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Qiu M, Chen Y, Zeng C. Biological functions of circRNA in regulating the hallmarks of gastrointestinal cancer (Review). Int J Oncol 2024; 64:49. [PMID: 38488023 PMCID: PMC10997371 DOI: 10.3892/ijo.2024.5637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2023] [Accepted: 02/06/2024] [Indexed: 03/19/2024] Open
Abstract
Circular RNA (circRNA) was first observed in the cytoplasm of eukaryotic cells in 1979, but it was not characterized in detail until 2012, when high‑throughput sequencing technology was more advanced and available. Consequently, the mechanism of circRNA formation and its biological function have been progressively elucidated by researchers. circRNA is abundant in eukaryotic cells and exhibits a certain degree of organization, timing and disease‑specificity. Additionally, it is poorly degradable, meeting the characteristics of an ideal clinical biomarker. In the present review, the recent research progress of circRNAs in digestive tract malignant tumors was primarily discussed. This included the roles, biological functions and clinical significance of circRNA, providing references for its research value and clinical potential in gastrointestinal cancer.
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Affiliation(s)
- Mengjun Qiu
- Department of Gastroenterology, Digestive Disease Hospital, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, Jiangxi 330006, P.R. China
| | - Youxiang Chen
- Department of Gastroenterology, Digestive Disease Hospital, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, Jiangxi 330006, P.R. China
| | - Chunyan Zeng
- Department of Gastroenterology, Digestive Disease Hospital, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, Jiangxi 330006, P.R. China
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2
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Liu J, Liang Y, Qiao L, Xia D, Pan Y, Liu W. MiR-128-1-5p regulates differentiation of ovine stromal vascular fraction by targeting the KLF11 5'-UTR. Domest Anim Endocrinol 2022; 80:106711. [PMID: 35338828 DOI: 10.1016/j.domaniend.2022.106711] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 01/25/2022] [Accepted: 02/01/2022] [Indexed: 11/22/2022]
Abstract
Fat content is an important index to evaluate the individual performance of livestock animals such as sheep for meat production purposes. Reducing the subcutaneous and visceral fat while increasing the intramuscular fat is a valuable goal to achieve for the meat production industry. Here, we investigated the effect of miR-128-1-5p on adipogenesis of subcutaneous fat by targeting 5'-UTR in KLF11, a rare mechanism where most miRNAs bind the 3'-UTR of mRNAs. A dual fluorescence reporter assay was conducted to validate the binding sites of miR-128-1-5p on 5'-UTR of KLF11 mRNA. Roles of miR-128-1-5p in KLF11 expression were measured through co-transfecting miRNA mimics with KLF11-expressing vectors (CDSs together with or without the 5'-UTR) into ovine stromal vascular fractions (SVF). Additionally, functional roles of miR-128-1-5p, and KLF11 in adipogenesis of ovine subcutaneous fat were investigated. Results showed that miR-128-1-5p targeted KLF11 5'-UTR, reduced the fluorescence activity of the dual fluorescent reporter vector, as well as KLF11 mRNA, and protein expression levels. During the differentiation of SVF, disturbing the expression of miR-128-1-5p and KLF11 changed the adipogenic differentiation of SVF as observed in the lipid formation, and adipogenic marker genes. This study indicates that miR-128-1-5p promotes the expression of lipogenic marker genes and the formation of lipid droplets by targeting KLF11 5'-UTR. Furthermore, overexpression, and inhibition of KLF11 indicate that KLF11 inhibited SVF differentiation. In summary, the 5'-UTR binding mechanism discovered in this study extends the understanding of miRNA functions. Key roles of miR-128-1-5p and KLF11 in the adipogenesis of sheep subcutaneous fat have potential values for improving the meat and/or fat ratio of domestic animals.
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Affiliation(s)
- Jianhua Liu
- College of Animal Science, Shanxi Agricultural University, Taigu 030801, China
| | - Yu Liang
- College of Animal Science, Shanxi Agricultural University, Taigu 030801, China
| | - Liying Qiao
- College of Animal Science, Shanxi Agricultural University, Taigu 030801, China
| | - Dong Xia
- Royal Veterinary College, University of London, London NW1 0TU, UK
| | - Yangyang Pan
- College of Animal Science, Shanxi Agricultural University, Taigu 030801, China
| | - Wenzhong Liu
- College of Animal Science, Shanxi Agricultural University, Taigu 030801, China.
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3
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Du M, Espinosa-Diez C, Liu M, Ahmed IA, Mahan S, Wei J, Handen AL, Chan SY, Gomez D. miRNA/mRNA co-profiling identifies the miR-200 family as a central regulator of SMC quiescence. iScience 2022; 25:104169. [PMID: 35465051 PMCID: PMC9018390 DOI: 10.1016/j.isci.2022.104169] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 03/01/2022] [Accepted: 03/24/2022] [Indexed: 12/14/2022] Open
Abstract
miRNAs are versatile regulators of smooth muscle cell (SMC) fate and behavior in vascular development and disease. Targeted loss-of-function studies have established the relevance of specific miRNAs in controlling SMC differentiation or mediating phenotypic modulation. Our goal was to characterize SMC miRNAome and its contribution to transcriptome changes during phenotypic modulation. Small RNA sequencing revealed that dedifferentiation led to the differential expression of over 50 miRNAs in cultured SMC. miRNA/mRNA comparison predicted that over a third of SMC transcript expression was regulated by differentially expressed miRNAs. Our screen identified the miR-200 cluster as highly downregulated during dedifferentiation. miR-200 maintains SMC quiescence and represses proliferation, migration, and neointima formation, in part by targeting Quaking, a central SMC phenotypic switching mediator. Our study unraveled the substantial contribution of miRNAs in regulating the SMC transcriptome and identified the miR-200 cluster as a pro-quiescence mechanism and a potential inhibitor of vascular restenosis.
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Affiliation(s)
- Mingyuan Du
- Pittsburgh Heart, Lung, Blood, and Vascular Medicine Institute, University of Pittsburgh, Pittsburgh, PA 15261, USA.,Department of Vascular Surgery, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Cristina Espinosa-Diez
- Pittsburgh Heart, Lung, Blood, and Vascular Medicine Institute, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Mingjun Liu
- Pittsburgh Heart, Lung, Blood, and Vascular Medicine Institute, University of Pittsburgh, Pittsburgh, PA 15261, USA.,Division of Cardiology, Department of Medicine, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Ibrahim Adeola Ahmed
- Pittsburgh Heart, Lung, Blood, and Vascular Medicine Institute, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Sidney Mahan
- Pittsburgh Heart, Lung, Blood, and Vascular Medicine Institute, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Jianxin Wei
- Pittsburgh Heart, Lung, Blood, and Vascular Medicine Institute, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Adam L Handen
- Pittsburgh Heart, Lung, Blood, and Vascular Medicine Institute, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Stephen Y Chan
- Pittsburgh Heart, Lung, Blood, and Vascular Medicine Institute, University of Pittsburgh, Pittsburgh, PA 15261, USA.,Division of Cardiology, Department of Medicine, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Delphine Gomez
- Pittsburgh Heart, Lung, Blood, and Vascular Medicine Institute, University of Pittsburgh, Pittsburgh, PA 15261, USA.,Division of Cardiology, Department of Medicine, University of Pittsburgh, Pittsburgh, PA 15261, USA
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4
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lncRNA STAT4-AS1 Inhibited TH17 Cell Differentiation by Targeting ROR γt Protein. J Immunol Res 2022; 2022:8307280. [PMID: 35528611 PMCID: PMC9071868 DOI: 10.1155/2022/8307280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Accepted: 04/05/2022] [Indexed: 11/18/2022] Open
Abstract
Objective From our previous study, we obtained long noncoding RNA (lncRNA) STAT4-AS1, which is related to asthma through high-throughput screening. However, we could not determine the specific mechanism involved and in response to this. We further designed this study. Results First, we found that lncRNA STAT4-AS1 was downregulated in T cells from patients with asthma when compared to healthy controls. Next, we confirmed that lncRNA STAT4-AS1 was significantly negatively correlated with T helper 17 (TH17) differentiation in vitro experiments. The decreases of STAT4-AS1 promoted TH17 differentiation, while the increases of STAT4-AS1 inhibited TH17 differentiation. Subsequently, through RNA pull-down, RNA-binding protein immunoprecipitation (RIP), and dual luciferase reporter assay, we found that STAT4-AS1 could inhibit the binding of retinoid-related orphan receptor-γt (RORγt) protein with an IL-17A promoter after binding with RORγt protein. Fluorescence in situ hybridization (FISH) and nuclear-cytoplasmic separation assay showed that STAT4-AS1 is bonded to RORγt in the cytoplasm, preventing RORγt from entering the nucleus. Conclusion Overall, STAT4-AS1 directly targets RORγt protein, inhibits the mutual binding of RORγt and IL-17 gene promoter, and eventually inhibits TH17 differentiation. To this end, STAT4-AS1 as a potential target may confer applications in the clinical treatment and diagnosis of TH17-related diseases.
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Ziel-Swier LJYM, Liu Y, Seitz A, de Jong D, Koerts J, Rutgers B, Veenstra R, Razak FRA, Dzikiewicz-Krawczyk A, van den Berg A, Kluiver J. The Role of the MYC/miR-150/MYB/ZDHHC11 Network in Hodgkin Lymphoma and Diffuse Large B-Cell Lymphoma. Genes (Basel) 2022; 13:genes13020227. [PMID: 35205272 PMCID: PMC8871936 DOI: 10.3390/genes13020227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 01/21/2022] [Accepted: 01/24/2022] [Indexed: 12/04/2022] Open
Abstract
We previously described involvement of the MYC/miR-150/MYB/ZDHHC11 network in the growth of Burkitt lymphoma (BL) cells. Here we studied the relevance of this network in the two other B-cell lymphomas: Hodgkin lymphoma (HL) and diffuse large B-cell lymphoma (DLBCL). Expression levels of the network components were assessed at the RNA and protein level. The effect of modulating levels of the network components on cell growth was determined through GFP competition assay. AGO2-RNA immunoprecipitation was performed to validate targeting by miR-150. Expression levels of MYC, MYB and ZDHHC11 were increased, while miR-150 levels were decreased similar to the pattern observed in BL. The knockdown of MYC, MYB and ZDHHC11 decreased the growth of HL and DLBCL cells. In contrast, overexpression of miR-150 did not induce clear phenotypes in HL, and limited the effects in DLBCL. This could not be explained by the differences in overexpression levels. Furthermore, we showed that in HL, ZDHHC11 and MYB are efficiently targeted by miR-150. To conclude, MYC, MYB and ZDHHC11 are critical for the growth of HL and DLBCL cells consistent with the role observed in BL cells, while low endogenous miR-150 levels appeared to be less critical for the growth of HL and DLBCL cells despite the effective targeting of ZDHHC11 and MYB.
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Affiliation(s)
- Lotteke J. Y. M. Ziel-Swier
- Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, 9700 RB Groningen, The Netherlands; (L.J.Y.M.Z.-S.); (Y.L.); (A.S.); (D.d.J.); (J.K.); (B.R.); (R.V.); (A.v.d.B.)
| | - Yichen Liu
- Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, 9700 RB Groningen, The Netherlands; (L.J.Y.M.Z.-S.); (Y.L.); (A.S.); (D.d.J.); (J.K.); (B.R.); (R.V.); (A.v.d.B.)
| | - Annika Seitz
- Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, 9700 RB Groningen, The Netherlands; (L.J.Y.M.Z.-S.); (Y.L.); (A.S.); (D.d.J.); (J.K.); (B.R.); (R.V.); (A.v.d.B.)
| | - Debora de Jong
- Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, 9700 RB Groningen, The Netherlands; (L.J.Y.M.Z.-S.); (Y.L.); (A.S.); (D.d.J.); (J.K.); (B.R.); (R.V.); (A.v.d.B.)
| | - Jasper Koerts
- Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, 9700 RB Groningen, The Netherlands; (L.J.Y.M.Z.-S.); (Y.L.); (A.S.); (D.d.J.); (J.K.); (B.R.); (R.V.); (A.v.d.B.)
| | - Bea Rutgers
- Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, 9700 RB Groningen, The Netherlands; (L.J.Y.M.Z.-S.); (Y.L.); (A.S.); (D.d.J.); (J.K.); (B.R.); (R.V.); (A.v.d.B.)
| | - Rianne Veenstra
- Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, 9700 RB Groningen, The Netherlands; (L.J.Y.M.Z.-S.); (Y.L.); (A.S.); (D.d.J.); (J.K.); (B.R.); (R.V.); (A.v.d.B.)
| | | | | | - Anke van den Berg
- Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, 9700 RB Groningen, The Netherlands; (L.J.Y.M.Z.-S.); (Y.L.); (A.S.); (D.d.J.); (J.K.); (B.R.); (R.V.); (A.v.d.B.)
| | - Joost Kluiver
- Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, 9700 RB Groningen, The Netherlands; (L.J.Y.M.Z.-S.); (Y.L.); (A.S.); (D.d.J.); (J.K.); (B.R.); (R.V.); (A.v.d.B.)
- Correspondence:
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6
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Drillis G, Goulielmaki M, Spandidos DA, Aggelaki S, Zoumpourlis V. Non-coding RNAs (miRNAs and lncRNAs) and their roles in lymphogenesis in all types of lymphomas and lymphoid malignancies. Oncol Lett 2021; 21:393. [PMID: 33777216 PMCID: PMC7988683 DOI: 10.3892/ol.2021.12654] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 02/26/2021] [Indexed: 12/16/2022] Open
Abstract
Contemporary developments in molecular biology have been combined with discoveries on the analysis of the role of all non-coding RNAs (ncRNAs) in human diseases, particularly in cancer, by examining their roles in cells. Currently, included among these common types of cancer, are all the lymphomas and lymphoid malignancies, which represent a diverse group of neoplasms and malignant disorders. Initial data suggest that non-coding RNAs, particularly long ncRNAs (lncRNAs), play key roles in oncogenesis and that lncRNA-mediated biology is an important key pathway to cancer progression. Other non-coding RNAs, termed microRNAs (miRNAs or miRs), are very promising cancer molecular biomarkers. They can be detected in tissues, cell lines, biopsy material and all biological fluids, such as blood. With the number of well-characterized cancer-related lncRNAs and miRNAs increasing, the study of the roles of non-coding RNAs in cancer is bringing forth new hypotheses of the biology of cancerous cells. For the first time, to the best of our knowledge, the present review provides an up-to-date summary of the recent literature referring to all diagnosed ncRNAs that mediate the pathogenesis of all types of lymphomas and lymphoid malignancies.
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Affiliation(s)
- Georgios Drillis
- 1st Internal Medicine Clinic, Medical School, Laiko University Hospital of Athens, 115 27 Athens, Greece
| | - Maria Goulielmaki
- Biomedical Applications Unit, Institute of Chemical Biology, National Hellenic Research Foundation (NHRF), 116 35 Athens, Greece
| | - Demetrios A Spandidos
- Laboratory of Clinical Virology, Medical School, University of Crete, 71003 Heraklion, Greece
| | - Sofia Aggelaki
- Oncology Unit, Medical School, University of Crete, 71003 Heraklion, Greece
| | - Vassilios Zoumpourlis
- Biomedical Applications Unit, Institute of Chemical Biology, National Hellenic Research Foundation (NHRF), 116 35 Athens, Greece
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7
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Diggins NL, Crawford LB, Struthers HM, Hook LM, Landais I, Skalsky RL, Hancock MH. Techniques for Characterizing Cytomegalovirus-Encoded miRNAs. Methods Mol Biol 2021; 2244:301-342. [PMID: 33555594 DOI: 10.1007/978-1-0716-1111-1_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
microRNAs (miRNAs) are small noncoding RNAs that regulate gene expression at the posttranscriptional level by binding to sites within the 3' untranslated regions of messenger RNA (mRNA) transcripts. The discovery of this completely new mechanism of gene regulation necessitated the development of a variety of techniques to further characterize miRNAs, their expression, and function. In this chapter, we will discuss techniques currently used in the miRNA field to detect, express and inhibit miRNAs, as well as methods used to identify and validate their targets, specifically with respect to the miRNAs encoded by human cytomegalovirus.
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Affiliation(s)
- Nicole L Diggins
- Vaccine and Gene Therapy Institute, Oregon Health and Sciences University, Beaverton, OR, USA
| | - Lindsey B Crawford
- Vaccine and Gene Therapy Institute, Oregon Health and Sciences University, Beaverton, OR, USA
| | - Hillary M Struthers
- Vaccine and Gene Therapy Institute, Oregon Health and Sciences University, Beaverton, OR, USA
| | - Lauren M Hook
- Vaccine and Gene Therapy Institute, Oregon Health and Sciences University, Beaverton, OR, USA
| | - Igor Landais
- Vaccine and Gene Therapy Institute, Oregon Health and Sciences University, Beaverton, OR, USA
| | - Rebecca L Skalsky
- Vaccine and Gene Therapy Institute, Oregon Health and Sciences University, Beaverton, OR, USA
| | - Meaghan H Hancock
- Vaccine and Gene Therapy Institute, Oregon Health and Sciences University, Beaverton, OR, USA.
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Niu F, Dzikiewicz-Krawczyk A, Koerts J, de Jong D, Wijenberg L, Fernandez Hernandez M, Slezak-Prochazka I, Winkle M, Kooistra W, van der Sluis T, Rutgers B, Terpstra MM, Kok K, Kluiver J, van den Berg A. MiR-378a-3p Is Critical for Burkitt Lymphoma Cell Growth. Cancers (Basel) 2020; 12:E3546. [PMID: 33261009 PMCID: PMC7760147 DOI: 10.3390/cancers12123546] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 11/09/2020] [Accepted: 11/25/2020] [Indexed: 12/29/2022] Open
Abstract
MicroRNAs (miRNAs) are small RNA molecules with important gene regulatory roles in normal and pathophysiological cellular processes. Burkitt lymphoma (BL) is an MYC-driven lymphoma of germinal center B (GC-B) cell origin. To gain further knowledge on the role of miRNAs in the pathogenesis of BL, we performed small RNA sequencing in BL cell lines and normal GC-B cells. This revealed 26 miRNAs with significantly different expression levels. For five miRNAs, the differential expression pattern was confirmed in primary BL tissues compared to GC-B cells. MiR-378a-3p was upregulated in BL, and its inhibition reduced the growth of multiple BL cell lines. RNA immunoprecipitation of Argonaute 2 followed by microarray analysis (Ago2-RIP-Chip) upon inhibition and ectopic overexpression of miR-378a-3p revealed 63 and 20 putative miR-378a-3p targets, respectively. Effective targeting by miR-378a-3p was confirmed by luciferase reporter assays for MAX Network Transcriptional Repressor (MNT), Forkhead Box P1 (FOXP1), Interleukin 1 Receptor Associated Kinase 4 (IRAK4), and lncRNA Just Proximal To XIST (JPX), and by Western blot for IRAK4 and MNT. Overexpression of IRAK4 and MNT phenocopied the effect of miR-378a-3p inhibition. In summary, we identified miR-378a-3p as a miRNA with an oncogenic role in BL and identified IRAK4 and MNT as miR-378a-3p target genes that are involved in its growth regulatory role.
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Affiliation(s)
- Fubiao Niu
- Departments of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, 9700 RB Groningen, The Netherlands; (F.N.); (J.K.); (D.d.J.); (L.W.); (M.F.H.); (M.W.); (W.K.); (T.v.d.S.); (B.R.); (J.K.)
| | | | - Jasper Koerts
- Departments of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, 9700 RB Groningen, The Netherlands; (F.N.); (J.K.); (D.d.J.); (L.W.); (M.F.H.); (M.W.); (W.K.); (T.v.d.S.); (B.R.); (J.K.)
| | - Debora de Jong
- Departments of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, 9700 RB Groningen, The Netherlands; (F.N.); (J.K.); (D.d.J.); (L.W.); (M.F.H.); (M.W.); (W.K.); (T.v.d.S.); (B.R.); (J.K.)
| | - Laura Wijenberg
- Departments of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, 9700 RB Groningen, The Netherlands; (F.N.); (J.K.); (D.d.J.); (L.W.); (M.F.H.); (M.W.); (W.K.); (T.v.d.S.); (B.R.); (J.K.)
| | - Margot Fernandez Hernandez
- Departments of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, 9700 RB Groningen, The Netherlands; (F.N.); (J.K.); (D.d.J.); (L.W.); (M.F.H.); (M.W.); (W.K.); (T.v.d.S.); (B.R.); (J.K.)
| | | | - Melanie Winkle
- Departments of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, 9700 RB Groningen, The Netherlands; (F.N.); (J.K.); (D.d.J.); (L.W.); (M.F.H.); (M.W.); (W.K.); (T.v.d.S.); (B.R.); (J.K.)
| | - Wierd Kooistra
- Departments of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, 9700 RB Groningen, The Netherlands; (F.N.); (J.K.); (D.d.J.); (L.W.); (M.F.H.); (M.W.); (W.K.); (T.v.d.S.); (B.R.); (J.K.)
| | - Tineke van der Sluis
- Departments of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, 9700 RB Groningen, The Netherlands; (F.N.); (J.K.); (D.d.J.); (L.W.); (M.F.H.); (M.W.); (W.K.); (T.v.d.S.); (B.R.); (J.K.)
| | - Bea Rutgers
- Departments of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, 9700 RB Groningen, The Netherlands; (F.N.); (J.K.); (D.d.J.); (L.W.); (M.F.H.); (M.W.); (W.K.); (T.v.d.S.); (B.R.); (J.K.)
| | - Miente Martijn Terpstra
- Department of Genetics, University Medical Center Groningen, University of Groningen, 9700 RB Groningen, The Netherlands; (M.M.T.); (K.K.)
| | - Klaas Kok
- Department of Genetics, University Medical Center Groningen, University of Groningen, 9700 RB Groningen, The Netherlands; (M.M.T.); (K.K.)
| | - Joost Kluiver
- Departments of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, 9700 RB Groningen, The Netherlands; (F.N.); (J.K.); (D.d.J.); (L.W.); (M.F.H.); (M.W.); (W.K.); (T.v.d.S.); (B.R.); (J.K.)
| | - Anke van den Berg
- Departments of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, 9700 RB Groningen, The Netherlands; (F.N.); (J.K.); (D.d.J.); (L.W.); (M.F.H.); (M.W.); (W.K.); (T.v.d.S.); (B.R.); (J.K.)
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9
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Yang Q, Chu W, Yang W, Cheng Y, Chu C, Pan X, Ye J, Cao J, Gan S, Cui X. Identification of RNA Transcript Makers Associated With Prognosis of Kidney Renal Clear Cell Carcinoma by a Competing Endogenous RNA Network Analysis. Front Genet 2020; 11:540094. [PMID: 33193613 PMCID: PMC7593646 DOI: 10.3389/fgene.2020.540094] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Accepted: 09/04/2020] [Indexed: 12/16/2022] Open
Abstract
Objective This study aims to identify several RNA transcripts associated with the prognosis of kidney renal clear cell carcinoma (KIRC). Methods The differentially expressed mRNAs, lncRNAs, and miRNAs (DEmRNAs, DElncRNAs, and DEmiRNAs) between KIRC cases and controls were screened based on an RNA-seq dataset from The Cancer Genome Atlas (TCGA) database. Subsequently, miRcode, miRDB, and TargetScan database were used to predict interactions between lncRNAs, miRNAs and target mRNAs. Then, a ceRNA network was built using miRNAs-mRNAs and lncRNAs-miRNAs pairs. Functional analysis of mRNAs in ceRNA was performed. Finally, the survival analysis of RNA transcripts in ceRNA network and correlation analysis for key RNA regulators were carried out. Results There were 1527 DElncRNAs, 54 DEmiRNAs, and 2321 DEmRNAs. A ceRNA network was constructed among 81 lncRNAs, 9 miRNAs, and 197 mRNAs. Functional analysis showed that numerous mRNAs were significantly associated with regulation of cellular glucuronidation. In addition, 35 lncRNAs, 84 mRNAs and two miRNAs were significantly corelated to the survival of patients with KIRC (P < 0.05). Among them, miRNA-21 and miRNA-155 were negatively related to three lncRNAs (LINC00472, SLC25A5.AS1, and TCL6). Seven mRNA targets of miRNA-21 (FASLG, FGF1, TGFBI, ALX1, SLC30A10, ADCY2, and ABAT) and 12 mRNAs targets of miRNA-155 (STXBP5L, SCG2, SPI1, C12orf40, TYRP1, CTHRC1, TDO2, PTPRQ, TRPM8, ERMP1, CD36, and ST9SIA4) also acted as prognostic biomarkers for KIRC patients. Conclusion We screened numerous novel prognosis-related RNA markers for KIRC patients by a ceRNA network analysis, providing deeper understandings of prognostic values of RNA transcripts for KIRC.
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Affiliation(s)
- Qiwei Yang
- Department of Urology, Gongli Hospital, Shanghai, China.,Department of Urology, The Third Affiliated Hospital of Naval Military Medical University (Eastern Hepatobiliary Surgery Hospital), Shanghai, China
| | - Weiwei Chu
- Laboratory of Nano Biomedicine and International Joint Cancer Institute, Second Military Medical University, Shanghai, China
| | - Wei Yang
- Department of Urology, The Third Affiliated Hospital of Naval Military Medical University (Eastern Hepatobiliary Surgery Hospital), Shanghai, China
| | - Yanqiong Cheng
- Department of Pharmaceutical College, Naval Military Medical University, Shanghai, China
| | - Chuanmin Chu
- Department of Urology, The Third Affiliated Hospital of Naval Military Medical University (Eastern Hepatobiliary Surgery Hospital), Shanghai, China
| | - Xiuwu Pan
- Department of Urology, Gongli Hospital, Shanghai, China
| | - Jianqing Ye
- Department of Urology, The Third Affiliated Hospital of Naval Military Medical University (Eastern Hepatobiliary Surgery Hospital), Shanghai, China
| | - Jianwei Cao
- Department of Urology, The Third Affiliated Hospital of Naval Military Medical University (Eastern Hepatobiliary Surgery Hospital), Shanghai, China
| | - Sishun Gan
- Department of Urology, The Third Affiliated Hospital of Naval Military Medical University (Eastern Hepatobiliary Surgery Hospital), Shanghai, China
| | - Xingang Cui
- Department of Urology, Gongli Hospital, Shanghai, China.,Department of Urology, The Third Affiliated Hospital of Naval Military Medical University (Eastern Hepatobiliary Surgery Hospital), Shanghai, China
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10
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Li R, Deng Y, Liang J, Hu Z, Li X, Liu H, Wang G, Fu B, Zhang T, Zhang Q, Yang Y, Chen G, Liu W. Circular RNA circ-102,166 acts as a sponge of miR-182 and miR-184 to suppress hepatocellular carcinoma proliferation and invasion. Cell Oncol (Dordr) 2020; 44:279-295. [PMID: 33034848 DOI: 10.1007/s13402-020-00564-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/17/2020] [Indexed: 02/07/2023] Open
Abstract
PURPOSE Multiple circular RNAs (circRNAs) have been reported to be dysregulated in hepatocellular carcinoma (HCC). However, their functions and modes of action are still largely unclear. Identifying key circRNAs and revealing their potential functions and molecular mechanisms is considered important for improving the diagnosis and treatment of HCC. METHODS Dysregulated circRNAs in HCC were identified through integration of three human HCC circRNAs microarray datasets (GSE94508, GSE97332 and GSE 78520), followed by qRT-PCR validation in primary HCC tissues and cell lines. circRNA characteristics were verified through Sanger sequencing, RNase R treatment, northern blotting and intracellular localization analyses. In addition, circRNA functions in HCC development were assessed using CCK8, colony formation, EDU incorporation, flow cytometry, transwell and scratch wound healing assays in vitro and tumor xenograft assays in vivo. Next, underlying molecular mechanisms in HCC were assessed using dual-luciferase reporter, RNA pull-down, RNA immunoprecipitation and western blotting assays. RESULTS We found that a novel circular RNA, circ-102,166, was down-regulated in HCC and that its expression level was significantly associated with multiple clinicopathologic characteristics, as well as the clinical prognosis of HCC patients. In vitro and in vivo experiments revealed that circ-102,166 overexpression significantly inhibited the proliferation, invasion, migration and tumorigenicity of HCC cells. Furthermore, we found that circ-102,166 can bind to miR-182 and miR-184 to regulate the expression of several of their downstream targets (FOXO3a, MTSS1, SOX7, p-RB and c-MYC). CONCLUSION Our data revealed a tumor-suppressing role of circ-102,166 in HCC. Down-regulation of circ-102,166 enhanced the proliferation and invasion of HCC cells by releasing the oncomiRs miR-182 and miR-184.
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Affiliation(s)
- Rong Li
- Guangdong Provincial Key Laboratory of Liver Disease Research, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510630, China.,Organ Transplantation Research Center of Guangdong Province, Guangdong province engineering laboratory for transplantation medicine, Guangzhou, 510630, China
| | - Yinan Deng
- Department of Hepatic Surgery and Liver Transplantation Center, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510630, China
| | - Jinliang Liang
- Guangdong Provincial Key Laboratory of Liver Disease Research, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510630, China
| | - Zhongying Hu
- Guangdong Provincial Key Laboratory of Liver Disease Research, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510630, China
| | - Xuejiao Li
- Guangdong Provincial Key Laboratory of Liver Disease Research, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510630, China
| | - Huanyi Liu
- Guangdong Provincial Key Laboratory of Liver Disease Research, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510630, China
| | - Guoying Wang
- Department of Hepatic Surgery and Liver Transplantation Center, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510630, China
| | - Binsheng Fu
- Department of Hepatic Surgery and Liver Transplantation Center, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510630, China
| | - Tong Zhang
- Department of Hepatic Surgery and Liver Transplantation Center, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510630, China
| | - Qi Zhang
- Cell-gene Therapy Translational Medicine Research Center, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510630, China
| | - Yang Yang
- Organ Transplantation Research Center of Guangdong Province, Guangdong province engineering laboratory for transplantation medicine, Guangzhou, 510630, China.,Department of Hepatic Surgery and Liver Transplantation Center, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510630, China
| | - Guihua Chen
- Guangdong Provincial Key Laboratory of Liver Disease Research, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510630, China. .,Department of Hepatic Surgery and Liver Transplantation Center, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510630, China.
| | - Wei Liu
- Guangdong Provincial Key Laboratory of Liver Disease Research, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510630, China. .,Organ Transplantation Research Center of Guangdong Province, Guangdong province engineering laboratory for transplantation medicine, Guangzhou, 510630, China.
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11
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Niu F, Kazimierska M, Nolte IM, Terpstra MM, de Jong D, Koerts J, van der Sluis T, Rutgers B, O’Connell RM, Kok K, van den Berg A, Dzikiewicz-Krawczyk A, Kluiver J. The miR-26b-5p/KPNA2 Axis Is an Important Regulator of Burkitt Lymphoma Cell Growth. Cancers (Basel) 2020; 12:E1464. [PMID: 32512858 PMCID: PMC7352454 DOI: 10.3390/cancers12061464] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 05/29/2020] [Accepted: 05/31/2020] [Indexed: 12/26/2022] Open
Abstract
The expression of several microRNAs (miRNAs) is known to be changed in Burkitt lymphoma (BL), compared to its normal counterparts. Although for some miRNAs, a role in BL was demonstrated, for most of them, their function is unclear. In this study, we aimed to identify miRNAs that control BL cell growth. Two BL cell lines were infected with lentiviral pools containing either 58 miRNA inhibitors or 44 miRNA overexpression constructs. Eighteen constructs showed significant changes in abundance over time, indicating that they affected BL growth. The screening results were validated by individual green fluorescent protein (GFP) growth competition assays for fifteen of the eighteen constructs. For functional follow-up studies, we focused on miR-26b-5p, whose overexpression inhibited BL cell growth. Argonaute 2 RNA immunoprecipitation (Ago2-IP) in two BL cell lines revealed 47 potential target genes of miR-26b-5p. Overlapping the list of putative targets with genes showing a growth repression phenotype in a genome-wide CRISPR/Cas9 knockout screen, revealed eight genes. The top-5 candidates included EZH2, COPS2, KPNA2, MRPL15, and NOL12. EZH2 is a known target of miR-26b-5p, with oncogenic properties in BL. The relevance of the latter four targets was confirmed using sgRNAs targeting these genes in individual GFP growth competition assays. Luciferase reporter assay confirmed binding of miR-26b-5p to the predicted target site for KPNA2, but not to the other genes. In summary, we identified 18 miRNAs that affected BL cell growth in a loss- or gain-of-function screening. A tumor suppressor role was confirmed for miR-26b-5p, and this effect could at least in part be attributed to KPNA2, a known regulator of OCT4, c-jun, and MYC.
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Affiliation(s)
- Fubiao Niu
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, 9700RB Groningen, The Netherlands; (F.N.); (D.d.J.); (J.K.); (T.v.d.S.); (B.R.); (A.v.d.B.)
| | - Marta Kazimierska
- Institute of Human Genetics, Polish Academy of Sciences, 60-479 Poznan, Poland;
| | - Ilja M. Nolte
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, 9700RB Groningen, The Netherlands;
| | - Miente Martijn Terpstra
- Department of Genetics, University of Groningen, University Medical Center Groningen, 9700RB Groningen, The Netherlands; (M.M.T.); (K.K.)
| | - Debora de Jong
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, 9700RB Groningen, The Netherlands; (F.N.); (D.d.J.); (J.K.); (T.v.d.S.); (B.R.); (A.v.d.B.)
| | - Jasper Koerts
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, 9700RB Groningen, The Netherlands; (F.N.); (D.d.J.); (J.K.); (T.v.d.S.); (B.R.); (A.v.d.B.)
| | - Tineke van der Sluis
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, 9700RB Groningen, The Netherlands; (F.N.); (D.d.J.); (J.K.); (T.v.d.S.); (B.R.); (A.v.d.B.)
| | - Bea Rutgers
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, 9700RB Groningen, The Netherlands; (F.N.); (D.d.J.); (J.K.); (T.v.d.S.); (B.R.); (A.v.d.B.)
| | - Ryan M. O’Connell
- Division of Microbiology and Immunology, Huntsman Cancer Institute, Department of Pathology at the University of Utah, Salt Lake City, UT 84112, USA.;
| | - Klaas Kok
- Department of Genetics, University of Groningen, University Medical Center Groningen, 9700RB Groningen, The Netherlands; (M.M.T.); (K.K.)
| | - Anke van den Berg
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, 9700RB Groningen, The Netherlands; (F.N.); (D.d.J.); (J.K.); (T.v.d.S.); (B.R.); (A.v.d.B.)
| | | | - Joost Kluiver
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, 9700RB Groningen, The Netherlands; (F.N.); (D.d.J.); (J.K.); (T.v.d.S.); (B.R.); (A.v.d.B.)
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12
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High-Throughput Identification of MiR-145 Targets in Human Articular Chondrocytes. Life (Basel) 2020; 10:life10050058. [PMID: 32403239 PMCID: PMC7281014 DOI: 10.3390/life10050058] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 04/30/2020] [Accepted: 05/05/2020] [Indexed: 02/06/2023] Open
Abstract
MicroRNAs (miRNAs) play key roles in cartilage development and homeostasis and are dysregulated in osteoarthritis. MiR-145 modulation induces profound changes in the human articular chondrocyte (HAC) phenotype, partially through direct repression of SOX9. Since miRNAs can simultaneously silence multiple targets, we aimed to identify the whole targetome of miR-145 in HACs, critical if miR-145 is to be considered a target for cartilage repair. We performed RIP-seq (RNA-immunoprecipitation and high-throughput sequencing) of miRISC (miRNA-induced silencing complex) in HACs overexpressing miR-145 to identify miR-145 direct targets and used cWords to assess enrichment of miR-145 seed matches in the identified targets. Further validations were performed by RT-qPCR, Western immunoblot, and luciferase assays. MiR-145 affects the expression of over 350 genes and directly targets more than 50 mRNAs through the 3′UTR or, more commonly, the coding region. MiR-145 targets DUSP6, involved in cartilage organization and development, at the translational level. DUSP6 depletion leads to MMP13 upregulation, suggesting a contribution towards the effect of miR-145 on MMP13 expression. In conclusion, miR-145 directly targets several genes involved in the expression of the extracellular matrix and inflammation in primary chondrocytes. Thus, we propose miR-145 as an important regulator of chondrocyte function and a new target for cartilage repair.
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13
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MicroRNA 27a Is a Key Modulator of Cholesterol Biosynthesis. Mol Cell Biol 2020; 40:MCB.00470-19. [PMID: 32071155 DOI: 10.1128/mcb.00470-19] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Accepted: 02/10/2020] [Indexed: 12/25/2022] Open
Abstract
Hypercholesterolemia is a strong predictor of cardiovascular diseases. The 3-hydroxy-3-methylglutaryl coenzyme A reductase gene (Hmgcr) coding for the rate-limiting enzyme in the cholesterol biosynthesis pathway is a crucial regulator of plasma cholesterol levels. However, the posttranscriptional regulation of Hmgcr remains poorly understood. The main objective of this study was to explore the role of microRNAs (miRNAs) in the regulation of Hmgcr expression. Systematic in silico predictions and experimental analyses reveal that miRNA 27a (miR-27a) specifically interacts with the Hmgcr 3' untranslated region in murine and human hepatocytes. Moreover, our data show that Hmgcr expression is inversely correlated with miR-27a levels in various cultured cell lines and in human and rodent tissues. Actinomycin D chase assays and relevant experiments demonstrate that miR-27a regulates Hmgcr by translational attenuation followed by mRNA degradation. Early growth response 1 (Egr1) regulates miR-27a expression under basal and cholesterol-modulated conditions. miR-27a augmentation via tail vein injection of miR-27a mimic in high-cholesterol-diet-fed Apoe -/- mice shows downregulation of hepatic Hmgcr and plasma cholesterol levels. Pathway and gene expression analyses show that miR-27a also targets several other genes (apart from Hmgcr) in the cholesterol biosynthesis pathway. Taken together, miR-27a emerges as a key regulator of cholesterol biosynthesis and has therapeutic potential for the clinical management of hypercholesterolemia.
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14
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Wang F, Xu X, Zhang N, Chen Z. Identification and integrated analysis of hepatocellular carcinoma-related circular RNA signature. ANNALS OF TRANSLATIONAL MEDICINE 2020; 8:294. [PMID: 32355738 PMCID: PMC7186732 DOI: 10.21037/atm.2020.03.06] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Background Circular RNAs (circRNAs), a novel type of non-coding RNA, play a vital role in the pathogenesis and development of cancer. CircRNAs signatures may be useful as prognostic and predictive factors as well as clinical tools for evaluating disease status and prognosis. This study was carried out to explore novel circRNA signatures in hepatocellular carcinoma (HCC). Methods The expression profiles of circRNAs were retrieved from the Gene Expression Omnibus (GEO). The expression profiles of miRNAs and mRNAs were obtained from The Cancer Genome Atlas (TCGA) and the Genotype-Tissue Expression (GTEx) database. The results of the microarray were validated by quantitative real-time RCR (qPCR). Based on circRNA-miRNA pairs and miRNA-mRNA pairs, a competitive endogenous RNA (ceRNA) network was constructed. Functional analysis was performed via Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), gene set enrichment analysis (GSEA), and gene set variation analysis (GSVA). Furthermore, survival analysis was carried out using the Kaplan-Meier curve and the log-rank test. Results Differentially expressed circRNAs in HCC from GEO databases (GSE94508 and GSE97332) were screened and analyzed using the bioinformatics method. We detected a total of 26 differentially expressed circRNAs by qPCR and then selected 6 circRNAs to construct the circRNA-miRNA-mRNA networks. Through prognostic analysis, 3 target hub genes (AURKA, KIF5B, and RHOA) of circRNAs were discovered. Moreover, GSEA and GSVA were used to reveal the functions of AURKA, KIF5B, and RHOA in HCC. Conclusions We identified three hub genes, and our results suggest that the circHMGCS1/miR-581/AURKA, circHMGCS1/miR-892a/KIF5B, and circTMCO3/miR-577/RHOA axes may play a vital role in HCC progression.
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Affiliation(s)
- Feiran Wang
- Department of General Surgery, Affiliated Hospital of Nantong University, Nantong 226000, China
| | - Xiaodong Xu
- Department of General Surgery, the 4th Affiliated Hospital of Nantong University, Yancheng 224000, China
| | - Nannan Zhang
- Department of General Surgery, Affiliated Hospital of Nantong University, Nantong 226000, China
| | - Zhong Chen
- Department of General Surgery, Affiliated Hospital of Nantong University, Nantong 226000, China
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15
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Abstract
PURPOSE OF REVIEW Numerous signaling pathways and inflammatory responses in cells and tissues are under microRNA (miRNA) control. In the present review, the role of miRNAs and exosomes in the pathogenesis of asthma will be discussed. RECENT FINDINGS MiRNAs differentially expressed with asthma, for example, miRNA-34/449, let-7, miRNA-19, miRNA-21, and miRNA-455, were identified in various cell types and tissues including epithelial cells, T cells, type 2 innate lymphoid cells, lung tissues, and smooth muscles. Current data suggest the involvement of these miRNAs in epithelial differentiation, mucus production, airway remodeling, inflammation, etc. However, it is often difficult to predict which genes are targeted by a specific miRNA. We recently combined genome-wide miRNA analyses together with transcriptome in bronchial biopsies, in relation to chronic mucus hypersecretion, then performed a genome-wide miRNA-mRNA network analysis and identified the key miRNA regulators for chronic mucus hypersecretion. SUMMARY There is now growing evidence suggesting that miRNAs play critically important roles in asthma. Several asthma-associated miRNAs have already been identified. Although miRNAs are attractive targets for therapeutic intervention, a safe and effective delivery to target tissues and cells in humans remains a challenge.
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16
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Yang L, Liang H, Meng X, Shen L, Guan Z, Hei B, Yu H, Qi S, Wen X. mmu_circ_0000790 Is Involved in Pulmonary Vascular Remodeling in Mice with HPH via MicroRNA-374c-Mediated FOXC1. MOLECULAR THERAPY. NUCLEIC ACIDS 2020; 20:292-307. [PMID: 32199127 PMCID: PMC7082500 DOI: 10.1016/j.omtn.2019.12.027] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/05/2019] [Revised: 12/23/2019] [Accepted: 12/23/2019] [Indexed: 01/05/2023]
Abstract
Recently, the identification of several circular RNAs (circRNAs) as vital regulators of microRNAs (miRNAs) underlines the increasing complexity of non-coding RNA (ncRNA)-mediated regulatory networks. This study aimed to explore the effects of mmu_circ_0000790 on the biological behaviors of pulmonary artery smooth muscle cells (PASMCs) in hypoxic pulmonary hypertension (HPH). The HPH mouse model and hypoxia-induced PASMC model were initially established, and the expression of mmu_circ_0000790 in the pulmonary vascular tissues and hypoxic PASMCs was determined using quantitative reverse transcriptase polymerase chain reaction (qRT-PCR). A series of in vitro experiments such as dual-luciferase, RNA pull-down, and RNA-binding protein immunoprecipitation (RIP) assays were conducted to evaluate the interactions among mmu_circ_0000790, microRNA-374c (miR-374c), and forkhead transcription factor 1 (FOXC1). The potential physiological functions of mmu_circ_0000790, miR-374c, and FOXC1 in hypoxic PASMCs were investigated through gain- and loss-of function approaches. Upregulated mmu_circ_0000790 was found in both the HPH-pulmonary vascular tissues and hypoxic PASMCs. Additionally, mmu_circ_0000790 could competitively bind to miR-374c and consequently upregulate the target gene of miR-374c, FOXC1. It was also observed that mmu_circ_0000790 induced proliferation and inhibited apoptosis of hypoxic PASMCs, which further promoted the pulmonary vascular remodeling in mice with HPH. Therefore, we speculate that mmu_circ_0000790 may serve as a prospective target for the treatment of patients with HPH.
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Affiliation(s)
- Lei Yang
- ICU, The Third Affiliated Hospital of Qiqihar Medical University, Qiqihar 161002, P.R. China.
| | - Huan Liang
- ICU, The Third Affiliated Hospital of Qiqihar Medical University, Qiqihar 161002, P.R. China
| | - Xianguo Meng
- ICU, The Third Affiliated Hospital of Qiqihar Medical University, Qiqihar 161002, P.R. China
| | - Li Shen
- Glorious Community, The Third Affiliated Hospital of Qiqihar Medical University, Qiqihar 161002, P.R. China
| | - Zhanjiang Guan
- ICU, The Third Affiliated Hospital of Qiqihar Medical University, Qiqihar 161002, P.R. China
| | - Bingchang Hei
- ICU, The Third Affiliated Hospital of Qiqihar Medical University, Qiqihar 161002, P.R. China
| | - Haitao Yu
- ICU, The Third Affiliated Hospital of Qiqihar Medical University, Qiqihar 161002, P.R. China
| | - Shanshan Qi
- ICU, The Third Affiliated Hospital of Qiqihar Medical University, Qiqihar 161002, P.R. China
| | - Xianchun Wen
- Institute of Medical Science, Qiqihar Medical College, Qiqihar 161002, P.R. China.
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17
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RIP-Chip analysis supports different roles for AGO2 and GW182 proteins in recruiting and processing microRNA targets. BMC Bioinformatics 2019; 20:120. [PMID: 30999843 PMCID: PMC6471694 DOI: 10.1186/s12859-019-2683-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Background MicroRNAs (miRNAs) are small non-coding RNA molecules mediating the translational repression and degradation of target mRNAs in the cell. Mature miRNAs are used as a template by the RNA-induced silencing complex (RISC) to recognize the complementary mRNAs to be regulated. To discern further RISC functions, we analyzed the activities of two RISC proteins, AGO2 and GW182, in the MCF-7 human breast cancer cell line. Methods We performed three RIP-Chip experiments using either anti-AGO2 or anti-GW182 antibodies and compiled a data set made up of the miRNA and mRNA expression profiles of three samples for each experiment. Specifically, we analyzed the input sample, the immunoprecipitated fraction and the unbound sample resulting from the RIP experiment. We used the expression profile of the input sample to compute several variables, using formulae capable of integrating the information on miRNA binding sites, both in the 3’UTR and coding regions, with miRNA and mRNA expression level profiles. We compared immunoprecipitated vs unbound samples to determine the enriched or underrepresented genes in the immunoprecipitated fractions, independently for AGO2 and GW182 related samples. Results For each of the two proteins, we trained and tested several support vector machine algorithms capable of distinguishing the enriched from the underrepresented genes that were experimentally detected. The most efficient algorithm for distinguishing the enriched genes in AGO2 immunoprecipitated samples was trained by using variables involving the number of binding sites in both the 3’UTR and coding region, integrated with the miRNA expression profile, as expected for miRNA targets. On the other hand, we found that the best variable for distinguishing the enriched genes in the GW182 immunoprecipitated samples was the length of the coding region. Conclusions Due to the major role of GW182 in GW/P-bodies, our data suggests that the AGO2-GW182 RISC recruits genes based on miRNA binding sites in the 3’UTR and coding region, but only the longer mRNAs probably remain sequestered in GW/P-bodies, functioning as a repository for translationally silenced RNAs. Electronic supplementary material The online version of this article (10.1186/s12859-019-2683-y) contains supplementary material, which is available to authorized users.
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Dhorne-Pollet S, Crisci E, Mach N, Renson P, Jaffrézic F, Marot G, Maroilley T, Moroldo M, Lecardonnel J, Blanc F, Bertho N, Bourry O, Giuffra E. The miRNA-targeted transcriptome of porcine alveolar macrophages upon infection with Porcine Reproductive and Respiratory Syndrome Virus. Sci Rep 2019; 9:3160. [PMID: 30816147 PMCID: PMC6395673 DOI: 10.1038/s41598-019-39220-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Accepted: 01/18/2019] [Indexed: 12/20/2022] Open
Abstract
Host miRNAs are known to modulate the cell response to virus infections. We characterized the miRNA-targeted transcriptome of porcine alveolar macrophages (PAMs) at early times after infection with a subtype 1.1 strain of PRRSV (Porcine Reproductive and Respiratory Syndrome Virus). We performed the immunoprecipitation of RISC (RNA-induced Silencing Complex) followed by microarray analysis of the RISC-bound miRNA targets (RIP-Chip) to evaluate the relative enrichment or depletion of expressed genes in RISC. The miRNA-mediated regulation occurred early after PRRSV infection and decreased fast (1,241 and 141 RISC-bound genes at 7 h and 10 h post-infection, respectively); it affected several cell functions with evidence of miRNA buffering of upregulated interferon-related genes. Eight miRNAs were highly enriched in RISC of both control and infected cells with no evidence of differential expression. Although miR-335-5p was the miRNA with most predicted targets among enriched RISC-bound genes, no effects on surface markers, cytokine expression and PRRSV replication were detected upon miR-335-5p mimics of primary PAMs. Our results do not point to specific miRNA-driven mechanisms regulating the early response to infection with this PRRSV 1.1 strain and indicate that the miRNome expressed by steady-state PAMs reacts promptly to counterbalance PRRSV infection by a pervasive modulation of host functions.
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Affiliation(s)
- Sophie Dhorne-Pollet
- GABI, INRA, AgroParisTech, Université Paris Saclay, Jouy-en-Josas, 78350, France
| | - Elisa Crisci
- GABI, INRA, AgroParisTech, Université Paris Saclay, Jouy-en-Josas, 78350, France.,Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, Raleigh, NC, United States
| | - Nuria Mach
- GABI, INRA, AgroParisTech, Université Paris Saclay, Jouy-en-Josas, 78350, France
| | - Patricia Renson
- ANSES, Unité Virologie Immunologie Porcines, Ploufragan, 22440, France
| | - Florence Jaffrézic
- GABI, INRA, AgroParisTech, Université Paris Saclay, Jouy-en-Josas, 78350, France
| | - Guillemette Marot
- EA 2694 Biostatistiques, Université de Lille, Inria Lille Nord Europe, MODAL, Villeneuve d'Ascq, 59650, France
| | - Tatiana Maroilley
- GABI, INRA, AgroParisTech, Université Paris Saclay, Jouy-en-Josas, 78350, France.,Departments of Medical Genetics and Biochemistry & Molecular Biology, Alberta Children's Hospital Research Institute (ACHRI), Cumming School of Medicine, University of Calgary, Calgary, Canada
| | - Marco Moroldo
- GABI, INRA, AgroParisTech, Université Paris Saclay, Jouy-en-Josas, 78350, France
| | - Jérôme Lecardonnel
- GABI, INRA, AgroParisTech, Université Paris Saclay, Jouy-en-Josas, 78350, France
| | - Fany Blanc
- GABI, INRA, AgroParisTech, Université Paris Saclay, Jouy-en-Josas, 78350, France
| | - Nicolas Bertho
- Virologie et Immunologie Moléculaire, Institut National de la Recherche Agronomique, Université Paris-Saclay, Jouy-en-Josas, France.,PIPAE, BIOEPAR, INRA, ONIRIS, Nantes Atlantic National College of Veterinary Medicine, Nantes, 44307, France
| | - Olivier Bourry
- ANSES, Unité Virologie Immunologie Porcines, Ploufragan, 22440, France
| | - Elisabetta Giuffra
- GABI, INRA, AgroParisTech, Université Paris Saclay, Jouy-en-Josas, 78350, France.
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Zhao X, Sun Y, Ding Y, Zhang J, Li K. miR-34a Inhibitor May Effectively Protect against Sevoflurane-Induced Hippocampal Apoptosis through the Wnt/β-Catenin Pathway by Targeting Wnt1. Yonsei Med J 2018; 59:1205-1213. [PMID: 30450855 PMCID: PMC6240572 DOI: 10.3349/ymj.2018.59.10.1205] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Revised: 08/27/2018] [Accepted: 09/21/2018] [Indexed: 12/20/2022] Open
Abstract
PURPOSE Research has shown that sevoflurane-induced toxicity causes neurodegeneration in the developing brain. miR-34a has been found to negatively regulate ketamine-induced hippocampal apoptosis and memory impairment. However, the role of miR-34a in sevoflurane-induced hippocampal neurodegeneration remains largely unclear. MATERIALS AND METHODS C57/BL6 mice (7-day-old) inhaled 2.3% sevoflurane for 2 h/day over 3 consecutive days. miR-34a expression was reduced through intracerebroventricular injection with miR-34a interference lentivirus vector (LV-anti-miR-34a) into mouse hippocampus after anesthesia on the first day of exposure. Hippocampal apoptosis was detected by TUNEL assay and flow cytometry analysis. Spatial memory ability was evaluated by the Morris water maze test. The interaction between miR-34a and Wnt1 was confirmed by luciferase reporter assay, RNA immunoprecipitation, Western blot, and immunofluorescence staining. The effects of miR-34a on protein levels of B-cell lymphoma 2 (Bcl-2), bcl-2-like protein 4 (Bax), and Wnt/β-catenin pathway-related proteins were evaluated using Western blot analysis. RESULTS Sevoflurane upregulated hippocampal miR-34a, and miR-34a inhibitor attenuated sevoflurane-induced hippocampal apoptosis and memory impairment. miR-34a negatively regulated Wnt1 expression by targeting miR-34a in hippocampal neurons. Moreover, forced expression of Wnt1 markedly undermined miR-34a-mediated enhancement of sevoflurane-induced apoptosis of hippocampal neurons, while Wnt1 silencing greatly restored anti-miR-34a-mediated repression of sevoflurane-induced apoptosis of hippocampal neurons. Increased expression of miR-34a inhibited the Wnt/β-catenin pathway in hippocampal neurons exposed to sevoflurane, while anti-miR-34a exerted the opposite effects. CONCLUSION miR-34a inhibitor may effectively protect against sevoflurane-induced hippocampal apoptosis via activation of the Wnt/β-catenin pathway by targeting Wnt1.
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Affiliation(s)
- Xiaoling Zhao
- School of Medicine, Shandong University, Jinan, China
- Department of Anesthesiology, Yantai Yuhuangding Hospital, Yantai, China
| | - Yue Sun
- Department of Anesthesiology, Shandong Provincial Hospital, Jinan, China
| | - Yongbo Ding
- Department of Anesthesiology, Yantai Yuhuangding Hospital, Yantai, China
| | - Jun Zhang
- Department of Anesthesiology, Yantai Yuhuangding Hospital, Yantai, China
| | - Kezhong Li
- Department of Anesthesiology, Yantai Yuhuangding Hospital, Yantai, China.
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20
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miR-143 and miR-145 promote hypoxia-induced proliferation and migration of pulmonary arterial smooth muscle cells through regulating ABCA1 expression. Cardiovasc Pathol 2018; 37:15-25. [DOI: 10.1016/j.carpath.2018.08.003] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Revised: 07/14/2018] [Accepted: 08/15/2018] [Indexed: 12/12/2022] Open
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21
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Tuerdi B, Zuo L, Ma Y, Wang K. Downregulation of miR-155 attenuates sepsis-induced acute lung injury by targeting SIRT1. INTERNATIONAL JOURNAL OF CLINICAL AND EXPERIMENTAL PATHOLOGY 2018; 11:4483-4492. [PMID: 31949845 PMCID: PMC6962949] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Accepted: 06/21/2018] [Indexed: 06/10/2023]
Abstract
Sepsis-induced acute lung injury (ALI) characterized by devastating hyperinflammatory response in the lungs is the ultimate cause of high mortality and mobility in septic patients. miR-155 was reported to be significantly upregulated in sepsis-induced ALI cases and alleviated inflammation in septic lung injury in mouse and cell models. However, the detailed role of miR-155 and its underlying mechanism in sepsis-associated ALI remain to be further explored. In vivo, a cecal ligation and puncture (CLP)-induced ALI mouse model was successfully established. miR-155 expression was significantly higher in CLP mice compared with control mice. miR-155 inhibitor attenuated histopathological changes, lung apoptosis, lung inflammation, and increased the survival rate in CLP-induced ALI mice. In vitro, miR-155 expression increased in murine alveolar epithelial cells MLE-12 stimulated with lipopolysaccharide (LPS) and downregulation of miR-155 suppressed apoptosis and the release of inflammatory cytokines in LPS-stimulated MLE-12 cells. In addition, luciferase reporter assay and RNA immunoprecipitation (RIP) demonstrated that SIRT1 was a direct target of miR-155 in LPS-treated MLE-12 cells. Moreover, miR-155 partially reversed the inhibitory effects of SIRT1 on apoptosis and inflammatory response in LPS-stimulated MLE-12 cells. In summary, these results demonstrated that downregulation of miR-155 attenuated sepsis-induced ALI in vivo and in vitro by targeting SIRT1.
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Affiliation(s)
- Baihetinisha Tuerdi
- Respiratory Intensive Care Unit, First Affiliated Hospital of Xinjiang Medical UniversityXinjiang, China
| | - Lei Zuo
- Respiratory Intensive Care Unit, First Affiliated Hospital of Xinjiang Medical UniversityXinjiang, China
| | - Yan Ma
- Intensive Care Unit, First Affiliated Hospital of Xinjiang Medical UniversityXinjiang, China
| | - Ke Wang
- Respiratory Intensive Care Unit, First Affiliated Hospital of Xinjiang Medical UniversityXinjiang, China
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22
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Argonaute 2 RNA Immunoprecipitation Reveals Distinct miRNA Targetomes of Primary Burkitt Lymphoma Tumors and Normal B Cells. THE AMERICAN JOURNAL OF PATHOLOGY 2018; 188:1289-1299. [DOI: 10.1016/j.ajpath.2018.01.018] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Revised: 01/23/2018] [Accepted: 01/30/2018] [Indexed: 12/19/2022]
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Inhibition of the JNK/MAPK signaling pathway by myogenesis-associated miRNAs is required for skeletal muscle development. Cell Death Differ 2018; 25:1581-1597. [PMID: 29449644 PMCID: PMC6143622 DOI: 10.1038/s41418-018-0063-1] [Citation(s) in RCA: 70] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2017] [Revised: 12/24/2017] [Accepted: 01/04/2018] [Indexed: 12/16/2022] Open
Abstract
Skeletal muscle differentiation is controlled by multiple cell signaling pathways, however, the JNK/MAPK signaling pathway dominating this process has not been fully elucidated. Here, we report that the JNK/MAPK pathway was significantly downregulated in the late stages of myogenesis, and in contrast to P38/MAPK pathway, it negatively regulated skeletal muscle differentiation. Based on the PAR-CLIP-seq analysis, we identified six elevated miRNAs (miR-1a-3p, miR-133a-3p, miR-133b-3p, miR-206-3p, miR-128-3p, miR-351-5p), namely myogenesis-associated miRNAs (mamiRs), negatively controlled the JNK/MAPK pathway by repressing multiple factors for the phosphorylation of the JNK/MAPK pathway, including MEKK1, MEKK2, MKK7, and c-Jun but not JNK protein itself, and as a result, expression of transcriptional factor MyoD and mamiRs were further promoted. Our study revealed a novel double-negative feedback regulatory pattern of cell-specific miRNAs by targeting phosphorylation kinase signaling cascade responsible for skeletal muscle development.
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24
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Pickl JMA, Tichy D, Kuryshev VY, Tolstov Y, Falkenstein M, Schüler J, Reidenbach D, Hotz-Wagenblatt A, Kristiansen G, Roth W, Hadaschik B, Hohenfellner M, Duensing S, Heckmann D, Sültmann H. Ago-RIP-Seq identifies Polycomb repressive complex I member CBX7 as a major target of miR-375 in prostate cancer progression. Oncotarget 2018; 7:59589-59603. [PMID: 27449098 PMCID: PMC5312160 DOI: 10.18632/oncotarget.10729] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2016] [Accepted: 07/09/2016] [Indexed: 01/02/2023] Open
Abstract
Prostate cancer is a heterogeneous disease. MiR-375 is a marker for prostate cancer progression, but its cellular function is not characterized. Here, we provide the first comprehensive investigation of miR-375 in prostate cancer. We show that miR-375 is enriched in prostate cancer compared to normal cells. Furthermore, miR-375 enhanced proliferation, migration and invasion in vitro and induced tumor growth and reduced survival in vivo showing that miR-375 has oncogenic properties in prostate cancer. On the molecular level, we provide the targetome and genome-wide transcriptional changes of miR-375 expression by applying a generalized linear model for Ago-RIP-Seq and RNA-Seq, and show that miR-375 is involved in tumorigenic networks and Polycomb regulation. Integration of tissue and gene ontology data prioritized miR-375 targets and identified the tumor suppressor gene CBX7, a member of Polycomb repressive complex 1, as a major miR-375 target. MiR-375-mediated repression of CBX7 was accompanied by increased expression of its homolog CBX8 and activated transcriptional programs linked to malignant progression in prostate cancer cells. Tissue analysis showed association of CBX7 loss with advanced prostate cancer. Our study indicates that miR-375 exerts its tumor-promoting role in prostate cancer by influencing the epigenetic regulation of transcriptional programs through its ability to directly target the Polycomb complex member CBX7.
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Affiliation(s)
- Julia M A Pickl
- Cancer Genome Research Group, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Diana Tichy
- Department of Biostatistics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Vladimir Y Kuryshev
- Cancer Genome Research Group, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Yanis Tolstov
- Section of Molecular Urooncology, Department of Urology, University of Heidelberg School of Medicine, Heidelberg, Germany
| | - Michael Falkenstein
- Section of Molecular Urooncology, Department of Urology, University of Heidelberg School of Medicine, Heidelberg, Germany
| | - Julia Schüler
- Oncotest GmbH, Institute for Experimental Oncology, Freiburg, Germany
| | - Daniel Reidenbach
- Cancer Genome Research Group, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Agnes Hotz-Wagenblatt
- Bioinformatics Group, Core Facility Genomics & Proteomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Glen Kristiansen
- Institute of Pathology, Center for Integrated Oncology, University of Bonn, Bonn, Germany
| | - Wilfried Roth
- NCT Tissue Bank of The National Center of Tumor Diseases (NCT) and Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
| | - Boris Hadaschik
- Department of Urology, University Hospital Heidelberg, Heidelberg, Germany
| | | | - Stefan Duensing
- Section of Molecular Urooncology, Department of Urology, University of Heidelberg School of Medicine, Heidelberg, Germany
| | - Doreen Heckmann
- Cancer Genome Research Group, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Holger Sültmann
- Cancer Genome Research Group, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
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25
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Ong J, Timens W, Rajendran V, Algra A, Spira A, Lenburg ME, Campbell JD, van den Berge M, Postma DS, van den Berg A, Kluiver J, Brandsma CA. Identification of transforming growth factor-beta-regulated microRNAs and the microRNA-targetomes in primary lung fibroblasts. PLoS One 2017; 12:e0183815. [PMID: 28910321 PMCID: PMC5599028 DOI: 10.1371/journal.pone.0183815] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Accepted: 08/10/2017] [Indexed: 12/05/2022] Open
Abstract
Background Lung fibroblasts are involved in extracellular matrix homeostasis, which is mainly regulated by transforming growth factor-beta (TGF-β), and are therefore crucial in lung tissue repair and remodeling. Abnormal repair and remodeling has been observed in lung diseases like COPD. As miRNA levels can be influenced by TGF-β, we hypothesized that TGF-β influences miRNA expression in lung fibroblasts, thereby affecting their function. Materials and methods We investigated TGF-β1-induced miRNA expression changes in 9 control primary parenchymal lung fibroblasts using miRNA arrays. TGF-β1-induced miRNA expression changes were validated and replicated in an independent set of lung fibroblasts composted of 10 controls and 15 COPD patients using qRT-PCR. Ago2-immunoprecipitation followed by mRNA expression profiling was used to identify the miRNA-targetomes of unstimulated and TGF-β1-stimulated primary lung fibroblasts (n = 2). The genes affected by TGF-β1-modulated miRNAs were identified by comparing the miRNA targetomes of unstimulated and TGF-β1-stimulated fibroblasts. Results Twenty-nine miRNAs were significantly differentially expressed after TGF-β1 stimulation (FDR<0.05). The TGF-β1-induced miR-455-3p and miR-21-3p expression changes were validated and replicated, with in addition, lower miR-455-3p levels in COPD (p<0.05). We identified 964 and 945 genes in the miRNA-targetomes of unstimulated and TGF-β1-stimulated lung fibroblasts, respectively. The TGF-β and Wnt pathways were significantly enriched among the Ago2-IP enriched and predicted targets of miR-455-3p and miR-21-3p. The miR-455-3p target genes HN1, NGF, STRADB, DLD and ANO3 and the miR-21-3p target genes HHEX, CHORDC1 and ZBTB49 were consistently more enriched after TGF-β1 stimulation. Conclusion Two miRNAs, miR-455-3p and miR-21-3p, were induced by TGF-β1 in lung fibroblasts. The significant Ago2-IP enrichment of targets of these miRNAs related to the TGF-β and/or Wnt pathways (NGF, DLD, HHEX) in TGF-β1-stimulated fibroblasts suggest a role for these miRNAs in lung diseases by affecting lung fibroblast function.
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Affiliation(s)
- Jennie Ong
- University of Groningen, University Medical Center Groningen, Department of Pathology and Medical Biology, Groningen, The Netherlands
- University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD (GRIAC), Groningen, The Netherlands
| | - Wim Timens
- University of Groningen, University Medical Center Groningen, Department of Pathology and Medical Biology, Groningen, The Netherlands
- University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD (GRIAC), Groningen, The Netherlands
| | - Vijay Rajendran
- University of Groningen, University Medical Center Groningen, Department of Pathology and Medical Biology, Groningen, The Netherlands
- University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD (GRIAC), Groningen, The Netherlands
| | - Arjan Algra
- University of Groningen, University Medical Center Groningen, Department of Pathology and Medical Biology, Groningen, The Netherlands
| | - Avrum Spira
- Boston University, School of Medicine, Department of Medicine, Section of Computational Biomedicine, Boston, Massachusetts, United States of America
| | - Marc E. Lenburg
- Boston University, School of Medicine, Department of Medicine, Section of Computational Biomedicine, Boston, Massachusetts, United States of America
| | - Joshua D. Campbell
- Boston University, School of Medicine, Department of Medicine, Section of Computational Biomedicine, Boston, Massachusetts, United States of America
| | - Maarten van den Berge
- University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD (GRIAC), Groningen, The Netherlands
- University of Groningen, University Medical Center Groningen, Department of Pulmonary Diseases, Groningen, The Netherlands
| | - Dirkje S. Postma
- University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD (GRIAC), Groningen, The Netherlands
- University of Groningen, University Medical Center Groningen, Department of Pulmonary Diseases, Groningen, The Netherlands
| | - Anke van den Berg
- University of Groningen, University Medical Center Groningen, Department of Pathology and Medical Biology, Groningen, The Netherlands
| | - Joost Kluiver
- University of Groningen, University Medical Center Groningen, Department of Pathology and Medical Biology, Groningen, The Netherlands
| | - Corry-Anke Brandsma
- University of Groningen, University Medical Center Groningen, Department of Pathology and Medical Biology, Groningen, The Netherlands
- University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD (GRIAC), Groningen, The Netherlands
- * E-mail:
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26
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MicroRNA in vivo precipitation identifies miR-151-3p as a computational unpredictable miRNA to target Stat3 and inhibits innate IL-6 production. Cell Mol Immunol 2017; 15:99-110. [PMID: 28890541 DOI: 10.1038/cmi.2017.82] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Revised: 07/20/2017] [Accepted: 07/20/2017] [Indexed: 12/13/2022] Open
Abstract
MicroRNAs (miRNAs) function as important regulators in the immune response and inflammation. Several approaches have been reported to computationally predict miRNAs and their potential targets. However, there are still many miRNA-target interactions that are unpredictable by using the current computational algorithms. We established a miRNA in vivo precipitation method (miRIP) to identify unpredictable miRNAs with definite targets in these cells. Because Stat3 is a well-known transcription factor involved in innate immunity and inflammation, we utilized the miRIP method to identify miRNAs that bind Stat3 mRNA in macrophages. Among the captured miRNAs, miR-151-3p was confirmed to interact with Stat3 mRNA 3'-UTR and downregulate the Stat3 protein levels. LPS stimulation decreased miR-151-3p expression, thereby increasing IL-6 production. Therefore, we found that miR-151-3p inhibited LPS-induced IL-6 production by targeting Stat3. These data further confirmed miRIP as an efficient method to identify unpredictable miRNAs and explore miRNAs-mediated regulation in innate immunity and inflammation.
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27
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Cai J, Fang L, Huang Y, Li R, Xu X, Hu Z, Zhang L, Yang Y, Zhu X, Zhang H, Wu J, Huang Y, Li J, Zeng M, Song E, He Y, Zhang L, Li M. Simultaneous overactivation of Wnt/β-catenin and TGFβ signalling by miR-128-3p confers chemoresistance-associated metastasis in NSCLC. Nat Commun 2017. [PMID: 28627514 PMCID: PMC5481840 DOI: 10.1038/ncomms15870] [Citation(s) in RCA: 130] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Cancer chemoresistance and metastasis are tightly associated features. However, whether they share common molecular mechanisms and thus can be targeted with one common strategy remain unclear in non-small cell lung cancer (NSCLC). Here, we report that high levels of microRNA-128-3p (miR-128-3p) is key to concomitant development of chemoresistance and metastasis in residual NSCLC cells having survived repeated chemotherapy and correlates with chemoresistance, aggressiveness and poor prognosis in NSCLC patients. Mechanistically, miR-128-3p induces mesenchymal and stemness-like properties through downregulating multiple inhibitors of Wnt/β-catenin and TGF-β pathways, leading to their overactivation. Importantly, antagonism of miR-128-3p potently reverses metastasis and chemoresistance of highly malignant NSCLC cells, which could be completely reversed by restoring Wnt/β-catenin and TGF-β activities. Notably, correlations among miR-128-3p levels, activated β-catenin and TGF-β signalling, and pro-epithelial-to-mesenchymal transition/pro-metastatic protein levels are validated in NSCLC patient specimens. These findings suggest that miR-128-3p might be a potential target against both metastasis and chemoresistance in NSCLC.
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Affiliation(s)
- Junchao Cai
- Department of Microbiology, Sun Yat-sen University Zhongshan School of Medicine, Guangzhou 510080, China.,Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Ministry of Education, Guangzhou 510080, China.,Guangdong Engineering and Technology Research Center for Disease-Model Animals, Sun Yat-sen University, Guangzhou 510006, China
| | - Lishan Fang
- Department of Microbiology, Sun Yat-sen University Zhongshan School of Medicine, Guangzhou 510080, China.,Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Ministry of Education, Guangzhou 510080, China.,Central Laboratory of The Eighth Affiliated Hospital of Sun Yat-sen University, Shenzhen 518033, China
| | - Yongbo Huang
- State Key Laboratory of Respiratory Diseases and Guangzhou Institute of Respiratory Diseases, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou 510120, China
| | - Rong Li
- Department of Microbiology, Sun Yat-sen University Zhongshan School of Medicine, Guangzhou 510080, China.,Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Ministry of Education, Guangzhou 510080, China
| | - Xiaonan Xu
- Department of Microbiology, Sun Yat-sen University Zhongshan School of Medicine, Guangzhou 510080, China.,Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Ministry of Education, Guangzhou 510080, China
| | - Zhihuang Hu
- Department of Medical Oncology, Fudan University Shanghai Cancer Center, Shanghai 200032, China
| | - Le Zhang
- Department of Microbiology, Sun Yat-sen University Zhongshan School of Medicine, Guangzhou 510080, China.,Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Ministry of Education, Guangzhou 510080, China
| | - Yi Yang
- Department of Pharmacology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China
| | - Xun Zhu
- Department of Microbiology, Sun Yat-sen University Zhongshan School of Medicine, Guangzhou 510080, China.,Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Ministry of Education, Guangzhou 510080, China
| | - Heng Zhang
- Neurosurgery Intensive Care Unit, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou 510080, China
| | - Jueheng Wu
- Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Ministry of Education, Guangzhou 510080, China
| | - Yan Huang
- Department of Medical Oncology, Fudan University Shanghai Cancer Center, Shanghai 200032, China
| | - Jun Li
- Department of Biochemistry, Sun Yat-sen University Zhongshan School of Medicine, Guangzhou 510080, China
| | - Musheng Zeng
- State Key Laboratory of Oncology in South China, Department of Experimental Research, Sun Yat-Sen University Cancer Center, Guangzhou 510060, China
| | - Erwei Song
- Department of Breast Surgery, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, China
| | - Yukai He
- Department of Medicine and Department of Biochemistry and Molecular Biology, Georgia Cancer Center, Augusta University, Augusta, Georgia 30912, USA
| | - Li Zhang
- Department of Medical Oncology, Fudan University Shanghai Cancer Center, Shanghai 200032, China
| | - Mengfeng Li
- Department of Microbiology, Sun Yat-sen University Zhongshan School of Medicine, Guangzhou 510080, China.,Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Ministry of Education, Guangzhou 510080, China
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Cordeiro A, Monzó M, Navarro A. Non-Coding RNAs in Hodgkin Lymphoma. Int J Mol Sci 2017; 18:ijms18061154. [PMID: 28555062 PMCID: PMC5485978 DOI: 10.3390/ijms18061154] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Revised: 05/23/2017] [Accepted: 05/26/2017] [Indexed: 12/22/2022] Open
Abstract
MicroRNAs (miRNAs), small non-coding RNAs that regulate gene expression by binding to the 3’-UTR of their target genes, can act as oncogenes or tumor suppressors. Recently, other types of non-coding RNAs—piwiRNAs and long non-coding RNAs—have also been identified. Hodgkin lymphoma (HL) is a B cell origin disease characterized by the presence of only 1% of tumor cells, known as Hodgkin and Reed-Stenberg (HRS) cells, which interact with the microenvironment to evade apoptosis. Several studies have reported specific miRNA signatures that can differentiate HL lymph nodes from reactive lymph nodes, identify histologic groups within classical HL, and distinguish HRS cells from germinal center B cells. Moreover, some signatures are associated with survival or response to chemotherapy. Most of the miRNAs in the signatures regulate genes related to apoptosis, cell cycle arrest, or signaling pathways. Here we review findings on miRNAs in HL, as well as on other non-coding RNAs.
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Affiliation(s)
- Anna Cordeiro
- Molecular Oncology and Embryology Laboratory, Human Anatomy and Embryology Unit, School of Medicine, University of Barcelona, C/Casanova 143, 08032 Barcelona, Spain.
| | - Mariano Monzó
- Molecular Oncology and Embryology Laboratory, Human Anatomy and Embryology Unit, School of Medicine, University of Barcelona, C/Casanova 143, 08032 Barcelona, Spain.
| | - Alfons Navarro
- Molecular Oncology and Embryology Laboratory, Human Anatomy and Embryology Unit, School of Medicine, University of Barcelona, C/Casanova 143, 08032 Barcelona, Spain.
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29
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Yuan Y, Kluiver J, Koerts J, de Jong D, Rutgers B, Abdul Razak FR, Terpstra M, Plaat BE, Nolte IM, Diepstra A, Visser L, Kok K, van den Berg A. miR-24-3p Is Overexpressed in Hodgkin Lymphoma and Protects Hodgkin and Reed-Sternberg Cells from Apoptosis. THE AMERICAN JOURNAL OF PATHOLOGY 2017; 187:1343-1355. [PMID: 28432871 DOI: 10.1016/j.ajpath.2017.02.016] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Accepted: 02/16/2017] [Indexed: 12/11/2022]
Abstract
miRNAs play important roles in biological processes, such as proliferation, metabolism, differentiation, and apoptosis, whereas altered expression levels contribute to diseases, such as cancers. We identified miRNAs with aberrant expression in Hodgkin lymphoma (HL) and investigated their role in pathogenesis. Small RNA sequencing revealed 84 significantly differentially expressed miRNAs in HL cell lines as compared to germinal center B cells. Three up-regulated miRNAs-miR-23a-3p, miR-24-3p, and miR-27a-3p-were derived from one primary miRNA transcript. Loss-of-function analyses for these miRNAs and their seed family members resulted in decreased growth on miR-24-3p inhibition in three HL cell lines and of miR-27a/b-3p inhibition in one HL cell line. Apoptosis analysis indicated that the effect of miR-24-3p on cell growth is at least in part caused by an increase of apoptotic cells. Argonaute 2 immunoprecipitation revealed 1142 genes consistently targeted by miRNAs in at least three of four HL cell lines. Furthermore, 52 of the 1142 genes were predicted targets of miR-24-3p. Functional annotation analysis revealed a function related to cell growth, cell death, and/or apoptosis for 15 of the 52 genes. Western blotting of the top five genes showed increased protein levels on miR-24-3p inhibition for CDKN1B/P27kip1 and MYC. In summary, we showed that miR-24-3p is up-regulated in HL and its inhibition impairs cell growth possibly via targeting CDKN1B/P27kip1 and MYC.
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Affiliation(s)
- Ye Yuan
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands; Institute of Clinical Pharmacology of the Second Affiliated Hospital, Harbin Medical University, Harbin, China
| | - Joost Kluiver
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Jasper Koerts
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Debora de Jong
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Bea Rutgers
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - F Reeny Abdul Razak
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Martijn Terpstra
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Boudewijn E Plaat
- Department of Otorhinolaryngology/Head and Neck Surgery, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Ilja M Nolte
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Arjan Diepstra
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Lydia Visser
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Klaas Kok
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Anke van den Berg
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands.
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30
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Wallaert A, Durinck K, Taghon T, Van Vlierberghe P, Speleman F. T-ALL and thymocytes: a message of noncoding RNAs. J Hematol Oncol 2017; 10:66. [PMID: 28270163 PMCID: PMC5341419 DOI: 10.1186/s13045-017-0432-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2017] [Accepted: 02/24/2017] [Indexed: 02/06/2023] Open
Abstract
In the last decade, the role for noncoding RNAs in disease was clearly established, starting with microRNAs and later expanded towards long noncoding RNAs. This was also the case for T cell acute lymphoblastic leukemia, which is a malignant blood disorder arising from oncogenic events during normal T cell development in the thymus. By studying the transcriptomic profile of protein-coding genes, several oncogenic events leading to T cell acute lymphoblastic leukemia (T-ALL) could be identified. In recent years, it became apparent that several of these oncogenes function via microRNAs and long noncoding RNAs. In this review, we give a detailed overview of the studies that describe the noncoding RNAome in T-ALL oncogenesis and normal T cell development.
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Affiliation(s)
- Annelynn Wallaert
- Center for Medical Genetics, Ghent University, Ghent, Belgium. .,Cancer Research Institute Ghent, Ghent, Belgium.
| | - Kaat Durinck
- Center for Medical Genetics, Ghent University, Ghent, Belgium.,Cancer Research Institute Ghent, Ghent, Belgium
| | - Tom Taghon
- Cancer Research Institute Ghent, Ghent, Belgium.,Department of Clinical Chemistry, Microbiology and Immunology, Ghent University, Ghent, Belgium
| | - Pieter Van Vlierberghe
- Center for Medical Genetics, Ghent University, Ghent, Belgium.,Cancer Research Institute Ghent, Ghent, Belgium
| | - Frank Speleman
- Center for Medical Genetics, Ghent University, Ghent, Belgium.,Cancer Research Institute Ghent, Ghent, Belgium
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31
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Snail-Modulated MicroRNA 493 Forms a Negative Feedback Loop with the Insulin-Like Growth Factor 1 Receptor Pathway and Blocks Tumorigenesis. Mol Cell Biol 2017; 37:MCB.00510-16. [PMID: 27956702 DOI: 10.1128/mcb.00510-16] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Accepted: 12/06/2016] [Indexed: 12/15/2022] Open
Abstract
In this study, we have identified one microRNA, microRNA 493 (miR-493), which could simultaneously and directly regulate multiple genes downstream of the insulin-like growth factor 1 receptor (IGF1R) pathway, including IGF1R, by binding with complementary sequences in the 3' untranslated region (UTR) of mRNAs of IGF1R, insulin receptor substrate 1 (IRS1), and mitogen-activated protein kinase 1 (MAPK1), thereby potentiating their inhibitory function at multiple levels in development and progression of cancers. This binding was further confirmed by pulldown of miR with AGO-2 antibody. Further, results from head and neck samples showed that miR-493 levels were significantly downregulated in tumors, with a concomitant increase in the expression of IGF1R and key downstream effectors. Functional studies from miR-493 overexpression cells and nude-mouse models revealed the tumor suppressor functions of miR-493. Regulation studies revealed that Snail binds to the miR-493 promoter and represses it. We found the existence of a dynamic negative feedback loop in the regulation of IGF1R and miR-493 mediated via Snail. Our study showed that nicotine treatment significantly decreases the levels of miR-493-with a concomitant increase in the levels of Snail-an indication of progression of cells toward tumorigenesis, reestablishing the role of tobacco as a major risk factor for head and neck cancers and elucidating the mechanism behind nicotine-mediated tumorigenesis.
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32
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Stepwise reprogramming of liver cells to a pancreas progenitor state by the transcriptional regulator Tgif2. Nat Commun 2017; 8:14127. [PMID: 28193997 PMCID: PMC5316826 DOI: 10.1038/ncomms14127] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2015] [Accepted: 11/11/2016] [Indexed: 12/12/2022] Open
Abstract
The development of a successful lineage reprogramming strategy of liver to pancreas holds promises for the treatment and potential cure of diabetes. The liver is an ideal tissue source for generating pancreatic cells, because of its close developmental origin with the pancreas and its regenerative ability. Yet, the molecular bases of hepatic and pancreatic cellular plasticity are still poorly understood. Here, we report that the TALE homeoprotein TGIF2 acts as a developmental regulator of the pancreas versus liver fate decision and is sufficient to elicit liver-to-pancreas fate conversion both ex vivo and in vivo. Hepatocytes expressing Tgif2 undergo extensive transcriptional remodelling, which represses the original hepatic identity and, over time, induces a pancreatic progenitor-like phenotype. Consistently, in vivo forced expression of Tgif2 activates pancreatic progenitor genes in adult mouse hepatocytes. This study uncovers the reprogramming activity of TGIF2 and suggests a stepwise reprogramming paradigm, whereby a 'lineage-restricted' dedifferentiation step precedes the identity switch.
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33
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Teteloshvili N, Smigielska-Czepiel K, Yuan Y, Seitz A, de Jong D, Rutgers B, Jellema P, van der Lei RJ, Slezak-Prochazka I, Brouwer E, Boots AMH, Kroesen BJ, van den Berg A, Kluiver J. Argonaute 2 immunoprecipitation revealed large tumor suppressor kinase 1 as a novel proapoptotic target of miR-21 in T cells. FEBS J 2017; 284:555-567. [PMID: 28075055 DOI: 10.1111/febs.14011] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Revised: 12/09/2016] [Accepted: 01/09/2017] [Indexed: 01/13/2023]
Abstract
MicroRNA (miR)-21 is an important suppressor of T-cell apoptosis that is also overexpressed in many types of cancers. The exact mechanisms underlying the antiapoptotic effects of miR-21 are not well understood. In this study, we used the Jurkat T-cell line as a model to identify apoptosis-associated miR-21 target genes. We showed that expression of miR-21 rapidly increases upon αCD3/αCD28 activation of Jurkat cells. Inhibition of miR-21 reduced cell growth which could be explained by an increase in apoptosis. MicroRNA target gene identification by AGO2 RNA-immunoprecipitation followed by gene expression microarray (RIP-Chip) resulted in the identification of 72 predicted miR-21 target genes that were at least twofold enriched in the AGO2-IP fraction of miR-21 overexpressing cells. Of these, 71 were at least twofold more enriched in the AGO2-IP fraction of miR-21 overexpressing cells as compared to AGO2-IP fraction of control cells. The target gene for which the AGO2-IP enrichment was most prominently increased upon miR-21 overexpression was the proapoptotic protein LATS1. Luciferase reporter assays and western blot analysis confirmed targeting of LATS1 by miR-21. qRT-PCR analysis in primary T cells showed an inverse expression pattern between LATS1 transcript levels and miR-21 upon T-cell stimulation. Finally, LATS1 knockdown partially rescued the miR-21 inhibition-induced impaired cell growth. Collectively, these data identify LATS1 as a miR-21 target important for the antiapoptotic function of miR-21 in T cells and likely also in many types of cancer.
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Affiliation(s)
- Nato Teteloshvili
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, The Netherlands.,Groningen Research initiative on healthy Ageing and Immune Longevity (GRAIL), University of Groningen, University Medical Center Groningen, The Netherlands
| | - Katarzyna Smigielska-Czepiel
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, The Netherlands.,Groningen Research initiative on healthy Ageing and Immune Longevity (GRAIL), University of Groningen, University Medical Center Groningen, The Netherlands
| | - Ye Yuan
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, The Netherlands.,Institute of Clinical Pharmacology of the Second Affiliated Hospital, Harbin Medical University, Heilongjiang Province, China
| | - Annika Seitz
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, The Netherlands
| | - Debora de Jong
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, The Netherlands
| | - Bea Rutgers
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, The Netherlands
| | - Pytrick Jellema
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, The Netherlands
| | - Roelof Jan van der Lei
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, The Netherlands
| | - Izabella Slezak-Prochazka
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, The Netherlands
| | - Elisabeth Brouwer
- Groningen Research initiative on healthy Ageing and Immune Longevity (GRAIL), University of Groningen, University Medical Center Groningen, The Netherlands.,Department of Rheumatology and Clinical Immunology, University of Groningen, University Medical Center Groningen, The Netherlands
| | - Annemieke M H Boots
- Groningen Research initiative on healthy Ageing and Immune Longevity (GRAIL), University of Groningen, University Medical Center Groningen, The Netherlands.,Department of Rheumatology and Clinical Immunology, University of Groningen, University Medical Center Groningen, The Netherlands
| | - Bart-Jan Kroesen
- Groningen Research initiative on healthy Ageing and Immune Longevity (GRAIL), University of Groningen, University Medical Center Groningen, The Netherlands.,Department of Laboratory Medicine, University of Groningen, University Medical Center Groningen, The Netherlands
| | - Anke van den Berg
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, The Netherlands.,Groningen Research initiative on healthy Ageing and Immune Longevity (GRAIL), University of Groningen, University Medical Center Groningen, The Netherlands
| | - Joost Kluiver
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, The Netherlands
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Slezak-Prochazka I, Kluiver J, de Jong D, Smigielska-Czepiel K, Kortman G, Winkle M, Rutgers B, Koerts J, Visser L, Diepstra A, Kroesen BJ, van den Berg A. Inhibition of the miR-155 target NIAM phenocopies the growth promoting effect of miR-155 in B-cell lymphoma. Oncotarget 2016; 7:2391-400. [PMID: 26497687 PMCID: PMC4823043 DOI: 10.18632/oncotarget.6165] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Accepted: 10/04/2015] [Indexed: 11/25/2022] Open
Abstract
Several studies have indicated an important role for miR-155 in the pathogenesis of B-cell lymphoma. Highly elevated levels of miR-155 were indeed observed in most B-cell lymphomas with the exception of Burkitt lymphoma (BL). However, the molecular mechanisms that underlie the oncogenic role of miR-155 in B-cell lymphoma are not well understood. To identify the miR-155 targets relevant for B-cell lymphoma, we performed RNA immunoprecipitation of Argonaute 2 in Hodgkin lymphoma (HL) cells upon miR-155 inhibition and in BL cells upon ectopic expression of miR-155. We identified 54 miR-155-specific target genes in BL cells and confirmed miR-155 targeting of DET1, NIAM, TRIM32, HOMEZ, PSIP1 and JARID2. Five of these targets are also regulated by endogenous miR-155 in HL cells. Both overexpression of miR-155 and inhibition of expression of the novel miR-155 target gene NIAM increased proliferation of BL cells. In primary B-cell lymphoma NIAM-positive cases have significant lower levels of miR-155 as compared to NIAM-negative cases, suggesting that NIAM is also regulated by miR-155 in primary B-cell lymphoma. Thus, our data indicate an oncogenic role for miR-155 in B-cell lymphoma which involves targeting the tumor suppressor NIAM.
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Affiliation(s)
- Izabella Slezak-Prochazka
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands.,Biosystems Group, Institute of Automatic Control, Silesian University of Technology, Gliwice, Poland
| | - Joost Kluiver
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Debora de Jong
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Katarzyna Smigielska-Czepiel
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Gertrud Kortman
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Melanie Winkle
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Bea Rutgers
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Jasper Koerts
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Lydia Visser
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Arjan Diepstra
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Bart-Jan Kroesen
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Anke van den Berg
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
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35
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Azevedo JA, Carter BS, Meng F, Turner DL, Dai M, Schatzberg AF, Barchas JD, Jones EG, Bunney WE, Myers RM, Akil H, Watson SJ, Thompson RC. The microRNA network is altered in anterior cingulate cortex of patients with unipolar and bipolar depression. J Psychiatr Res 2016; 82:58-67. [PMID: 27468165 PMCID: PMC5026930 DOI: 10.1016/j.jpsychires.2016.07.012] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/28/2015] [Revised: 07/08/2016] [Accepted: 07/12/2016] [Indexed: 11/26/2022]
Abstract
MicroRNAs (miRNAs) are small, non-coding RNAs acting as post-transcriptional regulators of gene expression. Though implicated in multiple CNS disorders, miRNAs have not been examined in any psychiatric disease state in anterior cingulate cortex (AnCg), a brain region centrally involved in regulating mood. We performed qPCR analyses of 29 miRNAs previously implicated in psychiatric illness (major depressive disorder (MDD), bipolar disorder (BP) and/or schizophrenia (SZ)) in AnCg of patients with MDD and BP versus controls. miR-132, miR-133a and miR-212 were initially identified as differentially expressed in BP, miR-184 in MDD and miR-34a in both MDD and BP (although none survived multiple correction testing and must be considered preliminary). In silico target prediction algorithms identified putative targets of differentially expressed miRNAs. Nuclear Co-Activator 1 (NCOA1), Nuclear Co-Repressor 2 (NCOR2) and Phosphodiesterase 4B (PDE4B) were selected based upon predicted targeting by miR-34a (with NCOR2 and PDE4B both targeted by miR-184) and published relevance to psychiatric illness. Luciferase assays identified PDE4B as a target of miR-34a and miR-184, while NCOA1 and NCOR2 were targeted by miR-34a and 184, respectively. qPCR analyses were performed to determine whether changes in miRNA levels correlated with mRNA levels of validated targets. NCOA1 showed an inverse correlation with miR-34a in BP, while NCOR2 demonstrated a positive correlation. In sum, this is the first study to demonstrate miRNA changes in AnCg in psychiatric illness and validate miR-34a as differentially expressed in CNS in MDD. These findings support a mechanistic role for miRNAs in the regulation of stress-responsive genes disrupted in psychiatric illness.
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Affiliation(s)
- Joshua A Azevedo
- Molecular and Behavioral Neuroscience Institute, University of Michigan, 205 Zina Pitcher Pl, Ann Arbor, MI, 48109, USA; Neuroscience Graduate Program, University of Michigan, 4137 Undergraduate Science Building (USB), 204 Washtenaw Avenue, Ann Arbor, MI, 48109, USA
| | - Bradley S Carter
- Molecular and Behavioral Neuroscience Institute, University of Michigan, 205 Zina Pitcher Pl, Ann Arbor, MI, 48109, USA; Neuroscience Graduate Program, University of Michigan, 4137 Undergraduate Science Building (USB), 204 Washtenaw Avenue, Ann Arbor, MI, 48109, USA; Neuroscience Program, Oberlin College, Science Center A261, 119 Woodland St., Oberlin, OH, 44074, USA
| | - Fan Meng
- Molecular and Behavioral Neuroscience Institute, University of Michigan, 205 Zina Pitcher Pl, Ann Arbor, MI, 48109, USA; Pritzker Neuropsychiatric Disorders Research Consortium, USA; Department of Psychiatry, University of Michigan, 530 Church St, Ann Arbor, MI, 48109, USA
| | - David L Turner
- Molecular and Behavioral Neuroscience Institute, University of Michigan, 205 Zina Pitcher Pl, Ann Arbor, MI, 48109, USA; Neuroscience Graduate Program, University of Michigan, 4137 Undergraduate Science Building (USB), 204 Washtenaw Avenue, Ann Arbor, MI, 48109, USA; Department of Biological Chemistry, University of Michigan, 5301 MSRB III, 1150 W. Medical Center Drive, Ann Arbor, MI, 48109, USA
| | - Manhong Dai
- Molecular and Behavioral Neuroscience Institute, University of Michigan, 205 Zina Pitcher Pl, Ann Arbor, MI, 48109, USA
| | - Alan F Schatzberg
- Pritzker Neuropsychiatric Disorders Research Consortium, USA; Department of Psychiatry and Behavioral Sciences, Stanford University, 401 Quarry Rd, Stanford, CA, 94305, USA
| | - Jack D Barchas
- Pritzker Neuropsychiatric Disorders Research Consortium, USA; Department of Psychiatry, Weill Cornell Medical College, 525 East 68th Street, New York, NY, 10065, USA
| | - Edward G Jones
- Pritzker Neuropsychiatric Disorders Research Consortium, USA; Center for Neuroscience, University of California - Davis, 1544 Newton Court, Davis, CA, 95618, USA
| | - William E Bunney
- Pritzker Neuropsychiatric Disorders Research Consortium, USA; Psychiatry and Human Behavior, University of California - Irvine, 101 The City Dr S, Orange, CA, 92868, USA
| | - Richard M Myers
- Pritzker Neuropsychiatric Disorders Research Consortium, USA; Hudson Alpha Institute for Biotechnology, 601 Genome Way Northwest, Huntsville, AL, 35806, USA
| | - Huda Akil
- Molecular and Behavioral Neuroscience Institute, University of Michigan, 205 Zina Pitcher Pl, Ann Arbor, MI, 48109, USA; Neuroscience Graduate Program, University of Michigan, 4137 Undergraduate Science Building (USB), 204 Washtenaw Avenue, Ann Arbor, MI, 48109, USA; Pritzker Neuropsychiatric Disorders Research Consortium, USA; Department of Psychiatry, University of Michigan, 530 Church St, Ann Arbor, MI, 48109, USA
| | - Stanley J Watson
- Molecular and Behavioral Neuroscience Institute, University of Michigan, 205 Zina Pitcher Pl, Ann Arbor, MI, 48109, USA; Neuroscience Graduate Program, University of Michigan, 4137 Undergraduate Science Building (USB), 204 Washtenaw Avenue, Ann Arbor, MI, 48109, USA; Pritzker Neuropsychiatric Disorders Research Consortium, USA; Department of Psychiatry, University of Michigan, 530 Church St, Ann Arbor, MI, 48109, USA
| | - Robert C Thompson
- Molecular and Behavioral Neuroscience Institute, University of Michigan, 205 Zina Pitcher Pl, Ann Arbor, MI, 48109, USA; Neuroscience Graduate Program, University of Michigan, 4137 Undergraduate Science Building (USB), 204 Washtenaw Avenue, Ann Arbor, MI, 48109, USA; Pritzker Neuropsychiatric Disorders Research Consortium, USA; Department of Psychiatry, University of Michigan, 530 Church St, Ann Arbor, MI, 48109, USA.
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36
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Fernandez-Mercado M, Manterola L, Lawrie CH. MicroRNAs in Lymphoma: Regulatory Role and Biomarker Potential. Curr Genomics 2016; 16:349-58. [PMID: 27047255 PMCID: PMC4763973 DOI: 10.2174/1389202916666150707160147] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2015] [Revised: 04/20/2015] [Accepted: 04/22/2015] [Indexed: 12/19/2022] Open
Abstract
Although it is now evident that microRNAs (miRNAs) play a critical regulatory role in many, if not all, pathological and physiological processes, remarkably they have only formally been recognized for less than fifteen years. These endogenously produced short non-coding RNAs have created a new paradigm of gene control and have utility as both novel biomarkers of cancer and as potential therapeutics. In this review we consider the role of miRNAs in lymphoid biology both under physiological (i.e. lymphopoiesis) and malignant (i.e. lymphomagenesis) conditions. In addition to the functional significance of aberrant miRNA expression in lymphomas we discuss their use as novel biomarkers, both as a in situ tumour biomarker and as a non-invasive surrogate for the tumour by testing miRNAs in the blood of patients. Finally we consider the use of these molecules as potential therapeutic agents for lymphoma (and other cancer) patients and discuss some of the hurdles yet to be overcome in order to translate this potential into clinical practice
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Affiliation(s)
| | - Lorea Manterola
- Oncology area, Biodonostia Research Institute, San Sebastián, Spain
| | - Charles H Lawrie
- Oncology area, Biodonostia Research Institute, San Sebastián, Spain; ; Nuffield Department of Clinical Laboratory Sciences, University of Oxford, Oxford, UK;; IKERBASQUE, Basque Foundation for Science, Bilbao, Spain
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37
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Gordillo GM, Biswas A, Khanna S, Spieldenner JM, Pan X, Sen CK. Multidrug Resistance-associated Protein-1 (MRP-1)-dependent Glutathione Disulfide (GSSG) Efflux as a Critical Survival Factor for Oxidant-enriched Tumorigenic Endothelial Cells. J Biol Chem 2016; 291:10089-103. [PMID: 26961872 DOI: 10.1074/jbc.m115.688879] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2015] [Indexed: 12/28/2022] Open
Abstract
Endothelial cell tumors are the most common soft tissue tumors in infants. Tumor-forming endothelial (EOMA) cells are able to escape cell death fate despite excessive nuclear oxidant burden. Our previous work recognized perinuclear Nox-4 as a key contributor to EOMA growth. The objective of this work was to characterize the mechanisms by which EOMA cells evade oxidant toxicity and thrive. In EOMA cells, compared with in the cytosol, the nuclear GSSG/GSH ratio was 5-fold higher. Compared to the ratio observed in healthy murine aortic endothelial (MAE) cells, GSSG/GSH was over twice as high in EOMA cells. Multidrug resistance-associated protein-1 (MRP-1), an active GSSG efflux mechanism, showed 2-fold increased activity in EOMA compared with MAE cells. Hyperactive YB-1 and Ape/Ref-1 were responsible for high MRP-1 expression in EOMA. Proximity ligand assay demonstrated MRP-1 and YB-1 binding. Such binding enabled the nuclear targeting of MRP-1 in EOMA in a leptomycin-B-sensitive manner. MRP-1 inhibition as well as knockdown trapped nuclear GSSG, causing cell death of EOMA. Disulfide loading of cells by inhibition of GSSG reductase (bischoloronitrosourea) or thioredoxin reductase (auranofin) was effective in causing EOMA death as well. In sum, EOMA cells survive a heavy oxidant burden by rapid efflux of GSSG, which is lethal if trapped within the cell. A hyperactive MRP-1 system for GSSG efflux acts as a critical survival factor for these cells, making it a potential target for EOMA therapeutics.
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Affiliation(s)
- Gayle M Gordillo
- From the Department of Plastic Surgery, Davis Heart and Lung Research Institute, and
| | - Ayan Biswas
- From the Department of Plastic Surgery, Davis Heart and Lung Research Institute, and
| | - Savita Khanna
- Davis Heart and Lung Research Institute, and Department of Surgery
| | | | - Xueliang Pan
- Center for Biostatistics, Ohio State University Wexner Medical Center, Columbus, Ohio 43212
| | - Chandan K Sen
- Davis Heart and Lung Research Institute, and Department of Surgery
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38
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MicroRNA-222 regulates muscle alternative splicing through Rbm24 during differentiation of skeletal muscle cells. Cell Death Dis 2016; 7:e2086. [PMID: 26844700 PMCID: PMC4849150 DOI: 10.1038/cddis.2016.10] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2015] [Revised: 12/15/2015] [Accepted: 01/03/2016] [Indexed: 02/01/2023]
Abstract
A number of microRNAs have been shown to regulate skeletal muscle development and differentiation. MicroRNA-222 is downregulated during myogenic differentiation and its overexpression leads to alteration of muscle differentiation process and specialized structures. By using RNA-induced silencing complex (RISC) pulldown followed by RNA sequencing, combined with in silico microRNA target prediction, we have identified two new targets of microRNA-222 involved in the regulation of myogenic differentiation, Ahnak and Rbm24. Specifically, the RNA-binding protein Rbm24 is a major regulator of muscle-specific alternative splicing and its downregulation by microRNA-222 results in defective exon inclusion impairing the production of muscle-specific isoforms of Coro6, Fxr1 and NACA transcripts. Reconstitution of normal levels of Rbm24 in cells overexpressing microRNA-222 rescues muscle-specific splicing. In conclusion, we have identified a new function of microRNA-222 leading to alteration of myogenic differentiation at the level of alternative splicing, and we provide evidence that this effect is mediated by Rbm24 protein.
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39
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Abstract
MicroRNA (miRNA) analysis has evolved over the past two decades to become a highly specialized field with broad-reaching applications across a multitude of diseases and cellular processes. The choice of an applicable approach for miRNA quantification will depend on a variety of factors such as cost, time constraints, and throughput. Here, we describe the methods of total RNA isolation, AGO2-bound RNA isolation, miRNA polyadenylation, miRNA-cDNA synthesis, and quantitative real-time polymerase chain reaction for the detection of known miRNAs in cultured cells or xenograft tissues of breast cancer.
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Affiliation(s)
- Martin Brown
- Departments of Pathology and Laboratory Medicine, University of Tennessee Health Science Center, 19 South Manassas Street, Memphis, TN, 38163, USA
| | - Meiyun Fan
- Departments of Pathology and Laboratory Medicine, University of Tennessee Health Science Center, 19 South Manassas Street, Memphis, TN, 38163, USA.
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40
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Yamagishi M, Katano H, Hishima T, Shimoyama T, Ota Y, Nakano K, Ishida T, Okada S, Watanabe T. Coordinated loss of microRNA group causes defenseless signaling in malignant lymphoma. Sci Rep 2015; 5:17868. [PMID: 26639163 PMCID: PMC4671098 DOI: 10.1038/srep17868] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Accepted: 11/06/2015] [Indexed: 01/16/2023] Open
Abstract
Biological robustness is exposed to stochastic perturbations, which should be controlled by intrinsic mechanisms; the promiscuous signaling network without appropriate alleviation is the true nature of cancer cells. B cell receptor (BCR) signaling is a major source of gene expression signature important for B cell. It is still unclear the mechanism by which the expression of functionally important genes is continuously deregulated in malignant lymphomas. Using RISC-capture assay, we reveal that multiple BCR signaling factors are persistently regulated by microRNA (miRNA) in human B cells. Clinical samples from patients with diffuse large B-cell lymphoma (DLBCL, n = 83) show loss of an essential miRNA set (miR-200c, miR-203, miR-31). Conventional screening and RISC profiling identify multiple targets (CD79B, SYK, PKCβII, PLCγ1, IKKβ, NIK, MYD88, PI3K class I (α/β/δ/γ), RasGRP3); signaling network habitually faces interference composed by miRNA group in normal B cells. We demonstrate that simultaneous depletion of the key miRNAs enhances translation of the multiple targets and causes chronic activation of NF-κB, PI3K-Akt, and Ras-Erk cascades, leading to B cell transformation. This study suggests that compensatory actions by multiple miRNAs rather than by a single miRNA ensure robustness of biological processes.
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Affiliation(s)
- Makoto Yamagishi
- Graduate School of Frontier Sciences, Department of Computational Biology and Medical Sciences, The University of Tokyo, Japan
| | - Harutaka Katano
- Department of Pathology, National Institute of Infectious Diseases, Japan
| | - Tsunekazu Hishima
- Department of Pathology, Tokyo Metropolitan Cancer and Infectious Diseases Center Komagome Hospital, Japan
| | - Tatsu Shimoyama
- Department of Clinical Medical Oncology, Tokyo Metropolitan Cancer and Infectious Diseases Center Komagome Hospital, Japan
| | - Yasunori Ota
- Institute of Medical Science, The University of Tokyo, Japan
| | - Kazumi Nakano
- Graduate School of Frontier Sciences, Department of Computational Biology and Medical Sciences, The University of Tokyo, Japan
| | - Takaomi Ishida
- Institute of Medical Science, The University of Tokyo, Japan
| | - Seiji Okada
- Center for AIDS Research, Kumamoto University, Japan
| | - Toshiki Watanabe
- Graduate School of Frontier Sciences, Department of Computational Biology and Medical Sciences, The University of Tokyo, Japan
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Aberrantly expressed miR-582-3p maintains lung cancer stem cell-like traits by activating Wnt/β-catenin signalling. Nat Commun 2015; 6:8640. [PMID: 26468775 PMCID: PMC4667703 DOI: 10.1038/ncomms9640] [Citation(s) in RCA: 90] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2015] [Accepted: 09/11/2015] [Indexed: 02/08/2023] Open
Abstract
Cancer stem cells (CSCs) are involved in tumorigenesis, tumour recurrence and therapy resistance and Wnt signalling is essential for the development of the biological traits of CSCs. In non-small cell lung carcinoma (NSCLC), unlike in colon cancer, mutations in β-catenin and APC genes are uncommon; thus, the mechanism underlying the constitutive activation of Wnt signalling in NSCLC remains unclear. Here we report that miR-582-3p expression correlates with the overall- and recurrence-free-survival of NSCLC patients, and miR-582-3p has an activating effect on Wnt/β-catenin signalling. miR-582-3p overexpression simultaneously targets multiple negative regulators of the Wnt/β-catenin pathway, namely, AXIN2, DKK3 and SFRP1. Consequently, miR-582-3p promotes CSC traits of NSCLC cells in vitro and tumorigenesis and tumour recurrence in vivo. Antagonizing miR-582-3p potently inhibits tumour initiation and progression in xenografted animal models. These findings suggest that miR-582-3p mediates the constitutive activation of Wnt/β-catenin signalling, likely serving as a potential therapeutic target for NSCLC. Despite the absence of frequent mutations of key components of Wnt/β-catenin signalling, this pathway is often constitutively activated in non-small cell lung carcinoma. In this study, the authors demonstrate the inhibitory effect of miR-582-3p on negative regulators of the Wnt/β-catenin pathway which is consequently triggered to sustain lung tumour growth.
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Chen W, Zhang B, Guo W, Gao L, Shi L, Li H, Lu S, Liu Y, Li X. miR-429 inhibits glioma invasion through BMK1 suppression. J Neurooncol 2015; 125:43-54. [PMID: 26272601 DOI: 10.1007/s11060-015-1887-x] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2015] [Accepted: 08/08/2015] [Indexed: 02/07/2023]
Abstract
The purpose of this research was to examine the relationship between big mitogen-activated protein kinase 1 (BMK1) and miRNA miR-429 and to determine the effect of miR-429 on glioma invasiveness. Immunohistochemistry was used to evaluate BMK1 expression in glioma tissues. Real-time PCR was used to measure the expression of miR-429 and other RNAs. Western blot was used to detect the expression of BMK1 and other related proteins. Wound healing, Matrigel invasion, and chemotaxis assays were performed to detect the invasion and migration of glioma cell lines. The actual binding site of miR-429 to the 3' untranslated region of BMK1 was confirmed by luciferase assay and RNA immunoprecipitation. BMK1 expression was associated with the World Health Organization grading of glioma and inversely correlated with patient survival. Suppression of BMK1 inhibited the migration and invasion of glioma cells by interfering with mesenchymal transition. Additionally, hepatocyte growth factor-induced GSK3β phosphorylation was suppressed through BMK1 knockdown. Interestingly, our findings validated a novel role for miR-429 in suppressing the migration and invasion of glioma by directly inhibiting BMK1 expression. We also found that miR-429 expression in glioma cells and tissues was lower than that in normal cells and adjacent non-neoplastic tissues, and miR-429 overexpression inhibited invasive activity of glioma cells both in vitro and in vivo. Furthermore, our data validated that miR-429 downregulation was due to the hypermethylation of its promoter region. Our results indicated that BMK1 modulation by miR-429 has an important function in glioma invasion both in vitro and in vivo.
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Affiliation(s)
- Weiyi Chen
- Department of Pathology, Weifang Medical University, Weifang, 261053, People's Republic of China
| | - Baogang Zhang
- Department of Pathology, Weifang Medical University, Weifang, 261053, People's Republic of China.
| | - Wenjun Guo
- Department of Pathology, Weifang Medical University, Weifang, 261053, People's Republic of China
| | - Linlin Gao
- Department of Internal Medicine, NO.3, Laixi Municipal Hospital, Laixi, 266600, People's Republic of China
| | - Lihong Shi
- Department of Pharmacology, Weifang Medical University, Weifang, 261053, People's Republic of China
| | - Hongli Li
- Department of Medicine Research Center, Weifang Medical University, Weifang, 261053, People's Republic of China
| | - Shijun Lu
- Department of Pathology, Weifang Medical University, Weifang, 261053, People's Republic of China
| | - Yuqing Liu
- Department of Pathology, Weifang Medical University, Weifang, 261053, People's Republic of China
| | - Xiaolong Li
- Department of Pathology, Weifang Medical University, Weifang, 261053, People's Republic of China
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Abuhatzira L, Xu H, Tahhan G, Boulougoura A, Schäffer AA, Notkins AL. Multiple microRNAs within the 14q32 cluster target the mRNAs of major type 1 diabetes autoantigens IA-2, IA-2β, and GAD65. FASEB J 2015; 29:4374-83. [PMID: 26148972 DOI: 10.1096/fj.15-273649] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2015] [Accepted: 06/30/2015] [Indexed: 12/25/2022]
Abstract
Islet antigen (IA)-2, IA-2β, and glutamate decarboxylase (GAD65) are major autoantigens in type 1 diabetes (T1D). Autoantibodies to these autoantigens appear years before disease onset and are widely used as predictive markers. Little is known, however, about what regulates the expression of these autoantigens. The present experiments were initiated to test the hypothesis that microRNAs (miRNAs) can target and affect the levels of these autoantigens. Bioinformatics was used to identify miRNAs predicted to target the mRNAs coding IA-2, IA-2β, and GAD65. RNA interference for the miRNA processing enzyme Dicer1 and individual miRNA mimics and inhibitors were used to confirm the effect in mouse islets and MIN6 cells. We show that the imprinted 14q32 miRNA cluster contains 56 miRNAs, 32 of which are predicted to target the mRNAs of T1D autoantigens and 12 of which are glucose-sensitive. Using miRNA mimics and inhibitors, we confirmed that at least 7 of these miRNAs modulate the mRNA levels of the T1D autoantigens. Dicer1 knockdown significantly reduced the mRNA levels of all 3 autoantigens, further confirming the importance of miRNAs in this regulation. We conclude that miRNAs are involved in regulating the expression of the major T1D autoantigens.
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Affiliation(s)
- Liron Abuhatzira
- *Experimental Medicine Section, Laboratory of Sensory Biology, National Institute of Dental and Craniofacial Research, and National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA
| | - Huanyu Xu
- *Experimental Medicine Section, Laboratory of Sensory Biology, National Institute of Dental and Craniofacial Research, and National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA
| | - Georges Tahhan
- *Experimental Medicine Section, Laboratory of Sensory Biology, National Institute of Dental and Craniofacial Research, and National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA
| | - Afroditi Boulougoura
- *Experimental Medicine Section, Laboratory of Sensory Biology, National Institute of Dental and Craniofacial Research, and National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA
| | - Alejandro A Schäffer
- *Experimental Medicine Section, Laboratory of Sensory Biology, National Institute of Dental and Craniofacial Research, and National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA
| | - Abner L Notkins
- *Experimental Medicine Section, Laboratory of Sensory Biology, National Institute of Dental and Craniofacial Research, and National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA
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Biswas A, Khanna S, Roy S, Pan X, Sen CK, Gordillo GM. Endothelial cell tumor growth is Ape/ref-1 dependent. Am J Physiol Cell Physiol 2015; 309:C296-307. [PMID: 26108661 DOI: 10.1152/ajpcell.00022.2015] [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: 01/26/2015] [Accepted: 06/17/2015] [Indexed: 01/12/2023]
Abstract
Tumor-forming endothelial cells have highly elevated levels of Nox-4 that release H2O2 into the nucleus, which is generally not compatible with cell survival. We sought to identify compensatory mechanisms that enable tumor-forming endothelial cells to survive and proliferate under these conditions. Ape-1/ref-1 (Apex-1) is a multifunctional protein that promotes DNA binding of redox-sensitive transcription factors, such as AP-1, and repairs oxidative DNA damage. A validated mouse endothelial cell (EOMA) tumor model was used to demonstrate that Nox-4-derived H2O2 causes DNA oxidation that induces Apex-1 expression. Apex-1 functions as a chaperone to keep transcription factors in a reduced state. In EOMA cells Apex-1 enables AP-1 binding to the monocyte chemoattractant protein-1 (mcp-1) promoter and expression of that protein is required for endothelial cell tumor formation. Intraperitoneal injection of the small molecule inhibitor E3330, which specifically targets Apex-1 redox-sensitive functions, resulted in a 50% decrease in tumor volume compared with mice injected with vehicle control (n = 6 per group), indicating that endothelial cell tumor proliferation is dependent on Apex-1 expression. These are the first reported results to establish Nox-4 induction of Apex-1 as a mechanism promoting endothelial cell tumor formation.
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Affiliation(s)
- Ayan Biswas
- Department of Plastic Surgery, The Ohio State University Wexner Medical Center, Columbus, Ohio; Davis Heart and Lung Research Institute, The Ohio State University Wexner Medical Center, Columbus, Ohio; and
| | - Savita Khanna
- Department of Surgery, The Ohio State University Wexner Medical Center, Columbus, Ohio; Davis Heart and Lung Research Institute, The Ohio State University Wexner Medical Center, Columbus, Ohio; and
| | - Sashwati Roy
- Department of Surgery, The Ohio State University Wexner Medical Center, Columbus, Ohio; Davis Heart and Lung Research Institute, The Ohio State University Wexner Medical Center, Columbus, Ohio; and
| | - Xueliang Pan
- Center for Biostatistics, The Ohio State University Wexner Medical Center, Columbus, Ohio
| | - Chandan K Sen
- Department of Surgery, The Ohio State University Wexner Medical Center, Columbus, Ohio; Davis Heart and Lung Research Institute, The Ohio State University Wexner Medical Center, Columbus, Ohio; and
| | - Gayle M Gordillo
- Department of Plastic Surgery, The Ohio State University Wexner Medical Center, Columbus, Ohio; Davis Heart and Lung Research Institute, The Ohio State University Wexner Medical Center, Columbus, Ohio; and
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Karnati HK, Raghuwanshi S, Sarvothaman S, Gutti U, Saladi RGV, Komati JK, Tummala PR, Gutti RK. microRNAs: Key Players in Hematopoiesis. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2015; 887:171-211. [DOI: 10.1007/978-3-319-22380-3_10] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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MiR-204 inhibits human NSCLC metastasis through suppression of NUAK1. Br J Cancer 2014; 111:2316-27. [PMID: 25412236 PMCID: PMC4264457 DOI: 10.1038/bjc.2014.580] [Citation(s) in RCA: 83] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2014] [Revised: 09/07/2014] [Accepted: 09/16/2014] [Indexed: 11/09/2022] Open
Abstract
Background: Lung cancer is a leading cause of cancer-related mortality worldwide and non-small-cell lung carcinoma (NSCLC) is responsible for almost 80% of lung cancer-related deaths. Identifying novel molecules that can repress the invasiveness and metastasis of lung cancer will facilitate the development of new antilung cancer strategies. The aim of this study is to determine the roles of NUAK1 (a downstream of Akt) and miR-204 in the invasiveness and metastasis of NSCLC and to reveal the correlation between NUAK1 and miR-204. Methods: The expression of NUAK1 in primary human NSCLC tissues was evaluated by immunohistochemistry. Real-time PCR was employed to measure the expression level of miR-204. The effect of NUAK1 and miR204 on the prognosis of NSCLC patients was evaluated by log-rank test. The siRNA transfection was used to manipulate the expression levels of NUAK1 and miR204 in cancer cells. Chemotaxis assay, Scratch assay, and Matrigel invasion assay were performed to evaluate the migration and invasion of cells. Cellular F-actin measurement was used to measure F-actin polymerisation in lung cancer cells. Western blot was used to detect the expression levels of corresponding proteins. The Luciferase assay and RNA immunoprecipitation were used to confirm the actual binding site of miR-204 to 3′UTR of NUAK1. Results: Increased expression of NUAK1 is correlated with the invasiveness and metastasis of human NSCLC. Knockdown of NUAK1 inhibited cell migration and invasion. In addition, this study showed that NUAK1 influenced mTOR phosphorylation and induced the phosphorylation of p70S6K1 and eukaryotic initiation factor 4E-binding protein1 (4E-BP1), two downstream targets of mTOR in NSCLC cells. At the same time, decreased expression of miR-204 promoted NSCLC progression and, contrarily, manipulated upregulation of miR-204-inhibited cell migration and invasion. There is clinical relevance between miR-204 downregulation and NUAK1 upregulation in human NSCLC. Furthermore, we found that miR-204 inhibited NSCLC tumour invasion by directly targeting and downregulating NUAK1 expression. Finally, our data suggested that the downregulation of miR-204 was due to hypermethylation of its promoter region. Conclusions: Our results indicate that NUAK1 is excessively expressed in NSCLC and plays important roles in NSCLC invasion. The miR-204 acts as a tumour suppressor by inhibiting NUAK1 expression in NSCLC. Both NUAK1 and miR-204 may serve as potential targets of NSCLC therapy.
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Ding Q, Yang LY. Perforin gene mutations in 77 Chinese patients with lymphomas. World J Emerg Med 2014; 4:128-32. [PMID: 25215106 PMCID: PMC4129835 DOI: 10.5847/wjem.j.issn.1920-8642.2013.02.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2012] [Accepted: 04/04/2013] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND: Perforin gene (PRF1) mutations have been reported in patients with lymphoma, but the prevalence and characteristics of PRF1 mutation have not been identified in Chinese patients with lymphoma. METHODS: Seventy-seven patients with lymphoma, including 6 patients with Hodgkin lymphoma and 71 patients with non-Hodgkin lymphoma, were recruited. DNA samples from peripheral blood were used for PRF1 mutation detection by the PCR-sequencing method. RESULTS: Eleven novel PRF1 mutations were found in 8 of the 77 patients with lymphoma. Biallelic or compound monoallelic missense mutations in 3 patients indicated the severe impairment of perforin function, monoallelic missense mutations in 3 patients possibly contributed a genetic predisposition to malignancies, and synonymous mutations in 2 patients showed unknown significance. CONCLUSIONS: The frequency of EBV infection was similar in lymphoma patients with PRF1 mutations and those without the mutations. The same PRF1 mutations were also found in DNA samples from nails or hair follicles from 4 patients with PRF1 mutations, suggesting that these mutations may be of germ-line origin.
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Affiliation(s)
- Qi Ding
- Department of Hematology, Peking University First Hospital, Beijing, China
| | - Li-Yun Yang
- Department of Hematology, Peking University First Hospital, Beijing, China ; Department of Clinical Laboratory, General Hospital of Armed Police, Beijing, China
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Androsavich JR, Chau BN. Non-inhibited miRNAs shape the cellular response to anti-miR. Nucleic Acids Res 2014; 42:6945-55. [PMID: 24810853 PMCID: PMC4066772 DOI: 10.1093/nar/gku344] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Identification of primary microRNA (miRNA) gene targets is critical for developing miRNA-based therapeutics and understanding their mechanisms of action. However, disentangling primary target derepression induced by miRNA inhibition from secondary effects on the transcriptome remains a technical challenge. Here, we utilized RNA immunoprecipitation (RIP) combined with competitive binding assays to identify novel primary targets of miR-122. These transcripts physically dissociate from AGO2-miRNA complexes when anti-miR is spiked into liver lysates. mRNA target displacement strongly correlated with expression changes in these genes following in vivo anti-miR dosing, suggesting that derepression of these targets directly reflects changes in AGO2 target occupancy. Importantly, using a metric based on weighted miRNA expression, we found that the most responsive mRNA target candidates in both RIP competition assays and expression profiling experiments were those with fewer alternative seed sites for highly expressed non-inhibited miRNAs. These data strongly suggest that miRNA co-regulation modulates the transcriptomic response to anti-miR. We demonstrate the practical utility of this ‘miR-target impact’ model, and encourage its incorporation, together with the RIP competition assay, into existing target prediction and validation pipelines.
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Affiliation(s)
- John R Androsavich
- Regulus Therapeutics Inc., 3545 John Hopkins Ct, San Diego, CA 92121, USA
| | - B Nelson Chau
- Regulus Therapeutics Inc., 3545 John Hopkins Ct, San Diego, CA 92121, USA
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Clark EA, Kalomoiris S, Nolta JA, Fierro FA. Concise review: MicroRNA function in multipotent mesenchymal stromal cells. Stem Cells 2014; 32:1074-82. [PMID: 24860868 PMCID: PMC10668871 DOI: 10.1002/stem.1623] [Citation(s) in RCA: 102] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Multipotent mesenchymal stromal cells (MSCs) are ideal candidates for different cellular therapies due to their simple isolation, extensive expansion potential, and low immunogenicity. For various therapeutic approaches, such as bone and cartilage repair, MSCs are expected to contribute by direct differentiation to replace the damaged tissue, while many other applications rely on the secretion of paracrine factors which modulate the immune response and promote angiogenesis. MicroRNAs (miRNAs), which target messenger RNA for cleavage or translational repression, have recently been shown to play critical functions in MSC to regulate differentiation, paracrine activity, and other cellular properties such as proliferation, survival, and migration. The global miRNA expression profile of MSC varies according to the tissue of origin, species, and detection methodology, while also certain miRNAs are consistently found in all types of MSC. The function in MSC of more than 60 different miRNAs has been recently described, which is the subject of this review. A special emphasis is given to miRNAs that have demonstrated a function in MSC in vivo. We also present in detail miRNAs with overlapping effects (i.e., common target genes) and discuss future directions to deepen our understanding of miRNA biology in MSC. These recent discoveries have opened the possibility of modulating miRNAs in MSC, in order to enhance their proregenerative, therapeutic potential.
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Gordillo GM, Biswas A, Khanna S, Pan X, Sinha M, Roy S, Sen CK. Dicer knockdown inhibits endothelial cell tumor growth via microRNA 21a-3p targeting of Nox-4. J Biol Chem 2014; 289:9027-38. [PMID: 24497637 DOI: 10.1074/jbc.m113.519264] [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
MicroRNAs (miR) are emerging as biomarkers and potential therapeutic targets in tumor management. Endothelial cell tumors are the most common soft tissue tumors in infants, yet little is known about the significance of miR in regulating their growth. A validated mouse endothelial cell (EOMA) tumor model was used to demonstrate that post-transcriptional gene silencing of dicer, the enzyme that converts pre-miR to mature miR, can prevent tumor formation in vivo. Tumors were formed in eight of eight mice injected with EOMA cells transfected with control shRNA but formed in only four of ten mice injected with EOMA cells transfected with dicer shRNA. Tumors that formed in the dicer shRNA group were significantly smaller than tumors in the control group. This response to dicer knockdown was mediated by up-regulated miR 21a-3p activity targeting the nox-4 3'-UTR. EOMA cells were transfected with miR 21a-3p mimic and luciferase reporter plasmids containing either intact nox-4 3'-UTR or with mutation of the proposed 3'-UTR miR21a-3p binding sites. Mean luciferase activity was decreased by 85% in the intact compared with the site mutated vectors (p < 0.01). Attenuated Nox-4 activity resulted in decreased cellular hydrogen peroxide production and decreased production of oxidant-inducible monocyte chemoattractant protein-1, which we have previously shown to be critically required for endothelial cell tumor formation. These findings provide the first evidence establishing the significance of dicer and microRNA in promoting endothelial cell tumor growth in vivo.
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