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Zheng Y, Li X, Huang Y, Jia L, Li W. Time series clustering of mRNA and lncRNA expression during osteogenic differentiation of periodontal ligament stem cells. PeerJ 2018; 6:e5214. [PMID: 30038865 PMCID: PMC6052852 DOI: 10.7717/peerj.5214] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2018] [Accepted: 06/21/2018] [Indexed: 12/12/2022] Open
Abstract
Background Long noncoding RNAs (lncRNAs) are regulatory molecules that participate in biological processes such as stem cell differentiation. Periodontal ligament stem cells (PDLSCs) exhibit great potential for the regeneration of periodontal tissue and the formation of new bone. However, although several lncRNAs have been found to be involved in the osteogenic differentiation of PDLSCs, the temporal transcriptomic landscapes of mRNAs and lncRNAs need to be mapped to obtain a complete picture of osteoblast differentiation. In this study, we aimed to characterize the time-course expression patterns of lncRNAs during the osteogenic differentiation of PDLSCs and to identify the lncRNAs that are related to osteoblastic differentiation. Methods We cultured PDLSCs in an osteogenic medium for 3, 7, or 14 days. We then used RNA sequencing (RNA-seq) to analyze the expression of the coding and non-coding transcripts in the PDLSCs during osteogenic differentiation. We also utilized short time-series expression miner (STEM) to describe the temporal patterns of the mRNAs and lncRNAs. We then performed Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analyses to assess the biological relevance of genes in each profile, and used quantitative real-time PCR (qRT-PCR) to validate the differentially expressed mRNAs and lncRNAs that were associated with osteoblast differentiation. Lastly, we performed a knock down of two lncRNAs, MEG8, and MIR22HG, and evaluated the expression of osteogenic markers. Results When PDLSCs were differentiated to osteoblasts, mRNAs associated with bone remodeling, cell differentiation, and cell apoptosis were upregulated while genes associated with cell proliferation were downregulated. lncRNAs showed stage-specific expression, and more than 200 lncRNAs were differentially expressed between the undifferentiated and osteogenically differentiated PDLSCs. Using STEM, we identified 25 temporal gene expression profiles, among which 14 mRNA and eight lncRNA profiles were statistically significant. We found that genes in pattern 12 were associated with osteoblast differentiation. The expression patterns of osteogenic mRNAs (COL6A1, VCAN, RRBP1, and CREB3L1) and lncRNAs (MEG8 and MIR22HG) were consistent between the qRT-PCR and RNA-seq results. Moreover, the knockdown of MEG8 and MIR22HG significantly decreased the expression of osteogenic markers (runt-related transcription factor 2 and osteocalcin). Discussion During the osteogenic differentiation of PDLSCs, both mRNAs and lncRNAs showed stage-specific expression. lncRNAs MEG8 and MIR22HG showed a high correlation with osteoblastogenesis. Our results can be used to gain a more comprehensive understanding of the molecular events regulating osteoblast differentiation and the identification of functional lncRNAs in PDLSCs.
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Affiliation(s)
- Yunfei Zheng
- Department of Orthodontics, Peking University School and Hospital of Stomatology, Beijing, China
| | - Xiaobei Li
- Department of Orthodontics, Peking University School and Hospital of Stomatology, Beijing, China
| | - Yiping Huang
- Department of Orthodontics, Peking University School and Hospital of Stomatology, Beijing, China
| | - Lingfei Jia
- Department of Oral and Maxillofacial Surgery, Peking University School and Hospital of Stomatology, Beijing, China.,Central Laboratory, Peking University School and Hospital of Stomatology, Beijing, China
| | - Weiran Li
- Department of Orthodontics, Peking University School and Hospital of Stomatology, Beijing, China
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Chen L, Dzakah EE, Shan G. Targetable long non-coding RNAs in cancer treatments. Cancer Lett 2018; 418:119-124. [PMID: 29341880 DOI: 10.1016/j.canlet.2018.01.042] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Revised: 12/25/2017] [Accepted: 01/09/2018] [Indexed: 02/09/2023]
Abstract
Aberrant expression of many long non-coding RNAs has been observed in various types of cancer, implicating their crucial roles in tumorigenesis and cancer progression. Emerging knowledge with regard to the critical physiological and pathological roles of long non-coding RNAs in cancers makes them potential targets in cancer treatments. In this review, we present a summary of the relatively well studied long non-coding RNAs that are involved in oncogenesis and outline their functions and functional mechanisms. Recent findings that may be utilized in therapeutic intervention are also highlighted. With the fast development in nucleic acid-based therapeutic reagents that can target disease associated RNAs, lncRNAs should be explored as potential targets in cancer treatments.
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Affiliation(s)
- Liang Chen
- CAS Key Laboratory of Innate Immunity and Chronic Disease, CAS Center for Excellence in Molecular Cell Science, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui Province 230027, China.
| | - Emmanuel Enoch Dzakah
- CAS Key Laboratory of Innate Immunity and Chronic Disease, CAS Center for Excellence in Molecular Cell Science, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui Province 230027, China
| | - Ge Shan
- CAS Key Laboratory of Innate Immunity and Chronic Disease, CAS Center for Excellence in Molecular Cell Science, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui Province 230027, China.
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Primate-specific Long Non-coding RNAs and MicroRNAs. GENOMICS PROTEOMICS & BIOINFORMATICS 2017; 15:187-195. [PMID: 28602844 PMCID: PMC5487532 DOI: 10.1016/j.gpb.2017.04.002] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Revised: 03/25/2017] [Accepted: 04/05/2017] [Indexed: 12/21/2022]
Abstract
Non-coding RNAs (ncRNAs) are critical regulators of gene expression in essentially all life forms. Long ncRNAs (lncRNAs) and microRNAs (miRNAs) are two important RNA classes possessing regulatory functions. Up to date, many primate-specific ncRNAs have been identified and investigated. Their expression specificity to primate lineage suggests primate-specific roles. It is thus critical to elucidate the biological significance of primate or even human-specific ncRNAs, and to develop potential ncRNA-based therapeutics. Here, we have summarized the studies regarding regulatory roles of some key primate-specific lncRNAs and miRNAs.
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Tan D, Wu Y, Hu L, He P, Xiong G, Bai Y, Yang K. Long noncoding RNA H19 is up-regulated in esophageal squamous cell carcinoma and promotes cell proliferation and metastasis. Dis Esophagus 2017; 30:1-9. [PMID: 27247022 DOI: 10.1111/dote.12481] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Long noncoding RNAs (lncRNAs) have been shown to play various roles in tumorigenesis, among which lncRNA H19 has been revealed as an ambivalent factor that acts as both an oncogene and a tumor suppressor in carcinogenesis. However, the exact biological role of H19 in esophageal squamous cell carcinoma (ESCC) remains to be determined. The aim of this study was to examine the expression pattern of H19 in ESCC and evaluate its biological role and clinical significance in the progression of ESCC. Expression of H19 was analyzed in 64 ESCC tissues and four ESCC cell lines by quantitative reverse-transcription polymerase chain reaction (qRT-PCR). Proliferation, cell cycle, migration, and invasion assays were performed in ESCC cell lines following knockdown of H19 to determine the biological function of H19 in the progression of ESCC both in vitro and in vivo. Western blot analysis was also performed to identify the potential mechanisms involved. H19 was highly expressed both in ESCC samples and cell lines compared with corresponding normal counterparts. The up-regulation of of H19 was significantly correlated with ESCC clinical stage and lymph node metastasis. Knockdown of H19 not only exerted inhibitory effect on tumor proliferation in vitro and in vivo, but also repressed the migratory and invasive capacity. G0/G1 phase arrest was also found in H19 knockdown cell lines. In addition, silencing of H19 up-regulated epithelial marker E-cadherin while down-regulating mesenchymal marker vimentin and metastasis-associated protein such as MMP-9. These findings indicate that H19 acts as an oncogene and promotes ESCC cell proliferation and metastasis, which may infer H19 as a marker of poor prognosis and, thus, a potential therapeutic target for treating ESCC patients.
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Affiliation(s)
- Deli Tan
- Department of Cardiothoracic Surgery, Southwest Hospital, Chongqing, China
| | - Yuanyuan Wu
- Department of Medical Genetics, College of Basic Medical Science, Third Military Medical University, Chongqing, China
| | - Liwen Hu
- Department of Cardiothoracic Surgery, Southwest Hospital, Chongqing, China
| | - Ping He
- Department of Cardiothoracic Surgery, Southwest Hospital, Chongqing, China
| | - Gang Xiong
- Department of Cardiothoracic Surgery, Southwest Hospital, Chongqing, China
| | - Yun Bai
- Department of Medical Genetics, College of Basic Medical Science, Third Military Medical University, Chongqing, China
| | - Kang Yang
- Department of Cardiothoracic Surgery, Southwest Hospital, Chongqing, China
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Jin H, Wang N, Wang C, Qin W. MicroRNAs in hypoxia and acidic tumor microenvironment. ACTA ACUST UNITED AC 2014. [DOI: 10.1007/s11434-014-0273-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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Meng L, Chen L, Li Z, Wu ZX, Shan G. Roles of microRNAs in the Caenorhabditis elegans nervous system. J Genet Genomics 2013; 40:445-52. [PMID: 24053946 DOI: 10.1016/j.jgg.2013.07.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2013] [Revised: 07/05/2013] [Accepted: 07/08/2013] [Indexed: 12/11/2022]
Abstract
The first microRNA was discovered in Caenorhabditis elegans in 1993, and since then, thousands of microRNAs have been identified from almost all eukaryotic organisms examined. MicroRNAs function in many biological events such as cell fate determination, metabolism, apoptosis, and carcinogenesis. So far, more than 250 microRNAs have been identified in C. elegans; however, functions for most of these microRNAs are still unknown. A small number of C. elegans microRNAs are associated with known physiological roles such as developmental timing, cell differentiation, stress response, and longevity. In this review, we summarize known roles of microRNAs in neuronal differentiation and function of C. elegans, and discuss interesting perspectives for future studies.
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Affiliation(s)
- Lingfeng Meng
- School of Life Science and Technology, Huazhong University of Science and Technology, 1037 Luoyu Road, Wuhan 430074, China
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Yang L, Meng Y, Bao C, Liu W, Ma C, Li A, Xuan Z, Shan G, Jia Y. Robustness and backbone motif of a cancer network regulated by miR-17-92 cluster during the G1/S transition. PLoS One 2013; 8:e57009. [PMID: 23469179 PMCID: PMC3585929 DOI: 10.1371/journal.pone.0057009] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2012] [Accepted: 01/16/2013] [Indexed: 11/18/2022] Open
Abstract
Based on interactions among transcription factors, oncogenes, tumor suppressors and microRNAs, a Boolean model of cancer network regulated by miR-17-92 cluster is constructed, and the network is associated with the control of G1/S transition in the mammalian cell cycle. The robustness properties of this regulatory network are investigated by virtue of the Boolean network theory. It is found that, during G1/S transition in the cell cycle process, the regulatory networks are robustly constructed, and the robustness property is largely preserved with respect to small perturbations to the network. By using the unique process-based approach, the structure of this network is analyzed. It is shown that the network can be decomposed into a backbone motif which provides the main biological functions, and a remaining motif which makes the regulatory system more stable. The critical role of miR-17-92 in suppressing the G1/S cell cycle checkpoint and increasing the uncontrolled proliferation of the cancer cells by targeting a genetic network of interacting proteins is displayed with our model.
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Affiliation(s)
- Lijian Yang
- Institute of Biophysics and Department of Physics, Central China Normal University, Wuhan, China
| | - Yan Meng
- Institute of Biophysics and Department of Physics, Central China Normal University, Wuhan, China
| | - Chun Bao
- Institute of Biophysics and Department of Physics, Central China Normal University, Wuhan, China
- School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Wangheng Liu
- Institute of Biophysics and Department of Physics, Central China Normal University, Wuhan, China
| | - Chengzhang Ma
- Institute of Biophysics and Department of Physics, Central China Normal University, Wuhan, China
| | - Anbang Li
- Institute of Biophysics and Department of Physics, Central China Normal University, Wuhan, China
| | - Zhan Xuan
- Institute of Biophysics and Department of Physics, Central China Normal University, Wuhan, China
| | - Ge Shan
- School of Life Sciences, University of Science and Technology of China, Hefei, China
- * E-mail: (YJ); (GS)
| | - Ya Jia
- Institute of Biophysics and Department of Physics, Central China Normal University, Wuhan, China
- * E-mail: (YJ); (GS)
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Hu S, Wu J, Chen L, Shan G. Signals from noncoding RNAs: unconventional roles for conventional pol III transcripts. Int J Biochem Cell Biol 2012; 44:1847-51. [PMID: 22819850 DOI: 10.1016/j.biocel.2012.07.013] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2012] [Revised: 07/06/2012] [Accepted: 07/09/2012] [Indexed: 12/29/2022]
Abstract
A range of noncoding RNAs are transcribed by pol III. A lot of them such as tRNA, 7SL RNA, 7SK RNA, 5S RNA, MRP RNA, Y RNAs, H1 RNA, and vault RNAs are considered as "house keeping" RNAs essential for eukaryotic cells. In recent years, researchers started to recognize the existence of unconventional functions of many pol III transcripts other than classical "house keeping" roles. Therefore, these ncRNAs could now be viewed as molecules with functional regulatory signals as well as cellular building blocks. These noncoding RNAs, all transcribed by pol III, may assemble regulatory networks with analogy to signaling pathways in eukaryotic cells. In this review we discuss these unconventional roles of pol III transcripts.
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Affiliation(s)
- Shanshan Hu
- School of Life Science, University of Science and Technology of China, 443 Huangshan Road, Hefei, Anhui Province 230027, China
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