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Kotzur R, Stein N, Kahlon S, Berhani O, Isaacson B, Mandelboim O. Eradication of CD48-positive tumors by selectively enhanced YTS cells harnessing the lncRNA NeST. iScience 2023; 26:107284. [PMID: 37609636 PMCID: PMC10440710 DOI: 10.1016/j.isci.2023.107284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 05/30/2023] [Accepted: 06/30/2023] [Indexed: 08/24/2023] Open
Abstract
Natural killer (NK) cells are currently used in clinical trials to treat tumors. However, such therapies still suffer from problems such as donor variability, reproducibility, and more, which prevent a wider use of NK cells therapeutics. Here we show a potential immunotherapy combining NK cell-mediated tumor eradiation and long non-coding (lnc) RNAs. We overexpressed the interferon (IFN) γ secretion-enhancing lncRNA nettoie Salmonella pas Theiler's (NeST) in the NK cell-like cell line YTS. YTS cells express the co-stimulatory receptor 2B4 whose main ligand is CD48. On YTS cells, 2B4 functions by direct activation. We showed that NeST overexpression in YTS cells resulted in increased IFNγ release upon interaction with CD48 (selectively enhanced (se)YTS cells). Following irradiation, the seYTS cells lost proliferation capacity but were still able to maintain their killing and IFNγ secretion capacities. Finally, we demonstrated that irradiated seYTS inhibit tumor growth in vivo. Thus, we propose seYTS cells as off-the-shelve therapy for CD48-expressing tumors.
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Affiliation(s)
- Rebecca Kotzur
- The Lautenberg Center for Immunology and Cancer Research, the Hebrew University, Medical School Hadassah Ein Karem, Israel, Jerusalem
| | - Natan Stein
- The Lautenberg Center for Immunology and Cancer Research, the Hebrew University, Medical School Hadassah Ein Karem, Israel, Jerusalem
| | - Shira Kahlon
- The Lautenberg Center for Immunology and Cancer Research, the Hebrew University, Medical School Hadassah Ein Karem, Israel, Jerusalem
| | - Orit Berhani
- The Lautenberg Center for Immunology and Cancer Research, the Hebrew University, Medical School Hadassah Ein Karem, Israel, Jerusalem
| | - Batya Isaacson
- The Lautenberg Center for Immunology and Cancer Research, the Hebrew University, Medical School Hadassah Ein Karem, Israel, Jerusalem
| | - Ofer Mandelboim
- The Lautenberg Center for Immunology and Cancer Research, the Hebrew University, Medical School Hadassah Ein Karem, Israel, Jerusalem
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2
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Ghamlouche F, Yehya A, Zeid Y, Fakhereddine H, Fawaz J, Liu YN, Al-Sayegh M, Abou-Kheir W. MicroRNAs as clinical tools for diagnosis, prognosis, and therapy in prostate cancer. Transl Oncol 2023; 28:101613. [PMID: 36608541 PMCID: PMC9827391 DOI: 10.1016/j.tranon.2022.101613] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 12/05/2022] [Accepted: 12/24/2022] [Indexed: 01/06/2023] Open
Abstract
Prostate cancer (PCa) is one of the most commonly diagnosed cancers among men worldwide. Despite the presence of accumulated clinical strategies for PCa management, limited prognostic/sensitive biomarkers are available to follow up on disease occurrence and progression. MicroRNAs (miRNAs) are small non-coding RNAs that control gene expression through post-transcriptional regulation of their complementary target messenger RNA (mRNA). MiRNAs modulate fundamental biological processes and play crucial roles in the pathology of various diseases, including PCa. Multiple evidence proved an aberrant miRNA expression profile in PCa, which is actively involved in the carcinogenic process. The robust and pleiotropic impact of miRNAs on PCa suggests them as potential candidates to help more understand the molecular landscape of the disease, which is likely to provide tools for early diagnosis and prognosis as well as additional therapeutic strategies to manage prostate tumors. Here, we emphasize the most consistently reported dysregulated miRNAs and highlight the contribution of their altered downstream targets with PCa hallmarks. Also, we report the potential effectiveness of using miRNAs as diagnostic/prognostic biomarkers in PCa and the high-throughput profiling technologies that are being used in their detection. Another key aspect to be discussed in this review is the promising implication of miRNAs molecules as therapeutic tools and targets for fighting PCa.
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Affiliation(s)
- Fatima Ghamlouche
- Department of Anatomy, Cell Biology, and Physiological Sciences, Faculty of Medicine, American University of Beirut, Beirut 1107-2020, Lebanon
| | - Amani Yehya
- Department of Anatomy, Cell Biology, and Physiological Sciences, Faculty of Medicine, American University of Beirut, Beirut 1107-2020, Lebanon
| | - Yousef Zeid
- Department of Anatomy, Cell Biology, and Physiological Sciences, Faculty of Medicine, American University of Beirut, Beirut 1107-2020, Lebanon
| | - Hiam Fakhereddine
- Department of Anatomy, Cell Biology, and Physiological Sciences, Faculty of Medicine, American University of Beirut, Beirut 1107-2020, Lebanon
| | - Jhonny Fawaz
- Department of Anatomy, Cell Biology, and Physiological Sciences, Faculty of Medicine, American University of Beirut, Beirut 1107-2020, Lebanon
| | - Yen-Nien Liu
- International Ph.D. Program in Medicine, College of Medicine, Taipei Medical University, Taipei 110, Taiwan.
| | - Mohamed Al-Sayegh
- Biology Division, New York University Abu Dhabi, Abu Dhabi 2460, United Arab Emirates.
| | - Wassim Abou-Kheir
- Department of Anatomy, Cell Biology, and Physiological Sciences, Faculty of Medicine, American University of Beirut, Beirut 1107-2020, Lebanon.
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3
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Andrographolide Exhibits Anticancer Activity against Breast Cancer Cells (MCF-7 and MDA-MB-231 Cells) through Suppressing Cell Proliferation and Inducing Cell Apoptosis via Inactivation of ER-α Receptor and PI3K/AKT/mTOR Signaling. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27113544. [PMID: 35684480 PMCID: PMC9182433 DOI: 10.3390/molecules27113544] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 05/26/2022] [Accepted: 05/27/2022] [Indexed: 11/16/2022]
Abstract
Breast cancer is the most common cancer among women worldwide. Chemotherapy followed by endocrine therapy is the standard treatment strategy after surgery or radiotherapy. However, breast cancer is highly resistant to the treatments leading to the recurrence of breast cancer. As a result, the development of alternative medicines derived from natural plants with fewer side effects is being emphasized. Andrographolide isolated from Andrographis paniculata is one of the potential substances with anti-cancer properties in a variety of cell types, including breast cancer cells. This study aims to investigate the anti-cancer effects of andrographolide in breast cancer cells by evaluating cell viability and apoptosis as well as its underlying mechanisms through estrogen receptor (ER)-dependent and PI3K/AKT/mTOR signaling pathways. Cell viability, cell apoptosis, mRNA or miRNA, and protein expression were examined by MTT assay, Annexin V-FITC, qRT-PCR, and Western blot analysis, respectively. MCF-7 and MDA-MB-231 cell viability was reduced in a concentration- and time-dependent manner after andrographolide treatment. Moreover, andrographolide induced cell apoptosis in both MCF-7 and MDA-MB-231 cells by inhibiting Bcl-2 and enhancing Bax expression at both mRNA and protein levels. In MCF-7 cells, the ER-positive breast cancer, andrographolide showed an inhibitory effect on cell proliferation through downregulation of ERα, PI3K, and mTOR expression levels. Andrographolide also inhibited MDA-MB-231 breast cancer cell proliferation via induction of cell apoptosis. However, the inhibition of MCF-7 and MDA-MB-231 cell proliferation of andrographolide treatment did not disrupt miR-21. Our findings showed that andrographolide possesses an anti-estrogenic effect by suppressing cell proliferation in MCF-7 cells. The effects were comparable to those of the anticancer drug fulvestrant in MCF-7 cells. This study provides new insights into the anti-cancer effect of andrographolide on breast cancer and suggests andrographolide as a potential alternative from the natural plant for treating breast cancer types that are resistant to tamoxifen and fulvestrant.
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Gibert MK, Sarkar A, Chagari B, Roig-Laboy C, Saha S, Bednarek S, Kefas B, Hanif F, Hudson K, Dube C, Zhang Y, Abounader R. Transcribed Ultraconserved Regions in Cancer. Cells 2022; 11:1684. [PMID: 35626721 PMCID: PMC9139194 DOI: 10.3390/cells11101684] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Revised: 05/11/2022] [Accepted: 05/17/2022] [Indexed: 11/25/2022] Open
Abstract
Transcribed ultraconserved regions are putative lncRNA molecules that are transcribed from DNA that is 100% conserved in human, mouse, and rat genomes. This is notable, as lncRNAs are typically poorly conserved. TUCRs remain very understudied in many diseases, including cancer. In this review, we summarize the current literature on TUCRs in cancer with respect to expression deregulation, functional roles, mechanisms of action, and clinical perspectives.
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Affiliation(s)
- Myron K. Gibert
- Department of Microbiology, Immunology, and Cancer Biology, School of Medicine, University of Virginia, Charlottesville, VA 22908, USA; (M.K.G.J.); (A.S.); (B.C.); (C.R.-L.); (S.S.); (S.B.); (B.K.); (F.H.); (K.H.); (C.D.); (Y.Z.)
| | - Aditya Sarkar
- Department of Microbiology, Immunology, and Cancer Biology, School of Medicine, University of Virginia, Charlottesville, VA 22908, USA; (M.K.G.J.); (A.S.); (B.C.); (C.R.-L.); (S.S.); (S.B.); (B.K.); (F.H.); (K.H.); (C.D.); (Y.Z.)
| | - Bilhan Chagari
- Department of Microbiology, Immunology, and Cancer Biology, School of Medicine, University of Virginia, Charlottesville, VA 22908, USA; (M.K.G.J.); (A.S.); (B.C.); (C.R.-L.); (S.S.); (S.B.); (B.K.); (F.H.); (K.H.); (C.D.); (Y.Z.)
| | - Christian Roig-Laboy
- Department of Microbiology, Immunology, and Cancer Biology, School of Medicine, University of Virginia, Charlottesville, VA 22908, USA; (M.K.G.J.); (A.S.); (B.C.); (C.R.-L.); (S.S.); (S.B.); (B.K.); (F.H.); (K.H.); (C.D.); (Y.Z.)
| | - Shekhar Saha
- Department of Microbiology, Immunology, and Cancer Biology, School of Medicine, University of Virginia, Charlottesville, VA 22908, USA; (M.K.G.J.); (A.S.); (B.C.); (C.R.-L.); (S.S.); (S.B.); (B.K.); (F.H.); (K.H.); (C.D.); (Y.Z.)
| | - Sylwia Bednarek
- Department of Microbiology, Immunology, and Cancer Biology, School of Medicine, University of Virginia, Charlottesville, VA 22908, USA; (M.K.G.J.); (A.S.); (B.C.); (C.R.-L.); (S.S.); (S.B.); (B.K.); (F.H.); (K.H.); (C.D.); (Y.Z.)
| | - Benjamin Kefas
- Department of Microbiology, Immunology, and Cancer Biology, School of Medicine, University of Virginia, Charlottesville, VA 22908, USA; (M.K.G.J.); (A.S.); (B.C.); (C.R.-L.); (S.S.); (S.B.); (B.K.); (F.H.); (K.H.); (C.D.); (Y.Z.)
| | - Farina Hanif
- Department of Microbiology, Immunology, and Cancer Biology, School of Medicine, University of Virginia, Charlottesville, VA 22908, USA; (M.K.G.J.); (A.S.); (B.C.); (C.R.-L.); (S.S.); (S.B.); (B.K.); (F.H.); (K.H.); (C.D.); (Y.Z.)
| | - Kadie Hudson
- Department of Microbiology, Immunology, and Cancer Biology, School of Medicine, University of Virginia, Charlottesville, VA 22908, USA; (M.K.G.J.); (A.S.); (B.C.); (C.R.-L.); (S.S.); (S.B.); (B.K.); (F.H.); (K.H.); (C.D.); (Y.Z.)
| | - Collin Dube
- Department of Microbiology, Immunology, and Cancer Biology, School of Medicine, University of Virginia, Charlottesville, VA 22908, USA; (M.K.G.J.); (A.S.); (B.C.); (C.R.-L.); (S.S.); (S.B.); (B.K.); (F.H.); (K.H.); (C.D.); (Y.Z.)
| | - Ying Zhang
- Department of Microbiology, Immunology, and Cancer Biology, School of Medicine, University of Virginia, Charlottesville, VA 22908, USA; (M.K.G.J.); (A.S.); (B.C.); (C.R.-L.); (S.S.); (S.B.); (B.K.); (F.H.); (K.H.); (C.D.); (Y.Z.)
| | - Roger Abounader
- Department of Microbiology, Immunology, and Cancer Biology, School of Medicine, University of Virginia, Charlottesville, VA 22908, USA; (M.K.G.J.); (A.S.); (B.C.); (C.R.-L.); (S.S.); (S.B.); (B.K.); (F.H.); (K.H.); (C.D.); (Y.Z.)
- Department of Neurology, School of Medicine, University of Virginia, Charlottesville, VA 22908, USA
- NCI Designated Comprehensive Cancer Center, University of Virginia, Charlottesville, VA 22908, USA
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Vannini I, Ferracin M, Fabbri F, Fabbri M. Overexpression of ultraconserved region 83- induces lung cancer tumorigenesis. PLoS One 2022; 17:e0261464. [PMID: 35015757 PMCID: PMC8752010 DOI: 10.1371/journal.pone.0261464] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 12/02/2021] [Indexed: 01/12/2023] Open
Abstract
The expression of non-coding RNAs (ncRNAs) is dysregulated in human cancers. The transcribed ultraconserved regions (T-UCRs) express long ncRNAs involved in human carcinogenesis. T-UCRs are non-coding genomic sequence that are 100% conserved across humans, rats and mice. Conservation of genomic sequences across species intrinsically implies an essential functional role and so we considered the expression of T-UCRs in lung cancer. Using a custom microarray we analyzed the global expression of T-UCRs. Among these T-UCRs, the greatest variation was observed for antisense ultraconserved element 83 (uc.83-), which was upregulated in human lung cancer tissues compared with adjacent non cancerous tissues. Even though uc.83- is located within the long intergenic non-protein coding RNA 1876 (LINC01876) gene, we found that the transcribed uc.83- is expressed independently of LINC01876 and was cloned as a 1143-bp RNA gene. In this study, functional analysis confirmed important effects of uc.83- on genes involved in cell growth of human cells. siRNA against uc.83- decreased the growth of lung cancer cells while the upregulation through a vector overexpressing the uc.83- RNA increased cell proliferation. We also show the oncogenic function of uc.83- is mediated by the phosphorylation of AKT and ERK 1/2, two important biomarkers of lung cancer cell proliferation. Based on our findings, inhibition against uc.83- could be a future therapeutic treatment for NSCLC to achieve simultaneous blockade of pathways involved in lung carcinogenesis.
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Affiliation(s)
- Ivan Vannini
- Biosciences Laboratory, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori", Meldola, Italy
| | - Manuela Ferracin
- Department of Experimental, Diagnostic and Specialty Medicine—DIMES, University of Bologna, Bologna, Italy
| | - Francesco Fabbri
- Biosciences Laboratory, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori", Meldola, Italy
| | - Muller Fabbri
- Center for Cancer and Immunology Research, Children’s National Hospital, Washington, DC, United States of America
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Mirahmadi Y, Nabavi R, Taheri F, Samadian MM, Ghale-Noie ZN, Farjami M, Samadi-khouzani A, Yousefi M, Azhdari S, Salmaninejad A, Sahebkar A. MicroRNAs as Biomarkers for Early Diagnosis, Prognosis, and Therapeutic Targeting of Ovarian Cancer. JOURNAL OF ONCOLOGY 2021; 2021:3408937. [PMID: 34721577 PMCID: PMC8553480 DOI: 10.1155/2021/3408937] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 09/27/2021] [Indexed: 02/06/2023]
Abstract
Ovarian cancer is the major cause of gynecologic cancer-related mortality. Regardless of outstanding advances, which have been made for improving the prognosis, diagnosis, and treatment of ovarian cancer, the majority of the patients will die of the disease. Late-stage diagnosis and the occurrence of recurrent cancer after treatment are the most important causes of the high mortality rate observed in ovarian cancer patients. Unraveling the molecular mechanisms involved in the pathogenesis of ovarian cancer may help find new biomarkers and therapeutic targets for ovarian cancer. MicroRNAs (miRNAs) are small noncoding RNAs that regulate gene expression, mostly at the posttranscriptional stage, through binding to mRNA targets and inducing translational repression or degradation of target via the RNA-induced silencing complex. Over the last two decades, the role of miRNAs in the pathogenesis of various human cancers, including ovarian cancer, has been documented in multiple studies. Consequently, these small RNAs could be considered as reliable markers for prognosis and early diagnosis. Furthermore, given the function of miRNAs in various cellular pathways, including cell survival and differentiation, targeting miRNAs could be an interesting approach for the treatment of human cancers. Here, we review our current understanding of the most updated role of the important dysregulation of miRNAs and their roles in the progression and metastasis of ovarian cancer. Furthermore, we meticulously discuss the significance of miRNAs as prognostic and diagnostic markers. Lastly, we mention the opportunities and the efforts made for targeting ovarian cancer through inhibition and/or stimulation of the miRNAs.
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Affiliation(s)
- Yegane Mirahmadi
- Department of Medical Genetics, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
- Medical Genetics Research Centre, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | | | - Fourough Taheri
- Department of Biology, Faculty of Basic Sciences, Shahrekord Branch, Islamic Azad University, Shahrekord, Iran
| | - Mohammad Mahdi Samadian
- Department of Medical Genetics, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Zari Naderi Ghale-Noie
- Department of Medical Genetics, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
- Medical Genetics Research Centre, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mahsa Farjami
- Department of Medical Genetics, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
- Medical Genetics Research Centre, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Abbas Samadi-khouzani
- Department of Biology, Faculty of Basic Sciences, Shahrekord Branch, Islamic Azad University, Shahrekord, Iran
| | - Meysam Yousefi
- Department of Medical Genetics, Faculty of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Sara Azhdari
- Department of Anatomy and Embryology, School of Medicine, Bam University of Medical Sciences, Bam, Iran
| | - Arash Salmaninejad
- Department of Medical Genetics, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
- Medical Genetics Research Centre, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
- Department of Medical Genetics, Faculty of Medicine, Guilan University of Medical Sciences, Guilan, Iran
| | - Amirhossein Sahebkar
- Applied Biomedical Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
- Biotechnology Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran
- School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
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Pereira Zambalde E, Bayraktar R, Schultz Jucoski T, Ivan C, Rodrigues AC, Mathias C, knutsen E, Silveira de Lima R, Fiori Gradia D, de Souza Fonseca Ribeiro EM, Hannash S, Adrian Calin G, Carvalhode Oliveira J. A novel lncRNA derived from an ultraconserved region: lnc- uc.147, a potential biomarker in luminal A breast cancer. RNA Biol 2021; 18:416-429. [PMID: 34387142 PMCID: PMC8677017 DOI: 10.1080/15476286.2021.1952757] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Revised: 06/02/2021] [Accepted: 07/04/2021] [Indexed: 02/06/2023] Open
Abstract
The human genome contains 481 ultraconserved regions (UCRs), which are genomic stretches of over 200 base pairs conserved among human, rat, and mouse. The majority of these regions are transcriptionally active (T-UCRs), and several have been found to be differentially expressed in tumours. Some T-UCRs have been functionally characterized, but of those few have been associated to breast cancer (BC). Using TCGA data, we found 302 T-UCRs related to clinical features in BC: 43% were associated with molecular subtypes, 36% with oestrogen-receptor positivity, 17% with HER2 expression, 12% with stage, and 10% with overall survival. The expression levels of 12 T-UCRs were further analysed in a cohort of 82 Brazilian BC patients using RT-qPCR. We found that uc.147 is high expressed in luminal A and B patients. For luminal A, a subtype usually associated with better prognosis, high uc.147 expression was associated with a poor prognosis and suggested as an independent prognostic factor. The lncRNA from uc.147 (lnc-uc.147) is located in the nucleus. Northern blotting results show that uc.147 is a 2,8 kb monoexonic trancript, and its sequence was confirmed by RACE. The silencing of uc.147 increases apoptosis, arrests cell cycle, and reduces cell viability and colony formation in BC cell lines. Additionally, we identifed 19 proteins that interact with lnc-uc.147 through mass spectrometry and demonstrated a high correlation of lnc-uc.147 with the neighbour gene expression and miR-18 and miR-190b. This is the first study to analyse the expression of all T-UCRs in BC and to functionally assess the lnc-uc.147.
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Affiliation(s)
- Erika Pereira Zambalde
- Laboratory of Human Cytogenetics and Oncogenetics, Department of Genetics, Universidade Federal Do Paraná, Curitiba, PR, Brazil
- Department of Experimental Therapeutics, MD Anderson Cancer Center, University of Texas, Houston, TX, USA
| | - Recep Bayraktar
- Department of Experimental Therapeutics, MD Anderson Cancer Center, University of Texas, Houston, TX, USA
| | - Tayana Schultz Jucoski
- Laboratory of Human Cytogenetics and Oncogenetics, Department of Genetics, Universidade Federal Do Paraná, Curitiba, PR, Brazil
| | - Cristina Ivan
- Center for RNA Interference and Non-coding RNAs, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ana Carolina Rodrigues
- Laboratory of Human Cytogenetics and Oncogenetics, Department of Genetics, Universidade Federal Do Paraná, Curitiba, PR, Brazil
| | - Carolina Mathias
- Laboratory of Human Cytogenetics and Oncogenetics, Department of Genetics, Universidade Federal Do Paraná, Curitiba, PR, Brazil
| | - Erik knutsen
- Department of Experimental Therapeutics, MD Anderson Cancer Center, University of Texas, Houston, TX, USA
- Department of Medical Biology, Faculty of Health Sciences, UiT - the Arctic University of Norway, Tromsø, Norway
| | | | - Daniela Fiori Gradia
- Laboratory of Human Cytogenetics and Oncogenetics, Department of Genetics, Universidade Federal Do Paraná, Curitiba, PR, Brazil
| | | | - Samir Hannash
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - George Adrian Calin
- Department of Experimental Therapeutics, MD Anderson Cancer Center, University of Texas, Houston, TX, USA
- Center for RNA Interference and Non-coding RNAs, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jaqueline Carvalhode Oliveira
- Laboratory of Human Cytogenetics and Oncogenetics, Department of Genetics, Universidade Federal Do Paraná, Curitiba, PR, Brazil
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8
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liu Y, Geng H, Liu X, Cao M, Zhang X. A meta-analysis of circulating microRNAs in the diagnosis of papillary thyroid carcinoma. PLoS One 2021; 16:e0251676. [PMID: 34019567 PMCID: PMC8139519 DOI: 10.1371/journal.pone.0251676] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Accepted: 04/29/2021] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND Aim of this meta-analysis was to evaluate the overall diagnostic value of circulating mini miRNAs for papillary thyroid carcinoma (PTC) and to find the possible molecular marker with higher diagnostic value for PTC. METHODS We searched the Pubmed, Cochrane and Embase database until June 2020. We selected relevant literatures associated with the diagnosis of PTC with circulating miRNAs. The number of cases in experimental group and the control group, sensitivity and specificity could be extracted from the literatures. RESULTS We got 9 literatures including 2114 cases of PTC. Comprehensive sensitivity was 0.79, comprehensive specificity was 0.82, positive likelihood ratio was 4.3, negative likelihood ratio was 0.26, diagnostic advantage ratio was 16. The summary receiver operating characteristic curve was drawn and the Area Under the Curve was 0.87. CONCLUSIONS Circulating microRNAs may be promising molecular markers for the diagnosis of papillary thyroid carcinoma. Combined detection of certain serum microRNAs can improve the diagnostic accuracy of papillary thyroid carcinoma. Especially MiR-222 and miR-146b may be prime candidates for the diagnosis of PTC in Asian population.
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Affiliation(s)
- Yan liu
- Shandong First Medical University & Shandong Academy of Medical Science, Tai’an, China
| | - Houfa Geng
- Department of Endocrinology, Xuzhou Central Hospital, Affiliated Hospital of Medical School of Southeast University, Xuzhou, China
| | - Xuekui Liu
- Department of Endocrinology, Xuzhou Central Hospital, Affiliated Hospital of Medical School of Southeast University, Xuzhou, China
| | - Mingfeng Cao
- Department of Endocrinology, The Second Affiliated Hospital of Shandong First Medical University & Shandong Academy of Medical Science, Tai’an, China
| | - Xinhuan Zhang
- Department of Endocrinology, The Second Affiliated Hospital of Shandong First Medical University & Shandong Academy of Medical Science, Tai’an, China
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9
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Ferrari L, Carugno M, Mensi C, Pesatori AC. Circulating Epigenetic Biomarkers in Malignant Pleural Mesothelioma: State of the Art and critical Evaluation. Front Oncol 2020; 10:445. [PMID: 32318342 PMCID: PMC7146237 DOI: 10.3389/fonc.2020.00445] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Accepted: 03/13/2020] [Indexed: 12/18/2022] Open
Abstract
Malignant pleural mesothelioma (MPM) is a rare and aggressive cancer, which originates from the mesothelial cells of the pleura and is associated with asbestos exposure. In light of its aggressive nature, late diagnosis and dismal prognosis, there is an urgent need for identification of biomarkers in easily accessible samples (such as blood) for early diagnosis of MPM. In the last 10 years, epigenetic markers, such as DNA methylation and microRNAs (miRNAs), have gained popularity as possible early diagnostic and prognostic biomarkers in cancer research. The aim of this review is to provide a critical analysis of the current evidences on circulating epigenetic biomarkers for MPM and on their translational potential to the clinical practice for early diagnosis and for prognosis.
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Affiliation(s)
- Luca Ferrari
- EPIGET LAB, Department of Clinical Sciences and Community Health, Università degli Studi di Milano, Milan, Italy
| | - Michele Carugno
- EPIGET LAB, Department of Clinical Sciences and Community Health, Università degli Studi di Milano, Milan, Italy.,Epidemiology Unit, Department of Preventive Medicine, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Carolina Mensi
- Epidemiology Unit, Department of Preventive Medicine, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Angela Cecilia Pesatori
- EPIGET LAB, Department of Clinical Sciences and Community Health, Università degli Studi di Milano, Milan, Italy.,Epidemiology Unit, Department of Preventive Medicine, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
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10
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The Transcribed-Ultra Conserved Regions: Novel Non-Coding RNA Players in Neuroblastoma Progression. Noncoding RNA 2019; 5:ncrna5020039. [PMID: 31167408 PMCID: PMC6631508 DOI: 10.3390/ncrna5020039] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Revised: 05/30/2019] [Accepted: 06/03/2019] [Indexed: 12/15/2022] Open
Abstract
The Transcribed-Ultra Conserved Regions (T-UCRs) are a class of novel non-coding RNAs that arise from the dark matter of the genome. T-UCRs are highly conserved between mouse, rat, and human genomes, which might indicate a definitive role for these elements in health and disease. The growing body of evidence suggests that T-UCRs contribute to oncogenic pathways. Neuroblastoma is a type of childhood cancer that is challenging to treat. The role of non-coding RNAs in the pathogenesis of neuroblastoma, in particular for cancer development, progression, and therapy resistance, has been documented. Exosmic non-coding RNAs are also involved in shaping the biology of the tumor microenvironment in neuroblastoma. In recent years, the involvement of T-UCRs in a wide variety of pathways in neuroblastoma has been discovered. Here, we present an overview of the involvement of T-UCRs in various cellular pathways, such as DNA damage response, proliferation, chemotherapy response, MYCN (v-myc myelocytomatosis viral related oncogene, neuroblastoma derived (avian)) amplification, gene copy number, and immune response, as well as correlate it to patient survival in neuroblastoma.
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11
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Mahmoudian-Sani MR, Jalali A, Jamshidi M, Moridi H, Alghasi A, Shojaeian A, Mobini GR. Long Non-Coding RNAs in Thyroid Cancer: Implications for Pathogenesis, Diagnosis, and Therapy. Oncol Res Treat 2019; 42:136-142. [PMID: 30799425 DOI: 10.1159/000495151] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Accepted: 10/21/2018] [Indexed: 12/16/2022]
Abstract
Thyroid cancer is a rare malignancy and accounts for less than 1% of malignant neoplasms in humans; however, it is the most common cancer of the endocrine system and responsible for most deaths from endocrine cancer. Long non-coding (Lnc)RNAs are defined as non-coding transcripts that are more than 200 nucleotides in length. Their expression deregulation plays an important role in the progress of cancer. These molecules are involved in physiologic cellular processes, genomic imprinting, inactivation of chromosome X, maintenance of pluripotency, and the formation of different organs via changes in chromatin, transcription, and translation. LncRNAs can act as a tumor suppressor genes or oncogenes. Several studies have shown that these molecules can interact with microRNAs and prevent their binding to messenger RNAs. Research has shown that these molecules play an important role in tumorigenicity, angiogenesis, proliferation, migration, apoptosis, and differentiation. In thyroid cancer, several lncRNAs (MALAT1, H19, BANCR, HOTAIR) have been identified as contributing factors to cancer development, and can be used as novel biomarkers for early diagnosis or even treatment. In this article, we study the newest lncRNAs and their role in thyroid cancer.
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12
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Abdollahzadeh S, Ghorbian S. Association of the study between LncRNA-H19 gene polymorphisms with the risk of breast cancer. J Clin Lab Anal 2018; 33:e22826. [PMID: 30485527 DOI: 10.1002/jcla.22826] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Revised: 10/08/2018] [Accepted: 11/04/2018] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND The H19 is a maternally expressed imprinted gene transcribing a long noncoding RNA (lncRNA), which has previously been reported to be involved in tumorigenesis and cancer progression. The aim of this study was to evaluate the associations between two lncRNA-H19 (rs3741219 T>C and rs217727 C>T) gene polymorphisms with the risk of breast cancer (BC). METHODS In a case-control investigation, we evaluated 150 BC patients and 100 cancer-free subjects in East Azerbaijan Province of Iran. To assess two gene polymorphisms, the polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method was used. RESULTS The genotype frequencies of two lncRNA-H19 (rs217727 C>T and rs3741219 T>C) gene polymorphisms TT + TC/CC and CC + CT/TT have not shown a statistically significant association with the risk of BC (P = 0.065; OR = 0.967; 95% CI, 0.938-0.996) and (P = 0.510; OR = 1.583; 95% CI, 0.399-6.726), respectively. In addition, our findings revealed a significant differences in allele frequencies in lncRNA-H19 rs217727 C>T polymorphism between groups (P = 0.033; OR = 1.985; 95% CI, 1.048-3.761). CONCLUSION Our findings suggested that rs217727 C>T polymorphism may be involved in the pathogenesis of BC, whereas rs3741219 T>C variation may not be involved in the genetic background of BC in Iranian.
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Affiliation(s)
- Safa Abdollahzadeh
- Department of Molecular Genetics, Ahar Branch, Islamic Azad University, Ahar, Iran
| | - Saeid Ghorbian
- Department of Molecular Genetics, Ahar Branch, Islamic Azad University, Ahar, Iran
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13
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O'Leary VB, Maugg D, Smida J, Baumhoer D, Nathrath M, Ovsepian SV, Atkinson MJ. The long non-coding RNA PARTICLE is associated with WWOX and the absence of FRA16D breakage in osteosarcoma patients. Oncotarget 2017; 8:87431-87441. [PMID: 29152092 PMCID: PMC5675644 DOI: 10.18632/oncotarget.21086] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Accepted: 08/31/2017] [Indexed: 01/18/2023] Open
Abstract
Breakage of the fragile site FRA16D disrupts the WWOX (WW Domain Containing Oxidoreductase) tumor suppressor gene in osteosarcoma. However, the frequency of breakage is not sufficient to explain the rate of WWOX loss in pathogenesis. The involvement of non-coding RNA transcripts is proposed due to their accumulation at fragile sites, where they are advocated to influence specific chromosomal regions associated with malignancy. The long ncRNA PARTICLE (promoter of MAT2A antisense radiation-induced circulating long non-coding RNA) is transiently elevated in response to irradiation and influences epigenetic silencing modification within WWOX. It now emerges that elevated PARTICLE levels are significantly associated with FRA16D non-breakage in OS patients. Although not associated with overall survival, high PARTICLE levels were found to be significantly linked to metastasis free outcome. The transcription of both PARTICLE and WWOX are transiently responsive to exposure to low doses of radiation in osteosarcoma cell lines. Herein, a relationship between WWOX and PARTICLE transcription is suggested in human osteosarcoma cell lines representing alternative genetic backgrounds. PARTICLE over-expression ameliorated WWOX promoter activity in U2OS harboring FRA16D non-breakage. It can be concluded that the lncRNA PARTICLE influences the WWOX tumor suppressor and in the absence of WWOX FRA16D breakage, it is associated with OS metastasis-free survival.
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Affiliation(s)
- Valerie Bríd O'Leary
- Institute of Radiation Biology, Helmholtz Zentrum Munich-German Research Center for Environmental Health, Neuherberg, Germany
| | - Doris Maugg
- Institute of Radiation Biology, Helmholtz Zentrum Munich-German Research Center for Environmental Health, Neuherberg, Germany.,Department of Pediatrics and Children's Cancer Research Center, Technical University Munich, Munich, Germany
| | - Jan Smida
- Institute of Radiation Biology, Helmholtz Zentrum Munich-German Research Center for Environmental Health, Neuherberg, Germany
| | - Daniel Baumhoer
- Bone Tumour Reference Center, Institute of Pathology, University Hospital Basel, Basel, Switzerland
| | - Michaela Nathrath
- Department of Pediatrics and Children's Cancer Research Center, Technical University Munich, Munich, Germany.,Pediatric Hematology and Oncology, Klinikum Kassel, Kassel, Germany
| | - Saak Victor Ovsepian
- Institute of Biological and Medical Imaging, Helmholtz Zentrum Munich-German Research Center for Environmental Health, Neuherberg, Germany.,Faculty for Electrical Engineering and Information Technology, Technical University Munich, Munich, Germany.,International Centre for Neurotherapeutics, Glasnevin, Dublin, Republic of Ireland
| | - Michael John Atkinson
- Institute of Radiation Biology, Helmholtz Zentrum Munich-German Research Center for Environmental Health, Neuherberg, Germany.,Chair of Radiation Biology, Technical University Munich, Munich, Germany
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14
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Deb B, Uddin A, Chakraborty S. miRNAs and ovarian cancer: An overview. J Cell Physiol 2017; 233:3846-3854. [PMID: 28703277 DOI: 10.1002/jcp.26095] [Citation(s) in RCA: 133] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Accepted: 07/11/2017] [Indexed: 12/16/2022]
Abstract
Ovarian cancer (OC) is the sixth most common cancer in women globally. However, even with the advances in detection and therapeutics it still represents the most dangerous gynecologic malignancy in women of the industrialized countries. The discovery of micro-RNAs (miRNA), a small noncoding RNA molecule targeting multiple mRNAs and regulation of gene expression by triggering translation repression and/or RNA degradation, has revealed the existence of a new array for regulation of genes involved in cancer. This review summarizes the current knowledge regarding the role of miRNAs expression in OC. It also provides information about potential clinical relevance of circulating miRNAs for OC diagnosis, prognosis, and therapeutics. The identification of functional targets for miRNAs represents a major obstacle in our understanding of microRNA function in OC, but significant progress is being made. The better understanding of the role of microRNA expression in ovarian cancer may provide new array for the detection, diagnosis, and therapy of the OC.
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Affiliation(s)
- Bornali Deb
- Department of Biotechnology, Assam University, Silchar, India
| | - Arif Uddin
- Department of Zoology, Moinul Hoque Choudhury Memorial Science College, Algapur, Hailakandi, India
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15
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Understanding the Genomic Ultraconservations: T-UCRs and Cancer. MIRNAS IN DIFFERENTIATION AND DEVELOPMENT 2017; 333:159-172. [DOI: 10.1016/bs.ircmb.2017.04.004] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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16
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Chi MN, Guo ST, Wilmott JS, Guo XY, Yan XG, Wang CY, Liu XY, Jin L, Tseng HY, Liu T, Croft A, Hondermarck H, Scolyer RA, Jiang CC, Zhang XD. INPP4B is upregulated and functions as an oncogenic driver through SGK3 in a subset of melanomas. Oncotarget 2016; 6:39891-907. [PMID: 26573229 PMCID: PMC4741868 DOI: 10.18632/oncotarget.5359] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2015] [Accepted: 10/27/2015] [Indexed: 01/15/2023] Open
Abstract
Inositol polyphosphate 4-phosphatase type II (INPP4B) negatively regulates PI3K/Akt signalling and has a tumour suppressive role in some types of cancers. However, we have found that it is upregulated in a subset of melanomas. Here we report that INPP4B can function as an oncogenic driver through activation of serum- and glucocorticoid-regulated kinase 3 (SGK3) in melanoma. While INPP4B knockdown inhibited melanoma cell proliferation and retarded melanoma xenograft growth, overexpression of INPP4B enhanced melanoma cell and melanocyte proliferation and triggered anchorage-independent growth of melanocytes. Noticeably, INPP4B-mediated melanoma cell proliferation was not related to activation of Akt, but was mediated by SGK3. Upregulation of INPP4B in melanoma cells was associated with loss of miRNA (miR)-494 and/or miR-599 due to gene copy number reduction. Indeed, overexpression of miR-494 or miR-599 downregulated INPP4B, reduced SGK3 activation, and inhibited melanoma cell proliferation, whereas introduction of anti-miR-494 or anti-miR-599 upregulated INPP4B, enhanced SGK3 activation, and promoted melanoma cell proliferation. Collectively, these results identify upregulation of INPP4B as an oncogenic mechanism through activation of SGK3 in a subset of melanomas, with implications for targeting INPP4B and restoring miR-494 and miR-599 as novel approaches in the treatment of melanomas with high INPP4B expression.
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Affiliation(s)
- Meng Na Chi
- School of Medicine and Public Health, The University of Newcastle, NSW 2308, Australia
| | - Su Tang Guo
- School of Biomedical Sciences and Pharmacy, The University of Newcastle, NSW 2308, Australia.,Department of Molecular Biology, Shanxi Cancer Hospital and Institute, Affiliated Hospital of Shanxi Medical University, Taiyuan, Shanxi 030013, China
| | - James S Wilmott
- Discipline of Pathology, The University of Sydney, and Tissue Pathology and Diagnostic Oncology, Royal Prince Alfred Hospital, Sydney, NSW 2006, Australia
| | - Xiang Yun Guo
- Department of Molecular Biology, Shanxi Cancer Hospital and Institute, Affiliated Hospital of Shanxi Medical University, Taiyuan, Shanxi 030013, China
| | - Xu Guang Yan
- School of Medicine and Public Health, The University of Newcastle, NSW 2308, Australia
| | - Chun Yan Wang
- School of Biomedical Sciences and Pharmacy, The University of Newcastle, NSW 2308, Australia.,Department of Molecular Biology, Shanxi Cancer Hospital and Institute, Affiliated Hospital of Shanxi Medical University, Taiyuan, Shanxi 030013, China
| | - Xiao Ying Liu
- School of Biomedical Sciences and Pharmacy, The University of Newcastle, NSW 2308, Australia
| | - Lei Jin
- School of Medicine and Public Health, The University of Newcastle, NSW 2308, Australia
| | - Hsin-Yi Tseng
- School of Biomedical Sciences and Pharmacy, The University of Newcastle, NSW 2308, Australia
| | - Tao Liu
- Children's Cancer Institute Australia for Medical Research, The University of New South Wales, Sydney, NSW 2052, Australia
| | - Amanda Croft
- School of Biomedical Sciences and Pharmacy, The University of Newcastle, NSW 2308, Australia
| | - Hubert Hondermarck
- School of Biomedical Sciences and Pharmacy, The University of Newcastle, NSW 2308, Australia
| | - Richard A Scolyer
- Discipline of Pathology, The University of Sydney, and Tissue Pathology and Diagnostic Oncology, Royal Prince Alfred Hospital, Sydney, NSW 2006, Australia
| | - Chen Chen Jiang
- School of Medicine and Public Health, The University of Newcastle, NSW 2308, Australia
| | - Xu Dong Zhang
- School of Medicine and Public Health, The University of Newcastle, NSW 2308, Australia.,School of Biomedical Sciences and Pharmacy, The University of Newcastle, NSW 2308, Australia
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17
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Ropio J, Merlio JP, Soares P, Chevret E. Telomerase Activation in Hematological Malignancies. Genes (Basel) 2016; 7:genes7090061. [PMID: 27618103 PMCID: PMC5039560 DOI: 10.3390/genes7090061] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Revised: 07/15/2016] [Accepted: 07/29/2016] [Indexed: 12/18/2022] Open
Abstract
Telomerase expression and telomere maintenance are critical for cell proliferation and survival, and they play important roles in development and cancer, including hematological malignancies. Transcriptional regulation of the rate-limiting subunit of human telomerase reverse transcriptase gen (hTERT) is a complex process, and unveiling the mechanisms behind its reactivation is an important step for the development of diagnostic and therapeutic applications. Here, we review the main mechanisms of telomerase activation and the associated hematologic malignancies.
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Affiliation(s)
- Joana Ropio
- Cutaneous Lymphoma Oncogenesis Team INSERM U1053 Bordeaux Research in Translational Oncology, Bordeaux University, Bordeaux 33076, France.
- Institute of Biomedical Sciences of Abel Salazar, University of Porto, Porto 4050-313, Portugal.
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto 4200-135, Portugal.
- Institute of Molecular Pathology and Immunology of the University of Porto (Ipatimup)-Cancer Biology, Rua Dr. Roberto Frias, s/n, Porto 4200-465, Portugal.
| | - Jean-Philippe Merlio
- Cutaneous Lymphoma Oncogenesis Team INSERM U1053 Bordeaux Research in Translational Oncology, Bordeaux University, Bordeaux 33076, France.
- Tumor Bank and Tumor Biology Laboratory, University Hospital Center Bordeaux, Pessac 33604, France.
| | - Paula Soares
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto 4200-135, Portugal.
- Institute of Molecular Pathology and Immunology of the University of Porto (Ipatimup)-Cancer Biology, Rua Dr. Roberto Frias, s/n, Porto 4200-465, Portugal.
- Department of Pathology and Oncology, Medical Faculty of Porto University, Porto 4200-319, Portugal.
| | - Edith Chevret
- Cutaneous Lymphoma Oncogenesis Team INSERM U1053 Bordeaux Research in Translational Oncology, Bordeaux University, Bordeaux 33076, France.
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18
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Ahadi A, Brennan S, Kennedy PJ, Hutvagner G, Tran N. Long non-coding RNAs harboring miRNA seed regions are enriched in prostate cancer exosomes. Sci Rep 2016; 6:24922. [PMID: 27102850 PMCID: PMC4840345 DOI: 10.1038/srep24922] [Citation(s) in RCA: 127] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2015] [Accepted: 03/21/2016] [Indexed: 12/22/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) form the largest transcript class in the human transcriptome. These lncRNA are expressed not only in the cells, but they are also present in the cell-derived extracellular vesicles such as exosomes. The function of these lncRNAs in cancer biology is not entirely clear, but they appear to be modulators of gene expression. In this study, we characterize the expression of lncRNAs in several prostate cancer exosomes and their parental cell lines. We show that certain lncRNAs are enriched in cancer exosomes with the overall expression signatures varying across cell lines. These exosomal lncRNAs are themselves enriched for miRNA seeds with a preference for let-7 family members as well as miR-17, miR-18a, miR-20a, miR-93 and miR-106b. The enrichment of miRNA seed regions in exosomal lncRNAs is matched with a concomitant high expression of the same miRNA. In addition, the exosomal lncRNAs also showed an over representation of RNA binding protein binding motifs. The two most common motifs belonged to ELAVL1 and RBMX. Given the enrichment of miRNA and RBP sites on exosomal lncRNAs, their interplay may suggest a possible function in prostate cancer carcinogenesis.
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Affiliation(s)
- Alireza Ahadi
- Centre for Human Centred Technology Design, University of Technology, Sydney.,Centre for Health Technologies, Faculty of Engineering and Information Technology, University of Technology, Sydney
| | - Samuel Brennan
- School of Life Sciences, Faculty of Science, University of Technology, Sydney
| | - Paul J Kennedy
- Centre for Health Technologies, Faculty of Engineering and Information Technology, University of Technology, Sydney.,Centre for Quantum Computation and Intelligent Systems, University of Technology, Sydney
| | - Gyorgy Hutvagner
- Centre for Health Technologies, Faculty of Engineering and Information Technology, University of Technology, Sydney
| | - Nham Tran
- Centre for Health Technologies, Faculty of Engineering and Information Technology, University of Technology, Sydney.,The Sydney Head and Neck Cancer Institute, Sydney Cancer Centre, Royal Prince Alfred Hospital, Australia
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19
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Manikandan M, Deva Magendhra Rao AK, Arunkumar G, Manickavasagam M, Rajkumar KS, Rajaraman R, Munirajan AK. Oral squamous cell carcinoma: microRNA expression profiling and integrative analyses for elucidation of tumourigenesis mechanism. Mol Cancer 2016; 15:28. [PMID: 27056547 PMCID: PMC4823852 DOI: 10.1186/s12943-016-0512-8] [Citation(s) in RCA: 139] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2015] [Accepted: 03/31/2016] [Indexed: 12/22/2022] Open
Abstract
Background The advantages and utility of microRNAs (miRNAs) as diagnostic and prognostic cancer markers is at the vanguard in recent years. In this study, we attempted to identify and validate the differential expression of miRNAs in oral squamous cell carcinoma (OSCC), to correlate their expression with the clinico-pathological profile of tumours and to identify the signaling pathways through which the aberrantly expressed miRNAs effect tumourigenesis. Methods miRCURY LNA™ array with probes specific to 1168 miRNAs and TaqMan assays specific for 10 miRNAs was employed to evaluate and validate miRNA expression in a discovery cohort (n = 29) and validation cohort (n = 61) of primary OSCC tissue specimens, respectively. A computational pipeline with sequential integration of data from miRTarBase, CytoScape, UniProtKB and DIANA-miRPath was utilized to map the target genes of deregulated miRNAs and associated molecular pathways. Results Microarray profiling identified 46 miRNAs that were differentially expressed in OSCC. Unsupervised clustering demonstrated a high degree of molecular heterogeneity across the tumour samples as the clusters did not represent any of their clinico-pathological characteristics. The differential expression of 10 miRNAs were validated by RT-qPCR (let-7a, let-7d, let-7f and miR-16 were downregulated while miR-29b, miR-142-3p, miR-144, miR-203, and miR-223 were upregulated in OSCC; the expression of miR-1275 was variable in tumours, with high levels associated to regional lymph node invasion; additionally, miR-223 exhibited an association with advanced tumour stage/size). In silico analyses of the experimentally confirmed target genes of miRNAs revamp the relationship of upregulated miRNAs with tumour suppressor genes and of downregulated miRNAs with oncogenes. Further, the differentially expressed miRNAs may play a role by simultaneously activating genes of PI3K/Akt signaling on one hand and by repressing genes of p53 signaling pathway on the other. Conclusions The identified differentially expressed miRNAs and signaling pathways deregulated in OSCC have implications for the development of novel therapeutic strategies. To the best of our knowledge, this is the first report to show the association of miR-1275 with nodal invasion and the upregulation of miR-144 in OSCC. Electronic supplementary material The online version of this article (doi:10.1186/s12943-016-0512-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Mayakannan Manikandan
- Department of Genetics, Dr. ALM PG Institute of Basic Medical Sciences, University of Madras, Taramani campus, Chennai, 600113, Tamil Nadu, India
| | - Arungiri Kuha Deva Magendhra Rao
- Department of Genetics, Dr. ALM PG Institute of Basic Medical Sciences, University of Madras, Taramani campus, Chennai, 600113, Tamil Nadu, India
| | - Ganesan Arunkumar
- Department of Genetics, Dr. ALM PG Institute of Basic Medical Sciences, University of Madras, Taramani campus, Chennai, 600113, Tamil Nadu, India
| | - Meenakshisundaram Manickavasagam
- Department of Medical Oncology, Government Arignar Anna Memorial Cancer Research Institute and Hospital, Karapettai, Kanchipuram, 631502, Tamil Nadu, India
| | | | - Ramamurthy Rajaraman
- Centre for Oncology, Government Royapettah Hospital & Kilpauk Medical College, Chennai, 600014, Tamil Nadu, India
| | - Arasambattu Kannan Munirajan
- Department of Genetics, Dr. ALM PG Institute of Basic Medical Sciences, University of Madras, Taramani campus, Chennai, 600113, Tamil Nadu, India.
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20
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Profiling cell-free and circulating miRNA: a clinical diagnostic tool for different cancers. Tumour Biol 2016; 37:5705-14. [PMID: 26831657 DOI: 10.1007/s13277-016-4907-3] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2015] [Accepted: 01/22/2016] [Indexed: 12/11/2022] Open
Abstract
Effective cancer management depends on early diagnosis and treatment. There are several microRNAs (miRNAs) which are used for detection of various cancers. Cell-free and circulating miRNAs originate from plasma, either from blood cells or endothelial cells. Cell-free and circulating miRNAs are very much important in the diagnosis and prognosis of cancer therapy. Admittedly, biological knowledge of extracellular miRNAs is still at its preliminary level. Recent discoveries of novel cell-free and circulating miRNAs from the body fluids are now being considered as important biomarkers that may help us in the early diagnosis of any cancer. In the present review, we highlight the biogenesis of miRNAs and their current extracellular pattern, the discovery of circulating miRNA, significant advantages, and different profiling techniques. Finally, we discuss the different circulating miRNAs such as miR-21, miR-20a, miR-155, miR‑221, miR-210, miR-218, miR-200-family, miR-141, miR-122, miR-486-5p, miR‑423-5p, miR-29a, and miR-500 for clinical diagnosis of various cancers. The present review may be beneficial for future researches concerned with miRNAs which are used for detection of various cancers.
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21
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Zamani-Ahmadmahmudi M. Relationship between microRNA genes incidence and cancer-associated genomic regions in canine tumors: a comprehensive bioinformatics study. Funct Integr Genomics 2016; 16:143-52. [DOI: 10.1007/s10142-016-0473-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Revised: 01/01/2016] [Accepted: 01/04/2016] [Indexed: 12/18/2022]
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22
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Jonsson P, Coarfa C, Mesmar F, Raz T, Rajapakshe K, Thompson JF, Gunaratne PH, Williams C. Single-Molecule Sequencing Reveals Estrogen-Regulated Clinically Relevant lncRNAs in Breast Cancer. Mol Endocrinol 2015; 29:1634-45. [PMID: 26426411 DOI: 10.1210/me.2015-1153] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Estrogen receptor (ER)α-positive tumors are commonly treated with ERα antagonists or inhibitors of estrogen synthesis, but most tumors develop resistance, and we need to better understand the pathways that underlie the proliferative and tumorigenic role of this estrogen-activated transcription factor. We here present the first single-molecule sequencing of the estradiol-induced ERα transcriptome in the luminal A-type human breast cancer cell lines MCF7 and T47D. Sequencing libraries were prepared from the polyadenylated RNA fraction after 8 hours of estrogen or vehicle treatment. Single-molecule sequencing was carried out in biological and technical replicates and differentially expressed genes were defined and analyzed for enriched processes. Correlation analysis with clinical expression and survival were performed, and follow-up experiments carried out using time series, chromatin immunoprecipitation and quantitative real-time PCR. We uncovered that ERα in addition to regulating approximately 2000 protein-coding genes, also regulated up to 1000 long noncoding RNAs (lncRNAs). Most of these were up-regulated, and 178 lncRNAs were regulated in both cell lines. We demonstrate that Long Intergenic Non-protein Coding RNA 1016 (LINC01016) and LINC00160 are direct transcriptional targets of ERα, correlate with ERα expression in clinical samples, and show prognostic significance in relation to breast cancer survival. We show that silencing of LINC00160 results in reduced proliferation, demonstrating that lncRNA expression have functional consequences. Our findings suggest that ERα regulation of lncRNAs is clinically relevant and that their functions and potential use as biomarkers for endocrine response are important to explore.
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Affiliation(s)
- Philip Jonsson
- Center for Nuclear Receptors and Cell Signaling (P.J., F.M., C.W.), Department of Biology and Biochemistry, and Department of Biology and Biochemistry (P.H.G.), University of Houston, Houston, Texas 77204; Molecular and Human Genetics (C.C., K.R.) and Human Genome Sequencing Center (P.H.G.), Baylor College of Medicine, Houston, Texas 77030; Helicos Biosciences (T.R., J.F.T.), Cambridge, Massachusetts 02139; SciLifeLab, School of Biotechnology (C.W.), The Royal Institute of Technology-KTH, 17121 Solna, Sweden; and Department of Biosciences and Nutrition (C.W.), Novum, Karolinska Institutet, 14183 Stockholm, Sweden
| | - Cristian Coarfa
- Center for Nuclear Receptors and Cell Signaling (P.J., F.M., C.W.), Department of Biology and Biochemistry, and Department of Biology and Biochemistry (P.H.G.), University of Houston, Houston, Texas 77204; Molecular and Human Genetics (C.C., K.R.) and Human Genome Sequencing Center (P.H.G.), Baylor College of Medicine, Houston, Texas 77030; Helicos Biosciences (T.R., J.F.T.), Cambridge, Massachusetts 02139; SciLifeLab, School of Biotechnology (C.W.), The Royal Institute of Technology-KTH, 17121 Solna, Sweden; and Department of Biosciences and Nutrition (C.W.), Novum, Karolinska Institutet, 14183 Stockholm, Sweden
| | - Fahmi Mesmar
- Center for Nuclear Receptors and Cell Signaling (P.J., F.M., C.W.), Department of Biology and Biochemistry, and Department of Biology and Biochemistry (P.H.G.), University of Houston, Houston, Texas 77204; Molecular and Human Genetics (C.C., K.R.) and Human Genome Sequencing Center (P.H.G.), Baylor College of Medicine, Houston, Texas 77030; Helicos Biosciences (T.R., J.F.T.), Cambridge, Massachusetts 02139; SciLifeLab, School of Biotechnology (C.W.), The Royal Institute of Technology-KTH, 17121 Solna, Sweden; and Department of Biosciences and Nutrition (C.W.), Novum, Karolinska Institutet, 14183 Stockholm, Sweden
| | - Tal Raz
- Center for Nuclear Receptors and Cell Signaling (P.J., F.M., C.W.), Department of Biology and Biochemistry, and Department of Biology and Biochemistry (P.H.G.), University of Houston, Houston, Texas 77204; Molecular and Human Genetics (C.C., K.R.) and Human Genome Sequencing Center (P.H.G.), Baylor College of Medicine, Houston, Texas 77030; Helicos Biosciences (T.R., J.F.T.), Cambridge, Massachusetts 02139; SciLifeLab, School of Biotechnology (C.W.), The Royal Institute of Technology-KTH, 17121 Solna, Sweden; and Department of Biosciences and Nutrition (C.W.), Novum, Karolinska Institutet, 14183 Stockholm, Sweden
| | - Kimal Rajapakshe
- Center for Nuclear Receptors and Cell Signaling (P.J., F.M., C.W.), Department of Biology and Biochemistry, and Department of Biology and Biochemistry (P.H.G.), University of Houston, Houston, Texas 77204; Molecular and Human Genetics (C.C., K.R.) and Human Genome Sequencing Center (P.H.G.), Baylor College of Medicine, Houston, Texas 77030; Helicos Biosciences (T.R., J.F.T.), Cambridge, Massachusetts 02139; SciLifeLab, School of Biotechnology (C.W.), The Royal Institute of Technology-KTH, 17121 Solna, Sweden; and Department of Biosciences and Nutrition (C.W.), Novum, Karolinska Institutet, 14183 Stockholm, Sweden
| | - John F Thompson
- Center for Nuclear Receptors and Cell Signaling (P.J., F.M., C.W.), Department of Biology and Biochemistry, and Department of Biology and Biochemistry (P.H.G.), University of Houston, Houston, Texas 77204; Molecular and Human Genetics (C.C., K.R.) and Human Genome Sequencing Center (P.H.G.), Baylor College of Medicine, Houston, Texas 77030; Helicos Biosciences (T.R., J.F.T.), Cambridge, Massachusetts 02139; SciLifeLab, School of Biotechnology (C.W.), The Royal Institute of Technology-KTH, 17121 Solna, Sweden; and Department of Biosciences and Nutrition (C.W.), Novum, Karolinska Institutet, 14183 Stockholm, Sweden
| | - Preethi H Gunaratne
- Center for Nuclear Receptors and Cell Signaling (P.J., F.M., C.W.), Department of Biology and Biochemistry, and Department of Biology and Biochemistry (P.H.G.), University of Houston, Houston, Texas 77204; Molecular and Human Genetics (C.C., K.R.) and Human Genome Sequencing Center (P.H.G.), Baylor College of Medicine, Houston, Texas 77030; Helicos Biosciences (T.R., J.F.T.), Cambridge, Massachusetts 02139; SciLifeLab, School of Biotechnology (C.W.), The Royal Institute of Technology-KTH, 17121 Solna, Sweden; and Department of Biosciences and Nutrition (C.W.), Novum, Karolinska Institutet, 14183 Stockholm, Sweden
| | - Cecilia Williams
- Center for Nuclear Receptors and Cell Signaling (P.J., F.M., C.W.), Department of Biology and Biochemistry, and Department of Biology and Biochemistry (P.H.G.), University of Houston, Houston, Texas 77204; Molecular and Human Genetics (C.C., K.R.) and Human Genome Sequencing Center (P.H.G.), Baylor College of Medicine, Houston, Texas 77030; Helicos Biosciences (T.R., J.F.T.), Cambridge, Massachusetts 02139; SciLifeLab, School of Biotechnology (C.W.), The Royal Institute of Technology-KTH, 17121 Solna, Sweden; and Department of Biosciences and Nutrition (C.W.), Novum, Karolinska Institutet, 14183 Stockholm, Sweden
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Li B, Chen H, Wu N, Zhang WJ, Shang LX. Deregulation of miR-128 in ovarian cancer promotes cisplatin resistance. Int J Gynecol Cancer 2015; 24:1381-8. [PMID: 25248111 DOI: 10.1097/igc.0000000000000252] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
OBJECTIVE Platinum-based chemotherapy is the standard treatment in advanced ovarian cancer, but most patients will relapse with drug-resistant disease. MicroRNAs have been demonstrated to function in chemoresistance in cancers. In this study, we focused on the role of miR-128 in cisplatin-resistant ovarian cancer. MATERIALS AND METHODS The expression of miR-128 RNA and its targeted genes, the polycomb ring finger oncogene Bmi-1 and ATP-binding cassette subfamily C member 5 (ABCC5), were investigated in the epithelial ovarian cancer cells and ovarian carcinomas. RESULTS miR-128 expression was significantly reduced in the cisplatin-resistant human epithelial ovarian cancer cell line SKOV3/CP compared with parental SKOV3 cells and decreased upon treatment with cisplatin in a concentration-dependent manner in SKOV3, OVCAR3, and PEO14 cells. Overexpression of miR-128 resensitized SKOV3/CP cells to cisplatin and reduced the expression of cisplatin-resistant-related proteins ABCC5 and Bmi-1, whereas miR-128 inhibitors increased cisplatin resistance in SKOV3 cells. Cisplatin combined with miR-128 agomirs inhibited the growth of SKOV3/CP xenograft tumors more effectively than cisplatin alone. Diminished expression of ABCC5 and Bmi-1 and higher cisplatin concentrations were observed in tumor tissue of mice treated with miR-128 agomirs in addition to cisplatin. CONCLUSIONS Taken together, our findings suggest that miR-128 may act as a promising therapeutic target for improvement of tumor sensitivity to cisplatin.
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Affiliation(s)
- Bing Li
- Departments of *Gynecology and Obstetrics, and †Anesthesiology, the Military General Hospital of Beijing PLA, Beijng, China
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24
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Alanazi I, Hoffmann P, Adelson DL. MicroRNAs are part of the regulatory network that controls EGF induced apoptosis, including elements of the JAK/STAT pathway, in A431 cells. PLoS One 2015; 10:e0120337. [PMID: 25781916 PMCID: PMC4364457 DOI: 10.1371/journal.pone.0120337] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2013] [Accepted: 02/05/2015] [Indexed: 12/20/2022] Open
Abstract
MiRNAs are known to regulate gene expression and in the context of cancer have been shown to regulate metastasis, cell proliferation and cell death. In this report we describe potential miRNA regulatory roles with respect to induction of cell death by pharmacologic dose of Epidermal Growth Factor (EGF). Our previous work suggested that multiple pathways are involved in the induction of apoptosis, including interferon induced genes, cytokines, cytoskeleton and cell adhesion and TP53 regulated genes. Using miRNA time course expression profiling of EGF treated A431 cells and coupling this to our previous gene expression and proteomic data, we have been able to implicate a number of additional miRNAs in the regulation of apoptosis. Specifically we have linked miR-134, miR-145, miR-146b-5p, miR-432 and miR-494 to the regulation of both apoptotic and anti-apoptotic genes expressed as a function of EGF treatment. Whilst additional miRNAs were differentially expressed, these had the largest number of apoptotic and anti-apoptotic targets. We found 5 miRNAs previously implicated in the regulation of apoptosis and our results indicate that an additional 20 miRNAs are likely to be involved based on their correlated expression with targets. Certain targets were linked to multiple miRNAs, including PEG10, BTG1, ID1, IL32 and NCF2. Some miRNAs that target the interferon pathway were found to be down regulated, consistent with a novel layer of regulation of interferon pathway components downstream of JAK/STAT. We have significantly expanded the repertoire of miRNAs that may regulate apoptosis in cancer cells as a result of this work.
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Affiliation(s)
- Ibrahim Alanazi
- School of Biological Sciences, The University of Adelaide, Adelaide, South Australia, Australia
| | - Peter Hoffmann
- School of Biological Sciences, The University of Adelaide, Adelaide, South Australia, Australia
| | - David L. Adelson
- School of Biological Sciences, The University of Adelaide, Adelaide, South Australia, Australia
- Zhendong Australia—China Centre for Molecular Chinese Medicine, The University of Adelaide, Adelaide, South Australia, Australia
- * E-mail:
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25
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Sciamanna I, Gualtieri A, Cossetti C, Osimo EF, Ferracin M, Macchia G, Aricò E, Prosseda G, Vitullo P, Misteli T, Spadafora C. A tumor-promoting mechanism mediated by retrotransposon-encoded reverse transcriptase is active in human transformed cell lines. Oncotarget 2014; 4:2271-87. [PMID: 24345856 PMCID: PMC3926826 DOI: 10.18632/oncotarget.1403] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
LINE-1 elements make up the most abundant retrotransposon family in the human genome. Full-length LINE-1 elements encode a reverse transcriptase (RT) activity required for their own retrotranpsosition as well as that of non-autonomous Alu elements. LINE-1 are poorly expressed in normal cells and abundantly in cancer cells. Decreasing RT activity in cancer cells, by either LINE-1-specific RNA interference, or by RT inhibitory drugs, was previously found to reduce proliferation and promote differentiation and to antagonize tumor growth in animal models. Here we have investigated how RT exerts these global regulatory functions. We report that the RT inhibitor efavirenz (EFV) selectively downregulates proliferation of transformed cell lines, while exerting only mild effects on non-transformed cells; this differential sensitivity matches a differential RT abundance, which is high in the former and undetectable in the latter. Using CsCl density gradients, we selectively identify Alu and LINE-1 containing DNA:RNA hybrid molecules in cancer but not in normal cells. Remarkably, hybrid molecules fail to form in tumor cells treated with EFV under the same conditions that repress proliferation and induce the reprogramming of expression profiles of coding genes, microRNAs (miRNAs) and ultraconserved regions (UCRs). The RT-sensitive miRNAs and UCRs are significantly associated with Alu sequences. The results suggest that LINE-1-encoded RT governs the balance between single-stranded and double-stranded RNA production. In cancer cells the abundant RT reverse-transcribes retroelement-derived mRNAs forming RNA:DNA hybrids. We propose that this impairs the formation of double-stranded RNAs and the ensuing production of small regulatory RNAs, with a direct impact on gene expression. RT inhibition restores the ‘normal’ small RNA profile and the regulatory networks that depend on them. Thus, the retrotransposon-encoded RT drives a previously unrecognized mechanism crucial to the transformed state in tumor cells.
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Affiliation(s)
- Ilaria Sciamanna
- Istituto Superiore di Sanità, Viale Regina Elena 299, Rome, Italy
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26
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Galasso M, Dama P, Previati M, Sandhu S, Palatini J, Coppola V, Warner S, Sana ME, Zanella R, Abujarour R, Desponts C, Teitell MA, Garzon R, Calin G, Croce CM, Volinia S. A large scale expression study associates uc.283-plus lncRNA with pluripotent stem cells and human glioma. Genome Med 2014; 6:76. [PMID: 25352916 PMCID: PMC4210590 DOI: 10.1186/s13073-014-0076-4] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2014] [Accepted: 09/16/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND There are 481 ultra-conserved regions (UCRs) longer than 200 bases in the genomes of human, mouse and rat. These DNA sequences are absolutely conserved and show 100% identity with no insertions or deletions. About half of these UCRs are reported as transcribed and many correspond to long non-coding RNAs (lncRNAs). METHODS We used custom microarrays with 962 probes representing sense and antisense sequences for the 481 UCRs to examine their expression across 374 normal samples from 46 different tissues and 510 samples representing 10 different types of cancer. The expression in embryonic stem cells of selected UCRs was validated by real time PCR. RESULTS We identified tissue selective UCRs and studied UCRs in embryonic and induced pluripotent stem cells. Among the normal tissues, the uc.283 lncRNA was highly specific for pluripotent stem cells. Intriguingly, the uc.283-plus lncRNA was highly expressed in some solid cancers, particularly in one of the most untreatable types, glioma. CONCLUSION Our results suggest that uc.283-plus lncRNA might have a role in pluripotency of stem cells and in the biology of glioma.
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Affiliation(s)
- Marco Galasso
- Biosystems Analysis, LTTA, Department of Morphology, Surgery and Experimental Medicine, Università degli Studi, Via Fossato di Mortara, 70, Ferrara, 44123 Italy
| | - Paola Dama
- Biosystems Analysis, LTTA, Department of Morphology, Surgery and Experimental Medicine, Università degli Studi, Via Fossato di Mortara, 70, Ferrara, 44123 Italy
| | - Maurizio Previati
- Biosystems Analysis, LTTA, Department of Morphology, Surgery and Experimental Medicine, Università degli Studi, Via Fossato di Mortara, 70, Ferrara, 44123 Italy
| | - Sukhinder Sandhu
- Comprehensive Cancer Center, Wexner Medical Center, and Biomedical Informatics, Ohio State University, Columbus, OH 43210 USA
| | - Jeff Palatini
- Comprehensive Cancer Center, Wexner Medical Center, and Biomedical Informatics, Ohio State University, Columbus, OH 43210 USA
| | - Vincenzo Coppola
- Comprehensive Cancer Center, Wexner Medical Center, and Biomedical Informatics, Ohio State University, Columbus, OH 43210 USA
| | - Sarah Warner
- Comprehensive Cancer Center, Wexner Medical Center, and Biomedical Informatics, Ohio State University, Columbus, OH 43210 USA
| | - Maria E Sana
- Biosystems Analysis, LTTA, Department of Morphology, Surgery and Experimental Medicine, Università degli Studi, Via Fossato di Mortara, 70, Ferrara, 44123 Italy
| | - Riccardo Zanella
- Biosystems Analysis, LTTA, Department of Morphology, Surgery and Experimental Medicine, Università degli Studi, Via Fossato di Mortara, 70, Ferrara, 44123 Italy
| | - Ramzey Abujarour
- Fate Therapeutics, 3535 General Atomics Ct, San Diego, CA 92121 USA
| | - Caroline Desponts
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037 USA
| | - Michael A Teitell
- Department of Pathology & Laboratory Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095 USA
| | - Ramiro Garzon
- Comprehensive Cancer Center, Wexner Medical Center, and Biomedical Informatics, Ohio State University, Columbus, OH 43210 USA
| | - George Calin
- Experimental Therapeutics & Cancer Genetics, MD Anderson Cancer Center, Houston, TX 77030 USA
| | - Carlo M Croce
- Comprehensive Cancer Center, Wexner Medical Center, and Biomedical Informatics, Ohio State University, Columbus, OH 43210 USA
| | - Stefano Volinia
- Biosystems Analysis, LTTA, Department of Morphology, Surgery and Experimental Medicine, Università degli Studi, Via Fossato di Mortara, 70, Ferrara, 44123 Italy ; Comprehensive Cancer Center, Wexner Medical Center, and Biomedical Informatics, Ohio State University, Columbus, OH 43210 USA ; Biomedical Informatics, Ohio State University, Columbus, OH 43210 USA
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Long non-coding RNA MALAT1 promotes tumour growth and metastasis in colorectal cancer through binding to SFPQ and releasing oncogene PTBP2 from SFPQ/PTBP2 complex. Br J Cancer 2014; 111:736-48. [PMID: 25025966 PMCID: PMC4134507 DOI: 10.1038/bjc.2014.383] [Citation(s) in RCA: 298] [Impact Index Per Article: 29.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2014] [Revised: 06/10/2014] [Accepted: 06/17/2014] [Indexed: 12/16/2022] Open
Abstract
Background: Metastasis associated with lung adenocarcinoma transcript-1 (MALAT1) is a functional long non-coding RNA (lncRNA), which is highly expressed in several tumours, including colorectal cancer (CRC). Its biological function and mechanism in the prognosis of human CRC is still largely under investigation. Methods: This study aimed to investigate the new effect mechanism of MALAT1 on the proliferation and migration of CRC cells in vitro and in vivo, and detect the expression of MALAT1, SFPQ (also known as PSF (PTB-associated splicing factor)), and PTBP2 (also known as PTB (polypyrimidine-tract-binding protein)) in CRC tumour tissues, followed by correlated analysis with clinicopathological parameters. Results: We found that overexpression of MALAT1 could promote cell proliferation and migration in vitro, and promote tumour growth and metastasis in nude mice. The underlying mechanism was associated with tumour suppressor gene SFPQ and proto-oncogene PTBP2. In CRC, MALAT1 could bind to SFPQ, thus releasing PTBP2 from the SFPQ/PTBP2 complex. In turn, the increased SFPQ-detached PTBP2 promoted cell proliferation and migration. SFPQ critically mediated the regulatory effects of MALAT1. Moreover, in CRC tissues, MALAT1 and PTBP2 were overexpressed, both of which were associated closely with the invasion and metastasis of CRC. However, the SFPQ showed unchanged expression either in CRC tissues or adjacent normal tissues. Conclusions: Our findings implied that MALAT1 might be a potential predictor for tumour metastasis and prognosis. Furthermore, the interaction between MALAT1 and SFPQ could be a novel therapeutic target for CRC.
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28
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Ghorai A, Ghosh U. miRNA gene counts in chromosomes vary widely in a species and biogenesis of miRNA largely depends on transcription or post-transcriptional processing of coding genes. Front Genet 2014; 5:100. [PMID: 24808907 PMCID: PMC4010735 DOI: 10.3389/fgene.2014.00100] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2013] [Accepted: 04/07/2014] [Indexed: 11/26/2022] Open
Abstract
MicroRNAs target specific mRNA(s) to silence its expression and thereby regulate various cellular processes. We have investigated miRNA gene counts in chromosomes for 20 different species and observed wide variation. Certain chromosomes have extremely high number of miRNA gene compared with others in all the species. For example, high number of miRNA gene in X chromosome and the least or absence of miRNA gene in Y chromosome was observed in all species. To search the criteria governing such variation of miRNA gene counts in chromosomes, we have selected three parameters- length, number of non-coding and coding genes in a chromosome. We have calculated Pearson's correlation coefficient of miRNA gene counts with length, number of non-coding and coding genes in a chromosome for all 20 species. Major number of species showed that number of miRNA gene was not correlated with chromosome length. Eighty five percent of species under study showed strong positive correlation coefficient (r ≥ 0.5) between the numbers of miRNA gene vs. non-coding gene in chromosomes as expected because miRNA is a sub-set of non-coding genes. 55% species under study showed strong positive correlation coefficient (r ≥ 0.5) between numbers of miRNA gene vs. coding gene. We hypothesize biogenesis of miRNA largely depends on coding genes, an evolutionary conserved process. Chromosomes having higher number of miRNA genes will be most likely playing regulatory roles in several cellular processes including different disorders. In humans, cancer and cardiovascular disease associated miRNAs are mostly intergenic and located in Chromosome 19, X, 14, and 1.
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Affiliation(s)
- Atanu Ghorai
- Department of Biochemistry and Biophysics, University of Kalyani Kalyani, India
| | - Utpal Ghosh
- Department of Biochemistry and Biophysics, University of Kalyani Kalyani, India
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29
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Veerappa AM, N MM, Vishweswaraiah S, Lingaiah K, Suresh RV, Nachappa SA, Prashali N, Yadav SN, Srikanta MA, Manjegowda DS, Seshachalam KB, Ramachandra NB. Copy number variations burden on miRNA genes reveals layers of complexities involved in the regulation of pathways and phenotypic expression. PLoS One 2014; 9:e90391. [PMID: 24587348 PMCID: PMC3938728 DOI: 10.1371/journal.pone.0090391] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2013] [Accepted: 01/28/2014] [Indexed: 12/21/2022] Open
Abstract
MicroRNAs are involved in post-transcriptional down-regulation of gene expression. Variations in miRNA genes can severely affect downstream-regulated genes and their pathways. However, population-specific burden of CNVs on miRNA genes and the complexities created towards the phenotype is not known. From a total of 44109 CNVs investigated from 1715 individuals across 12 populations using high-throughput arrays, 4007 miRNA-CNVs (∼ 9%) consisting 6542 (∼ 5%) miRNA genes with a total of 333 (∼ 5%) singleton miRNA genes were identified. We found miRNA-CNVs across the genomes of individuals showing multiple hits in many targets, co-regulated under the same pathway. This study proposes four mechanisms unraveling the many complexities in miRNA genes, targets and co-regulated miRNA genes towards establishment of phenotypic diversity.
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Affiliation(s)
- Avinash M. Veerappa
- Genetics and Genomics Lab, Department of Studies in Zoology, University of Mysore, Manasagangotri, Mysore, Karnataka, India
| | - Megha Murthy N
- Genetics and Genomics Lab, Department of Studies in Zoology, University of Mysore, Manasagangotri, Mysore, Karnataka, India
| | - Sangeetha Vishweswaraiah
- Genetics and Genomics Lab, Department of Studies in Zoology, University of Mysore, Manasagangotri, Mysore, Karnataka, India
| | - Kusuma Lingaiah
- Genetics and Genomics Lab, Department of Studies in Zoology, University of Mysore, Manasagangotri, Mysore, Karnataka, India
| | - Raviraj V. Suresh
- Genetics and Genomics Lab, Department of Studies in Zoology, University of Mysore, Manasagangotri, Mysore, Karnataka, India
| | - Somanna Ajjamada Nachappa
- Genetics and Genomics Lab, Department of Studies in Zoology, University of Mysore, Manasagangotri, Mysore, Karnataka, India
| | - Nelchi Prashali
- Genetics and Genomics Lab, Department of Studies in Zoology, University of Mysore, Manasagangotri, Mysore, Karnataka, India
| | - Sangeetha Nuggehalli Yadav
- Genetics and Genomics Lab, Department of Studies in Zoology, University of Mysore, Manasagangotri, Mysore, Karnataka, India
| | - Manjula Arsikere Srikanta
- Genetics and Genomics Lab, Department of Studies in Zoology, University of Mysore, Manasagangotri, Mysore, Karnataka, India
| | - Dinesh S. Manjegowda
- Department of Anatomy, Yenepoya Medical College, Yenepoya University, Mangalore, Karnataka, India
- Nitte University Centre for Science Education & Research, K S Hegde Medical Academy, Nitte University, Deralakatte, Mangalore, Karnataka, India
| | | | - Nallur B. Ramachandra
- Genetics and Genomics Lab, Department of Studies in Zoology, University of Mysore, Manasagangotri, Mysore, Karnataka, India
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30
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Cai J, Yang C, Yang Q, Ding H, Jia J, Guo J, Wang J, Wang Z. Deregulation of let-7e in epithelial ovarian cancer promotes the development of resistance to cisplatin. Oncogenesis 2013; 2:e75. [PMID: 24100610 PMCID: PMC3816216 DOI: 10.1038/oncsis.2013.39] [Citation(s) in RCA: 70] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2013] [Revised: 08/05/2013] [Accepted: 08/20/2013] [Indexed: 12/29/2022] Open
Abstract
Drug resistance remains a major clinical obstacle to successful treatment in ovarian cancer patients, and the evidence of microRNAs involvement in drug resistance has been emerging recently. In this report, we investigated the role of let-7e in the development of cisplatin-resistant ovarian cancer. On the cellular level, let-7e expression was significantly reduced in cisplatin-resistant human epithelial ovarian cancer (EOC) cell line A2780/CP compared with parental A2780 cell and decreased in a concentration-dependent manner in A2780, SKOV3 and ES2 cells treated with cisplatin. Overexpression of let-7e by transfection of agomir could resensitize A2780/CP and reduce the expression of cisplatin-resistant-related proteins enhancer of zeste 2 (EZH2) and cyclin D1 (CCND1), whereas let-7e inhibitors increased resistance to cisplatin in parental A2780 cells. Quantitative methylation-specific PCR analysis showed hypermethylation of the CpG island adjacent to let-7e in A2780/CP cells, and demethylation treatment with 5-aza-CdR or transfection of pYr-let-7e-shRNA plasmid containing unmethylated let-7e DNA sequence could restore let-7e expression and partly reduce the chemoresistance. In addition, cisplatin combined with let-7e agomirs inhibited the growth of A2780/CP xenograft more effectively than cisplatin alone. Diminished expression of EZH2 and CCND1 and higher cisplatin concentrations in tumor tissue of mice subjected to administration of let-7e agomirs in addition to cisplatin were revealed by immunohistochemistry and atomic absorption spectroscopy, respectively. Taken together, our findings suggest that let-7e may act as a promising therapeutic target for improvement of the sensibility to cisplatin in EOC.
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Affiliation(s)
- J Cai
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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31
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Persengiev S, Kondova I, Bontrop R. Insights on the functional interactions between miRNAs and copy number variations in the aging brain. Front Mol Neurosci 2013; 6:32. [PMID: 24106459 PMCID: PMC3788589 DOI: 10.3389/fnmol.2013.00032] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2013] [Accepted: 09/11/2013] [Indexed: 12/11/2022] Open
Abstract
MicroRNAs (miRNAs) are regulatory genetic elements that coordinate the expression of thousands of genes and play important roles in brain aging and neurodegeneration. DNA polymorphisms affecting miRNA biogenesis, dosage, and gene targeting may represent potentially functional variants. The consequences of single nucleotide polymorphisms affecting miRNA function were previously demonstrated by both experimental and computational methods. However, little is known about how copy number variations (CNVs) influence miRNA metabolism and regulatory networks. We discuss potential mechanisms of CNVs-mediated effects on miRNA function and regulation that might have consequences for brain aging. We argue that CNVs, which potentially can alter miRNA expression, regulation or target gene recognition, are possible functional variants and should be considered high priority candidates in genotype–phenotype mapping studies of brain-related disorders.
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Mazan-Mamczarz K, Gartenhaus RB. Role of microRNA deregulation in the pathogenesis of diffuse large B-cell lymphoma (DLBCL). Leuk Res 2013; 37:1420-8. [PMID: 24054860 DOI: 10.1016/j.leukres.2013.08.020] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2013] [Revised: 08/27/2013] [Accepted: 08/29/2013] [Indexed: 12/19/2022]
Abstract
MicroRNAs (miRNAs) are small endogenous RNA molecules that regulate gene expression at the post-transcriptional level through its sequence complementation with target mRNAs. An individual miRNA species can simultaneously influence the expression of multiple genes and conversely, several miRNAs can synchronously control expression of specific gene product mRNA levels. Thus, miRNAs expression in cells has to be precisely regulated and alterations in miRNA levels may cause an aberrant expression of genes involved in oncogenic pathways and consequently result in cancer development. Indeed, miRNA expression is often deregulated in many cancers, including B-cell lymphomas. Diffuse large B-cell lymphoma (DLBCL) is a heterogeneous group of B-cell lymphomas with different genetic backgrounds, morphologic features, and responses to therapy. Over the past decade, miRNAs emerged as a new tool for understanding DLBCL biology, and promising candidate molecular markers in DLBCL classification and treatment. In this review, we will focus on miRNAs aberrantly expressed in DLBCL and discuss the putative mechanisms of this deregulation. Additionally, we will summarize miRNAs' involvement in the identification of DLBCL subgroups, and their potential role as diagnostic/prognostic biomarkers as well as specific therapeutic targets for DLBCL.
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Affiliation(s)
- Krystyna Mazan-Mamczarz
- Marlene & Stewart Greenebaum Cancer Center, Department of Medicine, University of Maryland, Baltimore, MD 21201, USA.
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33
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Van Roosbroeck K, Pollet J, Calin GA. miRNAs and long noncoding RNAs as biomarkers in human diseases. Expert Rev Mol Diagn 2013; 13:183-204. [PMID: 23477558 DOI: 10.1586/erm.12.134] [Citation(s) in RCA: 108] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Noncoding RNAs (ncRNAs) are transcripts that have no apparent protein-coding capacity; however, many ncRNAs have been found to play a major biological role in human physiology. Their deregulation is implicated in many human diseases, but their exact roles are only beginning to be elucidated. Nevertheless, ncRNAs are extensively studied as a novel source of biomarkers, and the fact that they can be detected in body fluids makes them extremely suitable for this purpose. The authors mainly focus on ncRNAs as biomarkers in cancer, but also touch on other human diseases such as cardiovascular diseases, autoimmune diseases, neurological disorders and infectious diseases. The authors discuss the established methods and provide a selection of emerging new techniques that can be used to detect and quantify ncRNAs. Finally, the authors discuss ncRNAs as a new strategy for therapeutic interventions.
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Affiliation(s)
- Katrien Van Roosbroeck
- Department of Experimental Therapeutics, Unit 1950, The University of Texas MD Anderson Cancer Center, 1881 East Road, Houston, TX 77054, USA
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Garitano-Trojaola A, Agirre X, Prósper F, Fortes P. Long non-coding RNAs in haematological malignancies. Int J Mol Sci 2013; 14:15386-422. [PMID: 23887658 PMCID: PMC3759866 DOI: 10.3390/ijms140815386] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2013] [Revised: 06/28/2013] [Accepted: 07/09/2013] [Indexed: 12/20/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) are functional RNAs longer than 200 nucleotides in length. LncRNAs are as diverse as mRNAs and they normally share the same biosynthetic machinery based on RNA polymerase II, splicing and polyadenylation. However, lncRNAs have low coding potential. Compared to mRNAs, lncRNAs are preferentially nuclear, more tissue specific and expressed at lower levels. Most of the lncRNAs described to date modulate the expression of specific genes by guiding chromatin remodelling factors; inducing chromosomal loopings; affecting transcription, splicing, translation or mRNA stability; or serving as scaffolds for the organization of cellular structures. They can function in cis, cotranscriptionally, or in trans, acting as decoys, scaffolds or guides. These functions seem essential to allow cell differentiation and growth. In fact, many lncRNAs have been shown to exert oncogenic or tumor suppressor properties in several cancers including haematological malignancies. In this review, we summarize what is known about lncRNAs, the mechanisms for their regulation in cancer and their role in leukemogenesis, lymphomagenesis and hematopoiesis. Furthermore, we discuss the potential of lncRNAs in diagnosis, prognosis and therapy in cancer, with special attention to haematological malignancies.
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Affiliation(s)
- Andoni Garitano-Trojaola
- Laboratory of Myeloproliferative Syndromes, Oncology Area, Foundation for Applied Medical Research, University of Navarra, Pamplona 31008, Spain; E-Mails: (A.G.-T.); (X.A.); (F.P.)
| | - Xabier Agirre
- Laboratory of Myeloproliferative Syndromes, Oncology Area, Foundation for Applied Medical Research, University of Navarra, Pamplona 31008, Spain; E-Mails: (A.G.-T.); (X.A.); (F.P.)
| | - Felipe Prósper
- Laboratory of Myeloproliferative Syndromes, Oncology Area, Foundation for Applied Medical Research, University of Navarra, Pamplona 31008, Spain; E-Mails: (A.G.-T.); (X.A.); (F.P.)
- Hematology Service and Area of Cell Therapy, University of Navarra Clinic, University of Navarra, Pamplona 31008, Spain
| | - Puri Fortes
- Department of Hepatology and Gene Therapy, Foundation for Applied Medical Research, University of Navarra, Pamplona 31008, Spain
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Uchino K, Ochiya T, Takeshita F. RNAi therapeutics and applications of microRNAs in cancer treatment. Jpn J Clin Oncol 2013; 43:596-607. [PMID: 23592885 DOI: 10.1093/jjco/hyt052] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
RNA interference-based therapies are proving to be powerful tools for combating various diseases, including cancer. Scientists are researching the development of safe and efficient systems for the delivery of small RNA molecules, which are extremely fragile in serum, to target organs and cells in the human body. A dozen pre-clinical and clinical trials have been under way over the past few years involving biodegradable nanoparticles, lipids, chemical modification and conjugation. On the other hand, microRNAs, which control the balance of cellular biological processes, have been studied as attractive therapeutic targets in cancer treatment. In this review, we provide an overview of RNA interference-based therapeutics in clinical trials and discuss the latest technology for the systemic delivery of nucleic acid drugs. Furthermore, we focus on dysregulated microRNAs in human cancer, which have progressed in pre-clinical trials as therapeutic targets, and describe a wide range of strategies to control the expression levels of endogenous microRNAs. Further development of RNA interference technologies and progression of clinical trials will contribute to the achievement of practical applications of nucleic acid drugs.
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Affiliation(s)
- Keita Uchino
- Division of Molecular and Cellular Medicine, National Cancer Center Research Institute, 1-1, Tsukiji 5-chome, Chuo-ku, Tokyo 104-0045, Japan
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Frese KS, Katus HA, Meder B. Next-generation sequencing: from understanding biology to personalized medicine. BIOLOGY 2013; 2:378-98. [PMID: 24832667 PMCID: PMC4009863 DOI: 10.3390/biology2010378] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/21/2013] [Revised: 01/21/2013] [Accepted: 02/04/2013] [Indexed: 12/11/2022]
Abstract
Within just a few years, the new methods for high-throughput next-generation sequencing have generated completely novel insights into the heritability and pathophysiology of human disease. In this review, we wish to highlight the benefits of the current state-of-the-art sequencing technologies for genetic and epigenetic research. We illustrate how these technologies help to constantly improve our understanding of genetic mechanisms in biological systems and summarize the progress made so far. This can be exemplified by the case of heritable heart muscle diseases, so-called cardiomyopathies. Here, next-generation sequencing is able to identify novel disease genes, and first clinical applications demonstrate the successful translation of this technology into personalized patient care.
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Affiliation(s)
- Karen S Frese
- Department of Internal Medicine III, University of Heidelberg, Heidelberg 69120, Germany.
| | - Hugo A Katus
- Department of Internal Medicine III, University of Heidelberg, Heidelberg 69120, Germany.
| | - Benjamin Meder
- Department of Internal Medicine III, University of Heidelberg, Heidelberg 69120, Germany.
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Uchino K, Takeshita F, Takahashi RU, Kosaka N, Fujiwara K, Naruoka H, Sonoke S, Yano J, Sasaki H, Nozawa S, Yoshiike M, Kitajima K, Chikaraishi T, Ochiya T. Therapeutic effects of microRNA-582-5p and -3p on the inhibition of bladder cancer progression. Mol Ther 2013; 21:610-9. [PMID: 23295946 DOI: 10.1038/mt.2012.269] [Citation(s) in RCA: 91] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Many reports have indicated that the abnormal expression of microRNAs (miRNAs) is associated with the progression of disease and have identified miRNAs as attractive targets for therapeutic intervention. However, the bifunctional mechanisms of miRNA guide and passenger strands in RNA interference (RNAi) therapy have not yet been clarified. Here, we show that miRNA (miR)-582-5p and -3p, which are strongly decreased in high-grade bladder cancer clinical samples, regulate tumor progression in vitro and in vivo. Significantly, the overexpression of miR-582-5p or -3p reduced the proliferation and invasion of UM-UC-3 human bladder cancer cells. Furthermore, transurethral injections of synthetic miR-582 molecule suppressed tumor growth and metastasis in an animal model of bladder cancer. Most interestingly, our study revealed that both strands of miR-582-5p and -3p suppressed the expression of the same set of target genes such as protein geranylgeranyltransferase type I beta subunit (PGGT1B), leucine-rich repeat kinase 2 (LRRK2) and DIX domain containing 1 (DIXDC1). Knockdown of these genes using small interfering RNA (siRNA) resulted in the inhibition of cell growth and invasiveness of UM-UC-3. These findings uncover the unique regulatory pathway involving tumor suppression by both strands of a single miRNA that is a potential therapeutic target in the treatment of invasive bladder cancer.
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Affiliation(s)
- Keita Uchino
- National Cancer Center Research Institute, Chuo-ku, Tokyo, Japan
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NISHIKAWA SHIMPEI, ISHII HIDESHI, HARAGUCHI NAOTSUGU, KANO YOSHIHIRO, FUKUSUMI TAKAHITO, OHTA KATSUYA, OZAKI MIYUKI, DEWI DYAHLAKSMI, SAKAI DAISUKE, SATOH TAROH, NAGANO HIROAKI, DOKI YUICHIRO, MORI MASAKI. microRNA-based cancer cell reprogramming technology. Exp Ther Med 2012; 4:8-14. [PMID: 23060915 PMCID: PMC3460250 DOI: 10.3892/etm.2012.558] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2011] [Accepted: 03/05/2012] [Indexed: 02/07/2023] Open
Abstract
Epigenetic modifications play crucial roles in cancer initiation and development. Complete reprogramming can be achieved through the introduction of defined biological factors such as Oct4, Sox2, Klf4, and cMyc into mouse and human fibroblasts. Introduction of these transcription factors resulted in the modification of malignant phenotype behavior. Recent studies have shown that human and mouse somatic cells can be reprogrammed to become induced pluripotent stem cells using forced expression of microRNAs, which completely eliminates the need for ectopic protein expression. Considering the usefulness of RNA molecules, microRNA-based reprogramming technology may have future applications in regenerative and cancer medicine.
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Affiliation(s)
- SHIMPEI NISHIKAWA
- Departments of Frontier Science for Cancer and Chemotherapy and
- Gastroenterological Surgery, Osaka University, Graduate School of Medicine, Suita, Osaka 565-0871,
Japan
| | - HIDESHI ISHII
- Departments of Frontier Science for Cancer and Chemotherapy and
| | | | - YOSHIHIRO KANO
- Departments of Frontier Science for Cancer and Chemotherapy and
- Gastroenterological Surgery, Osaka University, Graduate School of Medicine, Suita, Osaka 565-0871,
Japan
| | - TAKAHITO FUKUSUMI
- Departments of Frontier Science for Cancer and Chemotherapy and
- Gastroenterological Surgery, Osaka University, Graduate School of Medicine, Suita, Osaka 565-0871,
Japan
| | - KATSUYA OHTA
- Departments of Frontier Science for Cancer and Chemotherapy and
- Gastroenterological Surgery, Osaka University, Graduate School of Medicine, Suita, Osaka 565-0871,
Japan
| | - MIYUKI OZAKI
- Departments of Frontier Science for Cancer and Chemotherapy and
- Gastroenterological Surgery, Osaka University, Graduate School of Medicine, Suita, Osaka 565-0871,
Japan
| | - DYAH LAKSMI DEWI
- Departments of Frontier Science for Cancer and Chemotherapy and
- Gastroenterological Surgery, Osaka University, Graduate School of Medicine, Suita, Osaka 565-0871,
Japan
| | - DAISUKE SAKAI
- Departments of Frontier Science for Cancer and Chemotherapy and
| | - TAROH SATOH
- Departments of Frontier Science for Cancer and Chemotherapy and
| | - HIROAKI NAGANO
- Gastroenterological Surgery, Osaka University, Graduate School of Medicine, Suita, Osaka 565-0871,
Japan
| | - YUICHIRO DOKI
- Gastroenterological Surgery, Osaka University, Graduate School of Medicine, Suita, Osaka 565-0871,
Japan
| | - MASAKI MORI
- Gastroenterological Surgery, Osaka University, Graduate School of Medicine, Suita, Osaka 565-0871,
Japan
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Costa FF, Seftor EA, Bischof JM, Kirschmann DA, Strizzi L, Arndt K, Bonaldo MDF, Soares MB, Hendrix MJC. Epigenetically reprogramming metastatic tumor cells with an embryonic microenvironment. Epigenomics 2012; 1:387-98. [PMID: 20495621 DOI: 10.2217/epi.09.25] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
UNLABELLED We have previously shown that the microenvironment of human embryonic stem cells (hESCs) is able to change and reprogram aggressive cancer cells to a less aggressive state. Some mechanisms implicated in the phenotypic changes observed after this exposure are mainly associated with the Nodal signaling pathway, which plays a key role in tumor cell plasticity. However, several other molecular mechanisms might be related directly and/or indirectly to these changes, including microRNA (miRNA) regulation and DNA methylation. AIM To further explore the epigenetic mechanisms potentially underlying the phenotypic changes that occur after exposing metastatic melanoma cells to a hESC microenvironment. MATERIALS & METHODS A total of 365 miRNAs were screened using the TaqMan® Low Density Arrays. We also evaluated whether DNA methylation could be one of the factors regulating the expression of the inhibitor of Nodal, Lefty, in hESCs (where it is highly expressed) vs melanoma cells (where it is not expressed). RESULTS Using these experimental approaches, we identified miRNAs that are up- and down-regulated in melanoma cells exposed to a hESC microenvironment, such as miR-302a and miR-27b, respectively. We also demonstrate that Notch4 is one of the targets of miR-302a, which is upstream of Nodal. Additionally, one of the mechanisms that might explain the absence of the inhibitor of Nodal, Lefty, in cancer cells is silencing by DNA methylation, which provides new insights into the unregulated expression of Nodal in melanoma. CONCLUSION These findings suggest that epigenetic changes such as DNA methylation and regulation by microRNAs might play a significant role in tumor cell plasticity and the metastatic phenotype.
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Affiliation(s)
- Fabricio F Costa
- Cancer Biology and Epigenomics Program, Children’s Memorial Research Center and Northwestern University’s Feinberg School of Medicine, 2300 Children’s Plaza, Chicago, IL 60614, USA.
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Mitra SA, Mitra AP, Triche TJ. A central role for long non-coding RNA in cancer. Front Genet 2012; 3:17. [PMID: 22363342 PMCID: PMC3279698 DOI: 10.3389/fgene.2012.00017] [Citation(s) in RCA: 132] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2011] [Accepted: 01/28/2012] [Indexed: 01/29/2023] Open
Abstract
Long non-coding RNAs (ncRNAs) have been shown to regulate important biological processes that support normal cellular functions. Aberrant regulation of these essential functions can promote tumor development. In this review, we underscore the importance of the regulatory role played by this distinct class of ncRNAs in cancer-associated pathways that govern mechanisms such as cell growth, invasion, and metastasis. We also highlight the possibility of using these unique RNAs as diagnostic and prognostic biomarkers in malignancies.
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Affiliation(s)
- Sheetal A Mitra
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles Los Angeles, CA, USA
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Abstract
The relevance of the non-coding genome to human disease has mainly been studied in the context of the widespread disruption of microRNA (miRNA) expression and function that is seen in human cancer. However, we are only beginning to understand the nature and extent of the involvement of non-coding RNAs (ncRNAs) in disease. Other ncRNAs, such as PIWI-interacting RNAs (piRNAs), small nucleolar RNAs (snoRNAs), transcribed ultraconserved regions (T-UCRs) and large intergenic non-coding RNAs (lincRNAs) are emerging as key elements of cellular homeostasis. Along with microRNAs, dysregulation of these ncRNAs is being found to have relevance not only to tumorigenesis, but also to neurological, cardiovascular, developmental and other diseases. There is great interest in therapeutic strategies to counteract these perturbations of ncRNAs.
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Abstract
miRNAs have been recently implicated as drivers in several carcinogenic processes, where they can act either as oncogenes or as tumor suppressors. Schwannomas arise from Schwann cells, the myelinating cells of the peripheral nervous system. These benign tumors typically result from loss of the neurofibromatosis type 2 (NF2) tumor suppressor gene. We have recently carried out high-throughput miRNA expression profiling of human vestibular schwannomas using an array representing 407 known miRNAs in order to explore the role of miRNAs in the tumorigenesis of schwannomas. We found that miR-7 functions as a "tumor suppressor" by targeting proteins in three major oncogenic pathways - EGFR, Pak1, and Ack1. Interestingly, in this study, we also observed that several previously described potential tumor suppressor miRNAs that are down-regulated in malignant tumors were up-regulated in schwannomas. Here we discuss the possibility that "tumor suppressor" miRNAs may play a role in the transition stage(s) of cancer from benign to malignant forms.
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Abstract
Since the discovery of microRNAs (miRNAs), the study of these small noncoding RNAs has steadily increased and more than 10,000 papers have already been published. The great interest in miRNAs reflects their central role in gene-expression regulation and the implication of miRNA-specific aberrant expression in the pathogenesis of cancer, cardiac, immune-related and other diseases. Another avenue of current research is the study of circulating miRNAs in serum, plasma, and other body fluids--miRNAs may act not only within cells, but also at other sites within the body. The presence of miRNAs in body fluids may represent a gold mine of noninvasive biomarkers in cancer. Since deregulated miRNA expression is an early event in tumorigenesis, measuring circulating miRNA levels may also be useful for early cancer detection, which can contribute greatly to the success of treatment. In this Review, we discuss the role of fluid-expressed miRNAs as reliable cancer biomarkers and treatment-response predictors as well as potential new patient selection criteria for clinical trials. In addition, we explore the concept that miRNAs could function as hormones.
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Marcinkowska M, Szymanski M, Krzyzosiak WJ, Kozlowski P. Copy number variation of microRNA genes in the human genome. BMC Genomics 2011; 12:183. [PMID: 21486463 PMCID: PMC3087710 DOI: 10.1186/1471-2164-12-183] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2010] [Accepted: 04/12/2011] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND MicroRNAs (miRNAs) are important genetic elements that regulate the expression of thousands of human genes. Polymorphisms affecting miRNA biogenesis, dosage and target recognition may represent potentially functional variants. The functional consequences of single nucleotide polymorphisms (SNPs) within critical miRNA sequences and outside of miRNA genes were previously demonstrated using both experimental and computational methods. However, little is known about how copy number variations (CNVs) affect miRNA genes. RESULTS In this study, we analyzed the co-localization of all miRNA loci with known CNV regions. Using bioinformatic tools we identified and validated 209 copy number variable miRNA genes (CNV-miRNAs) in CNV regions deposited in Database of Genomic Variations (DGV) and 11 CNV-miRNAs in two sets of CNVs defined as highly polymorphic. We propose potential mechanisms of CNV-mediated variation of functional copies of miRNAs (dosage) for different types of CNVs overlapping miRNA genes. We also showed that, consistent with their essential biological functions, miRNA loci are underrepresented in highly polymorphic and well-validated CNV regions. CONCLUSION We postulate that CNV-miRNAs are potential functional variants and should be considered high priority candidate variants in genotype-phenotype association studies.
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Shen H, Lu C, Jiang Y, Tang J, Chen W, Zhang H, Zhang Q, Wang J, Liang J, Hu Z, Shen H. Genetic variants in ultraconserved elements and risk of breast cancer in Chinese population. Breast Cancer Res Treat 2011; 128:855-61. [PMID: 21331621 DOI: 10.1007/s10549-011-1395-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2010] [Accepted: 02/04/2011] [Indexed: 01/13/2023]
Abstract
Ultraconserved elements (UCEs) are the most extreme representatives of conserved non-coding sequences. Recent studies have indicated that UCEs are not mutation cold regions and likely to be concerned with cancers, including breast cancer (BC). In this study, we first screened common single-nucleotide polymorphisms (SNPs) (minor allele frequency, MAF > 0.05) in Chinese population located in 481 UCEs sequences and selected seven SNPs (rs17049105, rs13020355, rs2682406, rs2056116, rs11190870, rs9572903, and rs8004379) of uc.51, uc.82, uc.133, uc.140, uc.302, uc.353, and uc.368, respectively. A two-stage case-control study of BC with a total of 1,497 cases and 1,497 controls in Chinese population was conducted to test the hypothesis that these SNPs of UCEs are associated with BC risk. Stage I with 735 cases and 735 controls was designed to discover the risk variants, followed by stage II with 762 cases and 762 controls to validate the significant variants. In stage I, although the genotype distributions of all seven SNPs were not significantly different between BC cases and controls, logistic regression analyses revealed that the variant genotypes of rs8004379 were significantly associated with the increased risk of BC (dominant model: adjusted OR = 1.27, 95% CI = 1.01-1.58, P = 0.039). We then selected two SNPs, rs8004379 A/C and rs2056116 A/G, with lowest P values of the associations into the stage II analysis. However, none of above two SNPs were significantly associated with BC risk in both stage II and pooled set (rs8004379 AC/CC vs. AA: adjusted OR = 0.88, 95% CI = 0.68-1.13 for stage II and adjusted OR = 1.09, 95% CI = 0.92-1.29 for the pooled set; rs2056116 AG/GG vs. AA: adjusted OR = 1.12, 95% CI = 0.87-1.45 for stage II and adjusted OR = 1.11, 95% CI = 0.94-1.31 for the pooled set). These findings did not support a significant association between UCEs SNPs and the risk of BC in Chinese population.
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Affiliation(s)
- Hao Shen
- Department of Epidemiology and Biostatistics, Nanjing Medical University, Nanjing, China
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Abstract
It is widely accepted that ncRNAs (non-coding RNAs), as opposed to protein-coding RNAs, represent the majority of human transcripts; and the regulatory roles of many of these ncRNAs have been elucidated over the past decade. One important role so far recognized for ncRNAs is their participation in the epigenetic regulation of genes. Indeed, it is becoming increasingly apparent that most epigenetic mechanisms of gene expression are controlled by ncRNAs. In this review, the different types of ncRNA that are strongly linked to epigenetic regulation are characterized and their possible mechanisms discussed.
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CpG island hypermethylation-associated silencing of non-coding RNAs transcribed from ultraconserved regions in human cancer. Oncogene 2010; 29:6390-401. [PMID: 20802525 PMCID: PMC3007676 DOI: 10.1038/onc.2010.361] [Citation(s) in RCA: 156] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Although only 1.5% of the human genome appears to code for proteins, much effort in cancer research has been devoted to this minimal fraction of our DNA. However, the last few years have witnessed the realization that a large class of non-coding RNAs (ncRNAs), named microRNAs, contribute to cancer development and progression by acting as oncogenes or tumor suppressor genes. Recent studies have also shown that epigenetic silencing of microRNAs with tumor suppressor features by CpG island hypermethylation is a common hallmark of human tumors. Thus, we wondered whether there were other ncRNAs undergoing aberrant DNA methylation-associated silencing in transformed cells. We focused on the transcribed-ultraconserved regions (T-UCRs), a subset of DNA sequences that are absolutely conserved between orthologous regions of the human, rat and mouse genomes and that are located in both intra- and intergenic regions. We used a pharmacological and genomic approach to reveal the possible existence of an aberrant epigenetic silencing pattern of T-UCRs by treating cancer cells with a DNA-demethylating agent followed by hybridization to an expression microarray containing these sequences. We observed that DNA hypomethylation induces release of T-UCR silencing in cancer cells. Among the T-UCRs that were reactivated upon drug treatment, Uc.160+, Uc283+A and Uc.346+ were found to undergo specific CpG island hypermethylation-associated silencing in cancer cells compared with normal tissues. The analysis of a large set of primary human tumors (n=283) demonstrated that hypermethylation of the described T-UCR CpG islands was a common event among the various tumor types. Our finding that, in addition to microRNAs, another class of ncRNAs (T-UCRs) undergoes DNA methylation-associated inactivation in transformed cells supports a model in which epigenetic and genetic alterations in coding and non-coding sequences cooperate in human tumorigenesis.
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Edwards JK, Pasqualini R, Arap W, Calin GA. MicroRNAs and ultraconserved genes as diagnostic markers and therapeutic targets in cancer and cardiovascular diseases. J Cardiovasc Transl Res 2010; 3:271-9. [PMID: 20560048 DOI: 10.1007/s12265-010-9179-5] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/12/2010] [Accepted: 03/01/2010] [Indexed: 12/19/2022]
Abstract
MicroRNAs (miRNAs), approximately 19-25 nucleotides in length, are posttranscriptional regulators of protein expression that target and inhibit translation of messenger (m) RNAs. Recent research on miRNAs has produced a plethora of new material on the role of miRNAs in disease. Deregulation or ablation of miRNA expression has led to major pathologies including heart disease and cancer. Signatures of differential miRNA expression have been uncovered for nearly every disease. Recent research has focused on exploitation of the selectivity of these signatures as markers of disease and for therapeutic applications. The significance of additional mechanisms of abnormal posttranscriptional regulation, such as ultraconserved genes (UCGs), has recently been recognized. This review focuses on the identification of aberrant posttranscriptional regulators (miRNAs and UCGs) in cancer and cardiovascular disease and addresses the applications of this work towards diagnosis and therapy.
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Affiliation(s)
- Julianna K Edwards
- David H. Koch Center, University of Texas M. D. Anderson Cancer Center, Houston, TX, USA
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Guo F, Li Y, Liu Y, Wang J, Li Y, Li G. Inhibition of metastasis-associated lung adenocarcinoma transcript 1 in CaSki human cervical cancer cells suppresses cell proliferation and invasion. Acta Biochim Biophys Sin (Shanghai) 2010; 42:224-9. [PMID: 20213048 DOI: 10.1093/abbs/gmq008] [Citation(s) in RCA: 188] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Metastasis-associated lung adenocarcinoma transcript 1 (MALAT1) is suggested to be a long (~7 kb) non-coding RNA. MALAT1 is overexpressed in many human carcinomas, but its function remains unknown. To investigate the role of MALAT1 in human cervical cancer progression, we designed and used short hairpin RNA to inhibit MALAT1 expression in CaSki cells and validated its effect on cell proliferation and invasion. Changes in gene expression were analyzed by reverse transcriptase- polymerase chain reaction. Our data demonstrated that MALAT1 was involved in cervical cancer cell growth, cell cycle progression, and invasion through the regulation of gene expression, such as caspase-3, -8, Bax, Bcl-2, and BclxL, suggesting that MALAT1 could have important implications in cervical cancer biology. Our findings illustrate the biological significance of MALAT1 in cervical cancer progression and provide novel evidence that MALAT1 may serve as a therapeutic target in the prevention of human cervical cancer.
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Affiliation(s)
- Fengjie Guo
- Cancer Research Institute, Xiangya Medical School, Central South University, Changsha 410078, China
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50
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Galasso M, Sana ME, Volinia S. Non-coding RNAs: a key to future personalized molecular therapy? Genome Med 2010; 2:12. [PMID: 20236487 PMCID: PMC2847703 DOI: 10.1186/gm133] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Continual discoveries on non-coding RNA (ncRNA) have changed the landscape of human genetics and molecular biology. Over the past ten years it has become clear that ncRNAs are involved in many physiological cellular processes and contribute to molecular alterations in pathological conditions. Several classes of ncRNAs, such as small interfering RNAs, microRNAs, PIWI-associated RNAs, small nucleolar RNAs and transcribed ultra-conserved regions, are implicated in cancer, heart diseases, immune disorders, and neurodegenerative and metabolic diseases. ncRNAs have a fundamental role in gene regulation and, given their molecular nature, they are thus both emerging therapeutic targets and innovative intervention tools. Next-generation sequencing technologies (for example SOLiD or Genome Analyzer) are having a substantial role in the high-throughput detection of ncRNAs. Tools for non-invasive diagnostics now include monitoring body fluid concentrations of ncRNAs, and new clinical opportunities include silencing and inhibition of ncRNAs or their replacement and re-activation. Here we review recent progress on our understanding of the biological functions of human ncRNAs and their clinical potential.
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Affiliation(s)
- Marco Galasso
- Data Mining for Analysis of Microarrays, Department of Morphology and Embryology, Università Degli Studi di Ferrara, 44100 Ferrara, Italy.
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