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Small RNA-directed epigenetic programming of embryonic stem cell cardiac differentiation. Sci Rep 2017; 7:41799. [PMID: 28165496 PMCID: PMC5292948 DOI: 10.1038/srep41799] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Accepted: 12/30/2016] [Indexed: 02/06/2023] Open
Abstract
Microinjection of small noncoding RNAs in one-cell embryos was reported in several instances to result in transcriptional activation of target genes. To determine the molecular mechanisms involved and to explore whether such epigenetic regulations could play a role in early development, we used a cell culture system as close as possible to the embryonic state. We report efficient cardiac differentiation of embryonic stem (ES) cells induced by small non-coding RNAs with sequences of Cdk9, a key player in cardiomyocyte differentiation. Transfer of oligoribonucleotides representing parts of the Cdk9 mRNA into ES and mouse embryo fibroblast cultures resulted in upregulation of transcription. Dependency on Argonaute proteins and endogenous antisense transcripts indicated that the inducer oligoribonucleotides were processed by the RNAi machinery. Upregulation of Cdk9 expression resulted in increased efficiency of cardiac differentiation suggesting a potential tool for stem cell-based regenerative medicine.
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52
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Target-Recognition Mechanism and Specificity of RNA Activation. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017. [DOI: 10.1007/978-981-10-4310-9_3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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53
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Bilichak A, Golubov A, Kovalchuk I. Small RNA Library Preparation and Illumina Sequencing in Plants. Methods Mol Biol 2017; 1456:189-196. [PMID: 27770367 DOI: 10.1007/978-1-4899-7708-3_15] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The discovery of small RNAs in plants and animals almost two decades ago attracted a significant interest towards epigenetic regulation of gene expression and the practical implementation of the gained knowledge in applied studies. New and sometimes unexpected functions have been ascribed to sRNAs almost every couple of years since their discovery, hence indicating that the complete role of sRNAs in plant and animal physiology is still barely understood. Next-generation sequencing technologies allow to generate high-resolution profiles of sRNAs for the consequent analysis and possibly to discover novel functions of sRNAs. In this chapter, we provide brief guidelines for sRNA library preparation in plants and a practical approach that can be implemented to overcome possible difficulties with sequencing library generation.
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Affiliation(s)
- Andriy Bilichak
- Lethbridge Research Centre, Agriculture and Agri-Food Canada, Lethbridge, AB, Canada
| | - Andrey Golubov
- Department of Biological Sciences, University of Lethbridge, 4401 University Drive, Lethbridge, AB, Canada, T1K 3M4
| | - Igor Kovalchuk
- Department of Biological Sciences, University of Lethbridge, 4401 University Drive, Lethbridge, AB, Canada, T1K 3M4.
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55
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Li B, Li C. Suppression of Prostate Cancer Metastasis by DPYSL3-Targeted saRNA. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017. [DOI: 10.1007/978-981-10-4310-9_15] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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56
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Xie D, Shang L, Peng L, Li L. Up-regulation of VEZT by small activating RNA inhibits the proliferation, invasion and migration of gastric cancer cells. Biochem Biophys Res Commun 2016; 482:542-548. [PMID: 27856244 DOI: 10.1016/j.bbrc.2016.11.071] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Accepted: 11/12/2016] [Indexed: 02/07/2023]
Abstract
OBJECTIVE To identify an effective saRNA sequence that can specifically up-regulate VEZT expression and to determine the influence of saRNA had on gastric cancer cell growth, proliferation, invasion and migration. METHODS Three various saRNAs, that target the VEZT gene promoter at different locations relative to the transcription start site were synthesized. A dsControl saRNA was synthesized as a negative control, and a specific shRNA was synthesized to knockdown VEZT and eliminate any off-target effects of the saRNA. Both SGC-7901 and M-28 cells were either transfected with the different saRNAs, or treated with Lipofectamine2000 alone. To determine the most effective saRNA, real-time PCR and Western blot were used to determine the VEZT mRNA and protein content, respectively, of each treatment group. After selection, both cell lines were treated with the chosen saRNA, dsControl or Lipofectamine2000. The saRNA treated cells were divided into two groups: the first group was used immediately in the experiments, and the second group was transfected with shRNA by using RNAi-Mate. The proliferation of cells transfected with saRNA, or saRNA and shRNA, as well as the other control cells, was detected by CCK-8. The invasive and migratory abilities were determined using the transwell chamber assay. RESULTS We identified the most effective saRNA via real-time PCR and Western blot. The selected saRNA inhibited the growth, invasion and migration of GC cells by specially reactivating VEZT. The real-time PCR and Western blot results showed that treatment with saRNA caused a significant up-regulation of VEZT, and an obvious decrease in the proliferative, invasive and migratory abilities; compared with the control groups (P < 0.01); furthermore, there were no significant differences among the control groups (P > 0.05). This phenomenon provides a theoretical basis for saRNA design and gene therapy for gastric cancer.
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Affiliation(s)
- Detian Xie
- Department of Gastrointestinal Surgery, Shandong Provincial Hospital Affiliated to Shandong University, Jinan 250000, Shandong, China
| | - Liang Shang
- Department of Gastrointestinal Surgery, Shandong Provincial Hospital Affiliated to Shandong University, Jinan 250000, Shandong, China
| | - Lipan Peng
- Department of Gastrointestinal Surgery, Shandong Provincial Hospital Affiliated to Shandong University, Jinan 250000, Shandong, China
| | - Leping Li
- Department of Gastrointestinal Surgery, Shandong Provincial Hospital Affiliated to Shandong University, Jinan 250000, Shandong, China.
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57
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Wu HL, Li SM, Hu J, Yu X, Xu H, Chen Z, Ye ZQ. Demystifying the mechanistic and functional aspects of p21 gene activation with double-stranded RNAs in human cancer cells. J Exp Clin Cancer Res 2016; 35:145. [PMID: 27639690 PMCID: PMC5027115 DOI: 10.1186/s13046-016-0423-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2016] [Accepted: 09/09/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The recently identified phenomenon of double-stranded RNA (dsRNA)-mediated gene activation (RNAa) has been studied extensively, as it is present in humans, mice, and Caenorhabditis elegans, suggesting that dsRNA-mediated RNAa is an evolutionarily conserved mechanism. Previous studies have shown that dsP21-322 can induce tumor suppressor gene p21 expression in several human cancer cells. Nonetheless, the role of dsRNAs in the activation of gene expression, including their target molecules and associated key factors, remains poorly understood. METHODS Oligonucleotides were used to overexpress dsRNAs and dsControl. Real-time PCR and Western blotting were used to detect corresponding mRNA and protein expression, respectively. Fluorescence microscopy was used to examine the kinetics of dsRNA subcellular distribution. Luciferase reporter assays were performed to verify dsRNA target molecules. Chromatin immunoprecipitation (ChIP) assays were carried out to determine whether histone modification and other associated key factors are involved in saRNA-mediated p21 expression. RESULTS We demonstrated that dsRNA-mediated p21 induction in human cell lines is a common phenomenon. This process occurs at the transcriptional level, and the complementary p21 promoter is the intended dsRNA target. Additionally, ChIP assays indicated that p21 activation was accompanied by an increased enrichment of AGO1 and the trimethylation of histone H3K4 at dsRNA-targeted genomic sites. CONCLUSION These data systematically reveal the mechanistic and functional aspects of ncRNA-mediated p21 activation in human cancer cells, which may be a useful tool to analyze gene function and aid in the development of novel drug targets for cancer therapeutics.
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Affiliation(s)
- Huan-Lei Wu
- Department of Geriatrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, People's Republic of China
| | - Sen-Mao Li
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Liberalization Avenue, No. 1095, Wuhan, 430030, People's Republic of China.,Institute of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, People's Republic of China
| | - Jia Hu
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Liberalization Avenue, No. 1095, Wuhan, 430030, People's Republic of China. .,Institute of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, People's Republic of China.
| | - Xiao Yu
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Liberalization Avenue, No. 1095, Wuhan, 430030, People's Republic of China.,Institute of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, People's Republic of China
| | - Hua Xu
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Liberalization Avenue, No. 1095, Wuhan, 430030, People's Republic of China.,Institute of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, People's Republic of China
| | - Zhong Chen
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Liberalization Avenue, No. 1095, Wuhan, 430030, People's Republic of China.,Institute of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, People's Republic of China
| | - Zhang-Qun Ye
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Liberalization Avenue, No. 1095, Wuhan, 430030, People's Republic of China.,Institute of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, People's Republic of China
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58
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Kalantari R, Hicks JA, Li L, Gagnon KT, Sridhara V, Lemoff A, Mirzaei H, Corey DR. Stable association of RNAi machinery is conserved between the cytoplasm and nucleus of human cells. RNA (NEW YORK, N.Y.) 2016; 22:1085-98. [PMID: 27198507 PMCID: PMC4911916 DOI: 10.1261/rna.056499.116] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Accepted: 04/25/2016] [Indexed: 05/25/2023]
Abstract
Argonaute 2 (AGO2), the catalytic engine of RNAi, is typically associated with inhibition of translation in the cytoplasm. AGO2 has also been implicated in nuclear processes including transcription and splicing. There has been little insight into AGO2's nuclear interactions or how they might differ relative to cytoplasm. Here we investigate the interactions of cytoplasmic and nuclear AGO2 using semi-quantitative mass spectrometry. Mass spectrometry often reveals long lists of candidate proteins, complicating efforts to rigorously discriminate true interacting partners from artifacts. We prioritized candidates using orthogonal analytical strategies that compare replicate mass spectra of proteins associated with Flag-tagged and endogenous AGO2. Interactions with TRNC6A, TRNC6B, TNRC6C, and AGO3 are conserved between nuclei and cytoplasm. TAR binding protein interacted stably with cytoplasmic AGO2 but not nuclear AGO2, consistent with strand loading in the cytoplasm. Our data suggest that interactions between functionally important components of RNAi machinery are conserved between the nucleus and cytoplasm but that accessory proteins differ. Orthogonal analysis of mass spectra is a powerful approach to streamlining identification of protein partners.
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Affiliation(s)
- Roya Kalantari
- Department of Pharmacology, Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Jessica A Hicks
- Department of Pharmacology, Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Liande Li
- Department of Pharmacology, Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Keith T Gagnon
- Department of Biochemistry and Molecular Biology, Southern Illinois University, Carbondale, Illinois 62901, USA
| | - Viswanadham Sridhara
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Andrew Lemoff
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Hamid Mirzaei
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - David R Corey
- Department of Pharmacology, Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
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Chaluvally-Raghavan P, Jeong KJ, Pradeep S, Silva AM, Yu S, Liu W, Moss T, Rodriguez-Aguayo C, Zhang D, Ram P, Liu J, Lu Y, Lopez-Berestein G, Calin GA, Sood AK, Mills GB. Direct Upregulation of STAT3 by MicroRNA-551b-3p Deregulates Growth and Metastasis of Ovarian Cancer. Cell Rep 2016; 15:1493-1504. [PMID: 27160903 PMCID: PMC4914391 DOI: 10.1016/j.celrep.2016.04.034] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2015] [Revised: 02/10/2016] [Accepted: 04/04/2016] [Indexed: 10/21/2022] Open
Abstract
3q26.2 amplification in high-grade serous ovarian cancer leads to increased expression of mature microRNA miR551b-3p, which is associated with poor clinical outcome. Importantly, miR551b-3p contributes to resistance to apoptosis and increased survival and proliferation of cancer cells in vitro and in vivo. miR551b-3p upregulates STAT3 protein levels, and STAT3 is required for the effects of miR551b-3p on cell proliferation. Rather than decreasing levels of target mRNA as expected, we demonstrate that miR551b-3p binds a complementary sequence on the STAT3 promoter, recruiting RNA polymerase II and the TWIST1 transcription factor to activate STAT3 transcription, and thus directly upregulates STAT3 expression. Furthermore, anti-miR551b reduced STAT3 expression in ovarian cancer cells in vitro and in vivo and reduced ovarian cancer growth in vivo. Together, our data demonstrate a role for miR551b-3p in transcriptional activation. Thus, miR551b-3p represents a promising candidate biomarker and therapeutic target in ovarian cancer.
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MESH Headings
- Animals
- Carcinoma, Ovarian Epithelial
- Cell Line, Tumor
- Cell Proliferation/genetics
- Cell Self Renewal
- Cell Survival/genetics
- Down-Regulation/genetics
- Female
- Gene Amplification
- Gene Expression Regulation, Neoplastic
- Gene Knockdown Techniques
- Gene Silencing
- Humans
- Mice, Nude
- MicroRNAs/metabolism
- Neoplasm Metastasis
- Neoplasms, Glandular and Epithelial/genetics
- Neoplasms, Glandular and Epithelial/pathology
- Nuclear Proteins/metabolism
- Ovarian Neoplasms/genetics
- Ovarian Neoplasms/pathology
- Promoter Regions, Genetic/genetics
- RNA Polymerase II/metabolism
- STAT3 Transcription Factor/genetics
- STAT3 Transcription Factor/metabolism
- Spheroids, Cellular/metabolism
- Spheroids, Cellular/pathology
- Transcription, Genetic
- Treatment Outcome
- Tumor Burden/genetics
- Twist-Related Protein 1/metabolism
- Up-Regulation/genetics
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Affiliation(s)
| | - Kang Jin Jeong
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
| | - Sunila Pradeep
- Department of Gynecologic Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA; Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
| | - Andreia Machado Silva
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
| | - Shuangxing Yu
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
| | - Wenbin Liu
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
| | - Tyler Moss
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
| | - Cristian Rodriguez-Aguayo
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
| | - Dong Zhang
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
| | - Prahlad Ram
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
| | - Jinsong Liu
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
| | - Yiling Lu
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
| | - Gabriel Lopez-Berestein
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA; Center for RNAi and Non-Coding RNA, The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
| | - George A Calin
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA; Center for RNAi and Non-Coding RNA, The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
| | - Anil K Sood
- Department of Gynecologic Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA; Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA; Center for RNAi and Non-Coding RNA, The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
| | - Gordon B Mills
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA.
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60
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Li M, Peng Z, Ren W, Wang Z. Small activating ribonucleic acid reverses tyrosine kinase inhibitor resistance in epidermal growth factor receptor-mutant lung cancer by increasing the expression of phosphatase and tensin homolog. Thorac Cancer 2016; 7:481-5. [PMID: 27385992 PMCID: PMC4930969 DOI: 10.1111/1759-7714.12356] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2016] [Accepted: 04/03/2016] [Indexed: 01/28/2023] Open
Abstract
BACKGROUND Epidermal growth factor receptor-tyrosine kinase inhibitors (TKI-EGFRs) present a new prospect for the treatment of lung cancer. However, in clinical application, the majority of patients become TKI resistant within a year. More and more studies have shown that a loss of phosphatase and tensin homolog (PTEN) expression is associated with TKI resistance. An alternative method of upregulating PTEN expression may reverse TKI resistance. METHODS We designed five candidate small activating ribonucleic acids (saRNAs) to target PTEN, and transfected them into H-157 cells to screen out functional saRNA. We used reverse transcriptase-polymerase chain reaction and Western blot to evaluate the effect of saRNA to PTEN expression. We then analyzed the growth and apoptosis of cells transfected with saRNA under the treatment of TKI to investigate whether saRNAs can reverse TKI resistance by upregulating PTEN expression. RESULTS The functional saRNA we designed could upregulate PTEN expression. The H-157 cells transfected with saRNA grew slower in the presence of TKI drugs than the cells that were not transfected with saRNA. The apoptosis rate was also obviously higher. CONCLUSIONS Our study proves that loss of PTEN expression is an important mechanism of TKI resistance. It is possible to control TKI resistance by upregulating PTEN expression using RNA activation technology.
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Affiliation(s)
- Meng Li
- Department of Thoracic Surgery Provincial Hospital Affiliated to Shandong University, Shandong University Jinan China
| | - Zhongmin Peng
- Department of Thoracic Surgery Provincial Hospital Affiliated to Shandong University, Shandong University Jinan China
| | - Wangang Ren
- Department of Thoracic Surgery Provincial Hospital Affiliated to Shandong University, Shandong University Jinan China
| | - Zhou Wang
- Department of Thoracic Surgery Provincial Hospital Affiliated to Shandong University, Shandong University Jinan China
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61
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Master A, Wójcicka A, Giżewska K, Popławski P, Williams GR, Nauman A. A Novel Method for Gene-Specific Enhancement of Protein Translation by Targeting 5'UTRs of Selected Tumor Suppressors. PLoS One 2016; 11:e0155359. [PMID: 27171412 PMCID: PMC4865139 DOI: 10.1371/journal.pone.0155359] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Accepted: 04/27/2016] [Indexed: 01/25/2023] Open
Abstract
BACKGROUND Translational control is a mechanism of protein synthesis regulation emerging as an important target for new therapeutics. Naturally occurring microRNAs and synthetic small inhibitory RNAs (siRNAs) are the most recognized regulatory molecules acting via RNA interference. Surprisingly, recent studies have shown that interfering RNAs may also activate gene transcription via the newly discovered phenomenon of small RNA-induced gene activation (RNAa). Thus far, the small activating RNAs (saRNAs) have only been demonstrated as promoter-specific transcriptional activators. FINDINGS We demonstrate that oligonucleotide-based trans-acting factors can also specifically enhance gene expression at the level of protein translation by acting at sequence-specific targets within the messenger RNA 5'-untranslated region (5'UTR). We designed a set of short synthetic oligonucleotides (dGoligos), specifically targeting alternatively spliced 5'UTRs in transcripts expressed from the THRB and CDKN2A suppressor genes. The in vitro translation efficiency of reporter constructs containing alternative TRβ1 5'UTRs was increased by up to more than 55-fold following exposure to specific dGoligos. Moreover, we found that the most folded 5'UTR has higher translational regulatory potential when compared to the weakly folded TRβ1 variant. This suggests such a strategy may be especially applied to enhance translation from relatively inactive transcripts containing long 5'UTRs of complex structure. SIGNIFICANCE This report represents the first method for gene-specific translation enhancement using selective trans-acting factors designed to target specific 5'UTR cis-acting elements. This simple strategy may be developed further to complement other available methods for gene expression regulation including gene silencing. The dGoligo-mediated translation-enhancing approach has the potential to be transferred to increase the translation efficiency of any suitable target gene and may have future application in gene therapy strategies to enhance expression of proteins including tumor suppressors.
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Affiliation(s)
- Adam Master
- The Centre of Postgraduate Medical Education, Department of Biochemistry and Molecular Biology, ul. Marymoncka 99/103, 01-813, Warsaw, Poland
- BioTe21, Laboratory of Molecular Medical Biology, ul. Krolowej Jadwigi 33/3b, 30-209, Cracow, Poland
| | - Anna Wójcicka
- The Centre of Postgraduate Medical Education, Department of Biochemistry and Molecular Biology, ul. Marymoncka 99/103, 01-813, Warsaw, Poland
- Centre of New Technologies, University of Warsaw, Banacha 2c, 02-089, Warsaw, Poland
- Genomic Medicine, Medical University of Warsaw, Zwirki i Wigury 61, 02-091, Warsaw, Poland
| | - Kamilla Giżewska
- BioTe21, Laboratory of Molecular Medical Biology, ul. Krolowej Jadwigi 33/3b, 30-209, Cracow, Poland
| | - Piotr Popławski
- The Centre of Postgraduate Medical Education, Department of Biochemistry and Molecular Biology, ul. Marymoncka 99/103, 01-813, Warsaw, Poland
| | - Graham R. Williams
- Molecular Endocrinology Group, Department of Medicine, Imperial College London, Hammersmith Campus, London, W12 0NN, United Kingdom
| | - Alicja Nauman
- The Centre of Postgraduate Medical Education, Department of Biochemistry and Molecular Biology, ul. Marymoncka 99/103, 01-813, Warsaw, Poland
- Centre of New Technologies, University of Warsaw, Banacha 2c, 02-089, Warsaw, Poland
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RNA Activation of the Vascular Endothelial Growth Factor Gene (VEGF) Promoter by Double-Stranded RNA and Hypoxia: Role of Noncoding VEGF Promoter Transcripts. Mol Cell Biol 2016; 36:1480-93. [PMID: 26976645 DOI: 10.1128/mcb.01096-15] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2015] [Accepted: 03/07/2016] [Indexed: 11/20/2022] Open
Abstract
RNA activation (RNAa) is a gene regulation process in which promoter-targeted short double-stranded RNAs (dsRNAs) or microRNAs (miRs) induce target gene expression at the transcriptional level. Here, we investigate the presence of cryptic promoter transcripts within the VEGF promoter. Single-strand sense and antisense noncoding vascular endothelial growth factor (NcVEGF) promoter transcripts are identified, and their respective expression is studied in cells transfected with a VEGF promoter targeted dsRNA, namely, dsVEGF706, in hypoxic cells and in human malignant lung tissues. Interestingly, in dsVEGF706-transfected, as well as in hypoxic cells, NcVEGF expression levels increase coordinately with coding VEGF expression. Ago2 interaction with both sense and antisense NcVEGFs is increased in hypoxic cells, whereas in dsVEGF706-transfected cells, Ago2 and the antisense strand of the dsRNA interact specifically with the sense NcVEGF transcript. Furthermore, both dsVEGF706 and ectopic NcVEGF transcripts are able to activate the VEGF promoter endogenously present or in a reporter construct. Finally, using small interfering RNA targeting Ago2, we show that RNAa plays a role in the maintenance of increased VEGF and NcVEGF expression after hypoxia. Given the central role of VEGF in major human diseases, including cancer, this novel molecular mechanism is poised to reveal promising possibilities for therapeutic interventions.
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63
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Li C, Jiang W, Hu Q, Li LC, Dong L, Chen R, Zhang Y, Tang Y, Thrasher JB, Liu CB, Li B. Enhancing DPYSL3 gene expression via a promoter-targeted small activating RNA approach suppresses cancer cell motility and metastasis. Oncotarget 2016; 7:22893-910. [PMID: 27014974 PMCID: PMC5008410 DOI: 10.18632/oncotarget.8290] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Accepted: 02/23/2016] [Indexed: 12/11/2022] Open
Abstract
To explore a novel strategy in suppressing tumor metastasis, we took the advantage of a recent RNA activation (RNAa) theory and used small double-strand RNA molecules, termed as small activating RNAs (saRNA) that are complimentary to target gene promoter, to enhance transcription of metastasis suppressor gene. The target gene in this study is Dihydro-pyrimidinase-like 3 (DPYSL3, protein name CRMP4), which was identified as a metastatic suppressor in prostate cancers. There are two transcriptional variants of DPYSL3 gene in human genome, of which the variant 2 is the dominant transcript (DPYSL3v2, CRMP4a) but is also significantly down-regulated in primary prostate cancers. A total of 8 saRNAs for DPYSL3v1 and 14 saRNAs for DPYSL3v2 were tested in multiple prostate cancer cell lines. While none of the saRNAs significantly altered DPYSL3v1 expression, 4 saRNAs showed a strong enhancing effect on DPYSL3v2 expression, resulting in reduced cell mobility in vitro. To achieve a prostate cancer-specific delivery for in vivo testing, we conjugated the most potent saV2-9 RNA molecule with the prostate-specific membrane antigen (PSMA)-targeting aptamer A10-3.2. The conjugates successful increased DPYSL3v2 gene expression in PSMA-positive but not PSMA-negative prostate cancer cells. In nude mice bearing orthotopic xenograft of prostate cancer, a 10-day consecutive treatment with the saV2-9 conjugates significantly suppress distal metastasis compared to the control saRNAs. Analysis of xenograft tissues revealed that DPYSL3v2 expression was largely increased in saV2-9 conjugate-treated group compared to the control group. In conclusion, DPYSL3v2 promoter-targeted saRNA molecules might be used as an adjunctive therapy to suppress prostate cancer metastasis.
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Affiliation(s)
- Changlin Li
- Department of Urology, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Wencong Jiang
- Department of Urology, University of Kansas Medical Center, Kansas City, KS 66160, USA
- Department of Urology, The Affiliated Hospital, Guangdong Medical University, Zhanjiang 524001, China
| | - Qingting Hu
- Department of Urology, University of Kansas Medical Center, Kansas City, KS 66160, USA
- Institute of Cell Therapy, China Three Gorges University, Yichang 443002, China
| | - Long-cheng Li
- Laboratory of Molecular Medicine, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing 100073, China
| | - Liang Dong
- Department of Urology, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Ruibao Chen
- Department of Urology, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Yinghong Zhang
- Department of Urology, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Yuzhe Tang
- Department of Urology, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - J. Brantley Thrasher
- Department of Urology, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Chang-Bai Liu
- Institute of Cell Therapy, China Three Gorges University, Yichang 443002, China
| | - Benyi Li
- Department of Urology, University of Kansas Medical Center, Kansas City, KS 66160, USA
- Department of Urology, The Affiliated Hospital, Guangdong Medical University, Zhanjiang 524001, China
- Institute of Cell Therapy, China Three Gorges University, Yichang 443002, China
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Wang C, Chen Z, Wu J, Zhang Y, Hu J, Ge Q, Yang W, Xu H, Liu J, Ye Z. Small activating RNA induces myogenic differentiation of rat adipose-derived stem cells by upregulating MyoD. Int Braz J Urol 2016; 41:764-72. [PMID: 26401871 PMCID: PMC4757007 DOI: 10.1590/s1677-5538.ibju.2014.0400] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2014] [Accepted: 11/08/2014] [Indexed: 01/17/2023] Open
Abstract
PURPOSE RNA activation (RNAa) is a mechanism of gene activation triggered by promoter-targeted small double stranded RNAs (dsRNAs), also known as small activating RNAs (saRNAs). Myogenic regulatory factor MyoD is regarded as the master activator of myogenic differentiation cascade by binding to enhancer of muscle specific genes. Stress urinary incontinence (SUI) is a condition primarily resulted from urethral sphincter deficiency. It is thus expected that by promoting differentiation of adipose-derived stem cells (ADSCs) into myoblasts by activating MyoD gene through RNAa may offer benefits to SUI. MATERIALS AND METHODS Rats ADSCs were isolated, proliferated in vitro, and identified by flow cytometry. Purified ADSCs were then transfected with a MyoD saRNA or control transfected. Real-time polymerase chain reaction (RT-PCR) and western blotting were used to detect MyoD mRNA and protein expression, respectively. Immunocytochemical staining was applied to determine the expression of desmin protein in transfected cells. Cell viability was measured by using CellTiter 96R AQueous One Solution Cell Proliferation Assay kit. RESULTS Transfection of a MyoD saRNA (dsMyoD) into ADSCs significantly induced the expression of MyoD at both the mRNA and protein levels, and inhibited cell proliferation. Desmin protein expression was detected in dsMyoD treated ADSCs 2 weeks later. CONCLUSION Our findings show that RNAa mediated overexpression of MyoD can promote transdifferentiation of ADSCs into myoblasts and may help treat stress urinary incontinence (SUI)-a condition primarily resulted from urethral sphincter deficiency.
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Affiliation(s)
- Chenghe Wang
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Hubei, China
| | - Zhong Chen
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Hubei, China
| | - Jia Wu
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Hubei, China
| | - Yan Zhang
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Hubei, China
| | - Jia Hu
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Hubei, China
| | - Qiangqiang Ge
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Hubei, China
| | - Weimin Yang
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Hubei, China
| | - Hua Xu
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Hubei, China
| | - Jihong Liu
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Hubei, China
| | - Zhangqun Ye
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Hubei, China
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Wang C, Ge Q, Zhang Q, Chen Z, Hu J, Li F, Ye Z. Targeted p53 activation by saRNA suppresses human bladder cancer cells growth and metastasis. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2016; 35:53. [PMID: 27012825 PMCID: PMC4807596 DOI: 10.1186/s13046-016-0329-8] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/16/2015] [Accepted: 03/21/2016] [Indexed: 01/01/2023]
Abstract
BACKGROUND Previous study showed that dsP53-285 has the capacity to induce tumor suppressor gene p53 expression by targeting promoter in non-human primates' cells. And it is well known that TP53 gene is frequently mutant or inactivated in human bladder cancer. Hereby, whether this small RNA can activate the expression of wild-type p53 and inhibit human bladder cancer cells remains to be elucidated. METHODS Oligonucleotide and lentivirus were used to overexpress dsP53-285 and dsControl. Real-time PCR and western blot were used to detect genes' mRNA and protein expression, respectively. Cell proliferation assay, colony formation, flow cytometry, transwell assay and wound healing assay were performed to determine the effects on bladder cancer cells proliferation and migration/invasion in vitro. Animal models were carried out to analyze the effects on cells growth and metastasis in vivo. RESULTS Transfection of dsP53-285 into human bladder cancer cell lines T24 and EJ readily activate wild-type p53 expression by targeting promoter. Moreover, dsP53-285 exhibited robust capacity to inhibit cells proliferation and colony formation, induce cells G0/G1 arrest, suppress migration and invasion. Besides, the Cyclin-CDK genes (Cyclin D1 and CDK4/6) were down-regulated and the EMT-associated genes (E-cadherin, β-catenin, ZEB1 and Vimentin) were also expressed inversely after dsP53-285 treatment. In addition, dsP53-285 could also significantly suppress the growth of bladder cancer xenografts and metastasis in nude mice. Most importantly, the anti-tumor effects mediated by dsP53-285 were mainly achieved by manipulating wild-type p53 expression. CONCLUSION Our findings indicate that the dsP53-285 can upregulate wild-type p53 expression in human bladder cancer cells through RNA activation, and suppresses cells proliferation and metastasis in vitro and in vivo.
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Affiliation(s)
- Chenghe Wang
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, No. 1095 JieFang Avenue, Wuhan, 430030, Hubei, China.,Department of Urology, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, No. 600 Yishan Road, Shanghai, 200233, China
| | - Qiangqiang Ge
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, No. 1095 JieFang Avenue, Wuhan, 430030, Hubei, China
| | - Qingsong Zhang
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, No. 1095 JieFang Avenue, Wuhan, 430030, Hubei, China
| | - Zhong Chen
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, No. 1095 JieFang Avenue, Wuhan, 430030, Hubei, China.
| | - Jia Hu
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, No. 1095 JieFang Avenue, Wuhan, 430030, Hubei, China
| | - Fan Li
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, No. 1095 JieFang Avenue, Wuhan, 430030, Hubei, China
| | - Zhangqun Ye
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, No. 1095 JieFang Avenue, Wuhan, 430030, Hubei, China
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66
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Wang B, Sun J, Shi J, Guo Q, Tong X, Zhang J, Hu N, Hu Y. Small-Activating RNA Can Change Nucleosome Positioning in Human Fibroblasts. ACTA ACUST UNITED AC 2016; 21:634-42. [PMID: 26993320 DOI: 10.1177/1087057116637562] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Accepted: 02/15/2016] [Indexed: 11/16/2022]
Abstract
RNA activation (RNAa) is a mechanism of positive gene expression regulation mediated by small-activating RNAs (saRNAs), which target gene promoters and have been used as tools to manipulate gene expression. Studies have shown that RNAa is associated with epigenetic modifications at promoter regions; however, it is unclear whether these modifications are the cause or a consequence of RNAa. In this study, we examined changes in nucleosome repositioning and the involvement of RNA polymerase II (RNAPII) in this process. We screened saRNAs for OCT4 (POU5F1), SOX2, and NANOG, and identified several novel saRNAs. We found that nucleosome positioning was altered after saRNA treatment and that the formation of nucleosome-depleted regions (NDRs) contributed to RNAa at sites of RNAPII binding, such as the TATA box, CpG islands (CGIs), proximal enhancers, and proximal promoters. Moreover, RNAPII appeared to be bound specifically to NDRs. These results suggested that changes in nucleosome positions resulted from RNAa. We thus propose a hypothesis that targeting promoter regions using exogenous saRNAs can induce the formation of NDRs, exposing regulatory binding sites to recruit RNAPII, a key component of preinitiation complex, and leading to increased initiation of transcription.
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Affiliation(s)
- Bin Wang
- Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, China Department of Biology, Kunming University, Kunming, China
| | - Jing Sun
- Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, China
| | - Jiandong Shi
- Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, China
| | - Qing Guo
- Department of Biology, Kunming University, Kunming, China
| | - Xiangrong Tong
- Department of Biology, Kunming University, Kunming, China
| | - Jin Zhang
- Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, China
| | - Ningzhu Hu
- Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, China
| | - YunZhang Hu
- Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, China
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67
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Portnoy V, Lin SHS, Li KH, Burlingame A, Hu ZH, Li H, Li LC. saRNA-guided Ago2 targets the RITA complex to promoters to stimulate transcription. Cell Res 2016; 26:320-35. [PMID: 26902284 PMCID: PMC4783471 DOI: 10.1038/cr.2016.22] [Citation(s) in RCA: 83] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2015] [Revised: 10/22/2015] [Accepted: 01/12/2016] [Indexed: 12/21/2022] Open
Abstract
Small activating RNAs (saRNAs) targeting specific promoter regions are able to stimulate gene expression at the transcriptional level, a phenomenon known as RNA activation (RNAa). It is known that RNAa depends on Ago2 and is associated with epigenetic changes at the target promoters. However, the precise molecular mechanism of RNAa remains elusive. Using human CDKN1A (p21) as a model gene, we characterized the molecular nature of RNAa. We show that saRNAs guide Ago2 to and associate with target promoters. saRNA-loaded Ago2 facilitates the assembly of an RNA-induced transcriptional activation (RITA) complex, which, in addition to saRNA-Ago2 complex, includes RHA and CTR9, the latter being a component of the PAF1 complex. RITA interacts with RNA polymerase II to stimulate transcription initiation and productive elongation, accompanied by monoubiquitination of histone 2B. Our results establish the existence of a cellular RNA-guided genome-targeting and transcriptional activation mechanism and provide important new mechanistic insights into the RNAa process.
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Affiliation(s)
- Victoria Portnoy
- Department of Urology and Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA 94158, USA
| | - Szu Hua Sharon Lin
- Department of Urology and Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA 94158, USA
| | - Kathy H Li
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA 94158, USA
| | - Alma Burlingame
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA 94158, USA
| | - Zheng-Hui Hu
- Department of Urology and Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA 94158, USA
| | - Hao Li
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA 94158, USA
| | - Long-Cheng Li
- Department of Urology and Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA 94158, USA.,Laboratory of Molecular Medicine, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing 100730, China
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68
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Meng X, Jiang Q, Chang N, Wang X, Liu C, Xiong J, Cao H, Liang Z. Small activating RNA binds to the genomic target site in a seed-region-dependent manner. Nucleic Acids Res 2016; 44:2274-82. [PMID: 26873922 PMCID: PMC4797303 DOI: 10.1093/nar/gkw076] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Accepted: 01/29/2016] [Indexed: 01/27/2023] Open
Abstract
RNA activation (RNAa) is the upregulation of gene expression by small activating RNAs (saRNAs). In order to investigate the mechanism by which saRNAs act in RNAa, we used the progesterone receptor (PR) gene as a model, established a panel of effective saRNAs and assessed the involvement of the sense and antisense strands of saRNA in RNAa. All active saRNAs had their antisense strand effectively incorporated into Ago2, whereas such consistency did not occur for the sense strand. Using a distal hotspot for saRNA targeting at 1.6-kb upstream from the PR transcription start site, we further established that gene activation mediated by saRNA depended on the complementarity of the 5' region of the antisense strand, and that such activity was largely abolished by mutations in this region of the saRNA. We found markedly reduced RNAa effects when we created mutations in the genomic target site of saRNA PR-1611, thus providing evidence that RNAa depends on the integrity of the DNA target. We further demonstrated that this saRNA bound the target site on promoter DNA. These results demonstrated that saRNAs work via an on-site mechanism by binding to target genomic DNA in a seed-region-dependent manner, reminiscent of miRNA-like target recognition.
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Affiliation(s)
- Xing Meng
- Institute of Molecular Medicine, Peking University, Beijing 100871, PR China
| | - Qian Jiang
- Institute of Molecular Medicine, Peking University, Beijing 100871, PR China
| | - Nannan Chang
- Institute of Molecular Medicine, Peking University, Beijing 100871, PR China
| | - Xiaoxia Wang
- Institute of Molecular Medicine, Peking University, Beijing 100871, PR China
| | - Chujun Liu
- Institute of Molecular Medicine, Peking University, Beijing 100871, PR China
| | - Jingwei Xiong
- Institute of Molecular Medicine, Peking University, Beijing 100871, PR China
| | - Huiqing Cao
- Institute of Molecular Medicine, Peking University, Beijing 100871, PR China
| | - Zicai Liang
- Institute of Molecular Medicine, Peking University, Beijing 100871, PR China Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin 300072, PR China
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69
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Kalantari R, Chiang CM, Corey DR. Regulation of mammalian transcription and splicing by Nuclear RNAi. Nucleic Acids Res 2016; 44:524-37. [PMID: 26612865 PMCID: PMC4737150 DOI: 10.1093/nar/gkv1305] [Citation(s) in RCA: 72] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2015] [Revised: 11/04/2015] [Accepted: 11/09/2015] [Indexed: 12/21/2022] Open
Abstract
RNA interference (RNAi) is well known as a mechanism for controlling mammalian mRNA translation in the cytoplasm, but what would be the consequences if it also functions in cell nuclei? Although RNAi has also been found in nuclei of plants, yeast, and other organisms, there has been relatively little progress towards understanding the potential involvement of mammalian RNAi factors in nuclear processes including transcription and splicing. This review summarizes evidence for mammalian RNAi factors in cell nuclei and mechanisms that might contribute to the control of gene expression. When RNAi factors bind small RNAs, they form ribonucleoprotein complexes that can be selective for target sequences within different classes of nuclear RNA substrates. The versatility of nuclear RNAi may supply a previously underappreciated layer of regulation to transcription, splicing, and other nuclear processes.
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Affiliation(s)
- Roya Kalantari
- Departments of Pharmacology & Biochemistry, University of Texas Southwestern Medical Center, 6001 Forest Park Road, Dallas, TX 75390-9041, USA
| | - Cheng-Ming Chiang
- Departments of Pharmacology & Biochemistry, University of Texas Southwestern Medical Center, 6001 Forest Park Road, Dallas, TX 75390-9041, USA Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, 6001 Forest Park Road, Dallas, TX 75390-8807, USA
| | - David R Corey
- Departments of Pharmacology & Biochemistry, University of Texas Southwestern Medical Center, 6001 Forest Park Road, Dallas, TX 75390-9041, USA
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70
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Yang K, Shen J, Chen SW, Qin J, Zheng XY, Xie LP. Upregulation of PAWR by small activating RNAs induces cell apoptosis in human prostate cancer cells. Oncol Rep 2016; 35:2487-93. [PMID: 26797252 DOI: 10.3892/or.2016.4582] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2015] [Accepted: 01/07/2016] [Indexed: 11/06/2022] Open
Abstract
RNA activation (RNAa) is a promising discovery whereby expression of a particular gene can be induced by targeting its promoter using small double-stranded RNAs (dsRNAs) also termed small activating RNAs (saRNAs). We previously reported that several small dsRNAs targeting the PRKC apoptosis WT1 regulator (PAWR) promoter can upregulate PAWR gene expression effectively in human cancer cells. The present study was conducted to evaluate the antitumor potential of PAWR gene induction by these saRNAs in prostate cancer cells. Promisingly, we found that upregulation of PAWR by saRNA inhibited the growth of prostate cancer cells by inducing cell apoptosis which was related to inactivation of the NF-κB and Akt pathways. The decreased anti‑apoptotic protein Bcl-2 and activation of the caspase cascade and poly(ADP-ribose) polymerase (PARP) also supported the efficacy of the treatment. Overall, these data suggest that activation of PAWR by saRNA may have a therapeutic benefit for prostate and other types of cancer.
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Affiliation(s)
- Kai Yang
- Department of Urology, The First Affiliated Hospital, Zhejiang University, Hangzhou, Zhejiang 310003, P.R. China
| | - Jie Shen
- Department of Pharmacy, Traditional Chinese Medical Hospital of Zhejiang Province, Hangzhou, Zhejiang 310006, P.R. China
| | - Shan-Wen Chen
- Department of Urology, The First Affiliated Hospital, Zhejiang University, Hangzhou, Zhejiang 310003, P.R. China
| | - Jie Qin
- Department of Urology, The First Affiliated Hospital, Zhejiang University, Hangzhou, Zhejiang 310003, P.R. China
| | - Xiang-Yi Zheng
- Department of Urology, The First Affiliated Hospital, Zhejiang University, Hangzhou, Zhejiang 310003, P.R. China
| | - Li-Ping Xie
- Department of Urology, The First Affiliated Hospital, Zhejiang University, Hangzhou, Zhejiang 310003, P.R. China
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71
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Ge Q, Wang C, Ruan Y, Chen Z, Liu J, Ye Z. Overexpression of p53 activated by small activating RNA suppresses the growth of human prostate cancer cells. Onco Targets Ther 2016; 9:231-41. [PMID: 26811691 PMCID: PMC4712973 DOI: 10.2147/ott.s96710] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Previous research has reported that a particular double-stranded RNA, named dsP53-285, has the capacity to induce expression of the tumor suppressor gene TP53 in chimpanzee cells by targeting its promoter. Usually, it is the wild-type p53 protein, rather than mutants, which exhibits potent cancer-inhibiting effects. In addition, nonhuman primates, such as chimpanzees, share almost identical genome sequences with humans. This prompted us to speculate whether dsP53-285 can trigger wild-type p53 protein expression in human prostate cancer (PCa) cells and consequently suppress cell growth. The human PCa cell lines LNCaP and DU145 were transfected with dsP53-285 for 72 hours. Compared with the dsControl and mock transfection groups, expression of both p53 messenger RNA and p53 protein was significantly enhanced after dsP53-285 transfection, and this enhancement was followed by upregulation of p21, which indirectly indicated that dsP53-285 induced wild-type p53 expression. Moreover, overexpression of wild-type p53 mediated by dsP53-285 downregulated the expression of Cyclin D1 and cyclin-dependent kinase 4/6, thereby inducing PCa cell cycle arrest in G0/G1 phase and then inhibiting cell proliferation and clonogenicity. More importantly, dsP53-285 suppressed PCa cells mainly by modulating wild-type p53 expression. In conclusion, our study provides evidence that dsP53-285 can significantly stimulate wild-type p53 expression in the human PCa cell lines LNCaP and DU145 and can exert potent antitumor effects.
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Affiliation(s)
- Qiangqiang Ge
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, People's Republic of China
| | - Chenghe Wang
- Department of Urology, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, People's Republic of China
| | - Yajun Ruan
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, People's Republic of China
| | - Zhong Chen
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, People's Republic of China
| | - Jihong Liu
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, People's Republic of China
| | - Zhangqun Ye
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, People's Republic of China
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Promoter-associated endogenous and exogenous small RNAs suppress human bladder cancer cell metastasis by activating p21 (CIP1/WAF1) expression. Tumour Biol 2015; 37:6589-98. [PMID: 26643891 DOI: 10.1007/s13277-015-4571-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2015] [Accepted: 12/01/2015] [Indexed: 01/28/2023] Open
Abstract
Accumulating data suggest that micro RNAs (miRNAs) or double-stranded RNAs (dsRNAs) can activate gene expression by targeting promoters. The cyclin-dependent kinase inhibitor p21 (CIP1/WAF1) (p21) has also been shown to suppress epithelial-mesenchymal transition (EMT) which plays a crucial role in the early stage of tumor metastases and invasiveness. In a previous study, we have reported that miR-370-5p is low-expressed in bladder cancer (BCa) tissues and cell lines. Here, we identified that miR-370-5p and sequence homology dsRNA (dsP21-555) fully complementary to promoter hold the potent abilities to induce p21 expression. Moreover, transfection of miR-370-5p or dsP21-555 into BCa cells remarkably inverts EMT-associated genes (increases epithelial cell makers E-cadherin and β-catenin, and decreases mesenchymal cell markers ZEB1 and Vimentin) expression mainly via regulating p21 expression. Besides, through manipulating p21, both the candidates can retard BCa cell migration and invasion. In summary, our results provide evidence that both endogenous and exogenous small RNAs may function to induce p21 expression by interacting with the similar promoter region and impede BCa metastasis.
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73
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Lim RSM, Kai T. A piece of the pi(e): The diverse roles of animal piRNAs and their PIWI partners. Semin Cell Dev Biol 2015; 47-48:17-31. [PMID: 26582251 DOI: 10.1016/j.semcdb.2015.10.025] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Small non-coding RNAs are indispensable to many biological processes. A class of endogenous small RNAs, termed PIWI-interacting RNAs (piRNAs) because of their association with PIWI proteins, has known roles in safeguarding the genome against inordinate transposon mobilization, embryonic development, and stem cell regulation, among others. This review discusses the biogenesis of animal piRNAs and their diverse functions together with their PIWI protein partners, both in the germline and in somatic cells, and highlights the evolutionarily conserved aspects of these molecular players in animal biology.
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Affiliation(s)
- Robyn S M Lim
- Temasek Life Sciences Laboratory, National University of Singapore, Singapore 117604, Singapore; Department of Biological Sciences, National University of Singapore, Singapore 117543, Singapore.
| | - Toshie Kai
- Temasek Life Sciences Laboratory, National University of Singapore, Singapore 117604, Singapore; Department of Biological Sciences, National University of Singapore, Singapore 117543, Singapore.
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74
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Husso T, Turunen MP, Parker N, Ylä-Herttuala S. Epigenetherapy, a new concept. Biomol Concepts 2015; 2:127-34. [PMID: 25962024 DOI: 10.1515/bmc.2011.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2010] [Accepted: 02/26/2011] [Indexed: 11/15/2022] Open
Abstract
Small RNAs have been shown to regulate gene transcription by interacting with the promoter region and modifying the histone code. The exact mechanism of function is still unclear but the feasibility to activate or repress endogenous gene expression with small RNA molecules has already been demonstrated in vitro and in vivo. In traditional gene therapy non-mutated or otherwise useful genes are inserted into patient's cells to treat a disease. In epigenetherapy the action of small RNAs is utilized by delivering only the small RNAs to patient's cells where they then regulate gene expression by epigenetic mechanisms. This method could be widely useful not only for basic research but also for clinical applications of small RNAs.
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75
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Laham-Karam N, Lalli M, Leinonen N, Ylä-Herttuala S. Differential Regulation of Vascular Endothelial Growth Factors by Promoter-targeted shRNAs. MOLECULAR THERAPY. NUCLEIC ACIDS 2015; 4:e243. [PMID: 25988242 PMCID: PMC4560792 DOI: 10.1038/mtna.2015.16] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Accepted: 04/16/2015] [Indexed: 02/06/2023]
Abstract
Vascular endothelial growth factors (VEGFs) and their receptors (VEGF-R) are central regulators of vasculogenesis, angiogenesis, and lymphangiogenesis. They contribute to many vascular-related pathologies, and hence VEGF-targeted therapies have been widely sought after. In this study, the authors investigated the ability of promoter-targeted small hairpin RNAs (shRNAs) to regulate VEGF-A, VEGF-C and VEGF-R1 in different cell lines. The authors identified shRNAs that can upregulate hVEGF-C at both the mRNA and protein levels, and differentially regulate hVEGF-A depending on the cell type. Likewise, the authors identified shRNA that downregulated VEGF-R1 gene expression. Hence, promoter-targeted shRNAs can affect endogenous gene expression not only bimodally, but also differentially in a cell-type specific manner. Importantly, all three genes tested were regulated by at least one shRNA, supporting the idea that nuclear RNA interference is a widespread phenomenon. The level of regulation across the panel of shRNAs varied maximally from a 2.2-fold increase to a 4-fold decrease. This level of change should be useful in fine-tuning and modulating target gene expression, which for potent molecules, such as VEGF-A and VEGF-C, can be very beneficial. These promoter-targeted shRNAs may facilitate the design and development of targeted, context-dependent strategies for both pro- and antiangiogenic therapies for the treatment of vascular-related pathologies.
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Affiliation(s)
- Nihay Laham-Karam
- Department of Biotechnology and Molecular Medicine, A.I. Virtanen Institute, University of Eastern Finland, Kuopio, Finland
| | - Marianne Lalli
- Department of Biotechnology and Molecular Medicine, A.I. Virtanen Institute, University of Eastern Finland, Kuopio, Finland
| | - Nastasia Leinonen
- Department of Biotechnology and Molecular Medicine, A.I. Virtanen Institute, University of Eastern Finland, Kuopio, Finland
| | - Seppo Ylä-Herttuala
- 1] Department of Biotechnology and Molecular Medicine, A.I. Virtanen Institute, University of Eastern Finland, Kuopio, Finland [2] Science Service Center, Kuopio University Hospital, Kuopio, Finland [3] Gene Therapy Unit, Kuopio University Hospital, Kuopio, Finland
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Wang J, Place RF, Portnoy V, Huang V, Kang MR, Kosaka M, Ho MKC, Li LC. Inducing gene expression by targeting promoter sequences using small activating RNAs. J Biol Methods 2015; 2. [PMID: 25839046 DOI: 10.14440/jbm.2015.39] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Vector-based systems comprised of exogenous nucleic acid sequences remain the standard for ectopic expression of a particular gene. Such systems offer robust overexpression, but have inherent drawbacks such as the tedious process of construction, excluding sequences (e.g. introns and untranslated regions) important for gene function and potential insertional mutagenesis of host genome associated with the use of viral vectors. We and others have recently reported that short double-stranded RNAs (dsRNAs) can induce endogenous gene expression by targeting promoter sequences in a phenomenon referred to as RNA activation (RNAa) and such dsRNAs are termed small activating RNAs (saRNAs). To date, RNAa has been successfully utilized to induce the expression of different genes such as tumor suppressor genes. Here, we describe a detailed protocol for target selection and dsRNA design with associated experiments to facilitate RNAa in cultured cells. This technique may be applied to selectively activate endogenous gene expression for studying gene function, interrogating molecular pathways and reprogramming cell fate.
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Affiliation(s)
- Ji Wang
- Department of Urology and Helen-Diller Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA 94158, USA
| | - Robert F Place
- Department of Urology and Helen-Diller Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA 94158, USA
| | - Victoria Portnoy
- Department of Urology and Helen-Diller Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA 94158, USA
| | - Vera Huang
- Department of Urology and Helen-Diller Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA 94158, USA
| | - Moo Rim Kang
- Department of Urology and Helen-Diller Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA 94158, USA
| | - Mika Kosaka
- Department of Urology and Helen-Diller Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA 94158, USA
| | - Maurice Kwok Chung Ho
- Biotechnology Research Institute and Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
| | - Long-Cheng Li
- Department of Urology and Helen-Diller Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA 94158, USA.,Laboratory of Molecular Medicine, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
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77
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Li T, Zhu YY, Chen L, Sun Y, Yuan J, Graham M, French P. Size unbiased representative enzymatically generated RNAi (SURER) library and application for RNAi therapeutic screens. Nucleic Acid Ther 2014; 25:35-46. [PMID: 25493330 DOI: 10.1089/nat.2014.0514] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
RNA interference (RNAi) libraries screens have become widely used for small RNA (sRNA) therapeutic targets development. However, conventional enzymatically libraries, typically prepared using the type 2 restriction enzyme MmeI, produce sRNAs between 18 and 20 bp, much shorter than the usual lengths of 19-23 bp. Here we develop a size unbiased representative enzymatically generated RNAi (SURER) library, which employs type 3 restriction modification enzyme EcoP15I to produce sRNAs ranging from 19 to 23 bp using a group of rationally designed linkers, which can completely mimic the length of sRNAs naturally generated by Dicer enzyme in living cells, and the screening results of SURER libraries showed high recombination rate and knockdown efficiency. SURER library provides a useful tool for RNAi therapeutics screening in a fast and simple way.
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Affiliation(s)
- Tiejun Li
- 1 Small RNA Technology and Application Institute, Nantong University , Nantong, China
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78
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Zheng L, Wang L, Gan J, Zhang H. RNA activation: promise as a new weapon against cancer. Cancer Lett 2014; 355:18-24. [PMID: 25261049 DOI: 10.1016/j.canlet.2014.09.004] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2014] [Revised: 08/30/2014] [Accepted: 09/04/2014] [Indexed: 02/05/2023]
Abstract
RNA activation (RNAa) is a novel mechanism in which short RNA duplexes, referred to as small activating RNAs (saRNAs), enable sequence-specific gene activation capable of lasting up to 2 weeks. RNAa was named in contrast to RNA interference (RNAi). Although many mysteries remain, increasing evidence demonstrates that RNAa not only provides a novel mechanism for the study of gene function and regulation, but also holds exciting potential for clinical translation to therapeutic modality against cancers. In this review, we will focus on the potential applications of RNAa in cancer studies and therapeutics.
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Affiliation(s)
- Lin Zheng
- Department of Biotherapy, Affiliated Cancer Hospital of Shantou University Medical College, Shantou, China; Cancer Research Center, Shantou University Medical College, Shantou, China
| | - Lu Wang
- Department of Biotherapy, Affiliated Cancer Hospital of Shantou University Medical College, Shantou, China; Cancer Research Center, Shantou University Medical College, Shantou, China
| | - Jinfeng Gan
- Cancer Research Center, Shantou University Medical College, Shantou, China
| | - Hao Zhang
- Department of Biotherapy, Affiliated Cancer Hospital of Shantou University Medical College, Shantou, China; Cancer Research Center, Shantou University Medical College, Shantou, China; Tumor Tissue Bank, Affiliated Cancer Hospital of Shantou University Medical College, Shantou, China.
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79
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Yang MH, Hu ZY, Xu C, Xie LY, Wang XY, Chen SY, Li ZG. MALAT1 promotes colorectal cancer cell proliferation/migration/invasion via PRKA kinase anchor protein 9. Biochim Biophys Acta Mol Basis Dis 2014; 1852:166-74. [PMID: 25446987 DOI: 10.1016/j.bbadis.2014.11.013] [Citation(s) in RCA: 154] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2014] [Revised: 10/24/2014] [Accepted: 11/12/2014] [Indexed: 02/08/2023]
Abstract
Our previous studies have shown that the 3' end of metastasis associated lung adenocarcinoma transcript 1 (MALAT1) is involved in colorectal cancer (CRC) cell proliferation and migration/invasion in vitro. The role and mechanism of MALAT1 in CRC metastasis in vivo, however, remain largely unknown. In the present study, we found that MALAT1 was up-regulated in human primary CRC tissues with lymph node metastasis. Overexpression of MALAT1 via RNA activation promoted CRC cell proliferation, invasion and migration in vitro, and stimulated tumor growth and metastasis in mice in vivo. Conversely, knockdown of MALAT1 inhibited CRC tumor growth and metastasis. MALAT1 regulated at least 243 genes in CRC cells in a genome-wide expression profiling. Among these genes, PRKA kinase anchor protein 9 (AKAP-9) was significantly up-regulated at both mRNA and protein levels. AKAP-9 was highly expressed in CRC cells with metastatic potential and human primary CRC tissues with lymph node metastasis, but not in normal cells or tissues. Importantly, knockdown of AKAP-9 blocked MALAT1-mediated CRC cell proliferation, migration and invasion. These data indicate that MALAT1 may promote CRC tumor development via its target protein AKAP-9.
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Affiliation(s)
- Min-Hui Yang
- Department of Pathology, Nanfang Hospital, Southern Medical University, China; Key Laboratory of Transcriptome and Proteome for Human Major Diseases of the Ministry of Education and Guangdong Province, Guangzhou 510515, Guangdong Province, China
| | - Zhi-Yan Hu
- Department of Pathology, Nanfang Hospital, Southern Medical University, China; Key Laboratory of Transcriptome and Proteome for Human Major Diseases of the Ministry of Education and Guangdong Province, Guangzhou 510515, Guangdong Province, China
| | - Chuan Xu
- Department of Pathology, Nanfang Hospital, Southern Medical University, China; Key Laboratory of Transcriptome and Proteome for Human Major Diseases of the Ministry of Education and Guangdong Province, Guangzhou 510515, Guangdong Province, China
| | - Lin-Ying Xie
- Department of Pathology, Nanfang Hospital, Southern Medical University, China; Key Laboratory of Transcriptome and Proteome for Human Major Diseases of the Ministry of Education and Guangdong Province, Guangzhou 510515, Guangdong Province, China
| | - Xiao-Yan Wang
- Department of Pathology, Nanfang Hospital, Southern Medical University, China; Key Laboratory of Transcriptome and Proteome for Human Major Diseases of the Ministry of Education and Guangdong Province, Guangzhou 510515, Guangdong Province, China
| | - Shi-You Chen
- Department of Physiology & Pharmacology, University of Georgia, Athens, GA, USA.
| | - Zu-Guo Li
- Department of Pathology, Nanfang Hospital, Southern Medical University, China; Key Laboratory of Transcriptome and Proteome for Human Major Diseases of the Ministry of Education and Guangdong Province, Guangzhou 510515, Guangdong Province, China.
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80
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Husso T, Ylä-Herttuala S, Turunen MP. A New Gene Therapy Approach for Cardiovascular Disease by Non-coding RNAs Acting in the Nucleus. MOLECULAR THERAPY. NUCLEIC ACIDS 2014; 3:e197. [PMID: 25405466 PMCID: PMC4461992 DOI: 10.1038/mtna.2014.48] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/09/2014] [Accepted: 08/14/2014] [Indexed: 11/26/2022]
Abstract
This review discusses recent developments in the use of non-coding RNAs (ncRNAs) for the regulation of therapeutically relevant genes, with special focus on applications for the treatment of cardiovascular diseases. The interest in using ncRNAs as therapeutics has steadily increased since the discovery of RNA interference. During the last decade it has become evident that these RNAs, delivered either as oligos or expressed as small hairpin RNAs (shRNAs) from vectors, can either upregulate (transcriptional gene activation, TGA) or downregulate (transcriptional gene silencing, TGS) gene expression, typically inducing epigenetic changes in their target sites in the chromatin. Also, the important role of naturally occurring long non-coding RNAs (lncRNAs) has been recently discovered and will likely provide new insights into cardiovascular pathology and provide new treatment strategies based on the manipulation of their expression. In this review, we discuss the possibility of using ncRNAs for activating or silencing therapeutically relevant genes, such as VEGF-A, for the treatment of cardiovascular disease.
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Affiliation(s)
- Tiia Husso
- Department of Biotechnology and Molecular Medicine, A.I.Virtanen Institute, University of Eastern Finland, Kuopio, Finland
| | - Seppo Ylä-Herttuala
- 1] Department of Biotechnology and Molecular Medicine, A.I.Virtanen Institute, University of Eastern Finland, Kuopio, Finland [2] Science Service Center and Gene Therapy Unit, Kuopio University Hospital, Kuopio, Finland
| | - Mikko P Turunen
- 1] Department of Biotechnology and Molecular Medicine, A.I.Virtanen Institute, University of Eastern Finland, Kuopio, Finland [2] Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, California, USA
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81
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Wang J, Huang V, Ye L, Bárcena A, Lin G, Lue TF, Li LC. Identification of small activating RNAs that enhance endogenous OCT4 expression in human mesenchymal stem cells. Stem Cells Dev 2014; 24:345-53. [PMID: 25232932 DOI: 10.1089/scd.2014.0290] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Ectopic overexpression of transcription factors has been used to reprogram cell fate. For example, virus-mediated overexpression of four transcription factors OCT4, SOX2, MYC, and KLF4, known as Yamanaka factors, can convert somatic cells to induced pluripotent stem (iPS) cells. However, gene-specific switch-on of endogenous gene production without the use of foreign DNA remains a challenge. The small RNA machinery that comprised small RNAs and Argonaute proteins is known to silence gene expression, but can be repurposed to activate gene expression when directed to gene promoters, a phenomenon known as RNA activation or RNAa. By screening of dsRNAs targeting OCT4 promoter, we identified a small activating RNA (saRNA) that activated OCT4 expression in several types of human mesenchymal stem cells (MSCs). We found that saRNA-induced OCT4 activation can be further enhanced by a histone deacetylase inhibitor, valproic acid. Furthermore, introducing OCT4 saRNA in combination with viruses encoding the remaining three Yamanaka factors (SOX2, MYC, and KLF4) into MSCs led to the derivation of partially reprogrammed iPS cells. Findings from this study suggest that, with further optimization, RNAa can be a powerful tool to reprogram cell fate by inducing the expression of endogenous genes.
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Affiliation(s)
- Ji Wang
- 1 Department of Urology, University of California , San Francisco, San Francisco, California
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82
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Zhao F, Pan S, Gu Y, Guo S, Dai Q, Yu Y, Zhang W. Reactivation of HIC-1 gene by saRNA inhibits clonogenicity and invasiveness in breast cancer cells. Oncol Lett 2014; 9:159-164. [PMID: 25435951 PMCID: PMC4246611 DOI: 10.3892/ol.2014.2633] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2014] [Accepted: 08/15/2014] [Indexed: 01/09/2023] Open
Abstract
Hypermethylated in cancer 1 (HIC-1) is a tumor suppressor gene, which is epigenetically silenced in breast cancer. It is known that the loss of HIC-1, caused by promoter hypermethylation, is associated with tumor aggression and poor survival in breast carcinoma. It has been shown that small activating RNA (saRNA) targeting promoter sequences may induce gene re-expression. In the current study, saRNA was used to restore HIC-1 expression, and the effects on colony formation, invasiveness and the cell cycle in breast cancer cells were explored. dsHIC1-2998, an saRNA, exhibited activating efficacy on MCF-7 and MDA-MB-231 cancer cell lines. A clonogenicity assay showed that evident colony inhibition was induced via saRNA-mediated re-expression of HIC-1 in the two cancer cell lines. Reactivation of HIC-1 significantly inhibited cell migration and invasion, resulting in G0/G1 cell cycle arrest in these cell lines. These findings suggest that HIC-1 may be a potential target in gene therapy for the treatment of breast cancer. saRNA may function as a therapeutic option for upregulating tumor suppressor genes in breast cancer.
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Affiliation(s)
- Feng Zhao
- Department of Surgery, The Ninth People's Hospital of Shanghai Jiao Tong University, School of Medicine, Shanghai 200011, P.R. China
| | - Shengli Pan
- Department of Surgery, Shanghai Ruijin Hospital of Shanghai Jiao Tong University, School of Medicine, Shanghai 200025, P.R. China
| | - Yan Gu
- Department of Surgery, The Ninth People's Hospital of Shanghai Jiao Tong University, School of Medicine, Shanghai 200011, P.R. China
| | - Shanyu Guo
- Department of Surgery, The Ninth People's Hospital of Shanghai Jiao Tong University, School of Medicine, Shanghai 200011, P.R. China
| | - Qiancheng Dai
- Department of Surgery, The Ninth People's Hospital of Shanghai Jiao Tong University, School of Medicine, Shanghai 200011, P.R. China
| | - Yingyan Yu
- Department of Surgery, Shanghai Ruijin Hospital of Shanghai Jiao Tong University, School of Medicine, Shanghai 200025, P.R. China
| | - Wei Zhang
- Department of Surgery, The Ninth People's Hospital of Shanghai Jiao Tong University, School of Medicine, Shanghai 200011, P.R. China
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83
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Ross JP, Kassir Z. The varied roles of nuclear argonaute-small RNA complexes and avenues for therapy. MOLECULAR THERAPY-NUCLEIC ACIDS 2014; 3:e203. [PMID: 25313622 PMCID: PMC4217078 DOI: 10.1038/mtna.2014.54] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2014] [Accepted: 08/22/2014] [Indexed: 12/14/2022]
Abstract
Argonautes are highly conserved proteins found in almost all eukaryotes and some bacteria and archaea. In humans, there are eight argonaute proteins evenly distributed across two clades, the Ago clade (AGO1-4) and the Piwi clade (PIWIL1-4). The function of Ago proteins is best characterized by their role in RNA interference (RNAi) and cytoplasmic post-transcriptional gene silencing (PTGS) – which involves the loading of siRNA or miRNA into argonaute to direct silencing of genes at the posttranscriptional or translational level. However, nuclear-localized, as opposed to cytoplasmic, argonaute-small RNA complexes may also orchestrate the mechanistically very different process of transcriptional gene silencing, which results in prevention of transcription from a gene locus by the formation of silent chromatin domains. More recently, the role of argonaute in other aspects of epigenetic regulation of chromatin, alternative splicing and DNA repair is emerging. This review focuses on the activity of nuclear-localized short RNA-argonaute complexes in a mammalian setting and discusses recent in vivo studies employing nuclear-directed sRNA for therapeutic interventions. These studies heed the potential development of RNA-based drugs which induce epigenetic changes in the cell.
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Affiliation(s)
- Jason P Ross
- CSIRO Food and Nutrition Flagship, Sydney, New South Wales, Australia
| | - Zena Kassir
- 1] CSIRO Food and Nutrition Flagship, Sydney, New South Wales, Australia [2] Garvan Institute of Medical Research, Sydney, New South Wales, Australia
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84
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Wojtasik W, Kulma A, Boba A, Szopa J. Oligonucleotide treatment causes flax β-glucanase up-regulation via changes in gene-body methylation. BMC PLANT BIOLOGY 2014; 14:261. [PMID: 25287293 PMCID: PMC4209061 DOI: 10.1186/s12870-014-0261-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2014] [Accepted: 09/23/2014] [Indexed: 05/29/2023]
Abstract
BACKGROUND Nowadays, the challenge for biotechnology is to develop tools for agriculture and industry to provide plants characterized by productivity and quality that will satisfy the growing demand for different kinds of natural products. To meet the challenge, the generation and application of genetically modified plants is justified. However, the strong social resistance to genetically modified organisms and restrictive regulations in European Union countries necessitated the development of a new technology for new plant types generation which uses the knowledge resulting from analysis of genetically modified plants to generate favourably altered plants while omitting the introduction of heterologous genes to their genome. Four-year experiments led to the development of a technology inducing heritable epigenetic gene activation without transgenesis. RESULTS The method comprises the induction of changes in methylation/demethylation of the endogenous gene by the plant's treatment with short oligodeoxynucleotides antisense to the coding region. In vitro cultured plants and F3 generation flax plants overproducing the β-1,3-glucanase gene (EMO-βGlu flax) were characterized by up-regulation of β-glucanase and chitinase genes, decreases in the methylation of CCGG sequences in the β-glucanase gene and in total DNA methylation and, more importantly, reasonable resistance against Fusarium infection. In addition, EMO-βGlu flax obtained by this technology showed similar features as those obtained by genetic engineering. CONCLUSION To our best knowledge, this is the first report on plant gene activation by treatment with oligodeoxynucleotides homologous to the coding region of the gene. Apart from the evident effectiveness, the most important issue is that the EMO method allows generation of favourably altered plants, whose cultivation makes the plant producer independent from the complicated procedure of obtaining an agreement on GMO release into the environment and whose products might be more easily introduced to the global market.
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Affiliation(s)
- Wioleta Wojtasik
- />Faculty of Biotechnology, University of Wroclaw, Przybyszewskiego 63/77, Wroclaw, 51-148 Poland
| | - Anna Kulma
- />Faculty of Biotechnology, University of Wroclaw, Przybyszewskiego 63/77, Wroclaw, 51-148 Poland
| | - Aleksandra Boba
- />Faculty of Biotechnology, University of Wroclaw, Przybyszewskiego 63/77, Wroclaw, 51-148 Poland
- />Wroclaw Research Center EIT+, Stablowicka 147/149, Wroclaw, 54-066 Poland
| | - Jan Szopa
- />Faculty of Biotechnology, University of Wroclaw, Przybyszewskiego 63/77, Wroclaw, 51-148 Poland
- />Linum Foundation, Stablowicka 147/149, Wroclaw, 54-066 Poland
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85
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Li MM, Li XM, Zheng XP, Yu JT, Tan L. MicroRNAs dysregulation in epilepsy. Brain Res 2014; 1584:94-104. [DOI: 10.1016/j.brainres.2013.09.049] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2013] [Revised: 09/26/2013] [Accepted: 09/28/2013] [Indexed: 10/26/2022]
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86
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Abstract
Microribonucleic acids, best known as microRNAs or miRNAs, are small, non-coding RNAs with important regulatory roles in eukaryotic cells. Here, I present a broad review on highly relevant but generally non-depicted features of miRNAs, among which stand out the non-conventional miRNA seed sites, the unusual messenger RNA (mRNA) target regions, the non-canonical miRNA-guided mechanisms of gene expression regulation, and the recently identified new class of miRNA ligands. Furthermore, I address the miRNA uncommon genomic location, transcription, and subcellular localization. Altogether, these unusual features and roles place the miRNA system as a very diverse, complex, and intriguing biological mechanism.
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Affiliation(s)
- Gabriel A Cipolla
- Laboratory of Human Molecular Genetics, Department of Genetics, Federal University of Paraná Curitiba, Brazil
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87
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Gagnon KT, Li L, Janowski BA, Corey DR. Analysis of nuclear RNA interference in human cells by subcellular fractionation and Argonaute loading. Nat Protoc 2014; 9:2045-60. [PMID: 25079428 PMCID: PMC4251768 DOI: 10.1038/nprot.2014.135] [Citation(s) in RCA: 143] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
RNAi is well known for its ability to regulate gene expression in the cytoplasm of mammalian cells. In mammalian cell nuclei, however, the impact of RNAi has remained more controversial. A key technical hurdle has been a lack of optimized protocols for the isolation and analysis of cell nuclei. Here we describe a simplified protocol for nuclei isolation from cultured cells that incorporates a method for obtaining nucleoplasmic and chromatin fractions and removing cytoplasmic contamination. Cell fractions can then be used to detect the presence and activity of RNAi factors in the nucleus. We include a method for investigating an early step in RNAi, Argonaute protein loading with small RNAs, which is enabled by our improved extract preparations. This protocol facilitates the characterization of nuclear RNAi, and it can be applied to the analysis of other nuclear proteins and pathways. From cellular fractionation to analysis of Argonaute loading results, this protocol takes 4-6 d to complete.
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Affiliation(s)
- Keith T Gagnon
- Department of Pharmacology, University of Texas Southwestern Medical Center at Dallas, Dallas, Texas, USA
| | - Liande Li
- Department of Pharmacology, University of Texas Southwestern Medical Center at Dallas, Dallas, Texas, USA
| | - Bethany A Janowski
- Department of Pharmacology, University of Texas Southwestern Medical Center at Dallas, Dallas, Texas, USA
| | - David R Corey
- 1] Department of Pharmacology, University of Texas Southwestern Medical Center at Dallas, Dallas, Texas, USA. [2] Department of Biochemistry, University of Texas Southwestern Medical Center at Dallas, Dallas, Texas, USA
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88
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Yang B, Duan X, Wu W, Ji W, Wu W, Zhong W, Zhao Z, Li S, Liu Y, Zeng G. Induction of TRPV5 expression by small activating RNA targeting gene promoter as a novel approach to regulate cellular calcium transportation. Life Sci 2014; 114:70-6. [PMID: 25139832 DOI: 10.1016/j.lfs.2014.08.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2014] [Revised: 08/04/2014] [Accepted: 08/06/2014] [Indexed: 10/24/2022]
Abstract
AIM Promoter-targeted small activating RNAs (saRNAs) have been shown to be able to induce target gene expression, a mechanism known as RNA activation (RNAa). The present study tested whether saRNA can induce the overexpression of TRPV5 in human cells derived from the kidney and subsequently manipulate cell calcium uptake. MAIN METHODS Three saRNAs complementary to the TRPV5 promoter were synthesized and transfected into cells. TRPV5 expression at the RNA and protein levels was analyzed by quantitative real-time PCR and Western blotting respectively. For functional study, transcellular Ca(2+) transportation was tested by fura-2 analysis. Dihydrotestosterone (DHT), a suppressor of cellular calcium transportation, was administered to challenge the activating effect of selected saRNA. KEY FINDINGS One of these synthesized saRNAs, ds-2939, significantly induced the expression of TRPV5 at both mRNA and protein levels. Fura-2 analysis revealed that the intracellular Ca(2+) concentration was elevated by ds-2939. DHT treatment reduced transmembrane Ca(2+) transport, which was partially antagonized by ds-2939. SIGNIFICANCE Our results suggest that a saRNA targeting TRPV5 promoter can be utilized to manipulate the transmembrane Ca(2+) transport by upregulating the expression of TRPV5 and may serve as an alternative for the treatment of Ca(2+) balance-related diseases.
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Affiliation(s)
- Bicheng Yang
- Department of Urology, Minimally Invasive Surgery Center, The First Affiliated Hospital of Guangzhou Medical University, Guangdong Key Laboratory of Urology, Guangzhou 510230, China
| | - Xiaolu Duan
- Department of Urology, Minimally Invasive Surgery Center, The First Affiliated Hospital of Guangzhou Medical University, Guangdong Key Laboratory of Urology, Guangzhou 510230, China
| | - Wenzheng Wu
- Department of Urology, Minimally Invasive Surgery Center, The First Affiliated Hospital of Guangzhou Medical University, Guangdong Key Laboratory of Urology, Guangzhou 510230, China
| | - Weidong Ji
- Department of Urology, Minimally Invasive Surgery Center, The First Affiliated Hospital of Guangzhou Medical University, Guangdong Key Laboratory of Urology, Guangzhou 510230, China
| | - Wenqi Wu
- Department of Urology, Minimally Invasive Surgery Center, The First Affiliated Hospital of Guangzhou Medical University, Guangdong Key Laboratory of Urology, Guangzhou 510230, China
| | - Wen Zhong
- Department of Urology, Minimally Invasive Surgery Center, The First Affiliated Hospital of Guangzhou Medical University, Guangdong Key Laboratory of Urology, Guangzhou 510230, China
| | - Zhijian Zhao
- Department of Urology, Minimally Invasive Surgery Center, The First Affiliated Hospital of Guangzhou Medical University, Guangdong Key Laboratory of Urology, Guangzhou 510230, China
| | - Shujue Li
- Department of Urology, Minimally Invasive Surgery Center, The First Affiliated Hospital of Guangzhou Medical University, Guangdong Key Laboratory of Urology, Guangzhou 510230, China
| | - Yang Liu
- Department of Urology, Minimally Invasive Surgery Center, The First Affiliated Hospital of Guangzhou Medical University, Guangdong Key Laboratory of Urology, Guangzhou 510230, China
| | - Guohua Zeng
- Department of Urology, Minimally Invasive Surgery Center, The First Affiliated Hospital of Guangzhou Medical University, Guangdong Key Laboratory of Urology, Guangzhou 510230, China.
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89
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Askou AL. Development of gene therapy for treatment of age-related macular degeneration. Acta Ophthalmol 2014; 92 Thesis3:1-38. [PMID: 24953666 DOI: 10.1111/aos.12452] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Intraocular neovascular diseases are the leading cause of blindness in the Western world in individuals over the age of 50. Age-related macular degeneration (AMD) is one of these diseases. Exudative AMD, the late-stage form, is characterized by abnormal neovessel development, sprouting from the choroid into the avascular subretinal space, where it can suddenly cause irreversible damage to the vulnerable photoreceptor (PR) cells essential for our high-resolution, central vision. The molecular basis of AMD is not well understood, but several growth factors have been implicated including vascular endothelial growth factor (VEGF), and the advent of anti-VEGF therapy has markedly changed the outcome of treatment. However, common to all current therapies for exudative AMD are the complications of repeated monthly intravitreal injections, which must be continued throughout one's lifetime to maintain visual benefits. Additionally, some patients do not benefit from established treatments. Strategies providing long-term suppression of inappropriate ocular angiogenesis are therefore needed, and gene therapy offers a potential powerful technique. This study aimed to develop a strategy based on RNA interference (RNAi) for the sustained attenuation of VEGF. We designed a panel of anti-VEGF short hairpin RNAs (shRNA), and based on the most potent shRNAs, microRNA (miRNA)-mimicked hairpins were developed. We demonstrated an additive VEGF silencing effect when we combined the miRNAs in a tricistronic miRNA cluster. To meet the requirements for development of medical treatments for AMD with long-term effects, the shRNA/miRNA is expressed from vectors based on adeno-associated virus (AAV) or lentivirus (LV). Both vector systems have been found superior in terms of transduction efficiency and persistence in gene expression in retinal cells. The capacity of AAV-encoded RNAi effector molecules to silence endogenous VEGF gene expression was evaluated in mouse models, including the model of laser-induced choroidal neovascularization (CNV), and we found that subretinal administration of self-complementary (sc)-AAV2/8 encoding anti-VEGF shRNAs can impair vessel formation. In parallel, a significant reduction of endogenous VEGF was demonstrated following injection of scAAV2/8 vectors expressing multiple anti-VEGF miRNAs into murine hind limb muscles. Furthermore, in an ongoing project we have designed versatile, multigenic LV vectors with combined expression of multiple miRNAs and proteins, including pigment epithelium-derived factor (PEDF), a multifunctional, secreted protein that has anti-angiogenic and neurotrophic functions. Co-expression of miRNAs and proteins from a single viral vector increases safety by minimizing the viral load necessary to obtain a therapeutic effect and thereby reduces the risk of insertional mutagenesis as well as the immune response against viral proteins. Our results show co-expression of functional anti-VEGF-miRNAs and PEDF in cell studies, and in vivo studies reveal an efficient retinal pigment epithelium (RPE)-specific gene expression following the incorporation of the vitelliform macular dystrophy 2 (VMD2) promoter, demonstrating the potential applicability of our multigenic LV vectors in ocular anti-VEGF gene therapy, including combination therapy for treatment of exudative AMD. In conclusion, these highly promising data clearly demonstrate that viral-encoded RNAi effector molecules can be used for the inhibition of neovascularization and will, in combination with the growing interest of applying DNA- or RNA-based technologies in the clinic, undoubtedly contribute to the development of efficacious long-term gene therapy treatment of intraocular neovascular diseases.
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90
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Girardi C, De Pittà C, Casara S, Calura E, Romualdi C, Celotti L, Mognato M. Integration analysis of microRNA and mRNA expression profiles in human peripheral blood lymphocytes cultured in modeled microgravity. BIOMED RESEARCH INTERNATIONAL 2014; 2014:296747. [PMID: 25045661 PMCID: PMC4090438 DOI: 10.1155/2014/296747] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/16/2014] [Revised: 05/22/2014] [Accepted: 05/22/2014] [Indexed: 01/07/2023]
Abstract
We analyzed miRNA and mRNA expression profiles in human peripheral blood lymphocytes (PBLs) incubated in microgravity condition, simulated by a ground-based rotating wall vessel (RWV) bioreactor. Our results show that 42 miRNAs were differentially expressed in MMG-incubated PBLs compared with 1 g incubated ones. Among these, miR-9-5p, miR-9-3p, miR-155-5p, miR-150-3p, and miR-378-3p were the most dysregulated. To improve the detection of functional miRNA-mRNA pairs, we performed gene expression profiles on the same samples assayed for miRNA profiling and we integrated miRNA and mRNA expression data. The functional classification of miRNA-correlated genes evidenced significant enrichment in the biological processes of immune/inflammatory response, signal transduction, regulation of response to stress, regulation of programmed cell death, and regulation of cell proliferation. We identified the correlation of miR-9-3p, miR-155-5p, miR-150-3p, and miR-378-3p expression with that of genes involved in immune/inflammatory response (e.g., IFNG and IL17F), apoptosis (e.g., PDCD4 and PTEN), and cell proliferation (e.g., NKX3-1 and GADD45A). Experimental assays of cell viability and apoptosis induction validated the results obtained by bioinformatics analyses demonstrating that in human PBLs the exposure to reduced gravitational force increases the frequency of apoptosis and decreases cell proliferation.
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Affiliation(s)
- C. Girardi
- Dipartimento di Biologia, Università degli Studi di Padova, Via U. Bassi 58/B, 35131 Padova, Italy
| | - C. De Pittà
- Dipartimento di Biologia, Università degli Studi di Padova, Via U. Bassi 58/B, 35131 Padova, Italy
| | - S. Casara
- Dipartimento di Biologia, Università degli Studi di Padova, Via U. Bassi 58/B, 35131 Padova, Italy
| | - E. Calura
- Dipartimento di Biologia, Università degli Studi di Padova, Via U. Bassi 58/B, 35131 Padova, Italy
| | - C. Romualdi
- Dipartimento di Biologia, Università degli Studi di Padova, Via U. Bassi 58/B, 35131 Padova, Italy
| | - L. Celotti
- Dipartimento di Biologia, Università degli Studi di Padova, Via U. Bassi 58/B, 35131 Padova, Italy
- Laboratori Nazionali di Legnaro, INFN, Viale dell'Università 2, Legnaro, 35020 Padova, Italy
| | - M. Mognato
- Dipartimento di Biologia, Università degli Studi di Padova, Via U. Bassi 58/B, 35131 Padova, Italy
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91
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Direct transcriptional regulation by nuclear microRNAs. Int J Biochem Cell Biol 2014; 54:304-11. [PMID: 24680896 DOI: 10.1016/j.biocel.2014.03.010] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2014] [Revised: 03/06/2014] [Accepted: 03/17/2014] [Indexed: 01/07/2023]
Abstract
The function of microRNAs is well characterized in the cytoplasm, where they direct an Argonaute-containing complex to target and repress mRNAs. More recently, regulatory roles for microRNAs and Argonaute have also been reported in the nucleus where microRNAs guide Argonaute to target gene promoters and directly regulate transcription in either a positive or a negative manner. Deep sequencing has revealed a high abundance of endogenous microRNAs within the nucleus, and in silico target prediction suggests thousands of potential microRNA:promoter interaction sites. The predicted high frequency of miRNA:promoter interactions is supported by chromatin immunoprecipitation, indicating the microRNA-dependent recruitment of Argonaute to thousands of transcriptional start sites and the subsequent regulation of RNA polymerase-II occupancy and chromatin modifiers. In this review we discuss the evidence for, and mechanisms associated with, direct transcriptional regulation by microRNAs which may represent a significant and largely unexplored aspect of microRNA function. This article is part of a Directed Issue entitled: The non-coding RNA revolution.
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92
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Upregulation of RECK gene expression by small double-stranded RNA targeting the promoter region. Cancer Gene Ther 2014; 21:164-70. [PMID: 24651481 DOI: 10.1038/cgt.2014.12] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2013] [Revised: 03/04/2014] [Accepted: 03/04/2014] [Indexed: 11/09/2022]
Abstract
Recent studies have demonstrated that small double-stranded RNAs (dsRNAs) complementary to the promoter region of target genes enhance the expression of those genes following transfection into cells. Here we show that expression of the matrix metalloproteinase (MMP) inhibitor RECK is activated in the cultured tumor cell lines by transfection with dsRNA complementary to the promoter of the RECK gene, leading to suppression of the expression of MMPs and it inhibited tumor cell invasion. These results support the suggestion that dsRNA complementary to the promoter region of tumor suppressor genes would have potential as a novel antitumor agent.
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93
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Dong Z, Dang Y, Chen Y. Small double-stranded RNA mediates the anti-cancer effects of p21WAF1/ClP1 transcriptional activation in a human glioma cell line. Yonsei Med J 2014; 55:324-30. [PMID: 24532499 PMCID: PMC3936623 DOI: 10.3349/ymj.2014.55.2.324] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
PURPOSE This study was conducted to investigate the small double-stranded RNA (dsRNA) mediated anti-tumor effects of p21WAF1/ClP1 (p21) transcriptional activation in vitro in the human glioma SHG-44 cell line. MATERIALS AND METHODS Human glioma SHG-44 cells were transfected with dsRNA using LipofectAMINE 2000 transfection reagent. Real-time PCR and Western blot analysis were conducted to detect p21 and survivin mRNA and protein levels, respectively. Cell proliferation was examined by MTT assay. Cell cycle distribution and apoptosis were detected by flow-cytometric analysis. RESULTS We found that dsRNA targeting p21 promoter (dsP21) significantly induced the expression of p21 at transcription and protein levels, and reduced the expression of survivin. AS well, dsP21 transcription significantly inhibited human glioma SHG-44 cell proliferation. Analysis of cell cycle distribution revealed that dsP21 transfection increased accumulation of cells in the G0/G1 phase and reduced accumulation of cells in the S phase. Further analysis revealed that dsP21 transcription led to an increase in both early and late stages of apoptosis in human glioma SHG-44 cells. CONCLUSION In the present study, P21 activation by RNA-induced gene activation (RNAa) induced anti-tumor activity in vitro in a human glioma SHG-44 cell line. The results suggested that RNAa could be used for human glioma treatment by targeted activation of tumor suppressor genes.
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Affiliation(s)
- Zhiqiang Dong
- Department of Urology, People's Hospital of Gansu Province, NO. 204 Donggang West Road, Chengguan District, Lanzhou 730000, China.
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94
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Cheng J, Wang X, Cai N, Ma Z, Zhang L, Lv Z. RNAs specifically affect gene expression in a length, position and sequence dependent manner. INTERNATIONAL JOURNAL OF CLINICAL AND EXPERIMENTAL PATHOLOGY 2014; 7:948-958. [PMID: 24696713 PMCID: PMC3971297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 12/18/2013] [Accepted: 02/10/2014] [Indexed: 06/03/2023]
Abstract
We aim to explore if RNA regulating gene expression is affected by length, sequence and position of RNA. HeLa cells were co-transfected with modulator plasmids (derived from pcDNA3.1 vector containing different length regulating sequences that produce RNAs) and reporter plasmids (derived from pEGFP-C1 vector); In addition, HeLa cells were transfected with plasmids that possess different sequences of downstream or adjacent genes of GFP reporter gene. We found that long inserting sequences of modulator plasmids induced stronger GFP gene activation than short inserting sequences. Changing of downstream sequences of GFP gene induced significant effects on GFP gene expression. Short sequences of adjacent genes of GFP activated GFP gene. Bioinformatics analysis of genes which is highly expressed in differentiating cells (thymocyte cells, germinal center B-cells) and quiescent cells (T cells, B cells) shows that differentiating cells produce longer RNA than quiescent cells. These findings demonstrate that the length, sequence and producing position of RNAs are important factors for RNA regulating gene expression.
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Affiliation(s)
- Jianjun Cheng
- Department of Genetics, Hebei Medical University, Hebei Key Lab of Laboratory AnimalShijiazhuang 050017, Hebei Province, China
| | - Xiufang Wang
- Department of Genetics, Hebei Medical University, Hebei Key Lab of Laboratory AnimalShijiazhuang 050017, Hebei Province, China
| | - Nianguang Cai
- Hebei North UniversityZhangjiakou 075000, Hebei Province, China
| | - Zhihong Ma
- Clinical Laboratory, The Second Hospital of TangshanTangshan 063000, Hebei Province, China
| | - Liyan Zhang
- Hebei North UniversityZhangjiakou 075000, Hebei Province, China
| | - Zhanjun Lv
- Department of Genetics, Hebei Medical University, Hebei Key Lab of Laboratory AnimalShijiazhuang 050017, Hebei Province, China
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95
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Small activating RNA restores the activity of the tumor suppressor HIC-1 on breast cancer. PLoS One 2014; 9:e86486. [PMID: 24489730 PMCID: PMC3904905 DOI: 10.1371/journal.pone.0086486] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2013] [Accepted: 12/09/2013] [Indexed: 12/20/2022] Open
Abstract
HIC-1 is a gene that is hypermethylated in cancer, and commonly downregulated in human breast cancer. However, the precise mechanisms and molecular pathways regulated by HIC-1 remain unclear. We assessed HIC-1 expression on a tissue microarray containing 80 cases of breast cancer. We also analyzed its biological function by restoring HIC-1 expression using 5-aza-2′ deoxycytidine (5-CdR) and small-activating RNAs for the reversal of HIC-1 tumor suppressive effects on MCF-7 and MDA-MB-231 cell lines. An Agilent Q44h global expressing microarray was probed after restoring the expression of HIC-1. Data demonstrated that HIC-1 expression was reduced significantly in breast cancer tissues. HIC-1 immunohistochemistry resulted in mean staining scores in cancer tissue and normal ductal epithelia of 3.54 and 8.2, respectively (p<0.01). 5-CdR partially reversed HIC-1 expression, and modulated cell growth and apoptosis. dsHIC1-2998, an saRNA, showed activating efficacy in breast cancer cells. A group of differentially expressed genes were characterized by cDNA microarray. Upon saRNA treatment, genes upregulated included those involved in immune activation, cell cycle interference, the induction of apoptosis, anti-metastasis, and cell differentiation. Downregulated genes included oncogenes and those that play roles in cell invasion, cell growth, and cell division. Our findings may provide valuable resources not only for gene functional studies, but also for potential clinical applications to develop novel drug targets.
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96
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Turner MJ, Jiao AL, Slack FJ. Autoregulation of lin-4 microRNA transcription by RNA activation (RNAa) in C. elegans. Cell Cycle 2014; 13:772-81. [PMID: 24398561 DOI: 10.4161/cc.27679] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
The conserved lin-4 microRNA (miRNA) regulates the proper timing of stem cell fate decisions in C. elegans by regulating stemness genes such as lin-14 and lin-28. (1)(-) (3) While lin-4 is upregulated toward the end of the first larval stage and functions as an essential developmental timing "switch", little is known about how lin-4 expression is regulated. (4) Here we show that in C. elegans hypodermal seam cells, transcription of lin-4 is positively regulated by lin-4 itself. In these cells, lin-4 activates its own transcription through a conserved lin-4-complementary element (LCE) in its promoter. We further show that lin-4 is required to recruit RNA polymerase II to its own promoter, and that lin-4 overexpression is sufficient for autoactivation. Finally, we show that a protein complex specifically binds the LCE in vitro, and that mutations that abolish this binding also reduce the in vivo expression of a plin-4:GFP reporter. Thus, we describe the first in vivo evidence of RNA activation (RNAa) by an endogenous miRNA, and provide new insights into an elegant autoregulatory mechanism that ensures the proper timing of stem cell fate decisions in development.
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Affiliation(s)
- Michael J Turner
- Department of Molecular, Cellular and Developmental Biology; Yale University; New Haven, CT USA
| | - Alan L Jiao
- Department of Molecular, Cellular and Developmental Biology; Yale University; New Haven, CT USA
| | - Frank J Slack
- Department of Molecular, Cellular and Developmental Biology; Yale University; New Haven, CT USA
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97
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A genetic program theory of aging using an RNA population model. Ageing Res Rev 2014; 13:46-54. [PMID: 24263168 DOI: 10.1016/j.arr.2013.11.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2013] [Accepted: 11/08/2013] [Indexed: 12/11/2022]
Abstract
Aging is a common characteristic of multicellular eukaryotes. Copious hypotheses have been proposed to explain the mechanisms of aging, but no single theory is generally acceptable. In this article, we refine the RNA population gene activating model (Lv et al., 2003) based on existing reports as well as on our own latest findings. We propose the RNA population model as a genetic theory of aging. The new model can also be applied to differentiation and tumorigenesis and could explain the biological significance of non-coding DNA, RNA, and repetitive sequence DNA. We provide evidence from the literature as well as from our own findings for the roles of repetitive sequences in gene activation. In addition, we predict several phenomena related to aging and differentiation based on this model.
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98
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Dharap A, Pokrzywa C, Murali S, Pandi G, Vemuganti R. MicroRNA miR-324-3p induces promoter-mediated expression of RelA gene. PLoS One 2013; 8:e79467. [PMID: 24265774 PMCID: PMC3827167 DOI: 10.1371/journal.pone.0079467] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2013] [Accepted: 09/28/2013] [Indexed: 12/31/2022] Open
Abstract
MicroRNAs (miRNAs) are known to repress translation by binding to the 3’UTRs of mRNAs. Using bioinformatics, we recently reported that several miRNAs also have target sites in DNA particularly in the promoters of the protein-coding genes. To understand the functional significance of this phenomenon, we tested the effects of miR-324-3p binding to RelA promoter. In PC12 cells, co-transfection with premiR-324-3p induced a RelA promoter plasmid in a dose-dependent manner and this effect was lost when the miR-324-3p binding site in the promoter was mutated. PremiR-324-3p transfection also significantly induced the endogenous RelA mRNA and protein expression in PC12 cells. Furthermore, transfection with premiR-324-3p increased the levels of cleaved caspase-3 which is a marker of apoptosis. Importantly, the miR-324-3p effects were Ago2 mediated as Ago2 knockdown prevented RelA expression and cleavage of caspase-3. Thus, our studies show that miRNA-mediated transcriptional activation can be seen in PC12 cells which are neural in origin.
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Affiliation(s)
- Ashutosh Dharap
- Department of Neurological Surgery, University of Wisconsin, Madison, Wisconsin, United States of America
- Neuroscience Training Program, University of Wisconsin, Madison, Wisconsin, United States of America
| | - Courtney Pokrzywa
- Department of Neurological Surgery, University of Wisconsin, Madison, Wisconsin, United States of America
| | - Shruthi Murali
- Department of Neurological Surgery, University of Wisconsin, Madison, Wisconsin, United States of America
| | - Gopal Pandi
- Department of Neurological Surgery, University of Wisconsin, Madison, Wisconsin, United States of America
| | - Raghu Vemuganti
- Department of Neurological Surgery, University of Wisconsin, Madison, Wisconsin, United States of America
- Neuroscience Training Program, University of Wisconsin, Madison, Wisconsin, United States of America
- * E-mail:
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99
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Human RNAi pathway: crosstalk with organelles and cells. Funct Integr Genomics 2013; 14:31-46. [PMID: 24197738 DOI: 10.1007/s10142-013-0344-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2013] [Revised: 10/03/2013] [Accepted: 10/07/2013] [Indexed: 12/12/2022]
Abstract
Understanding gene regulation mechanisms has been a serious challenge in biology. As a novel mechanism, small non-coding RNAs are an alternative means of gene regulation in a specific and efficient manner. There are growing reports on regulatory roles of these RNAs including transcriptional gene silencing/activation and post-transcriptional gene silencing events. Also, there are several known small non-coding RNAs which all work through RNA interference pathway. Interestingly, these small RNAs are secreted from cells toward targeted cells presenting new communication approach in cell-cell or cell-organ signal transduction. In fact, understanding cellular and molecular basis of these pathways will strongly improve developing targeted therapies and potent and specific regulatory tools. This study will review some of the most recent findings in this subject and will introduce a super-pathway RNA interference-based small RNA silencing network.
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100
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Abstract
The regulation of gene expression by non-coding RNAs (ncRNAs) has become a new paradigm in biology. RNA-mediated gene silencing pathways have been studied extensively, revealing diverse epigenetic and posttranscriptional mechanisms. In contrast, the roles of ncRNAs in activating gene expression remains poorly understood. In this review, we summarize the current knowledge of gene activation by small RNAs, long non-coding RNAs, and enhancer-derived RNAs, with an emphasis on epigenetic mechanisms.
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Affiliation(s)
- Alan L Jiao
- Department of Molecular, Cellular and Developmental Biology; Yale University; New Haven, CT USA
| | - Frank J Slack
- Department of Molecular, Cellular and Developmental Biology; Yale University; New Haven, CT USA
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