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Machine Learning Based Methods and Best Practices of microRNA-Target Prediction and Validation. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1385:109-131. [DOI: 10.1007/978-3-031-08356-3_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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2
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Abstract
MicroRNAs (miRNAs) are small noncoding elements that play essential roles in the posttranscriptional regulation of biochemical processes. miRNAs recognize and target multiple mRNAs; therefore, investigating miRNA dysregulation is an indispensable strategy to understand pathological conditions and to design innovative drugs. Targeting miRNAs in diseases improve outcomes of several therapeutic strategies thus, this present study highlights miRNA targeting methods through experimental assays and bioinformatics tools. The first part of this review focuses on experimental miRNA targeting approaches for elucidating key biochemical pathways. A growing body of evidence about the miRNA world reveals the fact that it is not possible to uncover these molecules' structural and functional characteristics related to the biological processes with a deterministic approach. Instead, a systemic point of view is needed to truly understand the facts behind the natural complexity of interactions and regulations that miRNA regulations present. This task heavily depends both on computational and experimental capabilities. Fortunately, several miRNA bioinformatics tools catering to nonexperts are available as complementary wet-lab approaches. For this purpose, this work provides recent research and information about computational tools for miRNA targeting research.
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Affiliation(s)
- Hossein Ghanbarian
- Biotechnology Department & Cellular and Molecular Biology Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mehmet Taha Yıldız
- Division of Molecular Medicine, Hamidiye Institute of Health Sciences, University of Health Sciences-Turkey, Istanbul, Turkey
| | - Yusuf Tutar
- Division of Biochemistry, Department of Basic Pharmaceutical Sciences, Hamidiye Faculty of Pharmacy & Division of Molecular Medicine, Hamidiye Institute of Health Sciences, University of Health Sciences-Turkey, Istanbul, Turkey.
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3
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Abstract
MicroRNAs (miRNAs), a class of small noncoding RNA, posttranscriptionally regulate the expression of genes. Aberrant expression of miRNA is reported in various types of cancer. Since the first report of oncomiR-21 involvement in the glioma, its upregulation was reported in multiple cancers and was allied with high oncogenic property. In addition to the downregulation of tumor suppressor genes, the miR-21 is also associated with cancer resistance to various chemotherapy. The recent research is appraising miR-21 as a promising cancer target and biomarker for early cancer detection. In this review, we briefly explain the biogenesis and regulation of miR-21 in cancer cells. Additionally, the review features the assorted genes/pathways regulated by the miR-21 in various cancer and cancer stem cells.
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Sindhu KJ, Venkatesan N, Karunagaran D. MicroRNA Interactome Multiomics Characterization for Cancer Research and Personalized Medicine: An Expert Review. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2021; 25:545-566. [PMID: 34448651 DOI: 10.1089/omi.2021.0087] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
MicroRNAs (miRNAs) that are mutually modulated by their interacting partners (interactome) are being increasingly noted for their significant role in pathogenesis and treatment of various human cancers. Recently, miRNA interactome dissected with multiomics approaches has been the subject of focus since individual tools or methods failed to provide the necessary comprehensive clues on the complete interactome. Even though single-omics technologies such as proteomics can uncover part of the interactome, the biological and clinical understanding still remain incomplete. In this study, we present an expert review of studies involving multiomics approaches to identification of miRNA interactome and its application in mechanistic characterization, classification, and therapeutic target identification in a variety of cancers, and with a focus on proteomics. We also discuss individual or multiple miRNA-based interactome identification in various pathological conditions of relevance to clinical medicine. Various new single-omics methods that can be integrated into multiomics cancer research and the computational approaches to analyze and predict miRNA interactome are also highlighted in this review. In all, we contextulize the power of multiomics approaches and the importance of the miRNA interactome to achieve the vision and practice of predictive, preventive, and personalized medicine in cancer research and clinical oncology.
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Affiliation(s)
- K J Sindhu
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, India
| | - Nalini Venkatesan
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, India
| | - Devarajan Karunagaran
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, India
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5
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A multi-omics analysis of the regulatory changes induced by miR-223 in a monocyte/macrophage cell line. Biochim Biophys Acta Mol Basis Dis 2018; 1864:2664-2678. [PMID: 29778662 DOI: 10.1016/j.bbadis.2018.05.010] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Accepted: 05/15/2018] [Indexed: 02/06/2023]
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6
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Seok H, Lee H, Jang ES, Chi SW. Evaluation and control of miRNA-like off-target repression for RNA interference. Cell Mol Life Sci 2018; 75:797-814. [PMID: 28905147 PMCID: PMC11105550 DOI: 10.1007/s00018-017-2656-0] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Revised: 09/06/2017] [Accepted: 09/07/2017] [Indexed: 01/08/2023]
Abstract
RNA interference (RNAi) has been widely adopted to repress specific gene expression and is easily achieved by designing small interfering RNAs (siRNAs) with perfect sequence complementarity to the intended target mRNAs. Although siRNAs direct Argonaute (Ago), a core component of the RNA-induced silencing complex (RISC), to recognize and silence target mRNAs, they also inevitably function as microRNAs (miRNAs) and suppress hundreds of off-targets. Such miRNA-like off-target repression is potentially detrimental, resulting in unwanted toxicity and phenotypes. Despite early recognition of the severity of miRNA-like off-target repression, this effect has often been overlooked because of difficulties in recognizing and avoiding off-targets. However, recent advances in genome-wide methods and knowledge of Ago-miRNA target interactions have set the stage for properly evaluating and controlling miRNA-like off-target repression. Here, we describe the intrinsic problems of miRNA-like off-target effects caused by canonical and noncanonical interactions. We particularly focus on various genome-wide approaches and chemical modifications for the evaluation and prevention of off-target repression to facilitate the use of RNAi with secured specificity.
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Affiliation(s)
- Heeyoung Seok
- Division of Life Sciences, College of Life Sciences and Biotechnology, Korea University, Seoul, 02841, Korea
| | - Haejeong Lee
- Division of Life Sciences, College of Life Sciences and Biotechnology, Korea University, Seoul, 02841, Korea
| | - Eun-Sook Jang
- Division of Life Sciences, College of Life Sciences and Biotechnology, Korea University, Seoul, 02841, Korea
- EncodeGEN Co. Ltd, Seoul, 06329, Korea
| | - Sung Wook Chi
- Division of Life Sciences, College of Life Sciences and Biotechnology, Korea University, Seoul, 02841, Korea.
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7
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Liu X, Zhang P, Ji K, Zhang J, Yang S, Du B, Hu S, Fan R. Cyclin-dependent kinase 5 regulates MAPK/ERK signaling in the skin of mice. Acta Histochem 2018; 120:15-21. [PMID: 29132690 DOI: 10.1016/j.acthis.2017.10.009] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Revised: 10/28/2017] [Accepted: 10/30/2017] [Indexed: 12/11/2022]
Abstract
Cyclin-dependent kinase 5 (CDK5) is a proline-directed serine/threonine kinase that has been shown to play important roles in many tissues except the nervous system. We previously reported that CDK5 showed differential expression in the transcriptome profiles of the skin of alpacas with different hair colors. To understand the functional role of CDK5 in hair color determination, we constructed CDK5-knockdown mice and identified the effect on the mitogen-activated protein kinase (MAPK) pathway in the mouse skin. Quantitative real-time polymerase chain reaction, co-immunoprecipitation, and western blotting were performed to analyze the effects of CDK5-knockdown on the MAPK pathway in mice. The results showed that MAP3K6 was inhibited by phosphorylated CDK5 through its activator CDK7. The decrease in MAP3K6 levels caused down-regulation of MEK1 and ERK expression, leading to the up-regulation of miR-143-3p, which targets MAP3K6 via Dicer. Taken together, our findings indicate that CDK5 functions in regulating the MAPK pathway. Given that MAP3K6 was inhibited in two directions, this mechanism can provide insight into the contributions of the MAPK/ERK pathway to the inhibition of melanin production.
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Affiliation(s)
- Xuexian Liu
- College of Animal Science and Veterinary Medicine, Shanxi Agricultural University, Mingxian South Road, Taigu 030801, China
| | - Pengqian Zhang
- Department of Ecology Research, Beijing Milu Ecological Research Center, Nanhaizi, Daxing District, Beijing 102600, China
| | - Kaiyuan Ji
- College of Animal Science and Veterinary Medicine, Shanxi Agricultural University, Mingxian South Road, Taigu 030801, China
| | - Junzhen Zhang
- College of Animal Science and Veterinary Medicine, Shanxi Agricultural University, Mingxian South Road, Taigu 030801, China
| | - Shanshan Yang
- College of Animal Science and Veterinary Medicine, Shanxi Agricultural University, Mingxian South Road, Taigu 030801, China
| | - Bin Du
- College of Animal Science and Veterinary Medicine, Shanxi Agricultural University, Mingxian South Road, Taigu 030801, China
| | - Shuaipeng Hu
- College of Animal Science and Veterinary Medicine, Shanxi Agricultural University, Mingxian South Road, Taigu 030801, China
| | - Ruiwen Fan
- College of Animal Science and Veterinary Medicine, Shanxi Agricultural University, Mingxian South Road, Taigu 030801, China.
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8
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miR-143 inhibits intracellular salmonella growth by targeting ATP6V1A in macrophage cells in pig. Res Vet Sci 2017; 117:138-143. [PMID: 29274513 DOI: 10.1016/j.rvsc.2017.12.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Revised: 10/16/2017] [Accepted: 12/14/2017] [Indexed: 12/27/2022]
Abstract
Salmonella infects many vertebrate species, and animals such as pigs can be colonized with Salmonella and become established carriers. Analyzing the roles of microRNA in intracellular proliferation is important for understanding the process of Salmonella infection. The objective of this study is to verify the regulation effect of miR-143 on ATP6V1A and its functions in the intracellular growth of Salmonella. A new miR-143 binding site was discovered in the 3' UTR of ATP6V1A using a newly developed prediction tool. The binding site was confirmed by binding site deletion assay. Real-time PCR results indicated that ATP6V1A was predominantly expressed in bone-marrow-derived macrophages, and the expression of miR-143 in different tissues was negatively correlated with ATP6V1A. The Salmonella proliferation assay showed that the expression of miR-143 could inhibit intracellular Salmonella growth in macrophages by target ATP6V1A. The results strongly suggest that miR-143 plays important regulatory roles in the development of Salmonella infection in animals.
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9
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Jimenez L, Lim J, Burd B, Harris TM, Ow TJ, Kawachi N, Belbin TJ, Angeletti R, Prystowsky MB, Childs G, Segall JE. miR-375 Regulates Invasion-Related Proteins Vimentin and L-Plastin. THE AMERICAN JOURNAL OF PATHOLOGY 2017; 187:1523-1536. [PMID: 28499703 PMCID: PMC5500828 DOI: 10.1016/j.ajpath.2017.02.019] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Accepted: 02/27/2017] [Indexed: 12/21/2022]
Abstract
Invasion is a hallmark of advanced head and neck squamous cell carcinoma (HNSCC). We previously determined that low relative miR-375 expression was associated with poor patient prognosis. HNSCC cells with increased miR-375 expression have lower invasive properties and impaired invadopodium activity. Using stable isotope labeling with amino acids in cell culture and reverse-phase liquid chromatography mass spectrometry, we assessed the impact of miR-375 expression on protein levels in UM-SCC-1 cells. Increased miR-375 expression was associated with down-regulation of proteins involved in cellular assembly and organization, death and survival, and movement. Two invasion-associated proteins, vimentin and L-plastin, were strongly down-regulated by miR-375. Luciferase reporter assays demonstrated that high miR-375 expression reduced vimentin promoter activity, suggesting that vimentin is an indirect target of miR-375. Runt-related transcription factor 1 (RUNX1) is a potential miR-375 direct target, and its knockdown reduced vimentin and L-plastin expression. Data in The Cancer Genome Atlas HNSCC database showed a significant inverse correlation between miR-375 expression and RUNX1, vimentin, and L-plastin RNA expression. These clinical correlations validate our in vitro model findings and support a mechanism in which miR-375 suppresses RUNX1 levels, resulting in reduced vimentin and L-plastin expression. Furthermore, knockdown of RUNX1, L-plastin, and vimentin resulted in significant reductions in cell invasion in vitro, indicating the functional significance of miR-375 regulation of specific proteins involved in HNSCC invasion.
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Affiliation(s)
- Lizandra Jimenez
- Department of Pathology, Albert Einstein College of Medicine, Bronx, New York; Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, New York
| | - Jihyeon Lim
- Department of Pathology, Albert Einstein College of Medicine, Bronx, New York; Laboratory for Macromolecular Analysis and Proteomics, Albert Einstein College of Medicine, Bronx, New York
| | - Berta Burd
- Laboratory for Macromolecular Analysis and Proteomics, Albert Einstein College of Medicine, Bronx, New York
| | - Thomas M Harris
- Department of Pathology, Albert Einstein College of Medicine, Bronx, New York
| | - Thomas J Ow
- Department of Pathology, Albert Einstein College of Medicine, Bronx, New York
| | - Nicole Kawachi
- Department of Pathology, Albert Einstein College of Medicine, Bronx, New York
| | - Thomas J Belbin
- Department of Pathology, Albert Einstein College of Medicine, Bronx, New York
| | - Ruth Angeletti
- Laboratory for Macromolecular Analysis and Proteomics, Albert Einstein College of Medicine, Bronx, New York
| | | | - Geoffrey Childs
- Department of Pathology, Albert Einstein College of Medicine, Bronx, New York
| | - Jeffrey E Segall
- Department of Pathology, Albert Einstein College of Medicine, Bronx, New York; Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, New York.
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Jin HY, Oda H, Chen P, Yang C, Zhou X, Kang SG, Valentine E, Kefauver JM, Liao L, Zhang Y, Gonzalez-Martin A, Shepherd J, Morgan GJ, Mondala TS, Head SR, Kim PH, Xiao N, Fu G, Liu WH, Han J, Williamson JR, Xiao C. Differential Sensitivity of Target Genes to Translational Repression by miR-17~92. PLoS Genet 2017; 13:e1006623. [PMID: 28241004 PMCID: PMC5348049 DOI: 10.1371/journal.pgen.1006623] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Revised: 03/13/2017] [Accepted: 02/08/2017] [Indexed: 12/19/2022] Open
Abstract
MicroRNAs (miRNAs) are thought to exert their functions by modulating the expression of hundreds of target genes and each to a small degree, but it remains unclear how small changes in hundreds of target genes are translated into the specific function of a miRNA. Here, we conducted an integrated analysis of transcriptome and translatome of primary B cells from mutant mice expressing miR-17~92 at three different levels to address this issue. We found that target genes exhibit differential sensitivity to miRNA suppression and that only a small fraction of target genes are actually suppressed by a given concentration of miRNA under physiological conditions. Transgenic expression and deletion of the same miRNA gene regulate largely distinct sets of target genes. miR-17~92 controls target gene expression mainly through translational repression and 5’UTR plays an important role in regulating target gene sensitivity to miRNA suppression. These findings provide molecular insights into a model in which miRNAs exert their specific functions through a small number of key target genes. MicroRNAs (miRNAs) are small RNAs encoded by our genome. Each miRNA binds hundreds of target mRNAs and performs specific functions. It is thought that miRNAs exert their function by reducing the expression of all these target genes and each to a small degree. However, these target genes often have very diverse functions. It has been unclear how small changes in hundreds of target genes with diverse functions are translated into the specific function of a miRNA. Here we take advantage of recent technical advances to globally examine the mRNA and protein levels of 868 target genes regulated by miR-17~92, the first oncogenic miRNA, in mutant mice with transgenic overexpression or deletion of this miRNA gene. We show that miR-17~92 regulates target gene expression mainly at the protein level, with little effect on mRNA. Surprisingly, only a small fraction of target genes respond to miR-17~92 expression changes. Further studies show that the sensitivity of target genes to miR-17~92 is determined by a non-coding region of target mRNA. Our findings demonstrate that not every target gene is equal, and suggest that the function of a miRNA is mediated by a small number of key target genes.
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Affiliation(s)
- Hyun Yong Jin
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, California, United States of America
- Kellogg School of Science and Technology, The Scripps Research Institute, La Jolla, California, United States of America
| | - Hiroyo Oda
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, California, United States of America
| | - Pengda Chen
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Xiamen, Fujian, China
| | - Chao Yang
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Xiamen, Fujian, China
| | - Xiaojuan Zhou
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Xiamen, Fujian, China
| | - Seung Goo Kang
- Division of Biomedical Convergence/Institute of Bioscience & Biotechnology, College of Biomedical Science, Kangwon National University, Chuncheon, Republic of Korea
| | - Elizabeth Valentine
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, United States of America
| | - Jennifer M. Kefauver
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, California, United States of America
- Kellogg School of Science and Technology, The Scripps Research Institute, La Jolla, California, United States of America
| | - Lujian Liao
- Shanghai Key Laboratory of Regulatory Biology, Shanghai Key Laboratory of Brain Functional Genomics (Ministry of Education), School of Life Sciences, East China Normal University, Shanghai, China
| | - Yaoyang Zhang
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, China
| | - Alicia Gonzalez-Martin
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, California, United States of America
| | - Jovan Shepherd
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, California, United States of America
| | - Gareth J. Morgan
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, California, United States of America
| | - Tony S. Mondala
- Next Generation Sequencing Core, The Scripps Research Institute, La Jolla, California, United States of America
| | - Steven R. Head
- Next Generation Sequencing Core, The Scripps Research Institute, La Jolla, California, United States of America
| | - Pyeung-Hyeun Kim
- Department of Molecular Bioscience/Institute of Bioscience & Biotechnology, College of Biomedical Science, Kangwon National University, Chuncheon, Republic of Korea
| | - Nengming Xiao
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Xiamen, Fujian, China
| | - Guo Fu
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Xiamen, Fujian, China
| | - Wen-Hsien Liu
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Xiamen, Fujian, China
| | - Jiahuai Han
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Xiamen, Fujian, China
| | - James R. Williamson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, United States of America
| | - Changchun Xiao
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, California, United States of America
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Xiamen, Fujian, China
- * E-mail:
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11
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Steinkraus BR, Toegel M, Fulga TA. Tiny giants of gene regulation: experimental strategies for microRNA functional studies. WILEY INTERDISCIPLINARY REVIEWS. DEVELOPMENTAL BIOLOGY 2016; 5:311-62. [PMID: 26950183 PMCID: PMC4949569 DOI: 10.1002/wdev.223] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/14/2015] [Revised: 11/19/2015] [Accepted: 11/28/2015] [Indexed: 12/11/2022]
Abstract
The discovery over two decades ago of short regulatory microRNAs (miRNAs) has led to the inception of a vast biomedical research field dedicated to understanding these powerful orchestrators of gene expression. Here we aim to provide a comprehensive overview of the methods and techniques underpinning the experimental pipeline employed for exploratory miRNA studies in animals. Some of the greatest challenges in this field have been uncovering the identity of miRNA-target interactions and deciphering their significance with regard to particular physiological or pathological processes. These endeavors relied almost exclusively on the development of powerful research tools encompassing novel bioinformatics pipelines, high-throughput target identification platforms, and functional target validation methodologies. Thus, in an unparalleled manner, the biomedical technology revolution unceasingly enhanced and refined our ability to dissect miRNA regulatory networks and understand their roles in vivo in the context of cells and organisms. Recurring motifs of target recognition have led to the creation of a large number of multifactorial bioinformatics analysis platforms, which have proved instrumental in guiding experimental miRNA studies. Subsequently, the need for discovery of miRNA-target binding events in vivo drove the emergence of a slew of high-throughput multiplex strategies, which now provide a viable prospect for elucidating genome-wide miRNA-target binding maps in a variety of cell types and tissues. Finally, deciphering the functional relevance of miRNA post-transcriptional gene silencing under physiological conditions, prompted the evolution of a host of technologies enabling systemic manipulation of miRNA homeostasis as well as high-precision interference with their direct, endogenous targets. For further resources related to this article, please visit the WIREs website.
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Affiliation(s)
- Bruno R Steinkraus
- Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Markus Toegel
- Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Tudor A Fulga
- Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
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Abstract
Challenges in the treatment of hepatocellular carcinoma Hepatocellular carcinoma (HCC) represents one of the most frequent types of cancer worldwide. Surgery, although only a part of the armamentarium against HCC, represents the cornerstone in the management of this aggressive disease. This article will review the current and future challenges in the surgical management of HCC, with a special emphasis on the following areas: (1) the evolution of staging of the disease and the importance of the biological nature and behavior of HCC, (2) the effort to increase resectability, (3) technical innovations and the role of image-guided surgery, and, finally, (4) the role of liver transplantation in the continuum of care for these patients. Although by no means an exhaustive list, the issues mentioned above represent some of the most promising prospects for significant progress in the management of HCC.
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Yao M, Gao W, Tao H, Yang J, Liu G, Huang T. Regulation signature of miR-143 and miR-26 in porcine Salmonella infection identified by binding site enrichment analysis. Mol Genet Genomics 2015; 291:789-99. [PMID: 26589421 DOI: 10.1007/s00438-015-1146-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2015] [Accepted: 11/11/2015] [Indexed: 12/21/2022]
Abstract
Salmonella infects many vertebrate species, and pigs colonized with Salmonella are typically Salmonella carriers. Transcriptomic analysis of the response to Salmonella infection in whole blood has been reported for the pig. The objective of this study is to identify the important miRNAs involved in Salmonella infection using binding site enrichment analysis. We predicted porcine microRNA (miRNA) binding sites in the 3' UTR of protein-coding genes for all miRNA families. Based on those predictions, we analyzed miRNA-binding sites for mRNAs expressed in peripheral blood to investigate the functional importance of miRNAs in Salmonella infection in pig. Enrichment analysis revealed that binding sites of five miRNAs (including miR-143, -9839, -26, -2483, and -4335) were significantly over represented for the differentially expressed gene sets. Real-time PCR results indicated that selected members of this miRNA group (miR-143, -26, and -4335) were differentially expressed in whole blood after Salmonella inoculation. The luciferase reporter assay showed that ATP6V1A and IL13RA1 were targets of miR-143 and that miR-26 regulates BINP3L and ARL6IP6. The results strongly suggest that miR-143 and miR-26 play important regulatory roles in the development of Salmonella infection in pig.
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Affiliation(s)
- Min Yao
- College of Animal Science, Yangtze University, Jingzhou, 434025, Hubei, China
| | - Weihua Gao
- College of Animal Science, Yangtze University, Jingzhou, 434025, Hubei, China
| | - Hengxun Tao
- College of Animal Science, Yangtze University, Jingzhou, 434025, Hubei, China
| | - Jun Yang
- College of Animal Science, Yangtze University, Jingzhou, 434025, Hubei, China
| | - Guoping Liu
- College of Animal Science, Yangtze University, Jingzhou, 434025, Hubei, China.,Black Pig Research Institute, Yangtze University, Jingzhou, 434025, Hubei, China
| | - Tinghua Huang
- College of Animal Science, Yangtze University, Jingzhou, 434025, Hubei, China.
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14
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Subasic D, Brümmer A, Wu Y, Pinto SM, Imig J, Keller M, Jovanovic M, Lightfoot HL, Nasso S, Goetze S, Brunner E, Hall J, Aebersold R, Zavolan M, Hengartner MO. Cooperative target mRNA destabilization and translation inhibition by miR-58 microRNA family in C. elegans. Genome Res 2015; 25:1680-91. [PMID: 26232411 PMCID: PMC4617964 DOI: 10.1101/gr.183160.114] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2014] [Accepted: 07/27/2015] [Indexed: 12/19/2022]
Abstract
In animals, microRNAs frequently form families with related sequences. The functional relevance of miRNA families and the relative contribution of family members to target repression have remained, however, largely unexplored. Here, we used the Caenorhabditis elegans miR-58 miRNA family, composed primarily of the four highly abundant members miR-58.1, miR-80, miR-81, and miR-82, as a model to investigate the redundancy of miRNA family members and their impact on target expression in an in vivo setting. We found that miR-58 family members repress largely overlapping sets of targets in a predominantly additive fashion. Progressive deletions of miR-58 family members lead to cumulative up-regulation of target protein and RNA levels. Phenotypic defects could only be observed in the family quadruple mutant, which also showed the strongest change in target protein levels. Interestingly, although the seed sequences of miR-80 and miR-58.1 differ in a single nucleotide, predicted canonical miR-80 targets were efficiently up-regulated in the mir-58.1 single mutant, indicating functional redundancy of distinct members of this miRNA family. At the aggregate level, target binding leads mainly to mRNA degradation, although we also observed some degree of translational inhibition, particularly in the single miR-58 family mutants. These results provide a framework for understanding how miRNA family members interact to regulate target mRNAs.
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Affiliation(s)
- Deni Subasic
- Institute of Molecular Life Sciences, University of Zurich, 8057 Zurich, Switzerland; Molecular Life Sciences PhD Program, Swiss Federal Institute of Technology and University of Zurich, 8057 Zurich, Switzerland
| | - Anneke Brümmer
- Biozentrum, University of Basel, 4056 Basel, Switzerland; Department of Integrative Biology and Physiology, University of California, Los Angeles, California 90095, USA
| | - Yibo Wu
- Department of Biology, Institute of Molecular Systems Biology, Swiss Federal Institute of Technology, 8093 Zurich, Switzerland
| | - Sérgio Morgado Pinto
- Institute of Molecular Life Sciences, University of Zurich, 8057 Zurich, Switzerland; Graduate Program in Areas of Basic and Applied Biology (GABBA), University of Porto, 4099-002 Porto, Portugal
| | - Jochen Imig
- Institute of Pharmaceutical Chemistry, Swiss Federal Institute of Technology, 8093 Zurich, Switzerland
| | - Martin Keller
- Institute of Molecular Life Sciences, University of Zurich, 8057 Zurich, Switzerland; Molecular Life Sciences PhD Program, Swiss Federal Institute of Technology and University of Zurich, 8057 Zurich, Switzerland
| | - Marko Jovanovic
- Institute of Molecular Life Sciences, University of Zurich, 8057 Zurich, Switzerland
| | - Helen Louise Lightfoot
- Institute of Pharmaceutical Chemistry, Swiss Federal Institute of Technology, 8093 Zurich, Switzerland
| | - Sara Nasso
- Department of Biology, Institute of Molecular Systems Biology, Swiss Federal Institute of Technology, 8093 Zurich, Switzerland
| | - Sandra Goetze
- Institute of Molecular Life Sciences, University of Zurich, 8057 Zurich, Switzerland; Department of Biology, Institute of Molecular Systems Biology, Swiss Federal Institute of Technology, 8093 Zurich, Switzerland
| | - Erich Brunner
- Institute of Molecular Life Sciences, University of Zurich, 8057 Zurich, Switzerland
| | - Jonathan Hall
- Institute of Pharmaceutical Chemistry, Swiss Federal Institute of Technology, 8093 Zurich, Switzerland
| | - Ruedi Aebersold
- Department of Biology, Institute of Molecular Systems Biology, Swiss Federal Institute of Technology, 8093 Zurich, Switzerland; Faculty of Science, University of Zurich, 8057 Zurich, Switzerland
| | | | - Michael O Hengartner
- Institute of Molecular Life Sciences, University of Zurich, 8057 Zurich, Switzerland
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15
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Wang L, Shi ZM, Jiang CF, Liu X, Chen QD, Qian X, Li DM, Ge X, Wang XF, Liu LZ, You YP, Liu N, Jiang BH. MiR-143 acts as a tumor suppressor by targeting N-RAS and enhances temozolomide-induced apoptosis in glioma. Oncotarget 2015; 5:5416-27. [PMID: 24980823 PMCID: PMC4170647 DOI: 10.18632/oncotarget.2116] [Citation(s) in RCA: 108] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Therapeutic applications of microRNAs (miRNAs) in RAS-driven glioma were valuable, but their specific roles and functions have yet to be fully elucidated. Here, we firstly report that miR-143 directly targets the neuroblastoma RAS viral oncogene homolog (N-RAS) and functions as a tumor-suppressor in glioma. Overexpression of miR-143 decreased the expression of N-RAS, inhibited PI3K/AKT, MAPK/ERK signaling, and attenuated the accumulation of p65 in nucleus of glioma cells. In human clinical specimens, miR-143 was downregulated where an adverse with N-RAS expression was observed. Furthermore, overexpression of miR-143 decreased glioma cell migration, invasion, tube formation and slowed tumor growth and angiogenesis in a manner associated with N-RAS downregulation in vitro and in vivo. Finally, miR-143 also sensitizes glioma cells to temozolomide (TMZ),the first-line drug for glioma treatment. Taken together, for the first time, our results demonstrate that miR-143 plays a significant role in inactivating the RAS signaling pathway through the inhibition of N-RAS, which may provide a novel therapeutic strategy for treatment of glioma and other RAS-driven cancers.
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Affiliation(s)
- Lin Wang
- State Key Lab of Reproductive Medicine, Department of Pathology, Nanjing Medical University, Nanjing, China. These authors contributed equally to this work
| | - Zhu-Mei Shi
- State Key Lab of Reproductive Medicine, Department of Pathology, Nanjing Medical University, Nanjing, China. Department of Neurosurgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China. These authors contributed equally to this work
| | - Cheng-Fei Jiang
- State Key Lab of Reproductive Medicine, Department of Pathology, Nanjing Medical University, Nanjing, China. These authors contributed equally to this work
| | - Xue Liu
- State Key Lab of Reproductive Medicine, Department of Pathology, Nanjing Medical University, Nanjing, China
| | - Qiu-Dan Chen
- State Key Lab of Reproductive Medicine, Department of Pathology, Nanjing Medical University, Nanjing, China
| | - Xu Qian
- State Key Lab of Reproductive Medicine, Department of Pathology, Nanjing Medical University, Nanjing, China
| | - Dong-Mei Li
- State Key Lab of Reproductive Medicine, Department of Pathology, Nanjing Medical University, Nanjing, China
| | - Xin Ge
- State Key Lab of Reproductive Medicine, Department of Pathology, Nanjing Medical University, Nanjing, China
| | - Xie-Feng Wang
- Department of Neurosurgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Ling-Zhi Liu
- Department of Pathology, Anatomy and Cell Biology, Thomas Jefferson University, Philadelphia, USA
| | - Yong-Ping You
- Department of Neurosurgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Ning Liu
- Department of Neurosurgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Bing-Hua Jiang
- State Key Lab of Reproductive Medicine, Department of Pathology, Nanjing Medical University, Nanjing, China. Department of Pathology, Anatomy and Cell Biology, Thomas Jefferson University, Philadelphia, USA
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16
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Murthy KR, Rajagopalan P, Pinto SM, Advani J, Murthy PR, Goel R, Subbannayya Y, Balakrishnan L, Dash M, Anil AK, Manda SS, Nirujogi RS, Kelkar DS, Sathe GJ, Dey G, Chatterjee A, Gowda H, Chakravarti S, Shankar S, Sahasrabuddhe NA, Nair B, Somani BL, Prasad TSK, Pandey A. Proteomics of Human Aqueous Humor. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2015; 19:283-93. [DOI: 10.1089/omi.2015.0029] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Affiliation(s)
- Krishna R. Murthy
- Institute of Bioinformatics, International Tech Park, Bangalore, India
- Department of Biotechnology, Amrita Vishwa Vidyapeetham, Kollam, India
- Vittala International Institute of Ophthalmology, Bangalore, India
| | - Pavithra Rajagopalan
- Institute of Bioinformatics, International Tech Park, Bangalore, India
- School of Biotechnology, KIIT University, Bhubaneswar, India
| | - Sneha M. Pinto
- Institute of Bioinformatics, International Tech Park, Bangalore, India
- Manipal University, Madhav Nagar, Manipal, Karnataka, India
| | - Jayshree Advani
- Institute of Bioinformatics, International Tech Park, Bangalore, India
- Manipal University, Madhav Nagar, Manipal, Karnataka, India
| | | | - Renu Goel
- Institute of Bioinformatics, International Tech Park, Bangalore, India
| | - Yashwanth Subbannayya
- Institute of Bioinformatics, International Tech Park, Bangalore, India
- Rajiv Gandhi University of Health Sciences, Bangalore, India
| | - Lavanya Balakrishnan
- Institute of Bioinformatics, International Tech Park, Bangalore, India
- Department of Biotechnology, Kuvempu University, Shankaraghatta, India
| | - Mahashweta Dash
- Department of Internal Medicine, Armed Forces Medical College, Pune, India
| | - Abhijith K. Anil
- Department of Internal Medicine, Armed Forces Medical College, Pune, India
| | - Srikanth S. Manda
- Institute of Bioinformatics, International Tech Park, Bangalore, India
- Centre of Excellence in Bioinformatics, School of Life Sciences, Pondicherry University, Puducherry, India
| | - Raja Sekhar Nirujogi
- Institute of Bioinformatics, International Tech Park, Bangalore, India
- Centre of Excellence in Bioinformatics, School of Life Sciences, Pondicherry University, Puducherry, India
| | | | - Gajanan J. Sathe
- Institute of Bioinformatics, International Tech Park, Bangalore, India
- Manipal University, Madhav Nagar, Manipal, Karnataka, India
| | - Gourav Dey
- Institute of Bioinformatics, International Tech Park, Bangalore, India
- Manipal University, Madhav Nagar, Manipal, Karnataka, India
| | - Aditi Chatterjee
- Institute of Bioinformatics, International Tech Park, Bangalore, India
- School of Biotechnology, KIIT University, Bhubaneswar, India
| | - Harsha Gowda
- Institute of Bioinformatics, International Tech Park, Bangalore, India
| | - Shukti Chakravarti
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Subramanian Shankar
- Department of Rheumatology, Medical Division, Command Hospital (Air Force), Bangalore, India
| | | | - Bipin Nair
- Department of Biotechnology, Amrita Vishwa Vidyapeetham, Kollam, India
| | - Babu Lal Somani
- Institute of Bioinformatics, International Tech Park, Bangalore, India
| | - T. S. Keshava Prasad
- Institute of Bioinformatics, International Tech Park, Bangalore, India
- Department of Biotechnology, Amrita Vishwa Vidyapeetham, Kollam, India
- Manipal University, Madhav Nagar, Manipal, Karnataka, India
- Centre of Excellence in Bioinformatics, School of Life Sciences, Pondicherry University, Puducherry, India
| | - Akhilesh Pandey
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland
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17
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Pekow J, Meckel K, Dougherty U, Butun F, Mustafi R, Lim J, Crofton C, Chen X, Joseph L, Bissonnette M. Tumor suppressors miR-143 and miR-145 and predicted target proteins API5, ERK5, K-RAS, and IRS-1 are differentially expressed in proximal and distal colon. Am J Physiol Gastrointest Liver Physiol 2015; 308:G179-87. [PMID: 25477374 PMCID: PMC4312953 DOI: 10.1152/ajpgi.00208.2014] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The colon differs regionally in local luminal environment, excretory function, and gene expression. Polycistronic microRNA (miR)-143 and miR-145 are downregulated early in colon cancer. We asked if these microRNAs (miRNAs) might be differentially expressed in the proximal vs. the distal colon, contributing to regional differences in protein expression. Primary transcripts and mature miR-143 and miR-145 were quantified by real-time PCR, putative targets were measured by Western blotting, and DNA methylation was assessed by sequencing bisulfite-treated DNA in proximal and distal normal colonic mucosa as well as colon cancers. Putative targets of these miRNAs were assessed following transfection with miR-143 or miR-145. Mean expression of mature miR-143 and miR-145 was 2.0-fold (P < 0.001) and 1.8-fold (P = 0.03) higher, respectively, in proximal than distal colon. DNA methylation or primary transcript expression of these miRNAs did not differ by location. In agreement with increased expression of miR-143 and miR-145 in proximal colon, predicted targets of these miRNAs, apoptosis inhibitor 5 (API5), ERK5, K-RAS, and insulin receptor substrate 1 (IRS-1), which are cell cycle and survival regulators, were expressed at a lower level in proximal than distal colon. Transfection of HCA-7 colon cancer cells with miR-145 downregulated IRS-1, and transfection of HT-29 colon cancer cells with miR-143 decreased K-RAS and ERK5 expression. In conclusion, miR-143 and miR-145 and the predicted target proteins API5, ERK5, K-RAS, and IRS-1 display regional differences in expression in the colon. We speculate that differences in these tumor suppressors might contribute to regional differences in normal colonic gene expression and modulate site-specific differences in malignant predisposition.
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Affiliation(s)
- Joel Pekow
- Section of Gastroenterology, Hepatology, and Nutrition, University of Chicago, Chicago, Illinois; and
| | - Katherine Meckel
- 1Section of Gastroenterology, Hepatology, and Nutrition, University of Chicago, Chicago, Illinois; and
| | - Urszula Dougherty
- 1Section of Gastroenterology, Hepatology, and Nutrition, University of Chicago, Chicago, Illinois; and
| | - Fatma Butun
- 1Section of Gastroenterology, Hepatology, and Nutrition, University of Chicago, Chicago, Illinois; and
| | - Reba Mustafi
- 1Section of Gastroenterology, Hepatology, and Nutrition, University of Chicago, Chicago, Illinois; and
| | - John Lim
- 1Section of Gastroenterology, Hepatology, and Nutrition, University of Chicago, Chicago, Illinois; and
| | - Charis Crofton
- 1Section of Gastroenterology, Hepatology, and Nutrition, University of Chicago, Chicago, Illinois; and
| | - Xindi Chen
- 1Section of Gastroenterology, Hepatology, and Nutrition, University of Chicago, Chicago, Illinois; and
| | - Loren Joseph
- 2Department of Pathology, University of Chicago, Chicago, Illinois
| | - Marc Bissonnette
- 1Section of Gastroenterology, Hepatology, and Nutrition, University of Chicago, Chicago, Illinois; and
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18
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Xuan Y, Yang H, Zhao L, Lau WB, Lau B, Ren N, Hu Y, Yi T, Zhao X, Zhou S, Wei Y. MicroRNAs in colorectal cancer: small molecules with big functions. Cancer Lett 2014; 360:89-105. [PMID: 25524553 DOI: 10.1016/j.canlet.2014.11.051] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2014] [Revised: 11/19/2014] [Accepted: 11/20/2014] [Indexed: 02/05/2023]
Abstract
Colorectal cancer (CRC) is the third most lethal malignancy, with pathogenesis intricately dependent upon microRNAs (miRNAs). miRNAs are short, non-protein coding RNAs, targeting the 3'-untranslated regions (3'-UTR) of certain mRNAs. They usually serve as tumor suppressors or oncogenes, and participate in tumor phenotype maintenance. Therefore, miRNAs consequently regulate CRC carcinogenesis and other biological functions, including apoptosis, development, angiogenesis, migration, and proliferation. Due to its differential expression and distinct stability, miRNAs are regarded as molecular biomarkers (for diagnosis/prognosis) and therapeutic targets for CRC. Recently, a remarkable number of miRNAs have been discovered with implications via incompletely understood mechanisms in CRC. As further study of relevant miRNAs continues, it is hopeful that novel miRNA-based therapeutic strategies may be available for CRC patients in the future.
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Affiliation(s)
- Yu Xuan
- Department of Gynecology and Obstetrics, Key Laboratory of Obstetrics & Gynecologic and Pediatric Diseases and Birth Defects of Ministry of Education, West China Second Hospital, Sichuan University, Chengdu 610041, China; The State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Huiliang Yang
- The State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Linjie Zhao
- The State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Wayne Bond Lau
- Department of Emergency Medicine, Thomas Jefferson University Hospital, USA
| | - Bonnie Lau
- Department of Surgery, Emergency Medicine, Kaiser Santa Clara Medial Center, Affiliate of Stanford University, USA
| | - Ning Ren
- College of Biological Sciences, Sichuan University, Chengdu 610041, China
| | - Yuehong Hu
- Department of Gynecology and Obstetrics, Key Laboratory of Obstetrics & Gynecologic and Pediatric Diseases and Birth Defects of Ministry of Education, West China Second Hospital, Sichuan University, Chengdu 610041, China
| | - Tao Yi
- Department of Gynecology and Obstetrics, Key Laboratory of Obstetrics & Gynecologic and Pediatric Diseases and Birth Defects of Ministry of Education, West China Second Hospital, Sichuan University, Chengdu 610041, China
| | - Xia Zhao
- Department of Gynecology and Obstetrics, Key Laboratory of Obstetrics & Gynecologic and Pediatric Diseases and Birth Defects of Ministry of Education, West China Second Hospital, Sichuan University, Chengdu 610041, China
| | - Shengtao Zhou
- Department of Gynecology and Obstetrics, Key Laboratory of Obstetrics & Gynecologic and Pediatric Diseases and Birth Defects of Ministry of Education, West China Second Hospital, Sichuan University, Chengdu 610041, China.
| | - Yuquan Wei
- The State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
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19
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Zhang H, Xu Y, Papanastasopoulos P, Stebbing J, Giamas G. Broader implications of SILAC-based proteomics for dissecting signaling dynamics in cancer. Expert Rev Proteomics 2014; 11:713-31. [PMID: 25345469 DOI: 10.1586/14789450.2014.971115] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Large-scale transcriptome and epigenome analyses have been widely utilized to discover gene alterations implicated in cancer development at the genetic level. However, mapping of signaling dynamics at the protein level is likely to be more insightful and needed to complement massive genomic data. Stable isotope labeling with amino acids in cell culture (SILAC)-based proteomic analysis represents one of the most promising comparative quantitative methods that has been extensively employed in proteomic research. This technology allows for global, robust and confident identification and quantification of signal perturbations important for the progress of human diseases, particularly malignancies. The present review summarizes the latest applications of in vitro and in vivo SILAC-based proteomics in identifying global proteome/phosphoproteome and genome-wide protein-protein interactions that contribute to oncogenesis, highlighting the recent advances in dissecting signaling dynamics in cancer.
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Affiliation(s)
- Hua Zhang
- Department of Surgery and Cancer, Division of Cancer, Imperial College London, Hammersmith Hospital Campus, ICTEM Building, Du Cane Road, London, W12 ONN, UK
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20
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Huang TC, Renuse S, Pinto S, Kumar P, Yang Y, Chaerkady R, Godsey B, Mendell JT, Halushka MK, Civin CI, Marchionni L, Pandey A. Identification of miR-145 targets through an integrated omics analysis. MOLECULAR BIOSYSTEMS 2014; 11:197-207. [PMID: 25354783 DOI: 10.1039/c4mb00585f] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
MicroRNAs (miRNAs) are small non-coding RNAs that regulate gene expression and protein synthesis. To characterize functions of miRNAs and to assess their potential applications, we carried out an integrated multi-omics analysis to study miR-145, a miRNA that has been shown to suppress tumor growth. We employed gene expression profiling, miRNA profiling and quantitative proteomic analysis of a pancreatic cancer cell line. In our transcriptomic analysis, overexpression of miR-145 was found to suppress the expression of genes that are implicated in development of cancer such as ITGA11 and MAGEA4 in addition to previously described targets such as FSCN1, YES1 and PODXL. Based on miRNA profiling, overexpression of miR-145 also upregulated other miRNAs including miR-124, miR-133b and miR-125a-3p, all of which are implicated in suppression of tumors and are generally co-regulated with miR-145 in other cancers. Using the SILAC system, we identified miR-145-induced downregulation of several oncoproteins/cancer biomarkers including SET, RPA1, MCM2, ABCC1, SPTBN1 and SPTLC1. Luciferase assay validation carried out on a subset of downregulated candidate targets confirmed them to be novel direct targets of miR-145. Overall, this multi-omics approach provided insights into miR-145-mediated tumor suppression and could be used as a general strategy to study the targets of individual miRNAs.
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Affiliation(s)
- Tai-Chung Huang
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
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21
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Marimuthu A, Huang TC, Selvan LDN, Renuse S, Nirujogi RS, Kumar P, Pinto SM, Rajagopalan S, Pandey A, Harsha H, Chatterjee A. Identification of targets of miR-200b by a SILAC-based quantitative proteomic approach. EUPA OPEN PROTEOMICS 2014. [DOI: 10.1016/j.euprot.2014.04.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
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22
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Murthy KR, Goel R, Subbannayya Y, Jacob HK, Murthy PR, Manda SS, Patil AH, Sharma R, Sahasrabuddhe NA, Parashar A, Nair BG, Krishna V, Prasad TK, Gowda H, Pandey A. Proteomic analysis of human vitreous humor. Clin Proteomics 2014; 11:29. [PMID: 25097467 PMCID: PMC4106660 DOI: 10.1186/1559-0275-11-29] [Citation(s) in RCA: 92] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2014] [Accepted: 05/16/2014] [Indexed: 12/11/2022] Open
Abstract
Background The vitreous humor is a transparent, gelatinous mass whose main constituent is water. It plays an important role in providing metabolic nutrient requirements of the lens, coordinating eye growth and providing support to the retina. It is in close proximity to the retina and reflects many of the changes occurring in this tissue. The biochemical changes occurring in the vitreous could provide a better understanding about the pathophysiological processes that occur in vitreoretinopathy. In this study, we investigated the proteome of normal human vitreous humor using high resolution Fourier transform mass spectrometry. Results The vitreous humor was subjected to multiple fractionation techniques followed by LC-MS/MS analysis. We identified 1,205 proteins, 682 of which have not been described previously in the vitreous humor. Most proteins were localized to the extracellular space (24%), cytoplasm (20%) or plasma membrane (14%). Classification based on molecular function showed that 27% had catalytic activity, 10% structural activity, 10% binding activity, 4% cell and 4% transporter activity. Categorization for biological processes showed 28% participate in metabolism, 20% in cell communication and 13% in cell growth. The data have been deposited to the ProteomeXchange with identifier PXD000957. Conclusion This large catalog of vitreous proteins should facilitate biomedical research into pathological conditions of the eye including diabetic retinopathy, retinal detachment and cataract.
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Affiliation(s)
- Krishna R Murthy
- Institute of Bioinformatics, International Technology Park, Bangalore 560 066, India.,Amrita School of Biotechnology, Amrita Vishwa Vidyapeetham, Kollam, Kerala 690 525, India.,Vittala International Institute Of Ophthalmology, Bangalore, Karnataka 560085, India
| | - Renu Goel
- Institute of Bioinformatics, International Technology Park, Bangalore 560 066, India.,Department of Biotechnology, Kuvempu University, Shankaraghatta, Karnataka 577 451, India
| | - Yashwanth Subbannayya
- Institute of Bioinformatics, International Technology Park, Bangalore 560 066, India
| | - Harrys Kc Jacob
- Institute of Bioinformatics, International Technology Park, Bangalore 560 066, India
| | - Praveen R Murthy
- Vittala International Institute Of Ophthalmology, Bangalore, Karnataka 560085, India
| | - Srikanth Srinivas Manda
- Institute of Bioinformatics, International Technology Park, Bangalore 560 066, India.,Centre of Excellence in Bioinformatics, Bioinformatics Centre, School of Life Sciences, Pondicherry University, Puducherry 605 014, India
| | - Arun H Patil
- Institute of Bioinformatics, International Technology Park, Bangalore 560 066, India
| | - Rakesh Sharma
- Department of Neurochemistry, National Institute of Mental Health and Neuro Sciences, Bangalore 560 006, India
| | | | | | - Bipin G Nair
- Amrita School of Biotechnology, Amrita Vishwa Vidyapeetham, Kollam, Kerala 690 525, India
| | | | - Ts Keshava Prasad
- Institute of Bioinformatics, International Technology Park, Bangalore 560 066, India.,Amrita School of Biotechnology, Amrita Vishwa Vidyapeetham, Kollam, Kerala 690 525, India.,Centre of Excellence in Bioinformatics, Bioinformatics Centre, School of Life Sciences, Pondicherry University, Puducherry 605 014, India
| | - Harsha Gowda
- Institute of Bioinformatics, International Technology Park, Bangalore 560 066, India
| | - Akhilesh Pandey
- Department of Biological Chemistry, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore 21205 MD, USA.,Department of Oncology and Pathology, Johns Hopkins University School of Medicine, Baltimore 21205 MD, USA
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23
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Du NH, Arpat AB, De Matos M, Gatfield D. MicroRNAs shape circadian hepatic gene expression on a transcriptome-wide scale. eLife 2014; 3:e02510. [PMID: 24867642 PMCID: PMC4032493 DOI: 10.7554/elife.02510] [Citation(s) in RCA: 82] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
A considerable proportion of mammalian gene expression undergoes circadian oscillations. Post-transcriptional mechanisms likely make important contributions to mRNA abundance rhythms. We have investigated how microRNAs (miRNAs) contribute to core clock and clock-controlled gene expression using mice in which miRNA biogenesis can be inactivated in the liver. While the hepatic core clock was surprisingly resilient to miRNA loss, whole transcriptome sequencing uncovered widespread effects on clock output gene expression. Cyclic transcription paired with miRNA-mediated regulation was thus identified as a frequent phenomenon that affected up to 30% of the rhythmic transcriptome and served to post-transcriptionally adjust the phases and amplitudes of rhythmic mRNA accumulation. However, only few mRNA rhythms were actually generated by miRNAs. Overall, our study suggests that miRNAs function to adapt clock-driven gene expression to tissue-specific requirements. Finally, we pinpoint several miRNAs predicted to act as modulators of rhythmic transcripts, and identify rhythmic pathways particularly prone to miRNA regulation. DOI:http://dx.doi.org/10.7554/eLife.02510.001 The rising and setting of the sun have long driven the schedules of humans and other mammals. This 24-hr cycle influences many behavioural and physiological changes, including alertness, body temperature, and sleep. A region in the brain acts as a master clock that regulates these daily cycles, which are called circadian rhythms. Signals from the brain's master clock turn on and off ‘core clock genes’ in cells, which trigger cycles that cause some proteins to be produced in a circadian rhythm. The rhythm is specialized to a particular tissue or organ, and may help them to carry out their designated daily tasks. However, circadian rhythms might also be produced in other ways that do not involve these genes. Messenger RNA (mRNA) molecules have a central role in the production of proteins, and in the mouse liver, up to 15% of mRNA molecules are produced in circadian cycles. The liver performs essential tasks that control metabolism–including that of carbohydrates, fats, and cholesterol. Precisely timing when certain mRNAs and proteins reach peaks and troughs in their activities to coincide with mealtimes is important for nutrients to be properly processed. Other RNA molecules called microRNAs influence how mRNA molecules are translated into proteins. Now Du, Arpat et al. have looked at the influence of microRNAs on circadian rhythms in the mouse liver in greater detail. These experiments, which involved ‘knocking out’ a gene that is essential for the production of microRNAs, show that rather than setting the mRNA rhythms, the microRNAs appear to adjust them to meet the specific needs of the liver. Targeting specific microRNA molecules may reveal new strategies to tweak these rhythms, which could help to improve conditions when metabolic functions go wrong. DOI:http://dx.doi.org/10.7554/eLife.02510.002
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Affiliation(s)
- Ngoc-Hien Du
- Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
| | - Alaaddin Bulak Arpat
- Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland Vital-IT, Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Mara De Matos
- Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
| | - David Gatfield
- Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
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24
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The miRNA-mediated cross-talk between transcripts provides a novel layer of posttranscriptional regulation. ADVANCES IN GENETICS 2014; 85:149-99. [PMID: 24880735 DOI: 10.1016/b978-0-12-800271-1.00003-2] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Endogenously expressed transcripts that are posttranscriptionally regulated by the same microRNAs (miRNAs) will, in principle, compete for the binding of their shared small noncoding RNA regulators and modulate each other's abundance. Recently, the levels of some coding as well as noncoding transcripts have indeed been found to be regulated in this way. Transcripts that engage in such regulatory interactions are referred to as competitive endogenous RNAs (ceRNAs). This novel layer of posttranscriptional regulation has been shown to contribute to diverse aspects of organismal and cellular biology, despite the number of functionally characterized ceRNAs being as yet relatively low. Importantly, increasing evidence suggests that the dysregulation of some ceRNA interactions is associated with disease etiology, most preeminently with cancer. Here we review how posttranscriptional regulation by miRNAs contributes to the cross-talk between transcripts and review examples of known ceRNAs by highlighting the features underlying their interactions and what might be their biological relevance.
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25
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Gallaher AM, Das S, Xiao Z, Andresson T, Kieffer-Kwon P, Happel C, Ziegelbauer J. Proteomic screening of human targets of viral microRNAs reveals functions associated with immune evasion and angiogenesis. PLoS Pathog 2013; 9:e1003584. [PMID: 24039573 PMCID: PMC3764211 DOI: 10.1371/journal.ppat.1003584] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2013] [Accepted: 07/14/2013] [Indexed: 01/11/2023] Open
Abstract
Kaposi's sarcoma (KS) is caused by infection with Kaposi's sarcoma-associated herpesvirus (KSHV). The virus expresses unique microRNAs (miRNAs), but the targets and functions of these miRNAs are not completely understood. In order to identify human targets of viral miRNAs, we measured protein expression changes caused by multiple KSHV miRNAs using pulsed stable labeling with amino acids in cell culture (pSILAC) in primary endothelial cells. This led to the identification of multiple human genes that are repressed at the protein level, but not at the miRNA level. Further analysis also identified that KSHV miRNAs can modulate activity or expression of upstream regulatory factors, resulting in suppressed activation of a protein involved in leukocyte recruitment (ICAM1) following lysophosphatidic acid treatment, as well as up-regulation of a pro-angiogenic protein (HIF1α), and up-regulation of a protein involved in stimulating angiogenesis (HMOX1). This study aids in our understanding of miRNA mechanisms of repression and miRNA contributions to viral pathogenesis.
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MESH Headings
- HEK293 Cells
- Herpesvirus 8, Human/genetics
- Herpesvirus 8, Human/metabolism
- Human Umbilical Vein Endothelial Cells
- Humans
- MicroRNAs/genetics
- MicroRNAs/metabolism
- Neoplasm Proteins/genetics
- Neoplasm Proteins/metabolism
- Neovascularization, Pathologic/genetics
- Neovascularization, Pathologic/metabolism
- Neovascularization, Pathologic/pathology
- Neovascularization, Pathologic/virology
- RNA, Neoplasm/genetics
- RNA, Neoplasm/metabolism
- RNA, Viral/genetics
- RNA, Viral/metabolism
- Sarcoma, Kaposi/genetics
- Sarcoma, Kaposi/metabolism
- Sarcoma, Kaposi/pathology
- Sarcoma, Kaposi/virology
- Tumor Escape
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Affiliation(s)
- Amelia M. Gallaher
- HIV and AIDS Malignancy Branch, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Sudipto Das
- Laboratory of Proteomics and Analytical Technologies, Advanced Technology Program, SAIC-Frederick Inc., National Cancer Institute at Frederick, Frederick, Maryland, United States of America
| | - Zhen Xiao
- Laboratory of Proteomics and Analytical Technologies, Advanced Technology Program, SAIC-Frederick Inc., National Cancer Institute at Frederick, Frederick, Maryland, United States of America
| | - Thorkell Andresson
- Laboratory of Proteomics and Analytical Technologies, Advanced Technology Program, SAIC-Frederick Inc., National Cancer Institute at Frederick, Frederick, Maryland, United States of America
| | - Philippe Kieffer-Kwon
- HIV and AIDS Malignancy Branch, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Christine Happel
- HIV and AIDS Malignancy Branch, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Joseph Ziegelbauer
- HIV and AIDS Malignancy Branch, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
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26
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Lemons D, Maurya MR, Subramaniam S, Mercola M. Developing microRNA screening as a functional genomics tool for disease research. Front Physiol 2013; 4:223. [PMID: 23986717 PMCID: PMC3753477 DOI: 10.3389/fphys.2013.00223] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2013] [Accepted: 08/02/2013] [Indexed: 02/04/2023] Open
Abstract
Originally discovered as regulators of developmental timing in C. elegans, microRNAs (miRNAs) have emerged as modulators of nearly every cellular process, from normal development to pathogenesis. With the advent of whole genome libraries of miRNA mimics suitable for high throughput screening, it is possible to comprehensively evaluate the function of each member of the miRNAome in cell-based assays. Since the relatively few microRNAs in the genome are thought to directly regulate a large portion of the proteome, miRNAome screening, coupled with the identification of the regulated proteins, might be a powerful new approach to gaining insight into complex biological processes.
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Affiliation(s)
- Derek Lemons
- Department of Bioengineering, Jacobs School of Engineering, University of California San Diego, La Jolla, CA, USA ; Muscle Development and Regeneration Program, Sanford-Burnham Medical Research Institute La Jolla, CA, USA
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27
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Pham H, Rodriguez CE, Donald GW, Hertzer KM, Jung XS, Chang HH, Moro A, Reber HA, Hines OJ, Eibl G. miR-143 decreases COX-2 mRNA stability and expression in pancreatic cancer cells. Biochem Biophys Res Commun 2013; 439:6-11. [PMID: 23973710 DOI: 10.1016/j.bbrc.2013.08.042] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2013] [Accepted: 08/13/2013] [Indexed: 12/14/2022]
Abstract
Small non-coding RNAs, microRNAs (miRNA), inhibit the translation or accelerate the degradation of message RNA (mRNA) by targeting the 3'-untranslated region (3'-UTR) in regulating growth and survival through gene suppression. Deregulated miRNA expression contributes to disease progression in several cancers types, including pancreatic cancers (PaCa). PaCa tissues and cells exhibit decreased miRNA, elevated cyclooxygenase (COX)-2 and increased prostaglandin E2 (PGE2) resulting in increased cancer growth and metastases. Human PaCa cell lines were used to demonstrate that restoration of miRNA-143 (miR-143) regulates COX-2 and inhibits cell proliferation. miR-143 were detected at fold levels of 0.41 ± 0.06 in AsPC-1, 0.20 ± 0.05 in Capan-2 and 0.10 ± 0.02 in MIA PaCa-2. miR-143 was not detected in BxPC-3, HPAF-II and Panc-1 which correlated with elevated mitogen-activated kinase (MAPK) and MAPK kinase (MEK) activation. Treatment with 10 μM of MEK inhibitor U0126 or PD98059 increased miR-143, respectively, by 187 ± 18 and 152 ± 26-fold in BxPC-3 and 182 ± 7 and 136 ± 9-fold in HPAF-II. miR-143 transfection diminished COX-2 mRNA stability at 60 min by 2.6 ± 0.3-fold in BxPC-3 and 2.5 ± 0.2-fold in HPAF-II. COX-2 expression and cellular proliferation in BxPC-3 and HPAF-II inversely correlated with increasing miR-143. PGE2 levels decreased by 39.3 ± 5.0% in BxPC-3 and 48.0 ± 3.0% in HPAF-II transfected with miR-143. Restoration of miR-143 in PaCa cells suppressed of COX-2, PGE2, cellular proliferation and MEK/MAPK activation, implicating this pathway in regulating miR-143 expression.
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Affiliation(s)
- Hung Pham
- Department of Surgery, UCLA Center of Excellence in Pancreatic Diseases, UCLA David Geffen School of Medicine, University of California - Los Angeles, Los Angeles, CA 90095, United States; Department of Medicine, Veterans Affair Greater Los Angeles Healthcare System, Los Angeles, CA 90073, United States
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28
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Li C, Xiong Q, Zhang J, Ge F, Bi LJ. Quantitative proteomic strategies for the identification of microRNA targets. Expert Rev Proteomics 2013. [PMID: 23194271 DOI: 10.1586/epr.12.49] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
MicroRNAs (miRNAs) are small noncoding RNAs, approximately 22 nucleotides in length, found in diverse organisms. They have emerged in recent years as key regulators of a broad spectrum of cellular functions. miRNAs regulate biological processes by inducing translational inhibition and degradation of their target mRNAs through base pairing to partially or fully complementary sites. In the field of miRNA research, the identification of the targets of individual miRNAs is of utmost importance. Our understanding of the molecular mechanisms by which individual miRNAs modulate cellular functions will remain incomplete until a full set of miRNA targets is identified and validated. Since a miRNA may regulate many of its targets at the translational level without affecting mRNA abundance, proteomic methods are best suited for revealing the full spectrum of miRNA targets. Quantitative proteomics is emerging as a powerful toolbox for identifying miRNA targets and for quantifying the contribution of translational repression by miRNAs. In this review, the authors summarize the quantitative proteomic approaches that have been employed for identification of miRNA targets and discuss current challenges as well as possible ways of overcoming them.
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Affiliation(s)
- Chongyang Li
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
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29
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Pan S, Brentnall TA, Kelly K, Chen R. Tissue proteomics in pancreatic cancer study: discovery, emerging technologies, and challenges. Proteomics 2013; 13:710-21. [PMID: 23125171 DOI: 10.1002/pmic.201200319] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2012] [Revised: 10/01/2012] [Accepted: 10/05/2012] [Indexed: 12/22/2022]
Abstract
Pancreatic cancer is a highly lethal disease that is difficult to diagnose and treat. The advances in proteomics technology, especially quantitative proteomics, have stimulated a great interest in applying this technology for pancreatic cancer study. A variety of tissue proteomics approaches have been applied to investigate pancreatic cancer and the associated diseases. These studies were carried out with various goals, aiming to better understand the molecular mechanisms underlying pancreatic tumorigenesis, to improve therapeutic treatment and to identify cancer associated protein signatures, signaling events as well as interactions between cancer cells and tumor microenvironment. Here, we provide an overview on the tissue proteomics studies of pancreatic cancer reported in the past few years in light of discovery and technology development.
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Affiliation(s)
- Sheng Pan
- Department of Medicine, University of Washington, Seattle, WA 98195, USA.
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30
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Lucas K, Raikhel AS. Insect microRNAs: biogenesis, expression profiling and biological functions. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2013; 43:24-38. [PMID: 23165178 PMCID: PMC3534889 DOI: 10.1016/j.ibmb.2012.10.009] [Citation(s) in RCA: 125] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2012] [Revised: 10/24/2012] [Accepted: 10/28/2012] [Indexed: 05/09/2023]
Abstract
MicroRNAs (miRNA) are a class of endogenous regulatory RNA molecules 21-24 nucleotides in length that modulate gene expression at the post-transcriptional level via base pairing to target sites within messenger RNAs (mRNA). Typically, the miRNA "seed sequence" (nucleotides 2-8 at the 5' end) binds complementary seed match sites within the 3' untranslated region of mRNAs, resulting in either translational inhibition or mRNA degradation. MicroRNAs were first discovered in Caenorhabditis elegans and were shown to be involved in the timed regulation of developmental events. Since their discovery in the 1990s, thousands of potential miRNAs have since been identified in various organisms through small RNA cloning methods and/or computational prediction, and have been shown to play functionally important roles of gene regulation in invertebrates, vertebrates, plants, fungi and viruses. Numerous functions of miRNAs identified in Drosophila melanogaster have demonstrated a great significance of these regulatory molecules. However, elucidation of miRNA roles in non-drosophilid insects presents a challenging and important task.
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Affiliation(s)
- Keira Lucas
- Department of Entomology, University of California Riverside, Riverside, CA 92521, U.S.A
- Institute for Integrative Genome Biology, University of California Riverside, Riverside, CA 92521, U.S.A
- Graduate Program in Genetics, Genomics and Bioinformatics, University of California Riverside, Riverside, CA 92521, U.S.A
| | - Alexander S. Raikhel
- Department of Entomology, University of California Riverside, Riverside, CA 92521, U.S.A
- Institute for Integrative Genome Biology, University of California Riverside, Riverside, CA 92521, U.S.A
- Corresponding author. Department of Entomology, University of California, Riverside, Riverside, CA 92521, U.S.A. Tel. +1 951 827 2129. (Keira Lucas); (Alexander S. Raikhel)
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31
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Huang TC, Pinto SM, Pandey A. Proteomics for understanding miRNA biology. Proteomics 2012; 13:558-67. [PMID: 23125164 DOI: 10.1002/pmic.201200339] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2012] [Revised: 10/01/2012] [Accepted: 10/05/2012] [Indexed: 12/19/2022]
Abstract
MicroRNAs (miRNAs) are small noncoding RNAs that play important roles in posttranscriptional regulation of gene expression. Mature miRNAs associate with the RNA interference silencing complex to repress mRNA translation and/or degrade mRNA transcripts. Mass spectrometry-based proteomics has enabled identification of several core components of the canonical miRNA processing pathway and their posttranslational modifications which are pivotal in miRNA regulatory mechanisms. The use of quantitative proteomic strategies has also emerged as a key technique for experimental identification of miRNA targets by allowing direct determination of proteins whose levels are altered because of translational suppression. This review focuses on the role of proteomics and labeling strategies to understand miRNA biology.
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Affiliation(s)
- Tai-Chung Huang
- Department of Biological Chemistry, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
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32
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Veraksa A. Regulation of developmental processes: insights from mass spectrometry-based proteomics. WILEY INTERDISCIPLINARY REVIEWS-DEVELOPMENTAL BIOLOGY 2012; 2:723-34. [PMID: 24014456 DOI: 10.1002/wdev.102] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Mass spectrometry (MS)-based proteomics has become an indispensable tool for protein identification and quantification. In this paper, common MS workflows are described, with an emphasis on applications of MS-based proteomics in developmental biology. Progress has been made in the analysis of proteome changes during tissue differentiation and in various genetic perturbations. MS-based proteomics has been particularly useful for identifying novel protein interactions by affinity purification-mass spectrometry (AP-MS), many of which have been subsequently functionally validated and led to the discovery of previously unknown modes of developmental regulation. Quantitative proteomics approaches can be used to study posttranslational modifications (PTMs) of proteins such as phosphorylation, to reveal the dynamics of intracellular signal transduction. Integrative approaches combine quantitative MS-based proteomics with other high-throughput methods, with the promise of a systems level understanding of developmental regulation.
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Affiliation(s)
- Alexey Veraksa
- Department of Biology, University of Massachusetts Boston, Boston, MA, USA.
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33
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Hu Y, Ou Y, Wu K, Chen Y, Sun W. miR-143 inhibits the metastasis of pancreatic cancer and an associated signaling pathway. Tumour Biol 2012; 33:1863-70. [PMID: 23070684 DOI: 10.1007/s13277-012-0446-8] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2012] [Accepted: 06/21/2012] [Indexed: 12/15/2022] Open
Abstract
Pancreatic cancer is characterized by early metastasis and high mortality. In this study, the role of miR-143 in invasion and metastasis was investigated in pancreatic cancer cells. miR-143 expression was established by an adenovirus-carried miR-143 expression cassette. mRNA and protein levels of gene expression were examined by RT-PCR and Western blot assay, respectively. Rho GTPases activity was measured by the pull down assay. The role of miR-143 in migration and invasion of Panc-1 cells was tested in vitro. The antimetastatic effect of miR-143 was tested in a liver metastasis model, while its antitumor growth effect was tested in a xenograft Panc-1 tumor model. Results demonstrated that ARHGEF1 (GEF1), ARHGEF2 (GEF2), and K-RAS genes are the targets of miR-143. miR-143 expression significantly decreased mRNA and protein levels of GEF1, GEF2, and K-RAS genes; lowered the constitutive activities of RhoA, Rac1, and Cdc42 GTPases; decreased the protein levels of MMP-2 and MMP-9; but significantly increased the protein level of E-cadherin. miR-143 expression also significantly inhibited the migration and invasion of Panc-1 cells in vitro, liver metastasis, and xenograft tumor growth in vivo. Our study suggested that miR-143 plays a central role in the invasion and metastasis of pancreatic cancer and miR-143 is a potential target for pancreatic cancer therapy.
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Affiliation(s)
- Yongjun Hu
- Department of General Surgery, Xiangya Hospital, Central South University, Changsha 410008, PR China
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34
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Bauer KM, Hummon AB. Effects of the miR-143/-145 microRNA cluster on the colon cancer proteome and transcriptome. J Proteome Res 2012; 11:4744-54. [PMID: 22897626 DOI: 10.1021/pr300600r] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The miR-143/-145 cluster is greatly reduced in several cancers, including colon cancer. Both miR-143 and miR-145 have been shown to possess antitumorigenic activity with involvement in various cancer-related events such as proliferation, invasion, and migration. As the deregulation of the miR-143/-145 cluster is implicated in tumorigenesis, we combined SILAC and microarray analyses to systematically interrogate the impact of miR-143/-145 on the colon cancer proteome and transcriptome. Using SILAC, we identified over 2000 proteins after reintroduction of miR-143 and miR-145, in the colon cancer cell line SW480, individually, and then, in concert. Our goal was to determine whether these microRNAs function individually or synergistically. The resulting regulated gene products showed evidence of both mRNA destabilization and translational inhibition with a bias toward the former mechanism of regulation. Numerous candidate targets were identified whose expression is attributable to an individual microRNA or whose regulation was more apparent following reintroduction of the miR-143/-145 cluster. In addition, several shared targets of miR-143 and miR-145 were identified. Overall, our results indicate that the summed effects of individually introduced microRNAs produce distinct molecular changes from the consequences of the assembled cluster. We conclude that there is a need to investigate both the individual and combined functional implications of a microRNA cluster.
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Affiliation(s)
- Kerry M Bauer
- Department of Chemistry and Biochemistry, University of Notre Dame, 251 Nieuwland Science Hall, Notre Dame, Indiana 46556, USA
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35
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Bargaje R, Gupta S, Sarkeshik A, Park R, Xu T, Sarkar M, Halimani M, Roy SS, Yates J, Pillai B. Identification of novel targets for miR-29a using miRNA proteomics. PLoS One 2012; 7:e43243. [PMID: 22952654 PMCID: PMC3428309 DOI: 10.1371/journal.pone.0043243] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2012] [Accepted: 07/18/2012] [Indexed: 12/21/2022] Open
Abstract
MicroRNAs (miRNAs) are short regulatory RNA molecules that interfere with the expression of target mRNA by binding to complementary sequences. Currently, the most common method for identification of targets of miRNAs is computational prediction based on free energy change calculations, target site accessibility and conservation. Such algorithms predict hundreds of targets for each miRNA, necessitating tedious experimentation to identify the few functional targets. Here we explore the utility of miRNA-proteomics as an approach to identifying functional miRNA targets. We used Stable Isotope Labeling by amino acids in cell culture (SILAC) based proteomics to detect differences in protein expression induced by the over-expression of miR-34a and miR-29a. Over-expression of miR-29a, a miRNA expressed in the brain and in cells of the blood lineage, resulted in the differential expression of a set of proteins. Gene Ontology based classification showed that a significant sub-set of these targets, including Voltage Dependent Anion Channel 1 and 2 (VDAC1 and VDAC2) and ATP synthetase, were mitochondrial proteins involved in apoptosis. Using reporter assays, we established that miR-29a targets the 3′ Untranslated Regions (3′ UTR) of VDAC1 and VDAC2. However, due to the limited number of proteins identified using this approach and the inability to differentiate between primary and secondary effects we conclude that miRNA-proteomics is of limited utility as a high-throughput alternative for sensitive and unbiased miRNA target identification. However, this approach was valuable for rapid assessment of the impact of the miRNAs on the cellular proteome and its biological role in apoptosis.
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Affiliation(s)
- Rhishikesh Bargaje
- Functional Genomics Unit, Council of Scientific Industrial Research - Institute of Genomics and Integrative Biology, Delhi, India
| | - Shivani Gupta
- Functional Genomics Unit, Council of Scientific Industrial Research - Institute of Genomics and Integrative Biology, Delhi, India
| | - Ali Sarkeshik
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, California, United States of America
| | - Robin Park
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, California, United States of America
| | - Tao Xu
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, California, United States of America
| | - Maharnob Sarkar
- Functional Genomics Unit, Council of Scientific Industrial Research - Institute of Genomics and Integrative Biology, Delhi, India
| | - Mahantappa Halimani
- Functional Genomics Unit, Council of Scientific Industrial Research - Institute of Genomics and Integrative Biology, Delhi, India
| | - Soumya Sinha Roy
- Functional Genomics Unit, Council of Scientific Industrial Research - Institute of Genomics and Integrative Biology, Delhi, India
| | - John Yates
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, California, United States of America
- * E-mail: (JY); (BP)
| | - Beena Pillai
- Functional Genomics Unit, Council of Scientific Industrial Research - Institute of Genomics and Integrative Biology, Delhi, India
- * E-mail: (JY); (BP)
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Abstract
MicroRNAs (miRNAs) are small noncoding RNAs that control the expression of around 60% of the human protein-coding genes. In the past decade, deregulation of miRNAs (by expression and/or function) has been associated with the pathogenesis, progression and prognosis of different diseases, including leukemia. The number of discovered genes encoding miRNAs has risen exponentially in this period, but the numbers of miRNA-target genes discovered and validated lag far behind. Scientists have gained more in-depth knowledge of the basic mechanism of action of miRNAs, but the main challenge still remaining is the identification of direct targets of these important 'micro-players', to understand how they fine-tune so many biological processes in both healthy and diseased tissue. Many technologies have been developed in the past few years, some with more potential than others, but all with their own pros and cons. Here, we review the most common and most potent computational and experimental approaches for miRNA-target gene discovery and discuss how the hunting of targets is challenging but possible by taking the experimental limitations in consideration and choosing the correct cellular context for identifying relevant target genes.
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37
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Fabian MR, Sonenberg N. The mechanics of miRNA-mediated gene silencing: a look under the hood of miRISC. Nat Struct Mol Biol 2012; 19:586-93. [PMID: 22664986 DOI: 10.1038/nsmb.2296] [Citation(s) in RCA: 730] [Impact Index Per Article: 60.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Since their discovery almost two decades ago, microRNAs (miRNAs) have been shown to function by post-transcriptionally regulating protein accumulation. Understanding how miRNAs silence targeted mRNAs has been the focus of intensive research. Multiple models have been proposed, with few mechanistic details having been worked out. However, the past few years have witnessed a quantum leap forward in our understanding of the molecular mechanics of miRNA-mediated gene silencing. In this review we describe recent discoveries, with an emphasis on how miRISC post-transcriptionally controls gene expression by inhibiting translation and/or initiating mRNA decay, and how trans-acting factors control miRNA action.
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Affiliation(s)
- Marc R Fabian
- Department of Biochemistry, Goodman Cancer Centre, McGill University, Montreal, Quebec, Canada.
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38
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WANG XINWEI, HEEGAARD NIELSHH, ØRUM HENRIK. MicroRNAs in liver disease. Gastroenterology 2012; 142:1431-43. [PMID: 22504185 PMCID: PMC6311104 DOI: 10.1053/j.gastro.2012.04.007] [Citation(s) in RCA: 223] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/09/2011] [Revised: 04/04/2012] [Accepted: 04/09/2012] [Indexed: 02/06/2023]
Abstract
MicroRNAs are small noncoding RNA molecules that regulate gene expression posttranscriptionally through complementary base pairing with thousands of messenger RNAs. They regulate diverse physiological, developmental, and pathophysiological processes. Recent studies have uncovered the contribution of microRNAs to the pathogenesis of many human diseases, including liver diseases. Moreover, microRNAs have been identified as biomarkers that can often be detected in the systemic circulation. We review the role of microRNAs in liver physiology and pathophysiology, focusing on viral hepatitis, liver fibrosis, and cancer. We also discuss microRNAs as diagnostic and prognostic markers and microRNA-based therapeutic approaches for liver disease.
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Affiliation(s)
- XIN WEI WANG
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer institute, National Institutes of Health, Bethesda, Maryland
| | - NIELS H. H. HEEGAARD
- Department of Clinical Biochemistry and Immunology Statens Serum Institut, Copenhagen, Denmark
| | - HENRIK ØRUM
- Santaris Pharma, Kogle Allé 6, Hørsholm, Denmark
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39
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Ali S, Ahmad A, Aboukameel A, Bao B, Padhye S, Philip PA, Sarkar FH. RETRACTED: Increased Ras GTPase activity is regulated by miRNAs that can be attenuated by CDF treatment in pancreatic cancer cells. Cancer Lett 2012; 319:173-181. [PMID: 22261338 DOI: 10.1016/j.canlet.2012.01.013] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2011] [Revised: 01/09/2012] [Accepted: 01/10/2012] [Indexed: 01/07/2023]
Abstract
This article has been retracted: please see Elsevier Policy on Article Withdrawal (http://www.elsevier.com/locate/withdrawalpolicy).
This article has been retracted at the request of the Editor in Chief. An investigation by Wayne State University identified a discrepancy between the data reported in Figures 1 A and 3 and the original collected data. The investigation committee concluded that this undermined the scientific basis of the publication, that no credible replacement data were available, and advised that the publication should be retracted.
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Affiliation(s)
- Shadan Ali
- Department of Oncology, Karmanos Cancer Institute, Wayne State University School of Medicine, Detroit, MI, United States
| | - Aamir Ahmad
- Department of Pathology, Karmanos Cancer Institute, Wayne State University School of Medicine, Detroit, MI, United States
| | - Amro Aboukameel
- Department of Oncology, Karmanos Cancer Institute, Wayne State University School of Medicine, Detroit, MI, United States
| | - Bin Bao
- Department of Pathology, Karmanos Cancer Institute, Wayne State University School of Medicine, Detroit, MI, United States
| | - Subhash Padhye
- Interdisciplinary Science & Technology Research Academy, Abeda Inamdar Senior College, Azam Campus, Pune 411 001, India
| | - Philip A Philip
- Department of Oncology, Karmanos Cancer Institute, Wayne State University School of Medicine, Detroit, MI, United States
| | - Fazlul H Sarkar
- Department of Oncology, Karmanos Cancer Institute, Wayne State University School of Medicine, Detroit, MI, United States; Department of Pathology, Karmanos Cancer Institute, Wayne State University School of Medicine, Detroit, MI, United States.
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40
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Pekow JR, Dougherty U, Mustafi R, Zhu H, Kocherginsky M, Rubin DT, Hanauer SB, Hart J, Chang EB, Fichera A, Joseph LJ, Bissonnette M. miR-143 and miR-145 are downregulated in ulcerative colitis: putative regulators of inflammation and protooncogenes. Inflamm Bowel Dis 2012; 18:94-100. [PMID: 21557394 PMCID: PMC3931730 DOI: 10.1002/ibd.21742] [Citation(s) in RCA: 88] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/15/2011] [Accepted: 03/24/2011] [Indexed: 12/11/2022]
Abstract
BACKGROUND miR-143 and miR-145 are believed to function as colon cancer tumor suppressors, as they inhibit colon cancer cell growth and are downregulated in sporadic colonic tumors. We speculated that miR-143 and miR-145 might also be downregulated and contribute to malignant transformation of colonic epithelium in longstanding ulcerative colitis (UC). METHODS Biopsies were obtained 20 cm proximal to the anus from individuals with quiescent UC and from normal controls. RNA and proteins were extracted and measured. miR-143 and miR-145 were quantified by real-time polymerase chain reaction (PCR) and miR-145 was also assessed by in situ hybridization. Putative targets of these miRNAs, K-RAS, API5, MEK-2 (miR-143), and IRS-1 (miR-145) were determined by western blotting. To assess the effects of miR-143 and miR-145 on these predicted targets, HCT116 and HCA-7 colorectal cancer cells were transfected with miR-143 and miR-145 and expression levels of these proteins were measured. RESULTS In UC, miR-143 and miR-145 were significantly downregulated 8.3-fold (3.4-20.1) (P < 0.0001) and 4.3-fold (2.3-7.8) (P < 0.0001), respectively, compared to normal colon. In contrast, IRS-1, K-RAS, API5, and MEK-2 were upregulated in UC, consistent with their assignments as targets of these miRNAs. Furthermore, transfected miR-143 and miR-145 significantly downregulated these proteins in HCT116 or HCA-7 cells. CONCLUSIONS Compared to normal colonic mucosa, in chronic UC miR-143 and miR-145 were significantly downregulated and their predicted targets, IRS-1, K-RAS, API5, and MEK-2 were upregulated. We postulate that loss of these tumor suppressor miRNAs predispose to chronic inflammation and neoplastic progression in IBD.
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Affiliation(s)
- Joel R. Pekow
- Section of Gastroenterology, Hepatology, and Nutrition, University of Chicago; Chicago, IL
| | - Urszula Dougherty
- Section of Gastroenterology, Hepatology, and Nutrition, University of Chicago; Chicago, IL
| | - Reba Mustafi
- Section of Gastroenterology, Hepatology, and Nutrition, University of Chicago; Chicago, IL
| | - Hongyan Zhu
- Section of Gastroenterology, Hepatology, and Nutrition, University of Chicago; Chicago, IL
| | | | - David T. Rubin
- Section of Gastroenterology, Hepatology, and Nutrition, University of Chicago; Chicago, IL
| | - Stephen B. Hanauer
- Section of Gastroenterology, Hepatology, and Nutrition, University of Chicago; Chicago, IL
| | - John Hart
- Department of Pathology, University of Chicago; Chicago, IL
| | - Eugene B. Chang
- Section of Gastroenterology, Hepatology, and Nutrition, University of Chicago; Chicago, IL
| | | | | | - Marc Bissonnette
- Section of Gastroenterology, Hepatology, and Nutrition, University of Chicago; Chicago, IL
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41
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Abstract
MicroRNAs (miRNAs) are highly conserved, tiny (∼22 nucleotides) non-coding RNAs that have emerged as potent regulators of mRNA translation. miRNAs exhibit fine-tuning of the control of proteins involved in cell signalling (AE) pathways and in vital cellular and developmental processes. miRNAs are expressed in cardiovascular tissues, and multiple functional aspects of miRNAs underscore their key role in cardiovascular (patho)physiology. The development and increasing use of novel molecular biology tools have contributed to the recent success in miRNA research. In the present review, we discuss current updates on important and novel miRNA techniques, including: (i) miRNA screening tools; (ii) bioanalytical target prediction tools; (iii) target validation tools; and (iv) manipulative miRNA expression tools. We also present an update about recently identified miRNA targets that play a key role in cardiovascular development and disorders.
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Affiliation(s)
- S Dangwal
- Institute of Molecular and Translational Therapeutic Strategies, Hannover Medical School, Carl-Neuberg-Straße 1, 30625 Hannover, Germany
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42
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Identification of cardiovascular microRNA targetomes. J Mol Cell Cardiol 2011; 51:674-81. [DOI: 10.1016/j.yjmcc.2011.08.017] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/12/2011] [Revised: 08/11/2011] [Accepted: 08/12/2011] [Indexed: 11/19/2022]
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43
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Lößner C, Meier J, Warnken U, Rogers MA, Lichter P, Pscherer A, Schnölzer M. Quantitative proteomics identify novel miR-155 target proteins. PLoS One 2011; 6:e22146. [PMID: 21799781 PMCID: PMC3143118 DOI: 10.1371/journal.pone.0022146] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2010] [Accepted: 06/17/2011] [Indexed: 12/02/2022] Open
Abstract
Background MicroRNAs are 22 nucleotides long non-coding RNAs and exert their function either by transcriptional or translational inhibition. Although many microRNA profiles in different tissues and disease states have already been discovered, only little is known about their target proteins. The microRNA miR-155 is deregulated in many diseases, including cancer, where it might function as an oncoMir. Methodology/Principal Findings We employed a proteomics technique called “stable isotope labelling by amino acids in cell culture” (SILAC) allowing relative quantification to reliably identify target proteins of miR-155. Using SILAC, we identified 46 putative miR-155 target proteins, some of which were previously reported. With luciferase reporter assays, CKAP5 was confirmed as a new target of miR-155. Functional annotation of miR-155 target proteins pointed to a role in cell cycle regulation. Conclusions/Significance To the best of our knowledge we have investigated for the first time miR-155 target proteins in the HEK293T cell line in large scale. In addition, by comparing our results to previously identified miR-155 target proteins in other cell lines, we provided further evidence for the cell line specificity of microRNAs.
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Affiliation(s)
- Christopher Lößner
- Functional Proteome Analysis, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Jan Meier
- Division of Molecular Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Uwe Warnken
- Functional Proteome Analysis, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Michael A. Rogers
- Division of Molecular Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Peter Lichter
- Division of Molecular Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Armin Pscherer
- Division of Molecular Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Martina Schnölzer
- Functional Proteome Analysis, German Cancer Research Center (DKFZ), Heidelberg, Germany
- * E-mail:
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44
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Lieber D, Haas J. Viruses and microRNAs: a toolbox for systematic analysis. WILEY INTERDISCIPLINARY REVIEWS-RNA 2011; 2:787-801. [DOI: 10.1002/wrna.92] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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45
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Zhu H, Dougherty U, Robinson V, Mustafi R, Pekow J, Kupfer S, Li YC, Hart J, Goss K, Fichera A, Joseph L, Bissonnette M. EGFR signals downregulate tumor suppressors miR-143 and miR-145 in Western diet-promoted murine colon cancer: role of G1 regulators. Mol Cancer Res 2011; 9:960-75. [PMID: 21653642 PMCID: PMC3819602 DOI: 10.1158/1541-7786.mcr-10-0531] [Citation(s) in RCA: 98] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Epidermal growth factor receptors (EGFR) contribute to colonic tumorigenesis in experimental models of colon cancer. We previously showed that EGFR was also required for colonic tumor promotion by Western diet. The goal of this study was to identify EGFR-regulated microRNAs that contribute to diet-promoted colonic tumorigenesis. Murine colonic tumors from Egfr(wt) and hypomorphic Egfr(wa2) mice were screened using micro RNA (miRNA) arrays and miR-143 and miR-145 changes confirmed by Northern, real-time PCR, and in situ analysis. Rodent and human sporadic and ulcerative colitis (UC)-associated colon cancers were examined for miR-143 and miR-145. Effects of EGFR on miR-143 and miR-145 expression were assessed in murine and human colonic cells and their putative targets examined in vitro and in vivo. miR-143 and miR-145 were readily detected in normal colonocytes and comparable in Egfr(wt) and Egfr(wa2) mice. These miRNAs were downregulated in azoxymethane and inflammation-associated colonic tumors from Egfr(wt) mice but upregulated in Egfr(wa2) tumors. They were also reduced in human sporadic and UC colon cancers. EGFR signals suppressed miR-143 and miR-145 in human and murine colonic cells. Transfected miR-143 and miR-145 inhibited HCT116 cell growth in vitro and in vivo and downregulated G(1) regulators, K-Ras, MYC, CCND2, cdk6, and E2F3, putative or established targets of these miRNAs. miRNA targets Ras and MYC were increased in colonic tumors from Egfr(wt) but not Egfr(wa2) mice fed a Western diet. EGFR suppresses miR-143 and miR-145 in murine models of colon cancer. Furthermore, Western diet unmasks the tumor suppressor roles of these EGFR-regulated miRNAs.
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MESH Headings
- Animals
- Antibodies, Monoclonal/pharmacology
- Antibodies, Monoclonal, Humanized
- Azoxymethane/pharmacology
- Cetuximab
- Colitis, Ulcerative/complications
- Colitis, Ulcerative/metabolism
- Colonic Neoplasms/etiology
- Colonic Neoplasms/genetics
- Colonic Neoplasms/metabolism
- Dextran Sulfate/pharmacology
- Diet/adverse effects
- Down-Regulation
- ErbB Receptors/antagonists & inhibitors
- ErbB Receptors/genetics
- ErbB Receptors/metabolism
- G1 Phase/genetics
- Gene Expression Regulation, Neoplastic
- Genes, Tumor Suppressor
- HCT116 Cells
- Humans
- Mice
- MicroRNAs/genetics
- Neoplasms, Experimental/etiology
- Neoplasms, Experimental/genetics
- Neoplasms, Experimental/metabolism
- Rats
- Signal Transduction
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | - Marc Bissonnette
- To Whom Correspondence Should be Addressed: Marc Bissonnette, M.D, Department of Medicine, University of Chicago Hospitals and Clinics, 900 East 57 Street, Chicago, IL 60637; Telephone: (773) 702-8597 FAX: (773) 702-2281
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46
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Thomson DW, Bracken CP, Goodall GJ. Experimental strategies for microRNA target identification. Nucleic Acids Res 2011; 39:6845-53. [PMID: 21652644 PMCID: PMC3167600 DOI: 10.1093/nar/gkr330] [Citation(s) in RCA: 417] [Impact Index Per Article: 32.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
MicroRNAs (miRNAs) are important regulators of eukaryotic gene expression in most biological processes. They act by guiding the RNAi-induced silencing complex (RISC) to partially complementary sequences in target mRNAs to suppress gene expression by a combination of translation inhibition and mRNA decay. The commonly accepted mechanism of miRNA targeting in animals involves an interaction between the 5'-end of the miRNA called the 'seed region' and the 3' untranslated region (3'-UTR) of the mRNA. Many target prediction algorithms are based around such a model, though increasing evidence demonstrates that targeting can also be mediated through sites other than the 3'-UTR and that seed region base pairing is not always required. The power and validity of such in silico data can be therefore hindered by the simplified rules used to represent targeting interactions. Experimentation is essential to identify genuine miRNA targets, however many experimental modalities exist and their limitations need to be understood. This review summarizes and critiques the existing experimental techniques for miRNA target identification.
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Affiliation(s)
- Daniel W Thomson
- Centre for Cancer Biology, SA Pathology, Frome Road Adelaide, South Australia 5000, Australia
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47
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Seliger B, Jasinski S, Dressler SP, Marincola FM, Recktenwald CV, Wang E, Lichtenfels R. Linkage of microRNA and proteome-based profiling data sets: a perspective for the priorization of candidate biomarkers in renal cell carcinoma? J Proteome Res 2011; 10:191-9. [PMID: 21142213 DOI: 10.1021/pr1011137] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Despite recent advances in the understanding of the biology of renal cell carcinoma (RCC) and the implementation of novel targeted therapies, the overall 5 years' survival rate for RCC patients remains disappointing. Late presentation, tumor heterogeneity and in particular the lack of molecular biomarkers for early detection and classification represent major obstacles. Global, untargeted comparative analysis of RCC vs tumor adjacent renal epithelium (NN) samples by high throughput analyses both at the transcriptome and proteome level have identified signatures, which might further clarify the molecular differences of RCC subtypes and might allow the identification of suitable therapeutic targets and diagnostic/prognostic biomarkers, but none thereof has yet been implemented in routine clinical use. The increasing knowledge regarding the functional role of noncoding microRNA (miR) in physiological, developmental, and pathophysiological processes by shaping the protein expression profile might provide an important link to improve the definition of disease-relevant regulatory networks. Taking into account that miR profiling of RCC and NN provides robust signatures discriminating between malignant and normal tissues, the concept of evaluating and scoring miR/protein pairs might represent a strategy for the selection and prioritization of potential biomarkers and their translation into practical use.
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Affiliation(s)
- Barbara Seliger
- Martin-Luther-University Halle-Wittenberg, Institute of Medical Immunology, 06112 Halle (Saale), Germany.
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48
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Integration of transcriptomics, proteomics, and microRNA analyses reveals novel microRNA regulation of targets in the mammalian inner ear. PLoS One 2011; 6:e18195. [PMID: 21483685 PMCID: PMC3071727 DOI: 10.1371/journal.pone.0018195] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2011] [Accepted: 02/22/2011] [Indexed: 12/19/2022] Open
Abstract
We have employed a novel approach for the identification of functionally important microRNA (miRNA)-target interactions, integrating miRNA, transcriptome and proteome profiles and advanced in silico analysis using the FAME algorithm. Since miRNAs play a crucial role in the inner ear, demonstrated by the discovery of mutations in a miRNA leading to human and mouse deafness, we applied this approach to microdissected auditory and vestibular sensory epithelia. We detected the expression of 157 miRNAs in the inner ear sensory epithelia, with 53 miRNAs differentially expressed between the cochlea and vestibule. Functionally important miRNAs were determined by searching for enriched or depleted targets in the transcript and protein datasets with an expression consistent with the dogma of miRNA regulation. Importantly, quite a few of the targets were detected only in the protein datasets, attributable to regulation by translational suppression. We identified and experimentally validated the regulation of PSIP1-P75, a transcriptional co-activator previously unknown in the inner ear, by miR-135b, in vestibular hair cells. Our findings suggest that miR-135b serves as a cellular effector, involved in regulating some of the differences between the cochlear and vestibular hair cells.
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49
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Abstract
MicroRNA-21 (miR-21) is a key regulator of oncogenic processes. It is significantly elevated in the majority of human tumors and functionally linked to cellular proliferation, survival and migration. In this study, we used two experimental-based strategies to search for novel miR-21 targets. On the one hand, we performed a proteomic approach using two-dimensional differential gel electrophoresis (2D-DIGE) to identify proteins suppressed upon enhanced miR-21 expression in LNCaP human prostate carcinoma cells. The tumor suppressor acidic nuclear phosphoprotein 32 family, member A (ANP32A) (alias pp32 or LANP) emerged as the most strongly downregulated protein. On the other hand, we applied a mathematical approach to select correlated gene sets that are negatively correlated with primary-miR-21 (pri-miR-21) expression in published transcriptome data from 114 B-cell lymphoma cases. Among these candidates, we found tumor suppressor SMARCA4 (alias BRG1) together with the already validated miR-21 target, PDCD4. ANP32A and SMARCA4, which are both involved in chromatin remodeling processes, were confirmed as direct miR-21 targets by immunoblot analysis and reporter gene assays. Furthermore, knock down of ANP32A mimicked the effect of enforced miR-21 expression by enhancing LNCaP cell viability, whereas overexpression of ANP32A in the presence of high miR-21 levels abrogated the miR-21-mediated effect. In A172 glioblastoma cells, enhanced ANP32A expression compensated for the effects of anti-miR-21 treatment on cell viability and apoptosis. In addition, miR-21 expression clearly increased the invasiveness of LNCaP cells, an effect also seen in part upon downregulation of ANP32A. In conclusion, these results suggest that downregulation of ANP32A contributes to the oncogenic function of miR-21.
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50
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Abstract
MicroRNAs (miRNAs) and small interfering RNAs (siRNAs) act with the Argonaute family of proteins to regulate target messenger RNAs (mRNAs) posttranscriptionally. SiRNAs typically induce endonucleolytic cleavage of mRNA with near-perfect complementarity. For targets with less complementarity, both translational repression and mRNA destabilization mechanisms have been implicated in miRNA-mediated gene repression, although the timing, coupling, and relative importance of these events have not been determined. Here, we review gene-specific and global approaches that probe miRNA function and mechanism, looking for a unifying model. More systematic analyses of the molecular specificities of the core components coupled with analysis of the relative timing of the different events will ultimately shed light on the mechanism of miRNA-mediated repression.
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Affiliation(s)
- Sergej Djuranovic
- Howard Hughes Medical Institute (HHMI), Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
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