreds or thousands of single-stranded DNAs with different lengths can selectively be amplified and purified together. These oligonucleotides are used to fold several DNA nanostructures and as primary fluorescence in situ hybridization probes. The amplification cost is lower than other reported methods (typically around US$ 20 per nanomole total oligonucleotides produced) and is dominated by the use of commercial enzymes.
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Huo X, Wang C, Teng Y, Liu X. Identification of miRNAs associated with dark-induced senescence in Arabidopsis. BMC PLANT BIOLOGY 2015; 15:266. [PMID: 26530097 PMCID: PMC4632659 DOI: 10.1186/s12870-015-0656-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2015] [Accepted: 10/28/2015] [Indexed: 05/25/2023]
Abstract
BACKGROUND microRNAs (miRNAs) are endogenous small (~21 nucleotide) single-stranded non-coding RNAs that typically function by guiding cleavage of target genes. To find the miRNAs that may be involved in dark-induced leaf senescence, we identified miRNAs by microarray platform using Arabidopsis thaliana leaves from both whole darkened plants (DPs) and individually darkened leaves (IDLs). RESULTS We found that the expressions of 137 miRNAs (P < 0.01, signal intensity >0) were significantly changed both in DP and IDL leaves. Among them, the expression levels of 44 miRNAs were relative higher than others (P < 0.01, signal intensity > 500). Of these differentially expressed miRNAs, 6 miRNAs (miR319a, 319c, miR159, miR164a, miR164c and miR390a) have been previously reported to be involved in dark-induced leaf senescence, and the remaining 38 miRNAs have not been implicated in leaf senescence before. Target genes of all 44 miRNAs were predicted, and some of them, such as NAC1, At3g28690, At2g17640 and At2g45160, were found in the Leaf Senescence Database (LSD). GO and KEGG analysis of 137 miRNAs showed that the predicted target genes were significantly enriched in transcription regulation, development-related biological processes and metabolic pathways. Expression levels of some of the corresponding miRNA targets (At1g73440, At2g03220 and At5g54810) were analysed and found to be significantly different in DP/IDL than that in WT. CONCLUSIONS A microarray analysis about dark-induced miRNAs involved in leaf senescence are present here. Further expression analysis revealed that some new founding miRNAs maybe regulate leaf senescence in Arabidopsis, and the findings highlight the important role of miRNAs in dark-induced leaf senescence.
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Affiliation(s)
- Xiaoying Huo
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 310036, P. R. China.
| | - Chao Wang
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 310036, P. R. China.
| | - Yibo Teng
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 310036, P. R. China.
| | - Xunyan Liu
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 310036, P. R. China.
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Hirai H, Firpo M, Kikyo N. Establishment of leukemia inhibitory factor (LIF)-independent iPS cells with potentiated Oct4. Stem Cell Res 2015; 15:469-480. [PMID: 26413786 DOI: 10.1016/j.scr.2015.09.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/29/2015] [Revised: 09/02/2015] [Accepted: 09/09/2015] [Indexed: 11/30/2022] Open
Abstract
Leukemia inhibitory factor (LIF) is widely used to establish and maintain naïve pluripotent stem cells, including mouse embryonic stem cells (ESCs) and induced pluripotent stem cells (iPSCs). Although the combination of chemical inhibitors called 2i can establish mouse iPSCs without LIF from primed pluripotent stem cells, it has been difficult, if not impossible, to establish mouse iPSCs from differentiated somatic cells without LIF. We previously showed that the fusion gene of the transactivation domain of MyoD and the full-length Oct4 (M3O) increases the efficiency of making iPSCs when transduced into fibroblasts along with Sox2, Klf4, and c-Myc (M3O-SKM). Here, we report that M3O-SKM allows for establishment of iPSCs without exogenous LIF from mouse embryonic fibroblasts. The established iPSCs remained undifferentiated and maintained pluripotency over 90 days without LIF as long as M3O was expressed. The iPSCs upregulated miR-205-5p, which was potentially involved in the LIF-independence by suppressing the two signaling pathways inhibited by 2i. The result indicates that potentiated Oct4 can substitute for the LIF signaling pathway, providing a novel model to link Oct4 and LIF, two of the most significant players in naïve pluripotency.
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Affiliation(s)
- Hiroyuki Hirai
- Stem Cell Institute, University of Minnesota, Minneapolis, Minnesota 55455, USA; Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, Minnesota 55455, USA
| | - Meri Firpo
- Stem Cell Institute, University of Minnesota, Minneapolis, Minnesota 55455, USA; Division of Endocrinology, Department of Medicine, University of Minnesota, Minneapolis, Minnesota 55455, USA
| | - Nobuaki Kikyo
- Stem Cell Institute, University of Minnesota, Minneapolis, Minnesota 55455, USA; Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, Minnesota 55455, USA.
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Gutiérrez-Escolano A, Santacruz-Vázquez E, Gómez-Pérez F. Dysregulated microRNAs involved in contrast-induced acute kidney injury in rat and human. Ren Fail 2015; 37:1498-506. [PMID: 26337190 DOI: 10.3109/0886022x.2015.1077322] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Contrast-induced nephropathy (CIN) is a complex syndrome of acute nephropathy that occurs following infusion of intravascular contrast agents, and is associated with an increased risk for adverse cardiovascular events. While there is no ideal biomarker for making an early diagnosis of CIN, we hypothesized that levels of specific circulating microRNA (miRNA) species might serve such a role. METHODS miRNA microarray assays were used to detect miRNAs in the kidney tissue of rats studied as an animal model of CIN. Real-time PCR was performed to validate results of the microarray assays. Kidney-enriched miRNAs detected in rat plasma were used as biomarkers to screen for CIN. Results obtained from the rat model of CIN were further validated in human patients with CIN. RESULTS Fifty-one miRNAs were aberrantly expressed in the kidney tissues between CIN and control rats; and among these, 17 miRNAs showed a >2-fold change of expression in the kidney tissues of CIN rats when compared with their expressions in non-CIN control rats. Among the 17 miRNAs aberrantly-expressed miRNAs screened from kidney tissue, only six also showed significantly different expression in the plasma of CIN rats. When compared with their levels in non-CIN control rats, the levels of three miR-30 family members (miR-30a, miR-30c, and miR-30e), as well as miR-320, were significantly increased in the plasma of CIN rats, while the plasma levels of miRNAs let-7a and miR-200a were significantly decreased. In a validation study of these results conducted with human plasma samples, only miR-30a, miR-30c, and miR-30e showed > 2-fold increases in CIN patients when compared with non-CIN patients. Receiver operating curves constructed to examine the abilities of miR-30a, miR-30c, and miR-30e to discriminate CIN patients from non-CIN patients showed AUCs of 0.954, 0.888, and 0.835, respectively. CONCLUSIONS Our study provides the first evidence that plasma miRNAs, and especially three miR-30 family members (miR-30a, miR-30c, and miR-30e), might serve as early biomarkers and (or) target candidates for CIN.
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Affiliation(s)
- A Gutiérrez-Escolano
- a Posgrado en Ciencias Genómicas, Universidad Autónoma de la Ciudad de México , México DF , Mexico
| | - E Santacruz-Vázquez
- a Posgrado en Ciencias Genómicas, Universidad Autónoma de la Ciudad de México , México DF , Mexico
| | - F Gómez-Pérez
- a Posgrado en Ciencias Genómicas, Universidad Autónoma de la Ciudad de México , México DF , Mexico
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Yazdi SMHT, Kiah HM, Garcia-Ruiz E, Ma J, Zhao H, Milenkovic O. DNA-Based Storage: Trends and Methods. ACTA ACUST UNITED AC 2015. [DOI: 10.1109/tmbmc.2016.2537305] [Citation(s) in RCA: 117] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Evidence for Epigenetic Regulation of Gene Expression and Function in Chronic Experimental Diabetic Neuropathy. J Neuropathol Exp Neurol 2015; 74:804-17. [DOI: 10.1097/nen.0000000000000219] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
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Chen QY, Jiao DM, Zhu Y, Hu H, Wang J, Tang X, Chen J, Yan L. Identification of carcinogenic potential-associated molecular mechanisms in CD133(+) A549 cells based on microRNA profiles. Tumour Biol 2015; 37:521-30. [PMID: 26227219 DOI: 10.1007/s13277-015-3675-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2015] [Accepted: 06/15/2015] [Indexed: 12/16/2022] Open
Abstract
This study aimed to identify carcinogenic potential-related molecular mechanisms in cancer stem cells (CSCs) in lung cancer. CD133(+) and CD133(-) subpopulations were sorted from A549 cells using magnetic-activated cell sorting. The abilities to form sphere and clone, proliferate, migrate, and invade were compared between CD133(+) and CD133(-) cells, as well as drug sensitivity. Thereafter, microRNA (miRNA) profiles were performed to identify differentially expressed miRNAs between CD133(+) and CD133(-) subpopulation. Following, bioinformatic methods were used to predict target genes for differentially expressed miRNAs and perform enrichment analysis. Furthermore, the mammalian target of rapamycin (mTOR) signaling pathways and CSC property-associated signaling pathways were explored and visualized in regulatory network among competitive endogenous RNA (ceRNA), miRNA, and target gene. CD133(+) subpopulation showed greater oncogenic potential than CD133(-) subpopulation. In all, 14 differentially expressed miRNAs were obtained and enriched in 119 pathways, including five upregulated (hsa-miR-23b-3p, -23a-3p, -15b-5p, -24-3p, and -4734) and nine downregulated (hsa-miR-1246, -30b-5p, -5096, -6510-5p, has-miR-7110-5p, -7641, -3197, -7108-5p, and -6791-5p). For mTOR signaling pathway, eight differential miRNAs (hsa-miR-23b-3p, -23a-3p, -15b-5p, -24-3p, -4734, -1246, -7641, and -3197) and 39 target genes (e.g., AKT1, AKT2, PIK3CB, PIK3CG, PIK3R1, PIK3CA, and PIK3CD) were involved, as well as some ceRNAs. Besides, for CSC property-related signaling pathways, six miRNAs (hsa-miR-1246, -15b-5p, -30b-5p, -3197, -4734, and -7110-5p) were dramatically enriched in Hedgehog, Notch, and Wnt signaling pathways via regulating 108 target genes (e.g., DVL1, DVL3, WNT3A, and WNT5A). The mTOR and CSC property-associated signaling pathways may be important oncogenic molecular mechanisms in CD133(+) A549 cells.
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Affiliation(s)
- Qing-Yong Chen
- The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325000, Zhejiang Province, People's Republic of China. .,Department of Respiratory Disease, The 117th Hospital of PLA, Hangzhou, 310013, Zhejiang Province, People's Republic of China.
| | - De-Min Jiao
- Department of Respiratory Disease, The 117th Hospital of PLA, Hangzhou, 310013, Zhejiang Province, People's Republic of China
| | - Ya Zhu
- Department of Oncology, The 117th Hospital of PLA, Hangzhou, 310013, Zhejiang Province, People's Republic of China
| | - Huizhen Hu
- Department of Respiratory Disease, The 117th Hospital of PLA, Hangzhou, 310013, Zhejiang Province, People's Republic of China
| | - Jian Wang
- Department of Respiratory Disease, The 117th Hospital of PLA, Hangzhou, 310013, Zhejiang Province, People's Republic of China
| | - Xiali Tang
- Department of Respiratory Disease, The 117th Hospital of PLA, Hangzhou, 310013, Zhejiang Province, People's Republic of China
| | - Jun Chen
- Department of Respiratory Disease, The 117th Hospital of PLA, Hangzhou, 310013, Zhejiang Province, People's Republic of China
| | - Li Yan
- Department of Oncology, The 117th Hospital of PLA, Hangzhou, 310013, Zhejiang Province, People's Republic of China.
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Sun W, Pei L. microRNA Expression Profiling of Propofol-Treated Developing Rat Hippocampal Astrocytes. DNA Cell Biol 2015; 34:511-23. [PMID: 26083276 DOI: 10.1089/dna.2015.2831] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Although propofol exerts toxic effects on the developing central nervous system (CNS), it remains a first-choice anesthetic in the pediatric population. Astrocytes represent a major glial cell population whose role in CNS development is widely appreciated and that has been recently shown to be mediated in large part by microRNAs (miRNAs). In contrast, relatively little is known about the roles of miRNAs in developing astrocytes during propofol treatment. Here, miRNA microarray was used to profile fluctuations in miRNA expression in immature hippocampal astrocytes in response to propofol treatment, and results were subsequently validated using quantitative real-time polymerase chain reaction. Predictive analysis of genes targeted by propofol-regulated miRNAs indicated enrichment of genes in the gene ontology (GO) nervous system development and differentiation category, and in the Kyoto encyclopedia of genes and genomes (KEGG) apoptotic pathway category. A total of 24 (10 short-term dosage and 14 long-term dosage) miRNAs were significantly regulated, one of which was rno-miR-665. Ectopic overexpression and silencing of rno-miR-665 demonstrated its role in the neurotoxic effects of propofol on hippocampal immature astrocytes. We present evidence that the role of rno-miR-665 in anesthesia-induced disturbances in astroglia development may involve direct downregulation of the anti-apoptotic gene Bcl2l1, and subsequent increased caspase-3-mediated apoptosis. Our results shed light on the anesthetic mechanism of propofol and have implications for its use in the clinical setting.
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Affiliation(s)
- Wenchong Sun
- Department of Anesthesiology, The First Affiliated Hospital, China Medical University , Shenyang, China
| | - Ling Pei
- Department of Anesthesiology, The First Affiliated Hospital, China Medical University , Shenyang, China
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Gong G, Sha Z, Chen S, Li C, Yan H, Chen Y, Wang T. Expression profiling analysis of the microRNA response of Cynoglossus semilaevis to Vibrio anguillarum and other stimuli. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2015; 17:338-352. [PMID: 25715708 DOI: 10.1007/s10126-015-9623-2] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2014] [Accepted: 01/14/2015] [Indexed: 06/04/2023]
Abstract
To investigate the roles of microRNAs (miRNA) of Cynoglossus semilaevis in response to Vibrio anguillarum that were previously identified using high-throughput sequencing, microarray analyses was performed on three small RNA libraries (CG, NOSG, and HOSG) prepared from C. semilaevis immune tissues. In total, of 1279 designed probes, 739 (57.78 %) were detectable. The expression levels of these miRNAs were analyzed using pairwise comparisons among the three libraries, and a total of 99 miRNAs were observed to be significantly differentially expressed. The expression patterns of 10 differentially expressed miRNAs were validated by real-time quantitative PCR (RT-qPCR). In addition, expression of miR-142-5p, miR-223, and miR-181a in response to V. anguillarum at numerous time-points in four tissues, as well as the responses to lipopolysaccharide (LPS), polyinosinic:polycytidylic acid (poly I:C), peptidoglycan (PGN), and red-spotted grouper nervous necrosis virus (RGNNV) in head kidney cells, were studied by qRT-PCR. Taken together, all of the expression profiles showed significant differences compared to the control group; both similarities and differences in the expression responses to the same pathogen were observed. Collectively, these findings highlighted the putative roles for miRNAs in the context of the innate immune response of C. semilaevis exposing to pathogens and that further studies are needed to understand the molecular mechanisms of miRNA regulation in C. semilaevis host-pathogen interactions.
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Affiliation(s)
- Guangye Gong
- Key Laboratory for Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, People's Republic of China
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Xun M, Ma CF, Du QL, Ji YH, Xu JR. Differential expression of miRNAs in enterovirus 71-infected cells. Virol J 2015; 12:56. [PMID: 25889836 PMCID: PMC4416288 DOI: 10.1186/s12985-015-0288-2] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2014] [Accepted: 03/24/2015] [Indexed: 12/17/2022] Open
Abstract
Background Enterovirus 71 (EV71) is one of the major etiological pathogens of hand, foot and mouth disease (HFMD) and can cause severe cerebral and pulmonary complications and even fatality. MicroRNAs (miRNAs), a class of small non-coding RNA molecules, play an important role in post-transcriptional regulation of gene expression and thereby influencing various physiological and pathological processes. Increasing evidence suggests that miRNAs act as key effector molecules in the complicated pathogen-host interactions. However, the roles of miRNAs in EV71 infection and pathogenesis are not well understood. Methods To identify special miRNAs involved in EV71 infection, a microarray assay was performed to study the expression pattern of miRNAs in EV71-infected human rhabdomyosarcoma cells (RD cells) and uninfected RD cells. We further predicted the putative target genes for the dysregulated miRNAs using the online bioinformatic algorithms (TargetScan, miRanda and PicTar) and carried out functional annotation including GO enrichment and KEGG pathway analysis for miRNA predicted targets. Then, the results of microarray were further confirmed by quantitative RT-PCR. Results Totally, 45 differentially expressed miRNAs ware identified by microarray, among which 36 miRNAs were up-regulated and 9 were down-regulated. 7166 predicted target genes for the dysregulated miRNAs were revealed by using TargetScan in conjunction with miRanda and PicTar. The GO annotation suggested that predicted targets of miRNAs were enriched into the category of signal transduction, regulation of transcription, metabolic process, protein phosphorylation, apoptotic process and immune response. KEGG pathway analysis suggested that these predicted target genes were involved in many important pathways, mainly including endocytosis and focal adhesion, MAPK signaling pathway, hypertrophic cardiomyopathy, melanogenesis and ErbB signaling pathway. The expression levels of 8 most differentially up-regulated miRNAs and 3 most differentially down-regulated miRNAs were confirmed by qRT-PCR. The expressions of hsa-miR-4530, hsa-miR-4492, hsa-miR-6125, hsa-miR-494-3p, hsa-miR-638, hsa-miR-6743-5p, hsa-miR-4459 and hsa-miR-4443 detected by qRT-PCR were consistent with the microarray data. Conclusion These results might extend our understanding to the regulatory mechanism of miRNAs underlying the pathogenesis of EV71 infection, thus strengthening the preventative and therapeutic strategies of HFMD caused by EV71.
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Affiliation(s)
- Meng Xun
- Department of Immunology and Microbiology, Medical School of Xi'an Jiaotong University, Xi'an, 710061, Shaanxi, China.
| | - Chao-Feng Ma
- Department of Viral Diseases Laboratory, Xi'an Center for Disease Control and Prevention, Xi'an, 710054, Shaanxi, China.
| | - Quan-Li Du
- Department of Viral Diseases Laboratory, Xi'an Center for Disease Control and Prevention, Xi'an, 710054, Shaanxi, China.
| | - Yan-Hong Ji
- Department of Immunology and Microbiology, Medical School of Xi'an Jiaotong University, Xi'an, 710061, Shaanxi, China.
| | - Ji-Ru Xu
- Department of Immunology and Microbiology, Medical School of Xi'an Jiaotong University, Xi'an, 710061, Shaanxi, China.
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Aptamer Microarrays—Current Status and Future Prospects. MICROARRAYS 2015; 4:115-32. [PMID: 27600216 PMCID: PMC4996391 DOI: 10.3390/microarrays4020115] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/30/2015] [Revised: 03/09/2015] [Accepted: 03/18/2015] [Indexed: 12/16/2022]
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