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Lee JS, Kim G, Lee JH, Ryu JY, Oh EJ, Kim HM, Kwak S, Hur K, Chung HY. MicroRNA-135b-5p Is a Pathologic Biomarker in the Endothelial Cells of Arteriovenous Malformations. Int J Mol Sci 2024; 25:4888. [PMID: 38732107 PMCID: PMC11084653 DOI: 10.3390/ijms25094888] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2024] [Revised: 04/23/2024] [Accepted: 04/26/2024] [Indexed: 05/13/2024] Open
Abstract
Arteriovenous malformations (AVMs) are congenital vascular anomalies with a poor prognosis. AVMs are considered intractable diseases, as there is no established approach for early diagnosis and treatment. Therefore, this study aimed to provide new evidence by analyzing microRNAs (miRNAs) associated with AVM. We present fundamental evidence for the early diagnosis and treatment of AVM by analyzing miRNAs in the endothelial cells of AVMs. This study performed sequencing and validation of miRNAs in endothelial cells from normal and AVM tissues. Five upregulated and two downregulated miRNAs were subsequently analyzed under hypoxia and vascular endothelial growth factor (VEGF) treatment by one-way analysis of variance (ANOVA). Under hypoxic conditions, miR-135b-5p was significantly upregulated in the AVM compared to that under normal conditions, corresponding to increased endothelial activity (p-value = 0.0238). VEGF treatment showed no significant increase in miR-135b-5p under normal conditions, however, a surge in AVM was observed. Under both hypoxia and VEGF treatment, comparison indicated a downregulation of miR-135b-5p in AVM. Therefore, miR-135b-5p was assumed to affect the pathophysiological process of AVM and might play a vital role as a potential biomarker of AVMs for application related to diagnosis and treatment.
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Affiliation(s)
- Joon Seok Lee
- Department of Plastic and Reconstructive Surgery, School of Medicine, Kyungpook National University, Daegu 41944, Republic of Korea; (J.S.L.); (J.H.L.); (J.Y.R.); (E.J.O.); (H.M.K.); (S.K.)
| | - Gyeonghwa Kim
- Department of Biochemistry and Cell Biology, School of Medicine, Kyungpook National University, Daegu 41199, Republic of Korea;
- Cell and Matrix Research Institute, School of Medicine, Kyungpook National University, Daegu 41944, Republic of Korea
| | - Jong Ho Lee
- Department of Plastic and Reconstructive Surgery, School of Medicine, Kyungpook National University, Daegu 41944, Republic of Korea; (J.S.L.); (J.H.L.); (J.Y.R.); (E.J.O.); (H.M.K.); (S.K.)
| | - Jeong Yeop Ryu
- Department of Plastic and Reconstructive Surgery, School of Medicine, Kyungpook National University, Daegu 41944, Republic of Korea; (J.S.L.); (J.H.L.); (J.Y.R.); (E.J.O.); (H.M.K.); (S.K.)
| | - Eun Jung Oh
- Department of Plastic and Reconstructive Surgery, School of Medicine, Kyungpook National University, Daegu 41944, Republic of Korea; (J.S.L.); (J.H.L.); (J.Y.R.); (E.J.O.); (H.M.K.); (S.K.)
- Cell and Matrix Research Institute, School of Medicine, Kyungpook National University, Daegu 41944, Republic of Korea
| | - Hyun Mi Kim
- Department of Plastic and Reconstructive Surgery, School of Medicine, Kyungpook National University, Daegu 41944, Republic of Korea; (J.S.L.); (J.H.L.); (J.Y.R.); (E.J.O.); (H.M.K.); (S.K.)
- Cell and Matrix Research Institute, School of Medicine, Kyungpook National University, Daegu 41944, Republic of Korea
| | - Suin Kwak
- Department of Plastic and Reconstructive Surgery, School of Medicine, Kyungpook National University, Daegu 41944, Republic of Korea; (J.S.L.); (J.H.L.); (J.Y.R.); (E.J.O.); (H.M.K.); (S.K.)
- Cell and Matrix Research Institute, School of Medicine, Kyungpook National University, Daegu 41944, Republic of Korea
| | - Keun Hur
- Department of Biochemistry and Cell Biology, School of Medicine, Kyungpook National University, Daegu 41199, Republic of Korea;
- Cell and Matrix Research Institute, School of Medicine, Kyungpook National University, Daegu 41944, Republic of Korea
| | - Ho Yun Chung
- Department of Plastic and Reconstructive Surgery, School of Medicine, Kyungpook National University, Daegu 41944, Republic of Korea; (J.S.L.); (J.H.L.); (J.Y.R.); (E.J.O.); (H.M.K.); (S.K.)
- Cell and Matrix Research Institute, School of Medicine, Kyungpook National University, Daegu 41944, Republic of Korea
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Matai L, Slack FJ. MicroRNAs in Age-Related Proteostasis and Stress Responses. Noncoding RNA 2023; 9:26. [PMID: 37104008 PMCID: PMC10143298 DOI: 10.3390/ncrna9020026] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 03/27/2023] [Accepted: 03/30/2023] [Indexed: 04/28/2023] Open
Abstract
Aging is associated with the accumulation of damaged and misfolded proteins through a decline in the protein homeostasis (proteostasis) machinery, leading to various age-associated protein misfolding diseases such as Huntington's or Parkinson's. The efficiency of cellular stress response pathways also weakens with age, further contributing to the failure to maintain proteostasis. MicroRNAs (miRNAs or miRs) are a class of small, non-coding RNAs (ncRNAs) that bind target messenger RNAs at their 3'UTR, resulting in the post-transcriptional repression of gene expression. From the discovery of aging roles for lin-4 in C. elegans, the role of numerous miRNAs in controlling the aging process has been uncovered in different organisms. Recent studies have also shown that miRNAs regulate different components of proteostasis machinery as well as cellular response pathways to proteotoxic stress, some of which are very important during aging or in age-related pathologies. Here, we present a review of these findings, highlighting the role of individual miRNAs in age-associated protein folding and degradation across different organisms. We also broadly summarize the relationships between miRNAs and organelle-specific stress response pathways during aging and in various age-associated diseases.
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Affiliation(s)
| | - Frank J. Slack
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02115, USA
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Yuan L, Jiang X, Gong Q, Gao N. Arsenic resistance protein 2 and microRNA biogenesis: Biological implications in cancer development. Pharmacol Ther 2023; 244:108386. [PMID: 36933704 DOI: 10.1016/j.pharmthera.2023.108386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2023] [Revised: 03/12/2023] [Accepted: 03/15/2023] [Indexed: 03/18/2023]
Abstract
Arsenic resistance protein 2 (Ars2) is a nuclear protein that plays a critical role in the regulation of microRNA (miRNA) biogenesis. Ars2 is required for cell proliferation and for the early stages of mammalian development through a possible effect on miRNA processing. Increasing evidence reveal that Ars2 is highly expressed in proliferating cancer cells, suggesting that Ars2 may be a potential therapeutic target for cancer. Therefore, development of the novel Ars2 inhibitors could represent the novel therapeutic strategies for treatment of cancer. In this review, we briefly discuss the mechanisms by which Ars2 regulates miRNA biogenesis and its impact on cell proliferation and cancer development. Particularly, we mainly discuss the role of Ars2 in the regulation of cancer development and highlight pharmacological targeting of Ars2 as a promising cancer therapeutic strategy.
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Affiliation(s)
- Liang Yuan
- Key Laboratory of Basic Pharmacology of Ministry of Education, Joint International Research Laboratory of Ethnomedicine of Ministry of Education, Zunyi Medical University, Zunyi, Guizhou 563006, China
| | - Xiuxing Jiang
- College of Pharmacy, Army Medical University, 30 Gaotanyan Street, Shapingba District, Chongqing 400038, China
| | - Qihai Gong
- Key Laboratory of Basic Pharmacology of Ministry of Education, Joint International Research Laboratory of Ethnomedicine of Ministry of Education, Zunyi Medical University, Zunyi, Guizhou 563006, China.
| | - Ning Gao
- Key Laboratory of Basic Pharmacology of Ministry of Education, Joint International Research Laboratory of Ethnomedicine of Ministry of Education, Zunyi Medical University, Zunyi, Guizhou 563006, China.
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4
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Ahmed U, Ashfaq UA, Qasim M, Ahmad I, Ahmad HU, Tariq M, Masoud MS, Khaliq S. Dysregulation of circulating miRNAs promotes the pathogenesis of diabetes-induced cardiomyopathy. PLoS One 2021; 16:e0250773. [PMID: 33909697 PMCID: PMC8081166 DOI: 10.1371/journal.pone.0250773] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Accepted: 04/13/2021] [Indexed: 12/12/2022] Open
Abstract
Diabetic Cardiomyopathy (DCM) is characterized by myocardial dysfunction caused by diabetes mellitus. After-effects of diabetic cardiomyopathy are far more lethal than non-diabetic cardiomyopathy. More than 300 million people suffer from diabetes and cardiovascular disorder which is expected to be elevated to an alarming figure of 450 million by 2030. Recent studies suggested that miRNA plays important role in the onset of diabetic cardiomyopathy. This study was designed to identify the miRNA that is responsible for the onset of diabetic cardiomyopathy using in silico and in vitro approaches. In this study, to identify the miRNA responsible for the onset of diabetic cardiomyopathy, in silico analysis was done to predict the role of these circulating miRNAs in type 2 diabetic cardiomyopathy. Shared miRNAs that are present in both diseases were selected for further analysis. Total RNA and miRNA were extracted from blood samples taken from type 2 diabetic patients as well as healthy controls to analyze the expression of important genes like AKT, VEGF, IGF, FGF1, ANGPT2 using Real-time PCR. The expression of ANGPT2 was up-regulated and AKT, VEGF, IGF, FGF1 were down-regulated in DCM patients as compared to healthy controls. The miRNA expression of miR-17 was up-regulated and miR-24, miR-150, miR-199a, miR-214, and miR-320a were down-regulated in the DCM patients as compared to healthy controls. This shows that dysregulation of target genes and miRNA may contribute towards the pathogenesis of DCM and more studies should be conducted to elucidate the role of circulating miRNAs to use them as therapeutic and diagnostic options.
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Affiliation(s)
- Uzair Ahmed
- Department of Bioinformatics and Biotechnology, Government College University, Faisalabad, Pakistan
- Department of Physiology and Cell Biology, University of Health Sciences, Lahore, Pakistan
| | - Usman Ali Ashfaq
- Department of Bioinformatics and Biotechnology, Government College University, Faisalabad, Pakistan
| | - Muhammad Qasim
- Department of Bioinformatics and Biotechnology, Government College University, Faisalabad, Pakistan
| | - Imtiaz Ahmad
- Department of Cardiology, Punjab Institute of Cardiology, Lahore, Pakistan
| | - Hafiz Usman Ahmad
- Department of Physiology and Cell Biology, University of Health Sciences, Lahore, Pakistan
| | - Muhammad Tariq
- Department of Biotechnology, Mirpur University of Sciences and Technology, Mirpur, AJK, Pakistan
| | - Muhammad Shareef Masoud
- Department of Bioinformatics and Biotechnology, Government College University, Faisalabad, Pakistan
| | - Saba Khaliq
- Department of Physiology and Cell Biology, University of Health Sciences, Lahore, Pakistan
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5
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Shirazi S, Huang CC, Kang M, Lu Y, Ravindran S, Cooper LF. The importance of cellular and exosomal miRNAs in mesenchymal stem cell osteoblastic differentiation. Sci Rep 2021; 11:5953. [PMID: 33723364 PMCID: PMC7960990 DOI: 10.1038/s41598-021-85306-2] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Accepted: 02/12/2021] [Indexed: 12/19/2022] Open
Abstract
The differentiation of osteoblasts is under complex regulation that includes autocrine and paracrine signaling from MSCs. Exosomes are important components of the MSC secretome and their cargo contains numerous miRNAs. In this study, the importance of MSC miRNAs in modulation of osteoblastic differentiation was examined by global reduction of miRNA biosynthesis in Dicer knock down hMSCs. We additionally impaired hMSC responses to miRNAs by knockdown of Argonaute 2 expression. Knockdown of Dicer and Argonaute 2 both reduced osteoblastic differentiation of hMSCs. This was observed at the levels of hMSC culture mineralization and osteoblastic gene expression. The treatment of Dicer deficient hMSCs with wild type hMSC exosomes effectively recovered the impaired osteoblastic differentiation. Dicer knockdown reduced the quantity and diversity of miRNAs present in hMSC exosomes. miRSeq data and KEGG analysis implicated the miRNA-dependent effects on multiple osteoinductive pathways in Dicer deficient cells, including the Hippo signaling and TGF-beta signaling pathways. Treatment of hMSCs with mimics of miRNAs significantly downregulated in Dicer knockdown cells recovered functions of exosome-mediated signaling in hMSCs. These results indicate that hMSC exosomes exert miRNA-dependent control that contributes to osteoblastic differentiation.
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Affiliation(s)
- Sajjad Shirazi
- Department of Oral Biology, College of Dentistry, University of Illinois at Chicago, 801 S Paulina St., Room 561C, Chicago, IL, 60612, USA
| | - Chun-Chieh Huang
- Department of Oral Biology, College of Dentistry, University of Illinois at Chicago, 801 S Paulina St., Room 561C, Chicago, IL, 60612, USA
| | - Miya Kang
- Department of Oral Biology, College of Dentistry, University of Illinois at Chicago, 801 S Paulina St., Room 561C, Chicago, IL, 60612, USA
| | - Yu Lu
- Department of Oral Biology, College of Dentistry, University of Illinois at Chicago, 801 S Paulina St., Room 561C, Chicago, IL, 60612, USA
| | - Sriram Ravindran
- Department of Oral Biology, College of Dentistry, University of Illinois at Chicago, 801 S Paulina St., Room 561C, Chicago, IL, 60612, USA.
| | - Lyndon F Cooper
- Department of Oral Biology, College of Dentistry, University of Illinois at Chicago, 801 S Paulina St., Room 561C, Chicago, IL, 60612, USA.
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6
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Domingo S, Solé C, Moliné T, Ferrer B, Cortés-Hernández J. MicroRNAs in Several Cutaneous Autoimmune Diseases: Psoriasis, Cutaneous Lupus Erythematosus and Atopic Dermatitis. Cells 2020; 9:cells9122656. [PMID: 33321931 PMCID: PMC7763020 DOI: 10.3390/cells9122656] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 12/01/2020] [Accepted: 12/05/2020] [Indexed: 02/06/2023] Open
Abstract
MicroRNAs (miRNAs) are endogenous small non-coding RNA molecules that regulate the gene expression at a post-transcriptional level and participate in maintaining the correct cell homeostasis and functioning. Different specific profiles have been identified in lesional skin from autoimmune cutaneous diseases, and their deregulation cause aberrant control of biological pathways, contributing to pathogenic conditions. Detailed knowledge of microRNA-affected pathways is of crucial importance for understating their role in skin autoimmune diseases. They may be promising therapeutic targets with novel clinical implications. They are not only present in skin tissue, but they have also been found in other biological fluids, such as serum, plasma and urine from patients, and therefore, they are potential biomarkers for the diagnosis, prognosis and response to treatment. In this review, we discuss the current understanding of the role of described miRNAs in several cutaneous autoimmune diseases: psoriasis (Ps, 33 miRNAs), cutaneous lupus erythematosus (CLE, 2 miRNAs) and atopic dermatitis (AD, 8 miRNAs). We highlight their role as crucial elements implicated in disease pathogenesis and their applicability as biomarkers and as a novel therapeutic approach in the management of skin inflammatory diseases.
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Affiliation(s)
- Sandra Domingo
- Rheumatology Research Group, Lupus Unit, Hospital Universitari Vall d’Hebron, Institut de Recerca (VHIR), Universitat Autònoma de Barcelona, 08035 Barcelona, Spain; (S.D.); (J.C.-H.)
| | - Cristina Solé
- Rheumatology Research Group, Lupus Unit, Hospital Universitari Vall d’Hebron, Institut de Recerca (VHIR), Universitat Autònoma de Barcelona, 08035 Barcelona, Spain; (S.D.); (J.C.-H.)
- Correspondence: ; Tel.: +34-9-3489-4045
| | - Teresa Moliné
- Department of Pathology, Hospital Universitari Vall d’Hebron, Institut de Recerca (VHIR), Universitat Autònoma de Barcelona, 08035 Barcelona, Spain; (T.M.); (B.F.)
| | - Berta Ferrer
- Department of Pathology, Hospital Universitari Vall d’Hebron, Institut de Recerca (VHIR), Universitat Autònoma de Barcelona, 08035 Barcelona, Spain; (T.M.); (B.F.)
| | - Josefina Cortés-Hernández
- Rheumatology Research Group, Lupus Unit, Hospital Universitari Vall d’Hebron, Institut de Recerca (VHIR), Universitat Autònoma de Barcelona, 08035 Barcelona, Spain; (S.D.); (J.C.-H.)
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7
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Wang P, Li Q, Sun N, Gao Y, Liu JS, Deng K, He J. MiRACLe: an individual-specific approach to improve microRNA-target prediction based on a random contact model. Brief Bioinform 2020; 22:5868068. [PMID: 34020537 DOI: 10.1093/bib/bbaa117] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2020] [Revised: 04/30/2020] [Accepted: 05/16/2020] [Indexed: 12/13/2022] Open
Abstract
Deciphering microRNA (miRNA) targets is important for understanding the function of miRNAs as well as miRNA-based diagnostics and therapeutics. Given the highly cell-specific nature of miRNA regulation, recent computational approaches typically exploit expression data to identify the most physiologically relevant target messenger RNAs (mRNAs). Although effective, those methods usually require a large sample size to infer miRNA-mRNA interactions, thus limiting their applications in personalized medicine. In this study, we developed a novel miRNA target prediction algorithm called miRACLe (miRNA Analysis by a Contact modeL). It integrates sequence characteristics and RNA expression profiles into a random contact model, and determines the target preferences by relative probability of effective contacts in an individual-specific manner. Evaluation by a variety of measures shows that fitting TargetScan, a frequently used prediction tool, into the framework of miRACLe can improve its predictive power with a significant margin and consistently outperform other state-of-the-art methods in prediction accuracy, regulatory potential and biological relevance. Notably, the superiority of miRACLe is robust to various biological contexts, types of expression data and validation datasets, and the computation process is fast and efficient. Additionally, we show that the model can be readily applied to other sequence-based algorithms to improve their predictive power, such as DIANA-microT-CDS, miRanda-mirSVR and MirTarget4. MiRACLe is publicly available at https://github.com/PANWANG2014/miRACLe.
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Affiliation(s)
- Pan Wang
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Qi Li
- Center for Statistical Science & Department of Industry Engineering, Tsinghua University, Beijing, China
| | - Nan Sun
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yibo Gao
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jun S Liu
- Department of Statistics, Harvard University, Cambridge, MA, USA
| | - Ke Deng
- Center for Statistical Science & Department of Industry Engineering, Tsinghua University, Beijing, China
| | - Jie He
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
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Kobayashi M, Benakis C, Anderson C, Moore MJ, Poon C, Uekawa K, Dyke JP, Fak JJ, Mele A, Park CY, Zhou P, Anrather J, Iadecola C, Darnell RB. AGO CLIP Reveals an Activated Network for Acute Regulation of Brain Glutamate Homeostasis in Ischemic Stroke. Cell Rep 2019; 28:979-991.e6. [PMID: 31340158 PMCID: PMC6784548 DOI: 10.1016/j.celrep.2019.06.075] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Revised: 12/11/2018] [Accepted: 06/21/2019] [Indexed: 12/17/2022] Open
Abstract
Post-transcriptional regulation by microRNAs (miRNAs) is essential for complex molecular responses to physiological insult and disease. Although many disease-associated miRNAs are known, their global targets and culminating network effects on pathophysiology remain poorly understood. We applied Argonaute (AGO) crosslinking immunoprecipitation (CLIP) to systematically elucidate altered miRNA-target interactions in brain following ischemia and reperfusion (I/R) injury. Among 1,190 interactions identified, the most prominent was the cumulative loss of target regulation by miR-29 family members. Integration of translational and time-course RNA profiles revealed a dynamic mode of miR-29 target de-regulation, led by acute translational activation and a later increase in RNA levels, allowing rapid proteomic changes to take effect. These functional regulatory events rely on canonical and non-canonical miR-29 binding and engage glutamate reuptake signals, such as glial glutamate transporter (GLT-1), to control local glutamate levels. These results uncover a miRNA target network that acts acutely to maintain brain homeostasis after ischemic stroke.
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Affiliation(s)
- Mariko Kobayashi
- Laboratory of Molecular Neuro-Oncology and Howard Hughes Medical Institute, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA.
| | - Corinne Benakis
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, 407 East 61(st) Street, New York, NY 10065, USA
| | - Corey Anderson
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, 407 East 61(st) Street, New York, NY 10065, USA
| | - Michael J Moore
- Laboratory of Molecular Neuro-Oncology and Howard Hughes Medical Institute, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Carrie Poon
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, 407 East 61(st) Street, New York, NY 10065, USA
| | - Ken Uekawa
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, 407 East 61(st) Street, New York, NY 10065, USA
| | - Jonathan P Dyke
- Department of Radiology, Citigroup Biomedical Imaging Center, Weill Cornell Medicine, 516 East 72(nd) Street, New York, NY 10021, USA
| | - John J Fak
- Laboratory of Molecular Neuro-Oncology and Howard Hughes Medical Institute, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Aldo Mele
- Laboratory of Molecular Neuro-Oncology and Howard Hughes Medical Institute, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Christopher Y Park
- Laboratory of Molecular Neuro-Oncology and Howard Hughes Medical Institute, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Ping Zhou
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, 407 East 61(st) Street, New York, NY 10065, USA
| | - Josef Anrather
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, 407 East 61(st) Street, New York, NY 10065, USA
| | - Costantino Iadecola
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, 407 East 61(st) Street, New York, NY 10065, USA
| | - Robert B Darnell
- Laboratory of Molecular Neuro-Oncology and Howard Hughes Medical Institute, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA.
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9
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Peng H, Wang L, Su Q, Yi K, Du J, Wang Z. MiR-31-5p promotes the cell growth, migration and invasion of colorectal cancer cells by targeting NUMB. Biomed Pharmacother 2019; 109:208-216. [PMID: 30396078 DOI: 10.1016/j.biopha.2018.10.048] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Revised: 10/08/2018] [Accepted: 10/09/2018] [Indexed: 02/07/2023] Open
Abstract
The aim of this study was to investigate the role and specific molecular mechanism of miR-31-5 in colorectal cancer. The relative expression of miR-31-5p and NUMB in colorectal cancer tissues was analyzed by qRT-PCR. To knock down the expression of miR-31-5p, the transfection of miR-31-5p inhibitor was performed. The transfection with miR-31-5p mimic was used for miR-31-5p overexpression and pcDNA3.0-NUMB plasmid was used for NUMB overexpression. CCK-8 assay was used to analyze the cell proliferation. Flow cytometry was used to evaluate the cell apoptosis and cell cycle. Matrigel invasion assay was performed to assess the invasion potency and migration assay was performed to assess the migration potency. Hoechst 33258 staining assay was performed to analyze the cell apoptosis of HT29 cells after the indicated transfection. Luciferase activity assays were performed to confirmed the potential binding site for miR-31-5p in 3'-UTR region of NUMB. MiR-31-5p is highly expressed in colorectal cancer and is critical for the cell proliferation, cell cycle, migration, invasion and apoptosis. NUMB is target of miR-31-5p and NUMB overexpression inhibited the cell proliferation, migration, invasion and induced cell cycle arrest and apoptosis in HT29 colorectal cancer cells. In conclusion, miR-31-5p promoted the cell growth, migration and invasion by targeting NUMB in colorectal cancer cells.
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Affiliation(s)
- Hong Peng
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, PR China; Department of Anorectal Surgery, Nanchong Central Hospital, Nanchong, Sichuan 637000, PR China
| | - Longfei Wang
- Department of Pharmacy, Nanchong Central Hospital, Nanchong, Sichuan 637000, PR China
| | - Qiang Su
- Department of Clinical Pharmacy, Nanchong Central Hospital, Nanchong, Sichuan 637000, PR China
| | - Kun Yi
- Department of Image Diagnoses, Nanchong Central Hospital, Nanchong, Sichuan 637000, PR China
| | - Jingwei Du
- Department of Otolaryngology, Nanchong Central Hospital, Nanchong, Sichuan 637000, PR China
| | - Ziwei Wang
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, PR China.
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10
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Mononuclear-cell-derived microparticles attenuate endothelial inflammation by transfer of miR-142-3p in a CD39 dependent manner. Purinergic Signal 2018; 14:423-432. [PMID: 30244433 DOI: 10.1007/s11302-018-9624-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Accepted: 08/29/2018] [Indexed: 12/22/2022] Open
Abstract
Plasma microparticles (MP) bear functional active ectonucleotidases of the CD39 family with implications in vascular inflammation. MP appear to be able to fuse with cells and transfer genetic information. Here, we tested whether levels of different immunomodulatory microRNAs (miRs) in plasma MP are modulated by CD39 after experimental hepatectomy. We further investigated whether horizontal transfer of miR-142-3p between mononuclear (MNC) and endothelial cells via MP is regulated by purinergic signaling. Partial hepatectomy was performed in C57BL/6 wild type and Cd39 null mice. MP were collected via ultracentrifugation. MNC were stimulated with nucleotides and nucleosides, in vitro, and tested for miR-142-3p levels. Fusion of MNC-derived MP and endothelial cells with subsequent transfer of miR-142-3p was imaged by flow cytometry and confocal microscopy. Endothelial inflammation and apoptosis were quantified after transfection with miR-142-3p. Significantly lower miR-142-3p levels were observed in plasma MP of Cd39 null mice after partial hepatectomy, when compared to C57BL/6 wild types (p < 0.05). In contrast to extracellular nucleotides, anti-inflammatory adenosine significantly increased miR-142-3p levels in MNC-derived MP, in vitro (p < 0.05). MNC-derived MP are able to transfer miR-142-3p to endothelial cells by fusion. Transfection of endothelial cells with miR-142-3p decreased TNF-α levels (p < 0.05) and endothelial apoptosis (p < 0.05). MiR-142-3p levels in MNC-derived MP are modulated by nucleoside signaling and might reflect compensatory responses in vascular inflammation. Our data suggest the transfer of genetic information via shed MP as a putative mechanism of intercellular communication-with implications in organ regeneration.
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11
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Bovaird S, Patel D, Padilla JCA, Lécuyer E. Biological functions, regulatory mechanisms, and disease relevance of RNA localization pathways. FEBS Lett 2018; 592:2948-2972. [PMID: 30132838 DOI: 10.1002/1873-3468.13228] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Revised: 08/06/2018] [Accepted: 08/17/2018] [Indexed: 12/12/2022]
Abstract
The asymmetric subcellular distribution of RNA molecules from their sites of transcription to specific compartments of the cell is an important aspect of post-transcriptional gene regulation. This involves the interplay of intrinsic cis-regulatory elements within the RNA molecules with trans-acting RNA-binding proteins and associated factors. Together, these interactions dictate the intracellular localization route of RNAs, whose downstream impacts have wide-ranging implications in cellular physiology. In this review, we examine the mechanisms underlying RNA localization and discuss their biological significance. We also review the growing body of evidence pointing to aberrant RNA localization pathways in the development and progression of diseases.
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Affiliation(s)
- Samantha Bovaird
- Institut de recherches cliniques de Montréal (IRCM), QC, Canada.,Division of Experimental Medicine, Faculty of Medicine, McGill University, Montreal, QC, Canada
| | - Dhara Patel
- Institut de recherches cliniques de Montréal (IRCM), QC, Canada.,Molecular Biology Program, Faculty of Medicine, Université de Montréal, QC, Canada
| | - Juan-Carlos Alberto Padilla
- Institut de recherches cliniques de Montréal (IRCM), QC, Canada.,Division of Experimental Medicine, Faculty of Medicine, McGill University, Montreal, QC, Canada
| | - Eric Lécuyer
- Institut de recherches cliniques de Montréal (IRCM), QC, Canada.,Division of Experimental Medicine, Faculty of Medicine, McGill University, Montreal, QC, Canada.,Molecular Biology Program, Faculty of Medicine, Université de Montréal, QC, Canada.,Department of Biochemistry and Molecular Medicine, Université de Montréal, QC, Canada
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12
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Nelson PT, Wang WX, Janse SA, Thompson KL. MicroRNA expression patterns in human anterior cingulate and motor cortex: A study of dementia with Lewy bodies cases and controls. Brain Res 2017; 1678:374-383. [PMID: 29146111 DOI: 10.1016/j.brainres.2017.11.009] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Revised: 11/08/2017] [Accepted: 11/10/2017] [Indexed: 02/07/2023]
Abstract
OVERVIEW MicroRNAs (miRNAs) have been implicated in neurodegenerative diseases including Parkinson's disease and Alzheimer's disease (AD). Here, we evaluated the expression of miRNAs in anterior cingulate (AC; Brodmann area [BA] 24) and primary motor (MO; BA 4) cortical tissue from aged human brains in the University of Kentucky AD Center autopsy cohort, with a focus on dementia with Lewy bodies (DLB). METHODS RNA was isolated from gray matter of brain samples with pathology-defined DLB, AD, AD + DLB, and low-pathology controls, with n = 52 cases initially included (n = 23 with DLB), all with low (<4 h) postmortem intervals. RNA was profiled using Exiqon miRNA microarrays. Quantitative PCR for post hoc replication was performed on separate cases (n = 6 controls) and included RNA isolated from gray matter of MO, AC, primary somatosensory (BA 3), and dorsolateral prefrontal (BA 9) cortical regions. RESULTS The miRNA expression patterns differed substantially according to anatomic location: of the relatively highly-expressed miRNAs, 150/481 (31%) showed expression that was different between AC versus MO (at p < .05 following correction for multiple comparisons), most (79%) with higher expression in MO. A subset of these results were confirmed in qPCR validation focusing on miR-7, miR-153, miR-133b, miR-137, and miR-34a. No significant variation in miRNA expression was detected in association with either neuropathology or sex after correction for multiple comparisons. CONCLUSION A subset of miRNAs (some previously associated with α-synucleinopathy and/or directly targeting α-synuclein mRNA) were differentially expressed in AC and MO, which may help explain why these brain regions show differences in vulnerability to Lewy body pathology.
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Affiliation(s)
- Peter T Nelson
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY 40536, USA; Department of Pathology, University of Kentucky, Lexington, KY 40536, USA.
| | - Wang-Xia Wang
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY 40536, USA
| | - Sarah A Janse
- Department of Statistics, University of Kentucky, Lexington, KY 40536, USA
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13
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Shi J, Fu Q, Yang P, Liu H, Ji L, Wang K. Downregulation of microRNA‐15a‐3p is correlated with clinical outcome and negatively regulates cancer proliferation and migration in human osteosarcoma. J Cell Biochem 2017; 119:1215-1222. [DOI: 10.1002/jcb.26294] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Accepted: 07/18/2017] [Indexed: 01/11/2023]
Affiliation(s)
- Jiyuan Shi
- Department of OrthopaedicsShanxi Provincial People's HospitalXi'anChina
- First Department of OrthopaedicsThe Second Affiliated Hospital of Xi'an Jiaotong UniversityXi'anChina
| | - Qiang Fu
- Department of HematologyXi'an Children's HospitalXi'anChina
| | - Pei Yang
- First Department of OrthopaedicsThe Second Affiliated Hospital of Xi'an Jiaotong UniversityXi'anChina
| | - Huitong Liu
- Department of OrthopaedicsShanxi Provincial People's HospitalXi'anChina
| | - Le Ji
- Department of OrthopaedicsShanxi Provincial People's HospitalXi'anChina
| | - Kunzheng Wang
- Department of OrthopaedicsShanxi Provincial People's HospitalXi'anChina
- First Department of OrthopaedicsThe Second Affiliated Hospital of Xi'an Jiaotong UniversityXi'anChina
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14
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MicroRNA-193-5p modulates angiogenesis through IGF2 in type 2 diabetic cardiomyopathy. Biochem Biophys Res Commun 2017; 491:876-882. [DOI: 10.1016/j.bbrc.2017.07.108] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Accepted: 07/19/2017] [Indexed: 12/31/2022]
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15
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Sells E, Pandey R, Chen H, Skovan BA, Cui H, Ignatenko NA. Specific microRNA-mRNA Regulatory Network of Colon Cancer Invasion Mediated by Tissue Kallikrein-Related Peptidase 6. Neoplasia 2017; 19:396-411. [PMID: 28431272 PMCID: PMC5397577 DOI: 10.1016/j.neo.2017.02.003] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Revised: 02/02/2017] [Accepted: 02/06/2017] [Indexed: 01/05/2023] Open
Abstract
Metastatic colon cancer is a major cause of deaths among colorectal cancer (CRC) patients. Elevated expression of kallikrein 6 (KLK6), a member of a kallikrein subfamily of peptidase S1 family serine proteases, has been reported in CRC and is associated with low patient survival rates and poor disease prognosis. We knocked down KLK6 expression in HCT116 colon cancer cells to determine the significance of KLK6 expression for metastatic dissemination and to identify the KLK6-associated microRNAs (miRNAs) signaling networks in metastatic colon cancer. KLK6 suppression resulted in decreased cells invasion in vitro with a minimal effect on the cell growth and viability. In vivo, animals with orthotopic colon tumors deficient in KLK6 expression had the statistically significant increase in survival rates (P = .005) and decrease in incidence of distant metastases. We further performed the integrated miRNA and messenger RNA (mRNA) expression profiling to identify functional miRNA-mRNA interactions associated with KLK6-mediated invasiveness of colon cancer. Through bioinformatics analysis we identified and functionally validated the top two up-regulated miRNAs, miR-182 and miR-203, and one down-regulated miRNA, miRNA-181d, and their seven mRNA effectors. The established miRNA-mRNA interactions modulate cellular proliferation, differentiation and epithelial–mesenchymal transition (EMT) in KLK6-expressing colon cancer cells via the TGF-β signaling pathway and RAS-related GTP-binding proteins. We confirmed the potential tumor suppressive properties of miR-181d and miR-203 in KLK6-expressing HCT116 cells using Matrigel invasion assay. Our data provide experimental evidence that KLK6 controls metastasis formation in colon cancer via specific downstream network of miRNA-mRNA effectors.
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Affiliation(s)
- Earlphia Sells
- Biochemistry and, Molecular and Cellular Biology Graduate Program, Department of Molecular and Cellular Biology, College of Science, University of Arizona, Tucson, AZ, USA
| | - Ritu Pandey
- University of Arizona, Cancer Center, University of Arizona, Tucson, AZ, USA; Department of Cellular and Molecular Medicine, University of Arizona, Tucson, AZ, USA
| | - Hwudaurw Chen
- University of Arizona, Cancer Center, University of Arizona, Tucson, AZ, USA
| | - Bethany A Skovan
- University of Arizona, Cancer Center, University of Arizona, Tucson, AZ, USA
| | - Haiyan Cui
- University of Arizona, Cancer Center, University of Arizona, Tucson, AZ, USA
| | - Natalia A Ignatenko
- Department of Cellular and Molecular Medicine, University of Arizona, Tucson, AZ, USA.
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16
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Vargas JNS, Kar AN, Kowalak JA, Gale JR, Aschrafi A, Chen CY, Gioio AE, Kaplan BB. Axonal localization and mitochondrial association of precursor microRNA 338. Cell Mol Life Sci 2016; 73:4327-4340. [PMID: 27229124 PMCID: PMC5056120 DOI: 10.1007/s00018-016-2270-6] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Revised: 04/28/2016] [Accepted: 05/06/2016] [Indexed: 12/22/2022]
Abstract
MicroRNAs (miRNAs) selectively localize to subcompartments of the neuron, such as dendrites, axons, and presynaptic terminals, where they regulate the local protein synthesis of their putative target genes. In addition to mature miRNAs, precursor miRNAs (pre-miRNAs) have also been shown to localize to somatodendritic and axonal compartments. miRNA-338 (miR-338) regulates the local expression of several nuclear-encoded mitochondrial mRNAs within axons of sympathetic neurons. Previous work has shown that precursor miR-338 (pre-miR-338) introduced into the axon can locally be processed into mature miR-338, where it can regulate local ATP synthesis. However, the mechanisms underlying the localization of pre-miRNAs to the axonal compartment remain unknown. In this study, we investigated the axonal localization of pre-miR-338. Using proteomic and biochemical approaches, we provide evidence for the localization of pre-miR-338 to distal neuronal compartments and identify several constituents of the pre-miR-338 ribonucleoprotein complex. Furthermore, we found that pre-miR-338 is associated with the mitochondria in axons of superior cervical ganglion (SCG) neurons. The maintenance of mitochondrial function within axons requires the precise spatiotemporal synthesis of nuclear-encoded mRNAs, some of which are regulated by miR-338. Therefore, the association of pre-miR-338 with axonal mitochondria could serve as a reservoir of mature, biologically active miRNAs, which could coordinate the intra-axonal expression of multiple nuclear-encoded mitochondrial mRNAs.
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Affiliation(s)
- Jose Norberto S Vargas
- Section on Neurobiology, Laboratory of Molecular Biology, Division of Intramural Research Programs, National Institute of Mental Health, National Institutes of Health, Bethesda, MD, 20892-4411, USA
| | - Amar N Kar
- Section on Neurobiology, Laboratory of Molecular Biology, Division of Intramural Research Programs, National Institute of Mental Health, National Institutes of Health, Bethesda, MD, 20892-4411, USA
| | - Jeffrey A Kowalak
- NINDS/NIMH Clinical Proteomics Unit, Division of Intramural Research Programs, National Institutes of Health, Bethesda, MD, USA
| | - Jenna R Gale
- Section on Neurobiology, Laboratory of Molecular Biology, Division of Intramural Research Programs, National Institute of Mental Health, National Institutes of Health, Bethesda, MD, 20892-4411, USA
| | - Armaz Aschrafi
- Section on Neurobiology, Laboratory of Molecular Biology, Division of Intramural Research Programs, National Institute of Mental Health, National Institutes of Health, Bethesda, MD, 20892-4411, USA
| | - Cai-Yun Chen
- Section on Neurobiology, Laboratory of Molecular Biology, Division of Intramural Research Programs, National Institute of Mental Health, National Institutes of Health, Bethesda, MD, 20892-4411, USA
| | - Anthony E Gioio
- Section on Neurobiology, Laboratory of Molecular Biology, Division of Intramural Research Programs, National Institute of Mental Health, National Institutes of Health, Bethesda, MD, 20892-4411, USA
| | - Barry B Kaplan
- Section on Neurobiology, Laboratory of Molecular Biology, Division of Intramural Research Programs, National Institute of Mental Health, National Institutes of Health, Bethesda, MD, 20892-4411, USA.
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17
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Gnazzo MM, Uhlemann EME, Villarreal AR, Shirayama M, Dominguez EG, Skop AR. The RNA-binding protein ATX-2 regulates cytokinesis through PAR-5 and ZEN-4. Mol Biol Cell 2016; 27:3052-3064. [PMID: 27559134 PMCID: PMC5063614 DOI: 10.1091/mbc.e16-04-0219] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Accepted: 08/17/2016] [Indexed: 12/15/2022] Open
Abstract
The mechanisms that mediate the temporal and spatial recruitment of cell division factors to the spindle midzone and midbody remain unclear. Cell division is regulated by the conserved RNA-binding protein, ATX-2/Ataxin-2, which facilitates the targeting of ZEN-4 to the spindle midzone by mediating PAR-5. The spindle midzone harbors both microtubules and proteins necessary for furrow formation and the completion of cytokinesis. However, the mechanisms that mediate the temporal and spatial recruitment of cell division factors to the spindle midzone and midbody remain unclear. Here we describe a mechanism governed by the conserved RNA-binding protein ATX-2/Ataxin-2, which targets and maintains ZEN-4 at the spindle midzone. ATX-2 does this by regulating the amount of PAR-5 at mitotic structures, particularly the spindle, centrosomes, and midbody. Preventing ATX-2 function leads to elevated levels of PAR-5, enhanced chromatin and centrosome localization of PAR-5–GFP, and ultimately a reduction of ZEN-4–GFP at the spindle midzone. Codepletion of ATX-2 and PAR-5 rescued the localization of ZEN-4 at the spindle midzone, indicating that ATX-2 mediates the localization of ZEN-4 upstream of PAR-5. We provide the first direct evidence that ATX-2 is necessary for cytokinesis and suggest a model in which ATX-2 facilitates the targeting of ZEN-4 to the spindle midzone by mediating the posttranscriptional regulation of PAR-5.
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Affiliation(s)
- Megan M Gnazzo
- Laboratory of Genetics and Medical Genetics, University of Wisconsin-Madison, Madison, WI 53706
| | - Eva-Maria E Uhlemann
- Laboratory of Genetics and Medical Genetics, University of Wisconsin-Madison, Madison, WI 53706
| | - Alex R Villarreal
- Laboratory of Genetics and Medical Genetics, University of Wisconsin-Madison, Madison, WI 53706
| | - Masaki Shirayama
- Program in Molecular Medicine, RNA Therapeutics Institute, and Howard Hughes Medical Institute, University of Massachusetts Medical School, Worcester, MA 01605
| | - Eddie G Dominguez
- Department of Medicine, University of Wisconsin-Madison, Madison, WI 53705
| | - Ahna R Skop
- Laboratory of Genetics and Medical Genetics, University of Wisconsin-Madison, Madison, WI 53706
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18
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de Groot S, Charehbili A, van Laarhoven HWM, Mooyaart AL, Dekker-Ensink NG, van de Ven S, Janssen LGM, Swen JJ, Smit VTHBM, Heijns JB, Kessels LW, van der Straaten T, Böhringer S, Gelderblom H, van der Hoeven JJM, Guchelaar HJ, Pijl H, Kroep JR. Insulin-like growth factor 1 receptor expression and IGF1R 3129G > T polymorphism are associated with response to neoadjuvant chemotherapy in breast cancer patients: results from the NEOZOTAC trial (BOOG 2010-01). Breast Cancer Res 2016; 18:3. [PMID: 26738606 PMCID: PMC4702399 DOI: 10.1186/s13058-015-0663-3] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2015] [Accepted: 12/12/2015] [Indexed: 11/10/2022] Open
Abstract
Background The insulin-like growth factor 1 (IGF-1) pathway is involved in cell growth and proliferation and is associated with tumorigenesis and therapy resistance. This study aims to elucidate whether variation in the IGF-1 pathway is predictive for pathologic response in early HER2 negative breast cancer (BC) patients, taking part in the phase III NEOZOTAC trial, randomizing between 6 cycles of neoadjuvant TAC chemotherapy with or without zoledronic acid. Methods Formalin-fixed paraffin-embedded tissue samples of pre-chemotherapy biopsies and operation specimens were collected for analysis of IGF-1 receptor (IGF-1R) expression (n = 216) and for analysis of 8 candidate single nucleotide polymorphisms (SNPs) in genes of the IGF-1 pathway (n = 184) using OpenArray® RealTime PCR. Associations with patient and tumor characteristics and chemotherapy response according to Miller and Payne pathologic response were performed using chi-square and regression analysis. Results During chemotherapy, a significant number of tumors (47.2 %) showed a decrease in IGF-1R expression, while in a small number of tumors an upregulation was seen (15.1 %). IGF-1R expression before treatment was not associated with pathological response, however, absence of IGF-1R expression after treatment was associated with a better response in multivariate analysis (P = 0.006) and patients with a decrease in expression during treatment showed a better response to chemotherapy as well (P = 0.020). Moreover, the variant T allele of 3129G > T in IGF1R (rs2016347) was associated with a better pathological response in multivariate analysis (P = 0.032). Conclusions Absent or diminished expression of IGF-1R after neoadjuvant chemotherapy was associated with a better pathological response. Additionally, we found a SNP (rs2016347) in IGF1R as a potential predictive marker for chemotherapy efficacy in BC patients treated with TAC. Trial registration ClinicalTrials.gov NCT01099436. Registered April 6, 2010.
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Affiliation(s)
- Stefanie de Groot
- Department of Medical Oncology, Leiden University Medical Center, Albinusdreef 2, P.O. Box 9600, 2300 RC, Leiden, The Netherlands
| | - Ayoub Charehbili
- Department of Medical Oncology, Leiden University Medical Center, Albinusdreef 2, P.O. Box 9600, 2300 RC, Leiden, The Netherlands.,Department of Surgery, Leiden University Medical Center, Albinusdreef 2, P.O. Box 9600, 2300 RC, Leiden, The Netherlands
| | - Hanneke W M van Laarhoven
- Department of Medical Oncology, Academic Medical Center, Meibergdreef 9, P.O. Box 22660, 1100 DD, Amsterdam, The Netherlands
| | - Antien L Mooyaart
- Department of Pathology, Leiden University Medical Center, Albinusdreef 2, P.O. Box 9600, 2300 RC, Leiden, The Netherlands
| | - N Geeske Dekker-Ensink
- Department of Surgery, Leiden University Medical Center, Albinusdreef 2, P.O. Box 9600, 2300 RC, Leiden, The Netherlands
| | - Saskia van de Ven
- Department of Radiotherapy, University Medical Center Utrecht, Heidelberglaan 100, P.O. Box 85500, 3508 GA, Utrecht, The Netherlands
| | - Laura G M Janssen
- Department of Endocrinology, Leiden University Medical Center, Albinusdreef 2, P.O. Box 9600, 2300 RC, Leiden, The Netherlands
| | - Jesse J Swen
- Department of Clinical Pharmacy and Toxicology, Leiden University Medical Center, Albinusdreef 2, P.O. Box 9600, 2300 RC, Leiden, The Netherlands
| | - Vincent T H B M Smit
- Department of Pathology, Leiden University Medical Center, Albinusdreef 2, P.O. Box 9600, 2300 RC, Leiden, The Netherlands
| | - Joan B Heijns
- Department of Medical Oncology, Amphia Hospital, Langendijk 75, P.O. Box 90157, 4800 RL, Breda, The Netherlands
| | - Lonneke W Kessels
- Department of Medical Oncology, Deventer Hospital, Nico Bolkesteinlaan 75, P.O. Box 5001, 7400 GC, Deventer, The Netherlands
| | - Tahar van der Straaten
- Department of Clinical Pharmacy and Toxicology, Leiden University Medical Center, Albinusdreef 2, P.O. Box 9600, 2300 RC, Leiden, The Netherlands
| | - Stefan Böhringer
- Department of Medical Statistics and Bioinformatics, Leiden University Medical Center, Albinusdreef 2, P.O. Box 9600, 2300 RC, Leiden, The Netherlands
| | - Hans Gelderblom
- Department of Medical Oncology, Leiden University Medical Center, Albinusdreef 2, P.O. Box 9600, 2300 RC, Leiden, The Netherlands
| | - Jacobus J M van der Hoeven
- Department of Medical Oncology, Leiden University Medical Center, Albinusdreef 2, P.O. Box 9600, 2300 RC, Leiden, The Netherlands
| | - Henk-Jan Guchelaar
- Department of Clinical Pharmacy and Toxicology, Leiden University Medical Center, Albinusdreef 2, P.O. Box 9600, 2300 RC, Leiden, The Netherlands
| | - Hanno Pijl
- Department of Endocrinology, Leiden University Medical Center, Albinusdreef 2, P.O. Box 9600, 2300 RC, Leiden, The Netherlands
| | - Judith R Kroep
- Department of Medical Oncology, Leiden University Medical Center, Albinusdreef 2, P.O. Box 9600, 2300 RC, Leiden, The Netherlands.
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Cui C, Xu G, Qiu J, Fan X. Up-regulation of miR-26a promotes neurite outgrowth and ameliorates apoptosis by inhibiting PTEN in bupivacaine injured mouse dorsal root ganglia. Cell Biol Int 2015; 39:933-42. [PMID: 25808510 DOI: 10.1002/cbin.10461] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2015] [Accepted: 03/10/2015] [Indexed: 01/09/2023]
Affiliation(s)
- Changlei Cui
- Department of Anesthesiology; The First Hospital of Jilin University; Changchun JiLin Province 130021 China
| | - Gong Xu
- Department of Anesthesiology; The First Hospital of Jilin University; Changchun JiLin Province 130021 China
| | - Jinpeng Qiu
- Department of Anesthesiology; The First Hospital of Jilin University; Changchun JiLin Province 130021 China
| | - Xiushuang Fan
- Department of Anesthesiology; The First Hospital of Jilin University; Changchun JiLin Province 130021 China
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20
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Deep sequencing and proteomic analysis of the microRNA-induced silencing complex in human red blood cells. Exp Hematol 2015; 43:382-392. [PMID: 25681748 DOI: 10.1016/j.exphem.2015.01.007] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2014] [Revised: 01/19/2015] [Accepted: 01/23/2015] [Indexed: 12/28/2022]
Abstract
During maturation, erythropoietic cells extrude their nuclei but retain their ability to respond to oxidant stress by tightly regulating protein translation. Several studies have reported microRNA-mediated regulation of translation during terminal stages of erythropoiesis, even after enucleation. In the present study, we performed a detailed examination of the endogenous microRNA machinery in human red blood cells using a combination of deep sequencing analysis of microRNAs and proteomic analysis of the microRNA-induced silencing complex. Among the 197 different microRNAs detected, miR-451a was the most abundant, representing more than 60% of all read sequences. In addition, miR-451a and its known target, 14-3-3ζ mRNA, were bound to the microRNA-induced silencing complex, implying their direct interaction in red blood cells. The proteomic characterization of endogenous Argonaute 2-associated microRNA-induced silencing complex revealed 26 cofactor candidates. Among these cofactors, we identified several RNA-binding proteins, as well as motor proteins and vesicular trafficking proteins. Our results demonstrate that red blood cells contain complex microRNA machinery, which might enable immature red blood cells to control protein translation independent of de novo nuclei information.
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21
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Griseri P, Pagès G. Regulation of the mRNA half-life in breast cancer. World J Clin Oncol 2014; 5:323-334. [PMID: 25114848 PMCID: PMC4127604 DOI: 10.5306/wjco.v5.i3.323] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/17/2013] [Revised: 03/31/2014] [Accepted: 05/14/2014] [Indexed: 02/06/2023] Open
Abstract
The control of the half-life of mRNA plays a central role in normal development and in disease progression. Several pathological conditions, such as breast cancer, correlate with deregulation of the half-life of mRNA encoding growth factors, oncogenes, cell cycle regulators and inflammatory cytokines that participate in cancer. Substantial stability means that a mRNA will be available for translation for a longer time, resulting in high levels of protein gene products, which may lead to prolonged responses that subsequently result in over-production of cellular mediators that participate in cancer. The stability of these mRNA is regulated at the 3’UTR level by different mechanisms involving mRNA binding proteins, micro-RNA, long non-coding RNA and alternative polyadenylation. All these events are tightly inter-connected to each other and lead to steady state levels of target mRNAs. Compelling evidence also suggests that both mRNA binding proteins and regulatory RNAs which participate to mRNA half-life regulation may be useful prognostic markers in breast cancers, pointing to a potential therapeutic approach to treatment of patients with these tumors. In this review, we summarize the main mechanisms involved in the regulation of mRNA decay and discuss the possibility of its implication in breast cancer aggressiveness and the efficacy of targeted therapy.
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Role of microRNA-29b in the ochratoxin A-induced enhanced collagen formation in human kidney cells. Toxicology 2014; 324:116-22. [PMID: 25091173 DOI: 10.1016/j.tox.2014.07.012] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2014] [Revised: 07/16/2014] [Accepted: 07/31/2014] [Indexed: 11/23/2022]
Abstract
Ochratoxin A (OTA) is an ubiquitous mycotoxin suspected to cause fibrotic kidney diseases. The involvement of mircoRNAs in these processes is unknown. Here, we investigated the role of the anti-fibrotic miR-29b in OTA-induced alterations of cellular collagen homeostasis. OTA exposure of human embryonic kidney cells (HEK293) cells led to an increase of collagen I, III and IV protein amounts without changes in collagen mRNA expression levels, indicating post-transcriptionally mediated mechanisms potentially involving microRNAs and 3'UTRs of collagen mRNAs. This was confirmed by enhanced luciferase activity of a collagen1A1-3'UTR reporter plasmid after OTA exposure. OTA also enhanced the luciferase activity of a reporter plasmid containing the seed region of miR-29b showing that OTA diminishes miR-29b action. Additionally, OTA induced an altered intracellular distribution of miR-29b leading to decreased cytoplasmic abundance of miR-29b. Abundantly added miR-29b (miR-29b clamp) completely prevented OTA-induced collagen formation. In summary, we show that OTA has the potential to initiate or support the development of fibrotic kidney diseases by involving post-transcriptional regulation mechanisms comprising miR-29b. OTA reduces the impact of miR-29b and thus enhances collagen protein expression. These findings allow a new perspective on how the exposure to nanomolar OTA concentrations can lead to fibrotic tissue alterations.
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Adjibade P, Mazroui R. Control of mRNA turnover: implication of cytoplasmic RNA granules. Semin Cell Dev Biol 2014; 34:15-23. [PMID: 24946962 DOI: 10.1016/j.semcdb.2014.05.013] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2014] [Accepted: 05/21/2014] [Indexed: 12/15/2022]
Abstract
The control of mRNA turnover is essential for the cell to rationalize its mRNA content both under physiological conditions and upon stress. Several mechanisms involved in the control of mRNA turnover have been elucidated. These include surveillance mechanisms such as nonsense-mediated decay, non-stop mediated decay and non-go-mediated decay that eliminate aberrant mRNAs, and regulatory mechanisms including AU-mediated decay, GU-mediated decay, and CDE-mediated decay that ensure mRNA plasticity. In general, the mechanisms of RNA decay rely on interactions between specific cis-acting RNA elements and selected RNA-binding proteins that either prevent the degradation of mRNA targets or induce the recruitment of decaying effectors leading to mRNA degradation. Formation of cytoplasmic RNA granules including processing bodies, stress granules, UV granules, and exosome granules have recently emerged as an additional mechanism that control mRNA turnover of selected mRNAs. Here we will review briefly review the main mechanisms that control mRNA decay and highlight possible implication of RNA granules in such mechanisms.
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Affiliation(s)
- Pauline Adjibade
- Centre de recherche du CHU de Québec, Département de biologie moléculaire, biochimie médicale et pathologie, Université Laval, Québec, PQ, Canada
| | - Rachid Mazroui
- Centre de recherche du CHU de Québec, Département de biologie moléculaire, biochimie médicale et pathologie, Université Laval, Québec, PQ, Canada.
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Gubin MM, Techasintana P, Magee JD, Dahm GM, Calaluce R, Martindale JL, Whitney MS, Franklin CL, Besch-Williford C, Hollingsworth JW, Abdelmohsen K, Gorospe M, Atasoy U. Conditional knockout of the RNA-binding protein HuR in CD4⁺ T cells reveals a gene dosage effect on cytokine production. Mol Med 2014; 20:93-108. [PMID: 24477678 DOI: 10.2119/molmed.2013.00127] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2013] [Accepted: 01/23/2014] [Indexed: 12/18/2022] Open
Abstract
The posttranscriptional mechanisms by which RNA binding proteins (RBPs) regulate T-cell differentiation and cytokine production in vivo remain unclear. The RBP HuR binds to labile mRNAs, usually leading to increases in mRNA stability and/or translation. Previous work demonstrated that HuR binds to the mRNAs encoding the Th2 transcription factor trans-acting T-cell-specific transcription factor (GATA-3) and Th2 cytokines interleukin (IL)-4 and IL-13, thereby regulating their expression. By using a novel conditional HuR knockout (KO) mouse in which HuR is deleted in activated T cells, we show that Th2-polarized cells from heterozygous HuR conditional (OX40-Cre HuR(fl/+)) KO mice had decreased steady-state levels of Gata3, Il4 and Il13 mRNAs with little changes at the protein level. Surprisingly, Th2-polarized cells from homozygous HuR conditional (OX40-Cre HuR(fl/fl)) KO mice showed increased Il2, Il4 and Il13 mRNA and protein via different mechanisms. Specifically, Il4 was transcriptionally upregulated in HuR KO T cells, whereas Il2 and Il13 mRNA stabilities increased. Additionally, when using the standard ovalbumin model of allergic airway inflammation, HuR conditional KO mice mounted a robust inflammatory response similar to mice with wild-type HuR levels. These results reveal a complex differential posttranscriptional regulation of cytokines by HuR in which gene dosage plays an important role. These findings may have significant implications in allergies and asthma, as well as autoimmune diseases and infection.
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Affiliation(s)
- Matthew M Gubin
- University of Missouri, Columbia, Missouri, United States of America
| | | | - Joseph D Magee
- University of Missouri, Columbia, Missouri, United States of America
| | - Garrett M Dahm
- University of Missouri, Columbia, Missouri, United States of America
| | - Robert Calaluce
- University of Missouri, Columbia, Missouri, United States of America
| | - Jennifer L Martindale
- National Institute on Aging, National Institutes of Health, Baltimore, Maryland, United States of America
| | - Maryln S Whitney
- University of Missouri, Columbia, Missouri, United States of America
| | - Craig L Franklin
- University of Missouri, Columbia, Missouri, United States of America
| | | | - John W Hollingsworth
- Department of Medicine, Duke University, Durham, North Carolina, United States of America
| | - Kotb Abdelmohsen
- National Institute on Aging, National Institutes of Health, Baltimore, Maryland, United States of America
| | - Myriam Gorospe
- National Institute on Aging, National Institutes of Health, Baltimore, Maryland, United States of America
| | - Ulus Atasoy
- University of Missouri, Columbia, Missouri, United States of America
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25
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Forloni M, Dogra SK, Dong Y, Conte D, Ou J, Zhu LJ, Deng A, Mahalingam M, Green MR, Wajapeyee N. miR-146a promotes the initiation and progression of melanoma by activating Notch signaling. eLife 2014; 3:e01460. [PMID: 24550252 PMCID: PMC3927633 DOI: 10.7554/elife.01460] [Citation(s) in RCA: 92] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2013] [Accepted: 01/11/2014] [Indexed: 02/07/2023] Open
Abstract
Oncogenic mutations in BRAF and NRAS occur in 70% of melanomas. In this study, we identify a microRNA, miR-146a, that is highly upregulated by oncogenic BRAF and NRAS. Expression of miR-146a increases the ability of human melanoma cells to proliferate in culture and form tumors in mice, whereas knockdown of miR-146a has the opposite effects. We show these oncogenic activities are due to miR-146a targeting the NUMB mRNA, a repressor of Notch signaling. Previous studies have shown that pre-miR-146a contains a single nucleotide polymorphism (C>G rs2910164). We find that the ability of pre-miR-146a/G to activate Notch signaling and promote oncogenesis is substantially higher than that of pre-miR-146a/C. Analysis of melanoma cell lines and matched patient samples indicates that during melanoma progression pre-miR-146a/G is enriched relative to pre-miR-146a/C, resulting from a C-to-G somatic mutation in pre-miR-146a/C. Collectively, our results reveal a central role for miR-146a in the initiation and progression of melanoma. DOI: http://dx.doi.org/10.7554/eLife.01460.001.
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Affiliation(s)
- Matteo Forloni
- Department of Pathology, Yale University School of Medicine, New Haven, United States
| | - Shaillay Kumar Dogra
- Singapore Institute of Clinical Sciences, Agency for Science Technology and Research (A*STAR), Singapore, Singapore
| | - Yuying Dong
- Department of Pathology, Yale University School of Medicine, New Haven, United States
| | - Darryl Conte
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, United States
| | - Jianhong Ou
- Program in Gene Function and Expression, University of Massachusetts Medical School, Worcester, United States
| | - Lihua Julie Zhu
- Programs in Gene Function and Expression, Molecular Medicine, and Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, United States
| | - April Deng
- Department of Pathology, University of Massachusetts Medical School, Worcester, United States
| | - Meera Mahalingam
- Dermatopathology Section, Department of Dermatology, Boston University School of Medicine, Boston, United States
| | - Michael R Green
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, United States
- Program in Gene Function and Expression, Howard Hughes Medical Institute, University of Massachusetts Medical School, Worcester, United States
| | - Narendra Wajapeyee
- Department of Pathology, Yale University School of Medicine, New Haven, United States
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Abstract
A growing body of evidence suggests that noncoding RNA (ncRNA) transcripts play a fundamental role in regulating gene expression via targeting epigenetic modifications to particular loci in the genome. Classical examples of such regulation are X-chromosome inactivation and genomic imprinting; however it is now clear that ncRNAs exert their influence over a wider array of genes throughout the metazoan genome. Accumulating evidence suggests that the ncRNAs act as guides for epigenetic silencing complexes to specific sites within the genome. Those ncRNAs involved in regulating the expression of particular protein-coding genes offer panoply of targets that when suppressed can result in derepression or activation of the ncRNA-targeted locus. Recent work has determined the underlying mechanisms involved in ncRNA-targeted epigenetic regulation in a subset of genes. These findings have resulted in a paradigm shift whereby targeted gene activation can be achieved, by targeting endogenous regulatory ncRNAs, producing potential novel treatments for genetic and infectious diseases where increases in gene expression are required.
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Affiliation(s)
- Caio Damski
- Biotechnology and Biomedical Sciences, The University of New South Wales, Sydney, NSW, 2052, Australia,
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27
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Mao Y, Keller ET, Garfield DH, Shen K, Wang J. Stromal cells in tumor microenvironment and breast cancer. Cancer Metastasis Rev 2013; 32:303-15. [PMID: 23114846 DOI: 10.1007/s10555-012-9415-3] [Citation(s) in RCA: 497] [Impact Index Per Article: 45.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Cancer is a systemic disease encompassing multiple components of both tumor cells themselves and host stromal cells. It is now clear that stromal cells in the tumor microenvironment play an important role in cancer development. Molecular events through which reactive stromal cells affect cancer cells can be defined so that biomarkers and therapeutic targets can be identified. Cancer-associated fibroblasts (CAFs) make up the bulk of cancer stroma and affect the tumor microenvironment such that they promote cancer initiation, angiogenesis, invasion, and metastasis. In breast cancer, CAFs not only promote tumor progression but also induce therapeutic resistance. Accordingly, targeting CAFs provides a novel way to control tumors with therapeutic resistance. This review summarizes the current understandings of tumor stroma in breast cancer with a particular emphasis on the role of CAFs and the therapeutic implications of CAFs. In addition, the effects of other stromal components such as endothelial cells, macrophages, and adipocytes in breast cancer are also discussed. Finally, we describe the biologic markers to categorize patients into a specific and confirmed subtype for personalized treatment.
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Affiliation(s)
- Yan Mao
- Shanghai Ruijin Hospital, Comprehensive Breast Health Center, Shanghai, China
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28
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Burroughs AM, Ando Y, Aravind L. New perspectives on the diversification of the RNA interference system: insights from comparative genomics and small RNA sequencing. WILEY INTERDISCIPLINARY REVIEWS-RNA 2013; 5:141-81. [PMID: 24311560 DOI: 10.1002/wrna.1210] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2013] [Revised: 10/03/2013] [Accepted: 11/01/2013] [Indexed: 12/19/2022]
Abstract
Our understanding of the pervasive involvement of small RNAs in regulating diverse biological processes has been greatly augmented by recent application of deep-sequencing technologies to small RNA across diverse eukaryotes. We review the currently known small RNA classes and place them in context of the reconstructed evolutionary history of the RNA interference (RNAi) protein machinery. This synthesis indicates that the earliest versions of eukaryotic RNAi systems likely utilized small RNA processed from three types of precursors: (1) sense-antisense transcriptional products, (2) genome-encoded, imperfectly complementary hairpin sequences, and (3) larger noncoding RNA precursor sequences. Structural dissection of PIWI proteins along with recent discovery of novel families (including Med13 of the Mediator complex) suggest that emergence of a distinct architecture with the N-terminal domains (also occurring separately fused to endoDNases in prokaryotes) formed via duplication of an ancestral unit was key to their recruitment as primary RNAi effectors and use of small RNAs of certain preferred lengths. Prokaryotic PIWI proteins are typically components of several RNA-directed DNA restriction or CRISPR/Cas systems. However, eukaryotic versions appear to have emerged from a subset that evolved RNA-directed RNAi. They were recruited alongside RNaseIII domains and RNA-dependent RNA polymerase (RdRP) domains, also from prokaryotic systems, to form the core eukaryotic RNAi system. Like certain regulatory systems, RNAi diversified into two distinct but linked arms concomitant with eukaryotic nucleocytoplasmic compartmentalization. Subsequent elaboration of RNAi proceeded via diversification of the core protein machinery through lineage-specific expansions and recruitment of new components from prokaryotes (nucleases and small RNA-modifying enzymes), allowing for diversification of associating small RNAs.
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Affiliation(s)
- Alexander Maxwell Burroughs
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
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29
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Li ZF, Liang YM, Lau PN, Shen W, Wang DK, Cheung WT, Xue CJ, Poon LM, Lam YW. Dynamic localisation of mature microRNAs in Human nucleoli is influenced by exogenous genetic materials. PLoS One 2013; 8:e70869. [PMID: 23940654 PMCID: PMC3735495 DOI: 10.1371/journal.pone.0070869] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2012] [Accepted: 06/26/2013] [Indexed: 11/18/2022] Open
Abstract
Although microRNAs are commonly known to function as a component of RNA-induced silencing complexes in the cytoplasm, they have been detected in other organelles, notably the nucleus and the nucleolus, of mammalian cells. We have conducted a systematic search for miRNAs in HeLa cell nucleoli, and identified 11 abundant miRNAs with a high level of nucleolar accumulation. Through in situ hybridisation, we have localised these miRNAs, including miR-191 and miR-484, in the nucleolus of a diversity of human and rodent cell lines. The nucleolar association of these miRNAs is resistant to various cellular stresses, but highly sensitive to the presence of exogenous nucleic acids. Introduction of both single- and double-stranded DNA as well as double stranded RNA rapidly induce the redistribution of nucleolar miRNAs to the cytoplasm. A similar change in subcellular distribution is also observed in cells infected with the influenza A virus. The partition of miRNAs between the nucleolus and the cytoplasm is affected by Leptomycin B, suggesting a role of Exportin-1 in the intracellular shuttling of miRNAs. This study reveals a previously unknown aspect of miRNA biology, and suggests a possible link between these small noncoding RNAs and the cellular management of foreign genetic materials.
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Affiliation(s)
- Zhou Fang Li
- Departments of Biology and Chemistry, City University of Hong Kong, Hong Kong, China
| | - Yi Min Liang
- Departments of Biology and Chemistry, City University of Hong Kong, Hong Kong, China
| | - Pui Ngan Lau
- Centre of Influenza Research and School of Public Health, The University of Hong Kong, Hong Kong, China
| | - Wei Shen
- Departments of Biology and Chemistry, City University of Hong Kong, Hong Kong, China
| | - Dai Kui Wang
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Wing Tai Cheung
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Chun Jason Xue
- Departments of Computer Science, City University of Hong Kong, Hong Kong, China
| | - Lit Man Poon
- Centre of Influenza Research and School of Public Health, The University of Hong Kong, Hong Kong, China
| | - Yun Wah Lam
- Departments of Biology and Chemistry, City University of Hong Kong, Hong Kong, China
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30
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Maurel M, Chevet E. Endoplasmic reticulum stress signaling: the microRNA connection. Am J Physiol Cell Physiol 2013; 304:C1117-26. [DOI: 10.1152/ajpcell.00061.2013] [Citation(s) in RCA: 96] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The endoplasmic reticulum (ER)-induced unfolded protein response (ERUPR) is an adaptive mechanism that is activated upon accumulation of misfolded proteins in the ER and aims at restoring ER homeostasis. The ERUPR is transduced by three major ER-resident stress sensors, namely PKR-like endoplasmic reticulum kinase (PERK), activating transcription factor 6 (ATF6), and inositol requiring enzyme 1 (IRE1). Activation of these ER stress sensors leads to transcriptional reprogramming of the cells. Recently, microRNAs (miRNAs), small noncoding RNAs that generally repress gene expression, have emerged as key regulators of ER homeostasis and important players in ERUPR-dependent signaling. Moreover, the miRNAs biogenesis machinery appears to also be regulated upon ER stress. Herein we extensively review the relationships existing between “canonical” ERUPR signaling, control of ER homeostasis, and miRNAs. We reveal an intricate signaling network that might confer specificity and selectivity to the ERUPR in tissue- or stress-dependent fashion. We discuss these issues in the context of the physiological and pathophysiological roles of ERUPR signaling.
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Affiliation(s)
- Marion Maurel
- INSERM U1053, Bordeaux, France; and
- Université Bordeaux-Segalen, Bordeaux, France
| | - Eric Chevet
- INSERM U1053, Bordeaux, France; and
- Université Bordeaux-Segalen, Bordeaux, France
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31
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Byrd AE, Brewer JW. Micro(RNA)managing endoplasmic reticulum stress. IUBMB Life 2013; 65:373-81. [PMID: 23554021 DOI: 10.1002/iub.1151] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2012] [Accepted: 01/12/2013] [Indexed: 01/11/2023]
Abstract
Cellular disturbances that cause accumulation of misfolded proteins in the endoplasmic reticulum (ER) lead to a condition referred to as "ER stress" and trigger the unfolded protein response (UPR), a signaling pathway that attempts to restore ER homeostasis. The complexity of UPR signaling can generate adaptive and apoptotic outputs, depending on the nature and duration of the ER stress. MicroRNAs (miRNAs), small non-coding RNAs that typically repress gene expression, have recently emerged as key gene regulators of the proadaptive/proapoptotic molecular switch emanating from the ER. Importantly, select miRNAs have been shown to directly regulate key UPR components.
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Affiliation(s)
- Andrew E Byrd
- Department of Microbiology and Immunology, College of Medicine, University of South Alabama, Mobile, AL 36688, USA
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32
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Serum microRNA 125b as a diagnostic or prognostic biomarker for advanced NSCLC patients receiving cisplatin-based chemotherapy. Acta Pharmacol Sin 2013; 34:309-13. [PMID: 22983388 DOI: 10.1038/aps.2012.125] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
AIM To investigate the expression profile of microRNAs in inoperable advanced non-small cell lung cancer (NSCLC) patients receiving chemotherapy and the potential relevance of microRNAs to clinicopathological characteristics and prognosis. METHODS Serum samples were taken from 260 inoperable advanced NSCLC patients and 260 healthy individuals. All the patients received cisplatin-based chemotherapy, including NP/NC regimens, GP/GC regimens, and TP/TC regimens. The serum levels of microRNAs (miR-125b, miR-10b, miR-34a and miR-155) were determined by quantitative real-time PCR. RESULTS Serum levels of the 4 microRNAs examined in NSCLC patients were significantly increased as compared with healthy individuals. The levels of miR-125b and miR-155 were changed in a similar pattern: the patients with stage IV disease had the highest one, while the patients with stage III A and stage III B disease showed similar increased levels. The levels of miR-10b and miR-34a in the patients with different stages were increased to similar extent. The level of miR-125b in poorly differentiated cancer was significantly higher than those in well and moderately differentiated cancers, while the levels of miR-10b, miR-34a, and miR-155 did not significantly differ with cancer differentiation. Among the 4 microRNAs examined, only miR-125b was significantly associated with therapeutic response, exhibiting higher expression levels in non-responsive patients. Furthermore, the high level of miR-125b was significantly correlated with poor patient survival. A multivariate Cox regression analysis showed that the expression level of miR-125b was an independent prognostic marker in NSCLC patients. CONCLUSION Our results suggest that miR-125b is a potential diagnostic or prognostic biomarker for NSCLC. This finding has important implications for development of targeted therapeutics to overcome chemotherapeutic resistance in NSCLC.
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33
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Leung AKL, Sharp PA. Quantifying Argonaute proteins in and out of GW/P-bodies: implications in microRNA activities. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2013; 768:165-82. [PMID: 23224970 DOI: 10.1007/978-1-4614-5107-5_10] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
MicroRNAs (miRNAs) are a class of ∼22nt non-coding RNAs that regulate the translational potential and stability of mRNAs. Though constituting only 1-4% of human genes, miRNAs are predicted to regulate more than 60% of all mRNAs. The action of miRNAs is mediated through their associations with Argonaute proteins and mRNA targets. Previous studies indicated that though the majority of Argonaute proteins is diffusely distributed in the cytoplasm, a small fraction is consistently observed to be concentrated in a cytoplasmic compartment called GW/P-bodies. In this chapter, we will provide a quantitative and dynamic view of the subcellular localization of miRNA function, followed by a discussion on the possible roles of PBs in miRNA silencing.
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Affiliation(s)
- Anthony K L Leung
- Department of Biochemistry and Molecular Biology, Johns Hopkins University, Baltimore, MD 21205, USA.
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34
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Stabilization of human interferon-α1 mRNA by its antisense RNA. Cell Mol Life Sci 2012; 70:1451-67. [PMID: 23224365 PMCID: PMC3607724 DOI: 10.1007/s00018-012-1216-x] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2012] [Revised: 10/31/2012] [Accepted: 11/19/2012] [Indexed: 12/15/2022]
Abstract
Antisense transcription is a widespread phenomenon in the mammalian genome and is believed to play a role in regulating gene expression. However, the exact functional significance of antisense transcription is largely unknown. Here, we show that natural antisense (AS) RNA is an important modulator of interferon-α1 (IFN-α1) mRNA levels. A ~4-kb, spliced IFN-α1 AS RNA targets a single-stranded region within a conserved secondary structure element of the IFN-α1 mRNA, an element which was previously reported to function as the nuclear export element. Following infection of human Namalwa lymphocytes with Sendai virus or infection of guinea pig 104C1 fetal fibroblasts with influenza virus A/PR/8/34, expression of IFN-α1 AS RNA becomes elevated. This elevated expression results in increased IFN-α1 mRNA stability because of the cytoplasmic (but not nuclear) interaction of the AS RNA with the mRNA at the single-stranded region. This results in increased IFN-α protein production. The silencing of IFN-α1 AS RNA by sense oligonucleotides or over-expression of antisense oligoribonucleotides, which were both designed from the target region, confirmed the critical role of the AS RNA in the post-transcriptional regulation of IFN-α1 mRNA levels. This AS RNA stabilization effect is caused by the prevention of the microRNA (miRNA)-induced destabilization of IFN-α1 mRNA due to masking of the miR-1270 binding site. This discovery not only reveals a regulatory pathway for controlling IFN-α1 gene expression during the host innate immune response against virus infection but also suggests a reason for the large number of overlapping complementary transcripts with previously unknown function.
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35
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MicroRNAs and unusual small RNAs discovered in Kaposi's sarcoma-associated herpesvirus virions. J Virol 2012; 86:12717-30. [PMID: 22973026 DOI: 10.1128/jvi.01473-12] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
It is widely held that any given virus uses only one type of nucleic acid for genetic information storage. However, this consensus has been challenged slightly by several recent studies showing that many RNA species are present within a range of DNA viruses that include Kaposi's sarcoma-associated herpesvirus (KSHV). RNAs extracted from purified DNA virus particles exhibit great diversity in terms of length, abundance, temporal expression, cellular localization, and coding capacity during viral infection. In addition to known RNA species, the current study showed that small regulatory RNAs were present in KSHV virions. A large number of viral and cellular microRNAs (miRNAs), as well as unusual small RNAs (usRNAs), were detected in KSHV virions by using deep sequencing. Both viral and host miRNAs detected in small RNAs extracted from KSHV virions were further shown to colocalize with KSHV virions directly by in situ hybridization (ISH)-electron microscopy (EM) (ISH-EM). Some of these miRNAs were differentially present in the host cells and KSHV virions, suggesting that they are not randomly present in KSHV virions. The virional miRNAs could be transported into host cells, and they are biologically functional during de novo viral infection. Our study revealed miRNAs and usRNAs as a novel group of components in KSHV virions.
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36
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Song FJ, Chen KX. Single-nucleotide polymorphisms among microRNA: big effects on cancer. CHINESE JOURNAL OF CANCER 2012; 30:381-91. [PMID: 21627860 PMCID: PMC4013412 DOI: 10.5732/cjc.011.10142] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
MicroRNAs (miRNAs) are small non-coding RNAs that regulate gene expression at the transcriptional or posttranscriptional level. Many miRNAs are found to play a significant role in cancer development either as tumor suppressor genes or as oncogenes. Examination of tumor-specific miRNA expression profiles in diverse cancers has revealed widespread deregulation of these molecules, whose loss and overexpression respectively have diagnostic and prognostic significance. Genetic variations, mostly single-nucleotide polymorphisms (SNPs) within miRNA sequences or their target sites, have been found to be associated with many kinds of cancers. In this review, we summarize the current knowledge of miRNAs including their biogenesis and role in cancer development, and finally, how SNPs among miRNAs affect miRNA biogenesis and contribute to cancer.
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Affiliation(s)
- Feng-Ju Song
- Department of Epidemiology and Biostatistics, Tianjin Medical University Cancer Hospital and Institute, Tianjin 300060, People's Republic of China
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37
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Induction of cytoprotective pathways is central to the extension of lifespan conferred by multiple longevity pathways. PLoS Genet 2012; 8:e1002792. [PMID: 22829775 PMCID: PMC3400582 DOI: 10.1371/journal.pgen.1002792] [Citation(s) in RCA: 88] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2012] [Accepted: 05/11/2012] [Indexed: 11/19/2022] Open
Abstract
Many genetic and physiological treatments that extend lifespan also confer resistance to a variety of stressors, suggesting that cytoprotective mechanisms underpin the regulation of longevity. It has not been established, however, whether the induction of cytoprotective pathways is essential for lifespan extension or merely correlated. Using a panel of GFP-fused stress response genes, we identified the suites of cytoprotective pathways upregulated by 160 gene inactivations known to increase Caenorhabditis elegans longevity, including the mitochondrial UPR (hsp-6, hsp-60), the ER UPR (hsp-4), ROS response (sod-3, gst-4), and xenobiotic detoxification (gst-4). We then screened for other gene inactivations that disrupt the induction of these responses by xenobiotic or genetic triggers, identifying 29 gene inactivations required for cytoprotective gene expression. If cytoprotective responses contribute directly to lifespan extension, inactivation of these genes would be expected to compromise the extension of lifespan conferred by decreased insulin/IGF-1 signaling, caloric restriction, or the inhibition of mitochondrial function. We find that inactivation of 25 of 29 cytoprotection-regulatory genes shortens the extension of longevity normally induced by decreased insulin/IGF-1 signaling, disruption of mitochondrial function, or caloric restriction, without disrupting normal longevity nearly as dramatically. These data demonstrate that induction of cytoprotective pathways is central to longevity extension and identify a large set of new genetic components of the pathways that detect cellular damage and couple that detection to downstream cytoprotective effectors. Many mutations that increase animal lifespan also confer stress tolerance, suggesting that cytoprotective mechanisms underpin the regulation of longevity. It has not been established, however, whether the induction of individual cytoprotective pathways is essential for lifespan extension, or merely correlated. To establish whether the regulatory pathways for the induction of cytoprotective responses are key in the extension of lifespan, we performed an RNAi screen for gene inactivations that decouple the activation of cytoprotective pathways from xenobiotic stimuli that normally induce them. The screen identified 29 genes that constitute the regulatory cascades of the unfolded protein response, oxidative stress response, and detoxification. These upstream regulatory genes are critical to stress tolerance and the extension of lifespan conferred by decreased insulin/IGF-1 signaling, disruption of mitochondrial function, or caloric restriction, but have little effect on normal longevity.
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38
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Small RNA expression profiling by high-throughput sequencing: implications of enzymatic manipulation. J Nucleic Acids 2012; 2012:360358. [PMID: 22778911 PMCID: PMC3388297 DOI: 10.1155/2012/360358] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2011] [Accepted: 03/05/2012] [Indexed: 01/20/2023] Open
Abstract
Eukaryotic regulatory small RNAs (sRNAs) play significant roles in many fundamental cellular processes. As such, they have emerged as useful biomarkers for diseases and cell differentiation states. sRNA-based biomarkers outperform traditional messenger RNA-based biomarkers by testing fewer targets with greater accuracy and providing earlier detection for disease states. Therefore, expression profiling of sRNAs is fundamentally important to further advance the understanding of biological processes, as well as diagnosis and treatment of diseases. High-throughput sequencing (HTS) is a powerful approach for both sRNA discovery and expression profiling. Here, we discuss the general considerations for sRNA-based HTS profiling methods from RNA preparation to sequencing library construction, with a focus on the causes of systematic error. By examining the enzymatic manipulation steps of sRNA expression profiling, this paper aims to demystify current HTS-based sRNA profiling approaches and to aid researchers in the informed design and interpretation of profiling experiments.
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39
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Stromal biomarkers in breast cancer development and progression. Clin Exp Metastasis 2012; 29:663-72. [DOI: 10.1007/s10585-012-9499-8] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2012] [Accepted: 05/28/2012] [Indexed: 12/21/2022]
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40
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Tan Gana NH, Victoriano AFB, Okamoto T. Evaluation of online miRNA resources for biomedical applications. Genes Cells 2011; 17:11-27. [PMID: 22077698 DOI: 10.1111/j.1365-2443.2011.01564.x] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
MicroRNAs (miRNAs) are endogenous single-stranded, 22-nt (nucleotide) RNAs which complement mRNA to initiate post-transcriptional regulation. This review presents updates and evaluations of the public domain resources available for miRNA identification and target prediction toward their utilization in the biomedical research approach. This study discusses the basic principles of miRNA computational studies based on the nature and mechanism of action of miRNAs. Furthermore, we have explored fifty-nine current online miRNA tools that can be categorized into three classes in this paper: (i) miRNA identification; (ii) miRNA target prediction; and (iii) specialized miRNA tools.
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Affiliation(s)
- Neil H Tan Gana
- Department of Molecular and Cell Biology, Nagoya City University Graduate School of Medical Sciences, 1-Kawasumi, Mizuho-cho, Mizuho-ku, Nagoya City 467-8601, Japan
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MicroRNA-binding is required for recruitment of human Argonaute 2 to stress granules and P-bodies. Biochem Biophys Res Commun 2011; 414:259-64. [DOI: 10.1016/j.bbrc.2011.09.068] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2011] [Accepted: 09/14/2011] [Indexed: 12/13/2022]
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Detzer A, Engel C, Wünsche W, Sczakiel G. Cell stress is related to re-localization of Argonaute 2 and to decreased RNA interference in human cells. Nucleic Acids Res 2010; 39:2727-41. [PMID: 21148147 PMCID: PMC3074141 DOI: 10.1093/nar/gkq1216] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Various kinds of stress on human cells induce the formation of endogenous stress granules (SGs). Human Argonaute 2 (hAgo2), the catalytic core component of the RNA-induced silencing complex (RISC), can be recruited to SGs as well as P-bodies (PBs) indicating that the dynamic intracellular distribution of hAgo2 in SGs, in PBs or at other sub-cellular sites could be related to the efficiency of the RNA interference (RNAi) machinery. Here, we studied the influence of heat shock, sodium arsenite (NaAsO2), cycloheximide (CHX) and LipofectamineTM 2000-mediated transfection of phosphorothioate (PS)-modified oligonucleotides (ON) on the intracellular localization of hAgo2 and the efficiency of RNAi. Fluorescence microscopy and sedimentation analysis of cell fractions indicate stress-induced accumulation of hAgo2 in SGs and the loss of distinctly composed complexes containing hAgo2 or their sub-cellular context. Transfection of cells with PS-ON induces cell stress that is phenotypically similar to the established inducers heat shock and NaAsO2. The intracellular re-distribution of hAgo2 is related to its increased metabolic stability and to decreased RNAi directed by microRNA or by short interfering RNA. Here, we propose a functional model of the relationship between cell stress, translocation of hAgo2 to SGs providing a depot function, and loss of RNAi activity.
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Affiliation(s)
- Anke Detzer
- Institut für Molekulare Medizin, Centre for Structural and Cell Biology in Medicine (CSCM), Universität zu Lübeck and UK S-H, Ratzeburger Allee 160, D-23538 Lübeck, Germany
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Neill D. A proposal in relation to a genetic control of lifespan in mammals. Ageing Res Rev 2010; 9:437-46. [PMID: 20553971 DOI: 10.1016/j.arr.2010.05.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2010] [Revised: 05/17/2010] [Accepted: 05/19/2010] [Indexed: 01/26/2023]
Abstract
This article proposes that behavioural advancement during mammalian evolution had been in part mediated through extension of total developmental time. Such time extensions would have resulted in increased numbers of neuronal precursor cells, hence larger brains and a disproportionate increase in the neocortex. Larger neocortical areas enabled new connections to be formed during development and hence expansion of existing behavioural circuits. To have been positively selected such behavioural advances would have required enough postdevelopmental time to enable the behaviour to be fully manifest. It is therefore proposed that the success of mammalian evolution depended on initiating a genetic control of total postdevelopmental time. This could have been mediated through the redeployment of gene regulatory networks controlling total developmental time to additionally control total postdevelopmental time. The result would be that any extension of developmental time, leading to a behavioural advancement, would be accompanied by a proportional extension to postdevelopmental time. In effect it is proposed that mammalian lifespan as a whole is genetically controlled.
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Affiliation(s)
- David Neill
- Department of Psychiatry, Newcastle University, Newcastle Upon Tyne NE1 7RU, United Kingdom.
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Fabian MR, Sonenberg N, Filipowicz W. Regulation of mRNA Translation and Stability by microRNAs. Annu Rev Biochem 2010; 79:351-79. [PMID: 20533884 DOI: 10.1146/annurev-biochem-060308-103103] [Citation(s) in RCA: 2333] [Impact Index Per Article: 166.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Marc Robert Fabian
- Department of Biochemistry and Goodman Cancer Research Center, McGill University, Montreal, Quebec, H3G 1Y6, Canada;
| | - Nahum Sonenberg
- Department of Biochemistry and Goodman Cancer Research Center, McGill University, Montreal, Quebec, H3G 1Y6, Canada;
| | - Witold Filipowicz
- Friedrich Miescher Institute for Biomedical Research, 4002 Basel, Switzerland;
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Watashi K, Yeung ML, Starost MF, Hosmane RS, Jeang KT. Identification of small molecules that suppress microRNA function and reverse tumorigenesis. J Biol Chem 2010; 285:24707-16. [PMID: 20529860 DOI: 10.1074/jbc.m109.062976] [Citation(s) in RCA: 92] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
MicroRNAs (miRNAs) act in post-transcriptional gene silencing and are proposed to function in a wide spectrum of pathologies, including cancers and viral diseases. Currently, to our knowledge, no detailed mechanistic characterization of small molecules that interrupt miRNA pathways have been reported. In screening a small chemical library, we identified compounds that suppress RNA interference activity in cultured cells. Two compounds were characterized; one impaired Dicer activity while the other blocked small RNA-loading into an Argonaute 2 (AGO2) complex. We developed a cell-based model of miRNA-dependent tumorigenesis, and using this model, we observed that treatment of cells with either of the two compounds effectively neutralized tumor growth. These findings indicate that miRNA pathway-suppressing small molecules could potentially reverse tumorigenesis.
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Affiliation(s)
- Koichi Watashi
- Molecular Virology Section, Laboratory of Molecular Microbiology, NIAID, National Institutes of Health, Bethesda, Maryland 20892, USA
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Evidence for natural antisense transcript-mediated inhibition of microRNA function. Genome Biol 2010; 11:R56. [PMID: 20507594 PMCID: PMC2898074 DOI: 10.1186/gb-2010-11-5-r56] [Citation(s) in RCA: 402] [Impact Index Per Article: 28.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2010] [Revised: 03/17/2010] [Accepted: 05/27/2010] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND MicroRNAs (miRNAs) have the potential to regulate diverse sets of mRNA targets. In addition, mammalian genomes contain numerous natural antisense transcripts, most of which appear to be non-protein-coding RNAs (ncRNAs). We have recently identified and characterized a highly conserved non-coding antisense transcript for beta-secretase-1 (BACE1), a critical enzyme in Alzheimer's disease pathophysiology. The BACE1-antisense transcript is markedly up-regulated in brain samples from Alzheimer's disease patients and promotes the stability of the (sense) BACE1 transcript. RESULTS We report here that BACE1-antisense prevents miRNA-induced repression of BACE1 mRNA by masking the binding site for miR-485-5p. Indeed, miR-485-5p and BACE1-antisense compete for binding within the same region in the open reading frame of the BACE1 mRNA. We observed opposing effects of BACE1-antisense and miR-485-5p on BACE1 protein in vitro and showed that Locked Nucleic Acid-antimiR mediated knockdown of miR-485-5p as well as BACE1-antisense over-expression can prevent the miRNA-induced BACE1 suppression. We found that the expression of BACE1-antisense as well as miR-485-5p are dysregulated in RNA samples from Alzheimer's disease subjects compared to control individuals. CONCLUSIONS Our data demonstrate an interface between two distinct groups of regulatory RNAs in the computation of BACE1 gene expression. Moreover, bioinformatics analyses revealed a theoretical basis for many other potential interactions between natural antisense transcripts and miRNAs at the binding sites of the latter.
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MicroRNAs as a target for novel antipsychotics: a systematic review of an emerging field. Int J Neuropsychopharmacol 2010; 13:395-404. [PMID: 19849891 DOI: 10.1017/s1461145709990800] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
The psychotic disorders of schizophrenia and bipolar affective disorder are among the most disabling of all medical conditions. Current drugs used to treat psychosis largely target monoamine receptors. Here we explore the possibility of developing new antipsychotics by targeting specific microRNAs (miRNAs). These are single-stranded RNA molecules, 21-23 nt in length that are not translated into proteins and function as regulatory molecules. A keyword search was performed using Medline, the ISI Web of Knowledge and Scopus for papers published up to June 2009. The search shows that to date studies of miRNAs have been far more abundant in schizophrenia than in bipolar affective disorder and the view that non-protein-coding genes have an important regulatory role with implications for the genetic liability to psychosis is gaining greater acceptance. The most promising miRNAs so far identified include miR-181, miR-346 and miR-195 in schizophrenia and miR-34a and miR-144 in bipolar disorder. It has been argued that miR-219 may be involved in both disorders. miRNAs offer an exciting potential for developing new antipsychotics, although research in the field is at an early stage. It will require a considerable advance in smart technologies to deliver either mimics or antagomirs to the appropriate site of action, but the development of selective small conventional molecules may negate this requirement.
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Wang X, Yan F, Du Q, Liang Z. siRNAs as potential drugs. DRUG DISCOVERY TODAY. TECHNOLOGIES 2010; 7:e95-e146. [PMID: 24103722 DOI: 10.1016/j.ddtec.2010.11.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
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Ebert PJR, Jiang S, Xie J, Li QJ, Davis MM. An endogenous positively selecting peptide enhances mature T cell responses and becomes an autoantigen in the absence of microRNA miR-181a. Nat Immunol 2009; 10:1162-9. [PMID: 19801983 PMCID: PMC3762483 DOI: 10.1038/ni.1797] [Citation(s) in RCA: 209] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2009] [Accepted: 09/01/2009] [Indexed: 11/09/2022]
Abstract
Thymic positive selection is based on the interactions of T cell antigen receptors (TCRs) with self peptide-major histocompatibility complex (MHC) ligands, but the identity of selecting peptides for MHC class II-restricted TCRs and the functional consequences of this peptide specificity are not clear. Here we identify several endogenous self peptides that positively selected the MHC class II-restricted 5C.C7 TCR. The most potent of these also enhanced mature T cell activation, which supports the hypothesis that one function of positive selection is to produce T cells that can use particular self peptide-MHC complexes for activation and/or homeostasis. We also show that inhibiting the microRNA miR-181a resulted in maturation of T cells that overtly reacted toward these erstwhile positively selecting peptides. Therefore, miR-181a helps to guarantee the clonal deletion of particular moderate-affinity clones by modulating the TCR signaling threshold of thymocytes.
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Affiliation(s)
- Peter J R Ebert
- The Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, California, USA
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