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Leblanc R, Ghossoub R, Goubard A, Castellano R, Fares J, Camoin L, Audebert S, Balzano M, Bou‐Tayeh B, Fauriat C, Vey N, Garciaz S, Borg J, Collette Y, Aurrand‐Lions M, David G, Zimmermann P. Downregulation of stromal syntenin sustains AML development. EMBO Mol Med 2023; 15:e17570. [PMID: 37819151 PMCID: PMC10630886 DOI: 10.15252/emmm.202317570] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 09/13/2023] [Accepted: 09/14/2023] [Indexed: 10/13/2023] Open
Abstract
The crosstalk between cancer and stromal cells plays a critical role in tumor progression. Syntenin is a small scaffold protein involved in the regulation of intercellular communication that is emerging as a target for cancer therapy. Here, we show that certain aggressive forms of acute myeloid leukemia (AML) reduce the expression of syntenin in bone marrow stromal cells (BMSC). Stromal syntenin deficiency, in turn, generates a pro-tumoral microenvironment. From serial transplantations in mice and co-culture experiments, we conclude that syntenin-deficient BMSC stimulate AML aggressiveness by promoting AML cell survival and protein synthesis. This pro-tumoral activity is supported by increased expression of endoglin, a classical marker of BMSC, which in trans stimulates AML translational activity. In short, our study reveals a vicious signaling loop potentially at the heart of AML-stroma crosstalk and unsuspected tumor-suppressive effects of syntenin that need to be considered during systemic targeting of syntenin in cancer therapy.
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Affiliation(s)
- Raphael Leblanc
- Team Spatio‐Temporal Regulation of Cell Signaling‐Scaffolds and Phosphoinositides, Equipe Labellisée Ligue 2018, Centre de Recherche en Cancérologie de Marseille (CRCM)Institut Paoli‐Calmettes, Aix‐Marseille Université, Inserm, CNRSMarseilleFrance
| | - Rania Ghossoub
- Team Spatio‐Temporal Regulation of Cell Signaling‐Scaffolds and Phosphoinositides, Equipe Labellisée Ligue 2018, Centre de Recherche en Cancérologie de Marseille (CRCM)Institut Paoli‐Calmettes, Aix‐Marseille Université, Inserm, CNRSMarseilleFrance
| | - Armelle Goubard
- TrGET Preclinical Platform, Centre de Recherche en Cancérologie de Marseille, Inserm, CNRSAix‐Marseille Université, Institut Paoli‐CalmettesMarseilleFrance
| | - Rémy Castellano
- TrGET Preclinical Platform, Centre de Recherche en Cancérologie de Marseille, Inserm, CNRSAix‐Marseille Université, Institut Paoli‐CalmettesMarseilleFrance
| | - Joanna Fares
- Team Spatio‐Temporal Regulation of Cell Signaling‐Scaffolds and Phosphoinositides, Equipe Labellisée Ligue 2018, Centre de Recherche en Cancérologie de Marseille (CRCM)Institut Paoli‐Calmettes, Aix‐Marseille Université, Inserm, CNRSMarseilleFrance
| | - Luc Camoin
- Proteomics and Mass Spectrometry Platform, Centre de Recherche en Cancérologie de MarseilleAix‐Marseille Université, Inserm, CNRS, Institut Paoli CalmettesMarseilleFrance
| | - Stephane Audebert
- Proteomics and Mass Spectrometry Platform, Centre de Recherche en Cancérologie de MarseilleAix‐Marseille Université, Inserm, CNRS, Institut Paoli CalmettesMarseilleFrance
| | - Marielle Balzano
- Team Spatio‐Temporal Regulation of Cell Signaling‐Scaffolds and Phosphoinositides, Equipe Labellisée Ligue 2018, Centre de Recherche en Cancérologie de Marseille (CRCM)Institut Paoli‐Calmettes, Aix‐Marseille Université, Inserm, CNRSMarseilleFrance
| | - Berna Bou‐Tayeh
- Team Immunity and Cancer, Centre de Recherche en Cancérologie de MarseilleAix‐Marseille Université, Inserm, CNRS, Institut Paoli CalmettesMarseilleFrance
| | - Cyril Fauriat
- Team Immunity and Cancer, Centre de Recherche en Cancérologie de MarseilleAix‐Marseille Université, Inserm, CNRS, Institut Paoli CalmettesMarseilleFrance
| | - Norbert Vey
- Aix‐Marseille Univ, Inserm, CNRS, Institut Paoli‐Calmettes, CRCMMarseilleFrance
| | - Sylvain Garciaz
- Aix‐Marseille Univ, Inserm, CNRS, Institut Paoli‐Calmettes, CRCMMarseilleFrance
| | - Jean‐Paul Borg
- Proteomics and Mass Spectrometry Platform, Centre de Recherche en Cancérologie de MarseilleAix‐Marseille Université, Inserm, CNRS, Institut Paoli CalmettesMarseilleFrance
| | - Yves Collette
- TrGET Preclinical Platform, Centre de Recherche en Cancérologie de Marseille, Inserm, CNRSAix‐Marseille Université, Institut Paoli‐CalmettesMarseilleFrance
| | - Michel Aurrand‐Lions
- Team Leuko/Stromal Interactions in Normal and Pathological Hematopoiesis, Centre de Recherche en Cancérologie de Marseille, Aix‐Marseille Université, Inserm, CNRS, Institut Paoli CalmettesMarseilleFrance
| | - Guido David
- Team Spatio‐Temporal Regulation of Cell Signaling‐Scaffolds and Phosphoinositides, Equipe Labellisée Ligue 2018, Centre de Recherche en Cancérologie de Marseille (CRCM)Institut Paoli‐Calmettes, Aix‐Marseille Université, Inserm, CNRSMarseilleFrance
- Department of Human GeneticsK U LeuvenLeuvenBelgium
| | - Pascale Zimmermann
- Team Spatio‐Temporal Regulation of Cell Signaling‐Scaffolds and Phosphoinositides, Equipe Labellisée Ligue 2018, Centre de Recherche en Cancérologie de Marseille (CRCM)Institut Paoli‐Calmettes, Aix‐Marseille Université, Inserm, CNRSMarseilleFrance
- Department of Human GeneticsK U LeuvenLeuvenBelgium
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Wilton J, de Mendonça FL, Pereira-Castro I, Tellier M, Nojima T, Costa AM, Freitas J, Murphy S, Oliveira MJ, Proudfoot NJ, Moreira A. Pro-inflammatory polarization and colorectal cancer modulate alternative and intronic polyadenylation in primary human macrophages. Front Immunol 2023; 14:1182525. [PMID: 37359548 PMCID: PMC10286830 DOI: 10.3389/fimmu.2023.1182525] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 05/09/2023] [Indexed: 06/28/2023] Open
Abstract
Introduction Macrophages are essential cells of the immune system that alter their inflammatory profile depending on their microenvironment. Alternative polyadenylation in the 3'UTR (3'UTR-APA) and intronic polyadenylation (IPA) are mechanisms that modulate gene expression, particularly in cancer and activated immune cells. Yet, how polarization and colorectal cancer (CRC) cells affect 3'UTR-APA and IPA in primary human macrophages was unclear. Methods In this study, we isolated primary human monocytes from healthy donors, differentiated and polarized them into a pro-inflammatory state and performed indirect co-cultures with CRC cells. ChrRNA-Seq and 3'RNA-Seq was performed to quantify gene expression and characterize new 3'UTR-APA and IPA mRNA isoforms. Results Our results show that polarization of human macrophages from naïve to a pro-inflammatory state causes a marked increase of proximal polyA site selection in the 3'UTR and IPA events in genes relevant to macrophage functions. Additionally, we found a negative correlation between differential gene expression and IPA during pro-inflammatory polarization of primary human macrophages. As macrophages are abundant immune cells in the CRC microenvironment that either promote or abrogate cancer progression, we investigated how indirect exposure to CRC cells affects macrophage gene expression and 3'UTR-APA and IPA events. Co-culture with CRC cells alters the inflammatory phenotype of macrophages, increases the expression of pro-tumoral genes and induces 3'UTR-APA alterations. Notably, some of these gene expression differences were also found in tumor-associated macrophages of CRC patients, indicating that they are physiologically relevant. Upon macrophage pro-inflammatory polarization, SRSF12 is the pre-mRNA processing gene that is most upregulated. After SRSF12 knockdown in M1 macrophages there is a global downregulation of gene expression, in particular in genes involved in gene expression regulation and in immune responses. Discussion Our results reveal new 3'UTR-APA and IPA mRNA isoforms produced during pro-inflammatory polarization of primary human macrophages and CRC co-culture that may be used in the future as diagnostic or therapeutic tools. Furthermore, our results highlight a function for SRSF12 in pro-inflammatory macrophages, key cells in the tumor response.
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Affiliation(s)
- Joana Wilton
- Graduate Program in Areas of Basic and Applied Biology (GABBA) PhD Program, ICBAS-Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, Porto, Portugal
- Gene Regulation - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- IBMC-Instituto de Biologia Molecular e Celular Universidade do Porto, Porto, Portugal
| | - Filipa Lopes de Mendonça
- Gene Regulation - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- IBMC-Instituto de Biologia Molecular e Celular Universidade do Porto, Porto, Portugal
| | - Isabel Pereira-Castro
- Gene Regulation - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- IBMC-Instituto de Biologia Molecular e Celular Universidade do Porto, Porto, Portugal
| | - Michael Tellier
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
| | - Takayuki Nojima
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
| | - Angela M. Costa
- Tumour and Microenvironment Interactions Group – Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- INEB-Instituto Nacional de Engenharia Biomédica Universidade do Porto, Porto, Portugal
| | - Jaime Freitas
- Gene Regulation - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
| | - Shona Murphy
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
| | - Maria Jose Oliveira
- Tumour and Microenvironment Interactions Group – Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- INEB-Instituto Nacional de Engenharia Biomédica Universidade do Porto, Porto, Portugal
- Faculdade de Medicina, Universidade do Porto, Porto, Portugal
- ICBAS- Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, Porto, Portugal
| | | | - Alexandra Moreira
- Gene Regulation - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- IBMC-Instituto de Biologia Molecular e Celular Universidade do Porto, Porto, Portugal
- ICBAS- Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, Porto, Portugal
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Time-resolved RNA signatures of CD4+ T cells in Parkinson's disease. Cell Death Dis 2023; 9:18. [PMID: 36681665 PMCID: PMC9867723 DOI: 10.1038/s41420-023-01333-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 01/10/2023] [Accepted: 01/12/2023] [Indexed: 01/22/2023]
Abstract
Parkinson's disease (PD) emerges as a complex, multifactorial disease. While there is increasing evidence that dysregulated T cells play a central role in PD pathogenesis, elucidation of the pathomechanical changes in related signaling is still in its beginnings. We employed time-resolved RNA expression upon the activation of peripheral CD4+ T cells to track and functionally relate changes on cellular signaling in representative cases of patients at different stages of PD. While only few miRNAs showed time-course related expression changes in PD, we identified groups of genes with significantly altered expression for each different time window. Towards a further understanding of the functional consequences, we highlighted pathways with decreased or increased activity in PD, including the most prominent altered IL-17 pathway. Flow cytometric analyses showed not only an increased prevalence of Th17 cells but also a specific subtype of IL-17 producing γδ-T cells, indicating a previously unknown role in PD pathogenesis.
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Wu Q, Michaels YS, Fulga TA. Interrogation of Functional miRNA-Target Interactions by CRISPR/Cas9 Genome Engineering. Methods Mol Biol 2023; 2630:243-264. [PMID: 36689187 DOI: 10.1007/978-1-0716-2982-6_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Posttranscriptional silencing by microRNAs (miRNAs) is a critical constituent of eukaryotic gene regulation. miRNAs are short (~22 nt) noncoding RNAs capable of specifically targeting the miRNA-induced silencing complex (miRISC) to transcripts bearing a complementary miRNA response element (MRE). Although recent methodological advances have greatly improved our understanding of miRNA biogenesis and the mechanisms by which miRNAs repress their cognate targets, exploring the physiological relevance of direct miRNA-target interactions in vivo has remained an outstanding challenge. Here we describe the experimental protocol underlying a novel approach, which allows direct in situ interrogation of specific miRNA-MRE interactions by CRISPR/Cas9-mediated genome engineering (Bassett G et al., Nat Commun 5, 4640, 2014). In this instance, the CRISPR/Cas9 system is first used to catalyze homology-directed replacement of candidate MREs with molecular barcodes at endogenous loci. Subsequently, the effect of MRE mutation on transcript abundance (i.e., MRE activity) can be rapidly evaluated by routine quantitative PCR. This strategy enables functional investigation of a putative miRNA-target pair in a pool of transiently transfected cells, obviating the need for generation of clonal cell lines or transgenic animals. This protocol can be implemented in any cell line in less than 2 weeks and can readily be scaled up for multiplex studies. To facilitate the conceptual workflow underlying this strategy, we also describe a genome-wide resource for automated design and computational evaluation of CRISPR/Cas9 guide RNAs targeting all predicted MREs in various species (miR-CRISPR).
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Affiliation(s)
| | - Yale S Michaels
- School of Biomedical Engineering, University of British Columbia, Vancouver, Canada.
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5
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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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Chen Y, Salem M, Boyd M, Bornholdt J, Li Y, Coskun M, Seidelin JB, Sandelin A, Nielsen OH. Relation between NOD2 genotype and changes in innate signaling in Crohn's disease on mRNA and miRNA levels. NPJ Genom Med 2017; 2:3. [PMID: 29263823 PMCID: PMC5642384 DOI: 10.1038/s41525-016-0001-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Revised: 11/11/2016] [Accepted: 11/11/2016] [Indexed: 02/07/2023] Open
Abstract
Crohn’s disease is associated with an altered innate immune response of pathogenic importance. This altered response can be associated to loss-of-function polymorphisms in the NOD2 (nucleotide-binding oligomerization domain-containing protein 2) gene, but also changes in transcriptional and post-transcriptional regulatory layers, including microRNA activity. Here, we characterized the link between NOD2 genotype and inflammatory-mediated changes in innate signaling by studying transcriptional and post-transcriptional activity in response to NOD2-agonist muramyl dipeptide in monocytes from healthy controls, and Crohn’s disease patients with and without NOD2 loss-of-function polymorphisms. We measured the expression of genes and microRNAs in monocytes from these subjects after stimulation with muramyl dipeptide. Gene expression profiles mainly distinguished the actual muramyl dipeptide response, but not the genotype. A hyper-responsive phenotype was found in Crohn’s disease patients without NOD2 mutations, characterized by upregulated cytokine receptors and general downregulation of microRNA expression. Conversely, microRNA expression could identify genotype-specific differences between subject groups but exhibited little change upon muramyl dipeptide treatment. Only two microRNAs showed muramyl dipeptide-induced response, including miR-155, which was found to regulate multiple genes and whose host gene was one of the highest muramyl dipeptide responders. miR-155 was upregulated in Crohn’s disease patients with NOD2 mutations following lipopolysaccharide and Escherichia coli treatment, but the upregulation was substantially reduced upon muramyl dipeptide treatment. While Crohn’s disease patients with NOD2 mutations on average showed a reduced muramyl dipeptide response, the cohort exhibited large individual variance: a small subset had inflammatory responses almost comparable to wild-type patients on both gene and miR-155 regulatory levels. The genetics of people with Crohn’s disease affects the molecular drivers of their dysregulated immune responses. Some individuals with Crohn’s harbor mutations in the NOD2 gene, which encodes a pathogen recognition receptor that binds to a molecule called muramyl dipeptide (MDP). To better understand how alternations in NOD2 can lead to increased susceptibility to gut inflammation, Yun Chen, Mohammad Salem and colleagues from the University of Copenhagen and Herlev Hospital, Denmark, analyzed the expression patterns of both genes and small, regulatory microRNAs in blood cells from healthy controls and from Crohn’s patients with and without NOD2 mutations. They exposed the cells to MDP, and saw that although gene acticity changed dramatically as a response, there was little difference between subjects, regardless of genetics. Conversely, microRNA expression showed genotype-specific differences that weren not impacted by MDP treatment. The findings underscore the importance of microRNAs in Crohn’s disease.
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Affiliation(s)
- Yun Chen
- The Bioinformatics Centre, Department of Biology and Biotech Research and Innovation Centre, University of Copenhagen, Ole Maaloes Vej 5, DK-2200 Copenhagen, Denmark
| | - Mohammad Salem
- Department of Gastroenterology, Medical Section, Herlev Hospital, University of Copenhagen, Herlev Ringvej 75, DK-2730 Herlev, Denmark
| | - Mette Boyd
- The Bioinformatics Centre, Department of Biology and Biotech Research and Innovation Centre, University of Copenhagen, Ole Maaloes Vej 5, DK-2200 Copenhagen, Denmark
| | - Jette Bornholdt
- The Bioinformatics Centre, Department of Biology and Biotech Research and Innovation Centre, University of Copenhagen, Ole Maaloes Vej 5, DK-2200 Copenhagen, Denmark
| | - Yuan Li
- Department of Gastroenterology, Medical Section, Herlev Hospital, University of Copenhagen, Herlev Ringvej 75, DK-2730 Herlev, Denmark
| | - Mehmet Coskun
- The Bioinformatics Centre, Department of Biology and Biotech Research and Innovation Centre, University of Copenhagen, Ole Maaloes Vej 5, DK-2200 Copenhagen, Denmark.,Department of Gastroenterology, Medical Section, Herlev Hospital, University of Copenhagen, Herlev Ringvej 75, DK-2730 Herlev, Denmark
| | - Jakob Benedict Seidelin
- Department of Gastroenterology, Medical Section, Herlev Hospital, University of Copenhagen, Herlev Ringvej 75, DK-2730 Herlev, Denmark
| | - Albin Sandelin
- The Bioinformatics Centre, Department of Biology and Biotech Research and Innovation Centre, University of Copenhagen, Ole Maaloes Vej 5, DK-2200 Copenhagen, Denmark
| | - Ole Haagen Nielsen
- Department of Gastroenterology, Medical Section, Herlev Hospital, University of Copenhagen, Herlev Ringvej 75, DK-2730 Herlev, Denmark
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Michaels YS, Wu Q, Fulga TA. Interrogation of Functional miRNA-Target Interactions by CRISPR/Cas9 Genome Engineering. Methods Mol Biol 2017; 1580:79-97. [PMID: 28439828 DOI: 10.1007/978-1-4939-6866-4_7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Post-transcriptional silencing by microRNAs (miRNAs) is a critical constituent of eukaryotic gene regulation. miRNAs are short (~22nt) noncoding RNAs capable of specifically targeting the miRNA-induced-silencing-complex (miRISC) to transcripts bearing a complementary miRNA response element (MRE). Although recent methodological advances have greatly improved our understanding of miRNA biogenesis and the mechanisms by which miRNAs repress their cognate targets, exploring the physiological relevance of direct miRNA-target interactions in vivo has remained an outstanding challenge. Here we describe the experimental protocol underlying a novel approach, which allows direct interrogation of specific miRNA-MRE interactions by CRISPR/Cas9-mediated genome engineering. In this instance, the CRISPR/Cas9 system is first used to catalyze homology-directed replacement of candidate MREs with molecular barcodes at endogenous loci. Subsequently, the effect of MRE mutation on transcript abundance (i.e., MRE activity) can be rapidly evaluated by routine quantitative PCR. This strategy enables functional investigation of a putative miRNA-target pair in a pool of transiently transfected cells, obviating the need for generation of clonal cell lines or transgenic animals. This protocol can be implemented in any cell line in less than 2 weeks, and can readily be scaled up for multiplex studies. To facilitate the conceptual workflow underlying this strategy, we also describe a genome-wide resource for automated design and computational evaluation of CRISPR/Cas9 guide RNAs targeting all predicted MREs in various species (miR-CRISPR).
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Affiliation(s)
- Yale S Michaels
- Radcliffe Department of Medicine, Weatherall Institute of Molecular Medicine, University of Oxford, OX3 9DS, Oxford, UK
| | - Qianxin Wu
- Radcliffe Department of Medicine, Weatherall Institute of Molecular Medicine, University of Oxford, OX3 9DS, Oxford, UK
| | - Tudor A Fulga
- Radcliffe Department of Medicine, Weatherall Institute of Molecular Medicine, University of Oxford, OX3 9DS, Oxford, UK.
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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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Basak I, Patil KS, Alves G, Larsen JP, Møller SG. microRNAs as neuroregulators, biomarkers and therapeutic agents in neurodegenerative diseases. Cell Mol Life Sci 2016; 73:811-27. [PMID: 26608596 PMCID: PMC11108480 DOI: 10.1007/s00018-015-2093-x] [Citation(s) in RCA: 78] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2015] [Revised: 10/14/2015] [Accepted: 11/09/2015] [Indexed: 01/03/2023]
Abstract
The last decade has experienced the emergence of microRNAs as a key molecular tool for the diagnosis and prognosis of human diseases. Although the focus has mostly been on cancer, neurodegenerative diseases present an exciting, yet less explored, platform for microRNA research. Several studies have highlighted the significance of microRNAs in neurogenesis and neurodegeneration, and pre-clinical studies have shown the potential of microRNAs as biomarkers. Despite this, no bona fide microRNAs have been identified as true diagnostic or prognostic biomarkers for neurodegenerative disease. This is mainly due to the lack of precisely defined patient cohorts and the variability within and between individual cohorts. However, the discovery that microRNAs exist as stable molecules at detectable levels in body fluids has opened up new avenues for microRNAs as potential biomarker candidates. Furthermore, technological developments in microRNA biology have contributed to the possible design of microRNA-mediated disease intervention strategies. The combination of these advancements, with the availability of well-defined longitudinal patient cohort, promises to not only assist in developing invaluable diagnostic tools for clinicians, but also to increase our overall understanding of the underlying heterogeneity of neurodegenerative diseases. In this review, we present a comprehensive overview of the existing knowledge of microRNAs in neurodegeneration and provide a perspective of the applicability of microRNAs as a basis for future therapeutic intervention strategies.
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Affiliation(s)
- Indranil Basak
- Department of Biological Sciences, St. John's University, 8000 Utopia Parkway, New York, NY, 11439, USA
| | - Ketan S Patil
- Department of Biological Sciences, St. John's University, 8000 Utopia Parkway, New York, NY, 11439, USA
| | - Guido Alves
- Norwegian Center for Movement Disorders, Stavanger University Hospital, 4068, Stavanger, Norway
| | - Jan Petter Larsen
- Norwegian Center for Movement Disorders, Stavanger University Hospital, 4068, Stavanger, Norway
| | - Simon Geir Møller
- Department of Biological Sciences, St. John's University, 8000 Utopia Parkway, New York, NY, 11439, USA.
- Norwegian Center for Movement Disorders, Stavanger University Hospital, 4068, Stavanger, Norway.
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Võsa U, Esko T, Kasela S, Annilo T. Altered Gene Expression Associated with microRNA Binding Site Polymorphisms. PLoS One 2015; 10:e0141351. [PMID: 26496489 PMCID: PMC4619707 DOI: 10.1371/journal.pone.0141351] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2015] [Accepted: 10/06/2015] [Indexed: 02/03/2023] Open
Abstract
Allele-specific gene expression associated with genetic variation in regulatory regions can play an important role in the development of complex traits. We hypothesized that polymorphisms in microRNA (miRNA) response elements (MRE-SNPs) that either disrupt a miRNA binding site or create a new miRNA binding site can affect the allele-specific expression of target genes. By integrating public expression quantitative trait locus (eQTL) data, miRNA binding site predictions, small RNA sequencing, and Argonaute crosslinking immunoprecipitation (AGO-CLIP) datasets, we identified genetic variants that can affect gene expression by modulating miRNA binding efficiency. We also identified MRE-SNPs located in regions associated with complex traits, indicating possible causative mechanisms associated with these loci. The results of this study expand the current understanding of gene expression regulation and help to interpret the mechanisms underlying eQTL effects.
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Affiliation(s)
- Urmo Võsa
- Estonian Genome Center, University of Tartu, Riia 23b, 51010 Tartu, Estonia
- * E-mail:
| | - Tõnu Esko
- Estonian Genome Center, University of Tartu, Riia 23b, 51010 Tartu, Estonia
- Division of Endocrinology, Children's Hospital, Boston, MA, United States of America
- Department of Genetics, Harvard Medical School, Boston, MA, United States of America
- Broad Institute, Cambridge, MA, United States of America
| | - Silva Kasela
- Estonian Genome Center, University of Tartu, Riia 23b, 51010 Tartu, Estonia
| | - Tarmo Annilo
- Estonian Genome Center, University of Tartu, Riia 23b, 51010 Tartu, Estonia
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Li Y, Liang C, Easterbrook S, Luo J, Zhang Z. Investigating the functional implications of reinforcing feedback loops in transcriptional regulatory networks. MOLECULAR BIOSYSTEMS 2015; 10:3238-48. [PMID: 25286350 DOI: 10.1039/c4mb00526k] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Transcription factors (TFs) and microRNAs (miRNAs) can jointly regulate transcriptional networks in the form of recurrent circuits or motifs. A motif can be divided into a feedforward loop (FFL) and a feedback loop (FBL). Incoherent FFLs have been the recent focus due to their potential to dampen gene expression noise in maintaining physiological norms. However, a cell is not only able to manage noise but also able to exploit it during development or tumorigenesis to initiate radical transformation such as cell differentiation or metastasis. A plausible mechanism may involve reinforcing FBLs (rFBLs), which amplify changes to a sufficient level in order to complete the state transition. To study the behaviour of rFBLs, we developed a novel theoretical framework based on biochemical kinetics. The proposed rFBL follows a parsimonious design, involving two TFs and two miRNAs. A simulation study based on our model suggested that a system with rFBLs is robust to only a certain level of fluctuation but prone to a complete paradigm shift when the change exceeds a threshold level. To investigate the natural occurrence of rFBLs, we performed a rigorous network motif analysis using a recently available TF/miRNA regulatory network from the Encyclopedia of DNA Elements (ENCODE). Our analysis suggested that the rFBL is significantly depleted in the observed network. Nonetheless, we identified 9 rFBL instances. Among them, we found a double-rFBL involving three TFs SUZ12/BCLAF1/ZBTB33 and three miRNAs miR-9/19a/129-5p, which together serve as an intriguing toggle switch between nerve development and telomere maintenance. Additionally, we investigated the interactions implicated in the rFBLs using expression profiles of cancer patients from The Cancer Genome Atlas (TCGA). Together, we provided a novel and comprehensive view of the profound impacts of rFBLs and highlighted several TFs and miRNAs as the leverage points for potential therapeutic targets in cancers due to their eminent roles in the identified rFBLs.
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Affiliation(s)
- Yue Li
- Department of Computer Science, University of Toronto, Toronto, Ontario M5S 3G4, Canada.
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12
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Abstract
MiRNAs regulate gene expression by binding predominantly to the 3' untranslated region (UTR) of target transcripts to prevent their translation and/or induce target degradation. In addition to the more than 1200 human miRNAs, human DNA tumor viruses such as Kaposi's sarcoma-associated herpesvirus (KSHV) and Epstein-Barr virus (EBV) encode miRNAs. Target predictions indicate that each miRNA targets hundreds of transcripts, many of which are regulated by multiple miRNAs. Thus, target identification is a big challenge for the field. Most methods used currently investigate single miRNA-target interactions and are not able to analyze complex miRNA-target networks. To overcome these challenges, cross-linking and immunoprecipitation (CLIP), a recently developed method to study direct RNA-protein interactions in living cells, has been successfully applied to miRNA target analysis. It utilizes Argonaute (Ago)-immunoprecipitation to isolate native Ago-miRNA-mRNA complexes. In four recent publications, two variants of the CLIP method (HITS-CLIP and PAR-CLIP) were utilized to determine the targetomes of human and viral miRNAs in cells infected with the gamma-herpesviruses KSHV and EBV, which are associated with a number of human cancers. Here, we briefly introduce herpesvirus-encoded miRNAs and then focus on how CLIP technology has largely impacted our understanding of viral miRNAs in viral biology and pathogenesis.
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Affiliation(s)
- Irina Haecker
- Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, FL, USA
| | - Rolf Renne
- Department of Molecular Genetics and Microbiology, Shands Cancer Center, Genetics Institute, University of Florida, Gainesville, FL, USA
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13
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Cheng CJ, Bahal R, Babar IA, Pincus Z, Barrera F, Liu C, Svoronos A, Braddock DT, Glazer PM, Engelman DM, Saltzman WM, Slack FJ. MicroRNA silencing for cancer therapy targeted to the tumour microenvironment. Nature 2014; 518:107-10. [PMID: 25409146 PMCID: PMC4367962 DOI: 10.1038/nature13905] [Citation(s) in RCA: 625] [Impact Index Per Article: 62.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2013] [Accepted: 10/02/2014] [Indexed: 02/07/2023]
Abstract
MicroRNAs are short non-coding RNAs expressed in different tissue and cell types that suppress the expression of target genes. As such, microRNAs are critical cogs in numerous biological processes, and dysregulated microRNA expression is correlated with many human diseases. Certain microRNAs, called oncomiRs, play a causal role in the onset and maintenance of cancer when overexpressed. Tumours that depend on these microRNAs are said to display oncomiR addiction. Some of the most effective anticancer therapies target oncogenes such as EGFR and HER2; similarly, inhibition of oncomiRs using antisense oligomers (that is, antimiRs) is an evolving therapeutic strategy. However, the in vivo efficacy of current antimiR technologies is hindered by physiological and cellular barriers to delivery into targeted cells. Here we introduce a novel antimiR delivery platform that targets the acidic tumour microenvironment, evades systemic clearance by the liver, and facilitates cell entry via a non-endocytic pathway. We find that the attachment of peptide nucleic acid antimiRs to a peptide with a low pH-induced transmembrane structure (pHLIP) produces a novel construct that could target the tumour microenvironment, transport antimiRs across plasma membranes under acidic conditions such as those found in solid tumours (pH approximately 6), and effectively inhibit the miR-155 oncomiR in a mouse model of lymphoma. This study introduces a new model for using antimiRs as anti-cancer drugs, which can have broad impacts on the field of targeted drug delivery.
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Affiliation(s)
- Christopher J Cheng
- 1] Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut 06511, USA [2] Department of Biomedical Engineering, Yale University, New Haven, Connecticut 06511, USA [3] Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06511, USA
| | - Raman Bahal
- Department of Therapeutic Radiology, Yale University, New Haven, Connecticut 06511, USA
| | - Imran A Babar
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut 06511, USA
| | - Zachary Pincus
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut 06511, USA
| | - Francisco Barrera
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06511, USA
| | - Connie Liu
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut 06511, USA
| | - Alexander Svoronos
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06511, USA
| | | | - Peter M Glazer
- Department of Therapeutic Radiology, Yale University, New Haven, Connecticut 06511, USA
| | - Donald M Engelman
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06511, USA
| | - W Mark Saltzman
- Department of Biomedical Engineering, Yale University, New Haven, Connecticut 06511, USA
| | - Frank J Slack
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut 06511, USA
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14
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Martin EC, Krebs AE, Burks HE, Elliott S, Baddoo M, Collins-Burow BM, Flemington EK, Burow ME. miR-155 induced transcriptome changes in the MCF-7 breast cancer cell line leads to enhanced mitogen activated protein kinase signaling. Genes Cancer 2014; 5:353-64. [PMID: 25352952 PMCID: PMC4209600 DOI: 10.18632/genesandcancer.33] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2014] [Accepted: 10/01/2014] [Indexed: 11/25/2022] Open
Abstract
A single microRNA (miRNA) has the potential to regulate thousands of genes and thus govern multiple signaling pathways at once. miR-155 is an oncogenic miRNA which regulates many cellular pathways, designating it as a multifaceted regulator of proliferation, chemo-resistance, and apoptosis. While many singular targeted effects of miR-155 have been defined and an oncogenic role has been attributed to miR-155 expression, the global effect of miR-155 on the cellular transcriptomes of an ER+ breast cancer cell line has yet to be determined. Here we demonstrate that miR-155 expression increases tumorigenesis in vivo and we determine miR-155 mediated transcriptome changes through next generation sequencing analysis. miR-155 expression alters many signaling pathways, with the chief altered pathway being the MAPK signaling cascade and miR-155 induces shortening of target mRNA 3′UTRs and alternative isoform expression of MAPK related genes. In addition there is an observed increase in protein phosphorylation of components of MAPK signaling including ERK1/2 and AP-1 complex members (Fra-1 and c-Fos) as well as elevated gene expression of MAPK regulated genes Zeb1, Snail, Plaur, and SerpinE1.
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Affiliation(s)
- Elizabeth C Martin
- Department of Medicine-Section of Hematology and Medical Oncology, Tulane University, New Orleans, LA
| | - Adrienne E Krebs
- Department of Medicine-Section of Hematology and Medical Oncology, Tulane University, New Orleans, LA
| | - Hope E Burks
- Department of Medicine-Section of Hematology and Medical Oncology, Tulane University, New Orleans, LA
| | - Steven Elliott
- Department of Medicine-Section of Hematology and Medical Oncology, Tulane University, New Orleans, LA
| | - Melody Baddoo
- Tulane Cancer Center, Tulane University, New Orleans, LA ; Department of Pathology, Tulane University, New Orleans, LA
| | - Bridgette M Collins-Burow
- Department of Medicine-Section of Hematology and Medical Oncology, Tulane University, New Orleans, LA
| | - Erik K Flemington
- Tulane Cancer Center, Tulane University, New Orleans, LA ; Department of Pathology, Tulane University, New Orleans, LA
| | - Matthew E Burow
- Department of Medicine-Section of Hematology and Medical Oncology, Tulane University, New Orleans, LA ; Tulane Cancer Center, Tulane University, New Orleans, LA ; Department of Pharmacology, Tulane University, New Orleans, LA
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15
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Abstract
Virus-host interactions highlight key regulatory steps in the control of gene expression. MicroRNAs (miRNAs) are small noncoding RNAs that regulate protein production via base pairing with mRNAs. Both DNA and RNA viruses have evolved mechanisms to degrade, boost, or hijack cellular miRNAs to benefit the viral life cycle. This minireview focuses on recent discoveries in virus-host miRNA interactions.
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16
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Lopez‐Ramirez MA, Wu D, Pryce G, Simpson JE, Reijerkerk A, King‐Robson J, Kay O, Vries HE, Hirst MC, Sharrack B, Baker D, Male DK, Michael GJ, Romero IA. MicroRNA‐155 negatively affects blood–brain barrier function during neuroinflammation. FASEB J 2014; 28:2551-65. [DOI: 10.1096/fj.13-248880] [Citation(s) in RCA: 187] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
| | - Dongsheng Wu
- Department of Life, Health, and Chemical Sciences, Biomedical Research NetworkThe Open UniversityMilton KeynesUK
| | - Gareth Pryce
- Center for Neuroscience and Trauma, Blizard InstituteBarts and The London School of Medicine and DentistryQueen Mary University of LondonLondonUK
| | - Julie E. Simpson
- Sheffield Institute for Translational NeuroscienceSheffield Teaching Hospitals National Health Service (NHS) TrustUniversity of SheffieldSheffieldUK
| | - Arie Reijerkerk
- Blood–Brain Barrier Research Group, Molecular Cell Biology and ImmunologyVU University Medical CenterAmsterdamThe Netherlands
| | - Josh King‐Robson
- Center for Neuroscience and Trauma, Blizard InstituteBarts and The London School of Medicine and DentistryQueen Mary University of LondonLondonUK
| | - Oliver Kay
- Center for Neuroscience and Trauma, Blizard InstituteBarts and The London School of Medicine and DentistryQueen Mary University of LondonLondonUK
| | - Helga E. Vries
- Blood–Brain Barrier Research Group, Molecular Cell Biology and ImmunologyVU University Medical CenterAmsterdamThe Netherlands
| | - Mark C. Hirst
- Department of Life, Health, and Chemical Sciences, Biomedical Research NetworkThe Open UniversityMilton KeynesUK
| | - Basil Sharrack
- Department of NeurologySheffield Teaching Hospitals National Health Service (NHS) TrustUniversity of SheffieldSheffieldUK
| | - David Baker
- Center for Neuroscience and Trauma, Blizard InstituteBarts and The London School of Medicine and DentistryQueen Mary University of LondonLondonUK
| | - David Kingsley Male
- Department of Life, Health, and Chemical Sciences, Biomedical Research NetworkThe Open UniversityMilton KeynesUK
| | - Gregory J. Michael
- Center for Neuroscience and Trauma, Blizard InstituteBarts and The London School of Medicine and DentistryQueen Mary University of LondonLondonUK
| | - Ignacio Andres Romero
- Department of Life, Health, and Chemical Sciences, Biomedical Research NetworkThe Open UniversityMilton KeynesUK
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17
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Rosa BA, Jasmer DP, Mitreva M. Genome-wide tissue-specific gene expression, co-expression and regulation of co-expressed genes in adult nematode Ascaris suum. PLoS Negl Trop Dis 2014; 8:e2678. [PMID: 24516681 PMCID: PMC3916258 DOI: 10.1371/journal.pntd.0002678] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2013] [Accepted: 12/18/2013] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND Caenorhabditis elegans has traditionally been used as a model for studying nematode biology, but its small size limits the ability for researchers to perform some experiments such as high-throughput tissue-specific gene expression studies. However, the dissection of individual tissues is possible in the parasitic nematode Ascaris suum due to its relatively large size. Here, we take advantage of the recent genome sequencing of Ascaris suum and the ability to physically dissect its separate tissues to produce a wide-scale tissue-specific nematode RNA-seq datasets, including data on three non-reproductive tissues (head, pharynx, and intestine) in both male and female worms, as well as four reproductive tissues (testis, seminal vesicle, ovary, and uterus). We obtained fundamental information about the biology of diverse cell types and potential interactions among tissues within this multicellular organism. METHODOLOGY/PRINCIPAL FINDINGS Overexpression and functional enrichment analyses identified many putative biological functions enriched in each tissue studied, including functions which have not been previously studied in detail in nematodes. Putative tissue-specific transcriptional factors and corresponding binding motifs that regulate expression in each tissue were identified, including the intestine-enriched ELT-2 motif/transcription factor previously described in nematode intestines. Constitutively expressed and novel genes were also characterized, with the largest number of novel genes found to be overexpressed in the testis. Finally, a putative acetylcholine-mediated transcriptional network connecting biological activity in the head to the male reproductive system is described using co-expression networks, along with a similar ecdysone-mediated system in the female. CONCLUSIONS/SIGNIFICANCE The expression profiles, co-expression networks and co-expression regulation of the 10 tissues studied and the tissue-specific analysis presented here are a valuable resource for studying tissue-specific biological functions in nematodes.
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Affiliation(s)
- Bruce A. Rosa
- The Genome Institute, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Douglas P. Jasmer
- Department of Veterinary Microbiology and Pathology, Washington State University, Pullman, Washington, United States of America
| | - Makedonka Mitreva
- The Genome Institute, Washington University School of Medicine, St. Louis, Missouri, United States of America
- Department of Medicine, Division of Infectious Diseases, Washington University School of Medicine, St. Louis, Missouri, United States of America
- Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, United States of America
- * E-mail:
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18
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Abstract
MicroRNAs (miRNAs) are a class of small noncoding RNAs expressed by plants, animals, and some viruses. miRNAs generally function as part of miRNA-induced silencing complexes to modestly repress mRNAs with imperfect sequence complementarity. Over the last years, many different roles of miRNA mediated regulation in the life cycles of mammalian viruses have been uncovered. In this chapter, I will mainly explore four different examples of how cellular miRNAs interact with viruses: the role of miR-155 in viral oncogenesis, viral strategies to eliminate cellular miR-27, the contribution of miR-122 to the replication of hepatitis C virus, and miRNAs as an experimental tool to control virus replication and vector transgene expression. In the final part of this chapter, I will give a brief overview of virally encoded microRNAs.
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19
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Koval ED, Shaner C, Zhang P, du Maine X, Fischer K, Tay J, Chau BN, Wu GF, Miller TM. Method for widespread microRNA-155 inhibition prolongs survival in ALS-model mice. Hum Mol Genet 2013; 22:4127-35. [PMID: 23740943 DOI: 10.1093/hmg/ddt261] [Citation(s) in RCA: 164] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
microRNAs (miRNAs) are dysregulated in a variety of disease states, suggesting that this newly discovered class of gene expression repressors may be viable therapeutic targets. A microarray of miRNA changes in ALS-model superoxide dismutase 1 (SOD1)(G93A) rodents identified 12 miRNAs as significantly changed. Six miRNAs tested in human ALS tissues were confirmed increased. Specifically, miR-155 was increased 5-fold in mice and 2-fold in human spinal cords. To test miRNA inhibition in the central nervous system (CNS) as a potential novel therapeutic, we developed oligonucleotide-based miRNA inhibitors (anti-miRs) that could inhibit miRNAs throughout the CNS and in the periphery. Anti-miR-155 caused global derepression of targets in peritoneal macrophages and, following intraventricular delivery, demonstrated widespread functional distribution in the brain and spinal cord. After treating SOD1(G93A) mice with anti-miR-155, we significantly extended survival by 10 days and disease duration by 15 days (38%) while a scrambled control anti-miR did not significantly improve survival or disease duration. Therefore, antisense oligonucleotides may be used to successfully inhibit miRNAs throughout the brain and spinal cord, and miR-155 is a promising new therapeutic target for human ALS.
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20
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Genome-wide analysis of 24-nt siRNAs dynamic variations during rice superior and inferior grain filling. PLoS One 2013; 8:e61029. [PMID: 23593380 PMCID: PMC3625182 DOI: 10.1371/journal.pone.0061029] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2012] [Accepted: 03/05/2013] [Indexed: 11/19/2022] Open
Abstract
24 nt-siRNAs are the most abundant small interfering RNAs in rice grains aside from microRNAs. To investigate the roles that 24 nt-siRNAs played in the poor grain filling of rice inferior grains, dynamic variations of 24 nt-siRNAs in inferior grains were compared with those of superior grains by using small RNA deep sequencing technology. The results showed that 24 nt-siRNAs derived from multiple regions of rice genome, and the maintenance of the two strands of 24 nt-siRNA duplex was a non-random process. The amounts of 24 nt-siRNAs declined with the process of grain filling in both superior and inferior grains, but 24 nt-siRNAs in inferior grains was much higher than that of superior grains in each period we sampled. Bioinformatics prediction indicated that 24 nt-siRNAs targeted on more genes involved in most of the known KEGG rice pathways, such as the starch and sucrose biosynthesis pathway. Combined with digital gene expression profiling of target genes, 24 nt-siRNAs mapped on the antisense strands of exons were specifically investigated, but the abundance of 24 nt-siRNAs did not show negative correlations with their corresponding target genes. The results indicated that 24 nt-siRNAs were not involved in down-regulation of target genes. The potential biological meanings for this inconsistency were probably the results of methylation directed gene expression activation, or competition for small RNA stability methylation.
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21
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Wu M, Piccini M, Koh CY, Lam KS, Singh AK. Single cell microRNA analysis using microfluidic flow cytometry. PLoS One 2013; 8:e55044. [PMID: 23383050 PMCID: PMC3559333 DOI: 10.1371/journal.pone.0055044] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2012] [Accepted: 12/18/2012] [Indexed: 11/29/2022] Open
Abstract
MicroRNAs (miRNAs) are non-coding small RNAs that have cell type and cell context-dependent expression and function. To study miRNAs at single-cell resolution, we have developed a novel microfluidic approach, where flow fluorescent in situ hybridization (flow-FISH) using locked-nucleic acid probes is combined with rolling circle amplification to detect the presence and localization of miRNA. Furthermore, our flow cytometry approach allows analysis of gene-products potentially targeted by miRNA together with the miRNA in the same cells. We demonstrate simultaneous measurement of miR155 and CD69 in 12-O-tetradecanoylphorbol 13-acetate (PMA) and Ionomycin stimulated Jurkat cells. The flow-FISH method can be completed in ∼10 h, utilizes only 170 nL of reagent per experimental condition, and is the first to directly detect miRNA in single cells using flow cytometry.
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Affiliation(s)
- Meiye Wu
- Department of Biotechnology and Bioengineering, Sandia National Laboratory, Livermore, CA, USA
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22
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Martinez-Sanchez A, Murphy CL. MicroRNA Target Identification-Experimental Approaches. BIOLOGY 2013; 2:189-205. [PMID: 24832658 PMCID: PMC4009854 DOI: 10.3390/biology2010189] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 10/29/2012] [Revised: 12/19/2012] [Accepted: 12/24/2012] [Indexed: 12/12/2022]
Abstract
MicroRNAs (miRNAs) are small non-coding RNA molecules of 21–23 nucleotides that control gene expression at the post-transcriptional level. They have been shown to play a vital role in a wide variety of biological processes and dysregulated expression of miRNAs is observed in many pathologies. Understanding the mechanism of action and identifying functionally important mRNA targets of a specific miRNA are essential to unravelling its biological function and to assist miRNA-based drug development. This review summarizes the current understanding of the mechanistic aspects of miRNA-mediated gene repression and focuses on the different approaches for miRNA target identification that have been proposed in recent years.
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Affiliation(s)
- Aida Martinez-Sanchez
- Kennedy Institute of Rheumatology, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, 65 Aspenlea Road, London W6 8LH, UK.
| | - Chris L Murphy
- Kennedy Institute of Rheumatology, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, 65 Aspenlea Road, London W6 8LH, UK.
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23
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Arvey A, Tempera I, Tsai K, Chen HS, Tikhmyanova N, Klichinsky M, Leslie C, Lieberman PM. An atlas of the Epstein-Barr virus transcriptome and epigenome reveals host-virus regulatory interactions. Cell Host Microbe 2013; 12:233-45. [PMID: 22901543 DOI: 10.1016/j.chom.2012.06.008] [Citation(s) in RCA: 180] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2011] [Revised: 04/13/2012] [Accepted: 06/01/2012] [Indexed: 02/06/2023]
Abstract
Epstein-Barr virus (EBV), which is associated with multiple human tumors, persists as a minichromosome in the nucleus of B lymphocytes and induces malignancies through incompletely understood mechanisms. Here, we present a large-scale functional genomic analysis of EBV. Our experimentally generated nucleosome positioning maps and viral protein binding data were integrated with over 700 publicly available high-throughput sequencing data sets for human lymphoblastoid cell lines mapped to the EBV genome. We found that viral lytic genes are coexpressed with cellular cancer-associated pathways, suggesting that the lytic cycle may play an unexpected role in virus-mediated oncogenesis. Host regulators of viral oncogene expression and chromosome structure were identified and validated, revealing a role for the B cell-specific protein Pax5 in viral gene regulation and the cohesin complex in regulating higher order chromatin structure. Our findings provide a deeper understanding of latent viral persistence in oncogenesis and establish a valuable viral genomics resource for future exploration.
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Affiliation(s)
- Aaron Arvey
- Computational Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA
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24
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Dahlke C, Maul K, Christalla T, Walz N, Schult P, Stocking C, Grundhoff A. A microRNA encoded by Kaposi sarcoma-associated herpesvirus promotes B-cell expansion in vivo. PLoS One 2012. [PMID: 23185331 PMCID: PMC3502504 DOI: 10.1371/journal.pone.0049435] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
The human gammaherpesvirus Kaposi sarcoma-associated herpesvirus is strongly linked to neoplasms of endothelial and B-cell origin. The majority of tumor cells in these malignancies are latently infected, and latency genes are consequently thought to play a critical role in virus-induced tumorigenesis. One such factor is kshv-miR-K12-11, a viral microRNA that is constitutively expressed in cell lines derived from KSHV-associated tumors, and that shares perfect homology of its seed sequence with the cellular miR-155. Since miR-155 is overexpressed in a number of human tumors, it is conceivable that mimicry of miR-155 by miR-K12-11 may contribute to cellular transformation in KSHV-associated disease. Here, we have performed a side-by-side study of phenotypic alterations associated with constitutive expression of either human miR-155 or viral miR-K12-11 in bone marrow-derived hematopoietic stem cells. We demonstrate that retroviral-mediated gene transfer and hematopoietic progenitor cell transplantation into C57BL/6 mice leads to increased B-cell fractions in lymphoid organs, as well as to enhanced germinal center formation in both microRNA-expressing mouse cohorts. We furthermore identify Jarid2, a component of Polycomb repressive complex 2, as a novel validated target of miR-K12-11, and confirm its downregulation in miR-K12-11 as well as miR-155 expressing bone marrow cells. Our findings confirm and extend previous observations made in other mouse models, and underscore the notion that miR-K12-11 may have arisen to mimic miR-155 functions in KSHV-infected B-cells. The expression of miR-K12-11 may represent one mechanism by which KSHV presumably aims to reprogram naïve B-cells towards supporting long-term latency, which at the same time is likely to pre-dispose infected lymphocytes to malignant transformation.
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Affiliation(s)
| | | | | | | | | | | | - Adam Grundhoff
- Heinrich-Pette-Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany
- * E-mail:
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25
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Wang M, Moisá S, Khan MJ, Wang J, Bu D, Loor JJ. MicroRNA expression patterns in the bovine mammary gland are affected by stage of lactation. J Dairy Sci 2012; 95:6529-35. [PMID: 22959945 DOI: 10.3168/jds.2012-5748] [Citation(s) in RCA: 88] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2012] [Accepted: 07/26/2012] [Indexed: 01/08/2023]
Abstract
The objective of this work was to determine the expression pattern of microRNA (miR) associated with cellular proliferation, lipid metabolism, and innate immunity in dairy cow mammary gland tissue at different stages of lactation. The expression of miR-10a, miR-15b, miR-16, miR-21, miR-31, miR-33b, miR-145, miR-146b, miR-155, miR-181a, miR-205, miR-221, and miR-223 was studied by real-time reverse-transcription PCR in tissue (n=7/stage) harvested via repeated biopsies during the dry period (-30 d prepartum), the fresh period (7 d postpartum), and early lactation (30 d postpartum). Except for miR-31, all miR studied increased in expression between the dry and fresh periods. Among those upregulated, the expression of miR-221 increased further at early lactation, suggesting a role in the control of endothelial cell proliferation or angiogenesis, whereas the expression of miR-223 decreased at early lactation but to a level that was greater than in the dry period, suggesting it could play a role in the mammary response to pathogens soon after parturition. The expression of miR-31, a hormonally regulated miR that inhibits cyclin gene expression, was greater at early lactation compared with the dry period. From a metabolic standpoint, the consistent upregulation of miR-33b during early lactation compared with the dry period suggests that this miR may exert some control over lipogenesis in mammary tissue. Overall, results indicate that expression of miR associated with transcriptional regulation of genes across diverse biological functions is altered by stage of lactation. The specific roles of these miR during lactation will require further research.
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Affiliation(s)
- M Wang
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, PR China
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26
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Feng J, Meyer CA, Wang Q, Liu JS, Shirley Liu X, Zhang Y. GFOLD: a generalized fold change for ranking differentially expressed genes from RNA-seq data. ACTA ACUST UNITED AC 2012; 28:2782-8. [PMID: 22923299 DOI: 10.1093/bioinformatics/bts515] [Citation(s) in RCA: 280] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
MOTIVATION RNA-seq has been widely used in transcriptome analysis to effectively measure gene expression levels. Although sequencing costs are rapidly decreasing, almost 70% of all the human RNA-seq samples in the gene expression omnibus do not have biological replicates and more unreplicated RNA-seq data were published than replicated RNA-seq data in 2011. Despite the large amount of single replicate studies, there is currently no satisfactory method for detecting differentially expressed genes when only a single biological replicate is available. RESULTS We present the GFOLD (generalized fold change) algorithm to produce biologically meaningful rankings of differentially expressed genes from RNA-seq data. GFOLD assigns reliable statistics for expression changes based on the posterior distribution of log fold change. In this way, GFOLD overcomes the shortcomings of P-value and fold change calculated by existing RNA-seq analysis methods and gives more stable and biological meaningful gene rankings when only a single biological replicate is available. AVAILABILITY The open source C/C++ program is available at http://www.tongji.edu.cn/∼zhanglab/GFOLD/index.html
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Affiliation(s)
- Jianxing Feng
- Department of Bioinformatics, School of Life sciences and Technology, Tongji University, 1239 Siping Road, Shanghai 20092, China
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Ago HITS-CLIP expands understanding of Kaposi's sarcoma-associated herpesvirus miRNA function in primary effusion lymphomas. PLoS Pathog 2012; 8:e1002884. [PMID: 22927820 PMCID: PMC3426530 DOI: 10.1371/journal.ppat.1002884] [Citation(s) in RCA: 134] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2012] [Accepted: 07/13/2012] [Indexed: 12/27/2022] Open
Abstract
KSHV is the etiological agent of Kaposi's sarcoma (KS), primary effusion lymphoma (PEL), and a subset of multicentricCastleman's disease (MCD). The fact that KSHV-encoded miRNAs are readily detectable in all KSHV-associated tumors suggests a potential role in viral pathogenesis and tumorigenesis. MiRNA-mediated regulation of gene expression is a complex network with each miRNA having many potential targets, and to date only few KSHV miRNA targets have been experimentally determined. A detailed understanding of KSHV miRNA functions requires high-through putribonomics to globally analyze putative miRNA targets in a cell type-specific manner. We performed Ago HITS-CLIP to identify viral and cellular miRNAs and their cognate targets in two latently KSHV-infected PEL cell lines. Ago HITS-CLIP recovered 1170 and 950 cellular KSHVmiRNA targets from BCBL-1 and BC-3, respectively. Importantly, enriched clusters contained KSHV miRNA seed matches in the 3′UTRs of numerous well characterized targets, among them THBS1, BACH1, and C/EBPβ. KSHV miRNA targets were strongly enriched for genes involved in multiple pathways central for KSHV biology, such as apoptosis, cell cycle regulation, lymphocyte proliferation, and immune evasion, thus further supporting a role in KSHV pathogenesis and potentially tumorigenesis. A limited number of viral transcripts were also enriched by HITS-CLIP including vIL-6 expressed only in a subset of PEL cells during latency. Interestingly, Ago HITS-CLIP revealed extremely high levels of Ago-associated KSHV miRNAs especially in BC-3 cells where more than 70% of all miRNAs are of viral origin. This suggests that in addition to seed match-specific targeting of cellular genes, KSHV miRNAs may also function by hijacking RISCs, thereby contributing to a global de-repression of cellular gene expression due to the loss of regulation by human miRNAs. In summary, we provide an extensive list of cellular and viral miRNA targets representing an important resource to decipher KSHV miRNA function. Kaposi's sarcoma-associated herpesvirus is the etiological agent of KS and two lymphoproliferative diseases: multicentricCastleman's disease and primary effusion lymphomas (PEL). KSHV tumors are the most prevalent AIDS malignancies and within Sub-Saharan Africa KS is the most common cancer in males, both in the presence and absence of HIV infection. KSHV encodes 12 miRNA genes whose function is largely unknown. Viral miRNAs are incorporated into RISCs, which regulate gene expression mostly by binding to 3′UTRs of mRNAs to inhibit their translation and/or induce degradation. The small subset of viral miRNA targets identified to date suggests that these small posttranscriptional regulators target important cellular pathways involved in pathogenesis and tumorgenesis. Using Ago HITS-CLIP, a technique which combines UV cross-linking, immunoprecipitation of Ago-miRNA-mRNA complexes, and high throughput sequencing, we performed a detailed analysis of the KSHV miRNA targetome in two commonly studied PEL cell lines, BCBL-1 and BC-3 and identified 1170 and 950 putative miRNA targets, respectively. This data set provides a valuable resource to decipher how KSHV miRNAs contribute to viral biology and pathogenesis.
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Martin EC, Elliott S, Rhodes LV, Antoon JW, Fewell C, Zhu Y, Driver JL, Jodari-Karimi M, Taylor CW, Flemington EK, Beckman BS, Collins-Burow BM, Burow ME. Preferential star strand biogenesis of pre-miR-24-2 targets PKC-alpha and suppresses cell survival in MCF-7 breast cancer cells. Mol Carcinog 2012; 53:38-48. [PMID: 22911661 DOI: 10.1002/mc.21946] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2012] [Revised: 07/06/2012] [Accepted: 07/11/2012] [Indexed: 12/21/2022]
Abstract
microRNAs (miRNA) are regulators of cellular pathways and alterations of normal miRNA expression levels have been shown to increase tumorigenesis. miR-24 has been demonstrated as having both tumor suppressive and oncogenic properties depending on cell context. Here, we demonstrate a possible role for pre-miR-24-2 as a tumor suppressor in the MCF-7 breast cancer cell line through the preferential processing of mature miR-24-2* over miR-24. Specifically, we show that the ectopic expression of miR-24-2* in MCF-7 breast cancer cells results in a suppression of cellular survival both in vivo and in vitro. Notably, the overexpression of miR-24-2* results in a dampening of cell survival through the targeted suppression of PKCα. In addition, a similar biological change is observed in vivo where MCF-7 cells overexpressing pre-miR-24-2 have decreased tumorigenicity and tumor incidence. Taken together our data demonstrate that when overexpressed biogenesis of the pre-miR-24-2 favors miR-24-2* in the MCF-7 breast cancer cell line and suggests a tumor suppressive role for miR-24-2* observed through the inhibition of PKCα-mediated cellular survival.
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Affiliation(s)
- Elizabeth C Martin
- Department of Medicine, Section of Hematology and Medical Oncology, Tulane University, New Orleans, Louisiaina
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29
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Abstract
Hematopoiesis is a dynamic and highly complex developmental process that gives rise to a multitude of the cell types that circulate in the blood of multicellular organisms. These cells provide tissues with oxygen, guard against infection, prevent bleeding by clotting, and mediate inflammatory reactions. Because the hematopoietic system plays such a central role in human diseases such as infections, cancer, autoimmunity, and anemia, it has been intensely studied for more than a century. This scrutiny has helped to shape many of the developmental paradigms that exist today and has identified specific protein factors that serve as master regulators of blood cell lineage specification. Despite this progress, many aspects of blood cell development remain obscure, suggesting that novel layers of regulation must exist. Consequently, the emergence of regulatory noncoding RNAs, such as the microRNAs (miRNAs), is beginning to provide new insights into the molecular control networks underlying hematopoiesis and diseases that stem from aberrations in this process. This review will discuss how miRNAs fit into our current understanding of hematopoietic development in mammals and how breakdowns in these pathways can trigger disease.
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Affiliation(s)
- Ryan M O'Connell
- Division of Microbiology and Immunology, Department of Pathology, University of Utah, Salt Lake City, Utah, USA
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30
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Neilsen PM, Noll JE, Mattiske S, Bracken CP, Gregory PA, Schulz RB, Lim SP, Kumar R, Suetani RJ, Goodall GJ, Callen DF. Mutant p53 drives invasion in breast tumors through up-regulation of miR-155. Oncogene 2012; 32:2992-3000. [DOI: 10.1038/onc.2012.305] [Citation(s) in RCA: 129] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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31
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Kumar R, Halder P, Sahu SK, Kumar M, Kumari M, Jana K, Ghosh Z, Sharma P, Kundu M, Basu J. Identification of a novel role of ESAT-6-dependent miR-155 induction during infection of macrophages withMycobacterium tuberculosis. Cell Microbiol 2012; 14:1620-31. [DOI: 10.1111/j.1462-5822.2012.01827.x] [Citation(s) in RCA: 123] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2012] [Revised: 06/06/2012] [Accepted: 06/11/2012] [Indexed: 12/21/2022]
Affiliation(s)
- Ranjeet Kumar
- Department of Chemistry; Bose Institute; 93/1 Acharya Prafulla Chandra Road; Kolkata; 700 009; India
| | - Priyanka Halder
- Department of Chemistry; Bose Institute; 93/1 Acharya Prafulla Chandra Road; Kolkata; 700 009; India
| | - Sanjaya K. Sahu
- Department of Chemistry; Bose Institute; 93/1 Acharya Prafulla Chandra Road; Kolkata; 700 009; India
| | - Manish Kumar
- Department of Chemistry; Bose Institute; 93/1 Acharya Prafulla Chandra Road; Kolkata; 700 009; India
| | - Mandavi Kumari
- Department of Chemistry; Bose Institute; 93/1 Acharya Prafulla Chandra Road; Kolkata; 700 009; India
| | - Kuladip Jana
- Division of Molecular Medicine; Bose Institute; A.J.C. Bose Centenary Building, P-1/12, CIT Scheme- VII M; Kolkata; 700 054; India
| | - Zhumur Ghosh
- Bioinformatics Centre; Bose Institute; A.J.C. Bose Centenary Building, P-1/12, CIT Scheme- VII M; Kolkata; 700 054; India
| | - Pawan Sharma
- Immunology Group; International Centre for Genetic Engineering and Biotechnology; New Delhi; India
| | - Manikuntala Kundu
- Department of Chemistry; Bose Institute; 93/1 Acharya Prafulla Chandra Road; Kolkata; 700 009; India
| | - Joyoti Basu
- Department of Chemistry; Bose Institute; 93/1 Acharya Prafulla Chandra Road; Kolkata; 700 009; India
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32
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Glaus P, Honkela A, Rattray M. Identifying differentially expressed transcripts from RNA-seq data with biological variation. Bioinformatics 2012; 28:1721-8. [PMID: 22563066 PMCID: PMC3381971 DOI: 10.1093/bioinformatics/bts260] [Citation(s) in RCA: 152] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2011] [Revised: 04/21/2012] [Accepted: 04/27/2012] [Indexed: 11/12/2022] Open
Abstract
MOTIVATION High-throughput sequencing enables expression analysis at the level of individual transcripts. The analysis of transcriptome expression levels and differential expression (DE) estimation requires a probabilistic approach to properly account for ambiguity caused by shared exons and finite read sampling as well as the intrinsic biological variance of transcript expression. RESULTS We present Bayesian inference of transcripts from sequencing data (BitSeq), a Bayesian approach for estimation of transcript expression level from RNA-seq experiments. Inferred relative expression is represented by Markov chain Monte Carlo samples from the posterior probability distribution of a generative model of the read data. We propose a novel method for DE analysis across replicates which propagates uncertainty from the sample-level model while modelling biological variance using an expression-level-dependent prior. We demonstrate the advantages of our method using simulated data as well as an RNA-seq dataset with technical and biological replication for both studied conditions. AVAILABILITY The implementation of the transcriptome expression estimation and differential expression analysis, BitSeq, has been written in C++ and Python. The software is available online from http://code.google.com/p/bitseq/, version 0.4 was used for generating results presented in this article.
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Affiliation(s)
- Peter Glaus
- School of Computer Science, University of Manchester, Oxford Road, Manchester M13 9PL, UK.
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33
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Mattiske S, Suetani RJ, Neilsen PM, Callen DF. The oncogenic role of miR-155 in breast cancer. Cancer Epidemiol Biomarkers Prev 2012; 21:1236-43. [PMID: 22736789 DOI: 10.1158/1055-9965.epi-12-0173] [Citation(s) in RCA: 198] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
miR-155 is an oncogenic miRNA with well described roles in leukemia. However, additional roles of miR-155 in breast cancer progression have recently been described. A thorough literature search was conducted to review all published data to date, examining the role of miR-155 in breast cancer. Data on all validated miR-155 target genes was collated to identify biologic pathways relevant to miR-155 and breast cancer progression. Publications describing the clinical relevance, functional characterization, and regulation of expression of miR-155 in the context of breast cancer are reviewed. A total of 147 validated miR-155 target genes were identified from the literature. Pathway analysis of these genes identified likely roles in apoptosis, differentiation, angiogenesis, proliferation, and epithelial-mesenchymal transition. The large number of validated miR-155 targets presented here provide many avenues of interest as to the clinical potential of miR-155. Further investigation of these target genes will be required to elucidate the specific mechanisms and functions of miR-155 in breast cancer. This is the first review examining the role of miR-155 in breast cancer progression. The collated data of target genes and biologic pathways of miR-155 identified in this review suggest new avenues of research for this oncogenic miRNA.
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Affiliation(s)
- Sam Mattiske
- Centre for Personalised Cancer Medicine, Cancer Therapeutics Laboratory, Department of Medicine, University of Adelaide, Australia.
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34
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Huang L, Zhou K, Yang Y, Shang Z, Wang J, Wang D, Wang N, Xu D, Zhou J. FLT3-ITD-associated gene-expression signatures in NPM1-mutated cytogenetically normal acute myeloid leukemia. Int J Hematol 2012; 96:234-40. [PMID: 22688855 DOI: 10.1007/s12185-012-1115-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2012] [Revised: 05/18/2012] [Accepted: 05/22/2012] [Indexed: 11/29/2022]
Abstract
Concomitance of the FLT3-ITD mutation is associated with poor prognosis in NPM1-mutated cytogenetically normal acute myeloid leukemia (CN-AML) patients, and precise studies on its role in leukemogenesis are needed; these may be elucidated at the molecular level by gene express profiling. In the present study, we built a gene-expression-based classifier using prediction analysis of microarray to characterize the FLT3-ITD signature in NPM1-mutated CN-AML patients, which comprised 10 annotated genes, and demonstrated an overall accuracy of 83.8 % in cross-validation. To characterize the signature in another way, differential expression was revealed for 34 genes by class comparison, and the up-regulation of LAPTM4B and MIR155HG was validated by quantitative RT-PCR in our small cohort of NPM1-mutated CN-AML samples, which appeared to be associated with this specific subtype. The 10-gene classifier and differentially expressed genes identified in this study indicate a potential utility for risk-assessed treatment stratification, and suggest new therapeutic targets for these high-risk AML patients.
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Affiliation(s)
- Liang Huang
- Department of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, Hubei, People's Republic of China
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35
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Inhibition of miR-29 by TGF-beta-Smad3 signaling through dual mechanisms promotes transdifferentiation of mouse myoblasts into myofibroblasts. PLoS One 2012; 7:e33766. [PMID: 22438993 PMCID: PMC3306299 DOI: 10.1371/journal.pone.0033766] [Citation(s) in RCA: 106] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2011] [Accepted: 02/21/2012] [Indexed: 12/13/2022] Open
Abstract
MicroRNAs (miRNAs) are non-coding RNAs that regulate gene expression in post-transcriptional fashion, and emerging studies support their importance in regulating many biological processes, including myogenic differentiation and muscle development. miR-29 is a promoting factor during myogenesis but its full spectrum of impact on muscle cells has yet to be explored. Here we describe an analysis of miR-29 affected transcriptome in C2C12 muscle cells using a high throughput RNA-sequencing platform. The results reveal that miR-29 not only functions to promote myogenic differentiation but also suppresses the transdifferentiation of myoblasts into myofibroblasts. miR-29 inhibits the fibrogenic differentiation through down-regulating both extracellular matrix genes and cell adhesion genes. We further demonstrate that miR-29 is under negative regulation by TGF-beta (TGF-β)-Smad3 signaling via dual mechanisms of both inhibiting MyoD binding and enhancing Yin Yang 1 (YY1)-recruited Polycomb association. Together, these results identify miR-29 as a pleiotropic molecule in both myogenic and fibrogenic differentiation of muscle cells.
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36
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Skalsky RL, Corcoran DL, Gottwein E, Frank CL, Kang D, Hafner M, Nusbaum JD, Feederle R, Delecluse HJ, Luftig MA, Tuschl T, Ohler U, Cullen BR. The viral and cellular microRNA targetome in lymphoblastoid cell lines. PLoS Pathog 2012; 8:e1002484. [PMID: 22291592 PMCID: PMC3266933 DOI: 10.1371/journal.ppat.1002484] [Citation(s) in RCA: 273] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2011] [Accepted: 11/29/2011] [Indexed: 12/13/2022] Open
Abstract
Epstein-Barr virus (EBV) is a ubiquitous human herpesvirus linked to a number of B cell cancers and lymphoproliferative disorders. During latent infection, EBV expresses 25 viral pre-microRNAs (miRNAs) and induces the expression of specific host miRNAs, such as miR-155 and miR-21, which potentially play a role in viral oncogenesis. To date, only a limited number of EBV miRNA targets have been identified; thus, the role of EBV miRNAs in viral pathogenesis and/or lymphomagenesis is not well defined. Here, we used photoactivatable ribonucleoside-enhanced crosslinking and immunoprecipitation (PAR-CLIP) combined with deep sequencing and computational analysis to comprehensively examine the viral and cellular miRNA targetome in EBV strain B95-8-infected lymphoblastoid cell lines (LCLs). We identified 7,827 miRNA-interaction sites in 3,492 cellular 3'UTRs. 531 of these sites contained seed matches to viral miRNAs. 24 PAR-CLIP-identified miRNA:3'UTR interactions were confirmed by reporter assays. Our results reveal that EBV miRNAs predominantly target cellular transcripts during latent infection, thereby manipulating the host environment. Furthermore, targets of EBV miRNAs are involved in multiple cellular processes that are directly relevant to viral infection, including innate immunity, cell survival, and cell proliferation. Finally, we present evidence that myc-regulated host miRNAs from the miR-17/92 cluster can regulate latent viral gene expression. This comprehensive survey of the miRNA targetome in EBV-infected B cells represents a key step towards defining the functions of EBV-encoded miRNAs, and potentially, identifying novel therapeutic targets for EBV-associated malignancies.
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Affiliation(s)
- Rebecca L. Skalsky
- Department of Molecular Genetics and Microbiology, Duke University, Durham, North Carolina, United States of America
| | - David L. Corcoran
- Duke Institute for Genome Sciences and Policy, Duke University, Durham, North Carolina, United States of America
| | - Eva Gottwein
- Department of Microbiology-Immunology, Northwestern University, Feinberg School of Medicine, Chicago, Illinois, United States of America
| | - Christopher L. Frank
- Department of Molecular Genetics and Microbiology, Duke University, Durham, North Carolina, United States of America
| | - Dong Kang
- Department of Molecular Genetics and Microbiology, Duke University, Durham, North Carolina, United States of America
| | - Markus Hafner
- Laboratory of RNA Molecular Biology, The Rockefeller University, New York, New York, United States of America
| | - Jeffrey D. Nusbaum
- Laboratory of RNA Molecular Biology, The Rockefeller University, New York, New York, United States of America
| | - Regina Feederle
- German Cancer Research Center, Department of Virus-Associated Tumours, Heidelberg, Germany
| | | | - Micah A. Luftig
- Department of Molecular Genetics and Microbiology, Duke University, Durham, North Carolina, United States of America
| | - Thomas Tuschl
- Laboratory of RNA Molecular Biology, The Rockefeller University, New York, New York, United States of America
| | - Uwe Ohler
- Duke Institute for Genome Sciences and Policy, Duke University, Durham, North Carolina, United States of America
- Department of Biostatistics and Bioinformatics, Duke University, Durham, North Carolina, United States of America
| | - Bryan R. Cullen
- Department of Molecular Genetics and Microbiology, Duke University, Durham, North Carolina, United States of America
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37
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Mestan KK, Ilkhanoff L, Mouli S, Lin S. Genomic sequencing in clinical trials. J Transl Med 2011; 9:222. [PMID: 22206293 PMCID: PMC3269395 DOI: 10.1186/1479-5876-9-222] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2011] [Accepted: 12/30/2011] [Indexed: 12/02/2022] Open
Abstract
Human genome sequencing is the process by which the exact order of nucleic acid base pairs in the 24 human chromosomes is determined. Since the completion of the Human Genome Project in 2003, genomic sequencing is rapidly becoming a major part of our translational research efforts to understand and improve human health and disease. This article reviews the current and future directions of clinical research with respect to genomic sequencing, a technology that is just beginning to find its way into clinical trials both nationally and worldwide. We highlight the currently available types of genomic sequencing platforms, outline the advantages and disadvantages of each, and compare first- and next-generation techniques with respect to capabilities, quality, and cost. We describe the current geographical distributions and types of disease conditions in which these technologies are used, and how next-generation sequencing is strategically being incorporated into new and existing studies. Lastly, recent major breakthroughs and the ongoing challenges of using genomic sequencing in clinical research are discussed.
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Affiliation(s)
- Karen K Mestan
- Department of Pediatrics, Division of Neonatology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA.
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38
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Forte E, Luftig MA. The role of microRNAs in Epstein-Barr virus latency and lytic reactivation. Microbes Infect 2011; 13:1156-67. [PMID: 21835261 PMCID: PMC4911174 DOI: 10.1016/j.micinf.2011.07.007] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2010] [Revised: 07/19/2011] [Accepted: 07/20/2011] [Indexed: 01/06/2023]
Abstract
Oncogenic viruses reprogram host gene expression driving proliferation, ensuring survival, and evading the immune response. The recent appreciation of microRNAs (miRNAs) as small non-coding RNAs that broadly regulate gene expression has provided new insight into this complex scheme of host control. This review highlights the role of viral and cellular miRNAs during the latent and lytic phases of the EBV life cycle.
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MESH Headings
- Animals
- B-Lymphocytes/immunology
- B-Lymphocytes/metabolism
- B-Lymphocytes/virology
- Conserved Sequence
- Epstein-Barr Virus Infections/complications
- Epstein-Barr Virus Infections/immunology
- Epstein-Barr Virus Infections/virology
- Exosomes/immunology
- Exosomes/metabolism
- Exosomes/virology
- Gene Expression Profiling
- Gene Expression Regulation, Viral
- Herpesvirus 4, Human/genetics
- Herpesvirus 4, Human/immunology
- Herpesvirus 4, Human/metabolism
- Host-Pathogen Interactions
- Humans
- Lymphoma, B-Cell/etiology
- Lymphoma, B-Cell/immunology
- Lymphoma, B-Cell/virology
- Mice
- MicroRNAs/genetics
- MicroRNAs/immunology
- MicroRNAs/metabolism
- Oligonucleotide Array Sequence Analysis
- RNA, Messenger/genetics
- RNA, Messenger/immunology
- RNA, Messenger/metabolism
- RNA, Viral/genetics
- RNA, Viral/immunology
- RNA, Viral/metabolism
- RNA-Induced Silencing Complex/immunology
- Viral Proteins/genetics
- Viral Proteins/immunology
- Viral Proteins/metabolism
- Virus Activation/physiology
- Virus Latency/physiology
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Affiliation(s)
- Eleonora Forte
- Department of Molecular Genetics and Microbiology and Center for Virology, Duke University Medical Center, Durham, NC, USA, 27712
| | - Micah A. Luftig
- Department of Molecular Genetics and Microbiology and Center for Virology, Duke University Medical Center, Durham, NC, USA, 27712
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39
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Huang R, Jaritz M, Guenzl P, Vlatkovic I, Sommer A, Tamir IM, Marks H, Klampfl T, Kralovics R, Stunnenberg HG, Barlow DP, Pauler FM. An RNA-Seq strategy to detect the complete coding and non-coding transcriptome including full-length imprinted macro ncRNAs. PLoS One 2011; 6:e27288. [PMID: 22102886 PMCID: PMC3213133 DOI: 10.1371/journal.pone.0027288] [Citation(s) in RCA: 89] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2011] [Accepted: 10/13/2011] [Indexed: 11/18/2022] Open
Abstract
Imprinted macro non-protein-coding (nc) RNAs are cis-repressor transcripts that silence multiple genes in at least three imprinted gene clusters in the mouse genome. Similar macro or long ncRNAs are abundant in the mammalian genome. Here we present the full coding and non-coding transcriptome of two mouse tissues: differentiated ES cells and fetal head using an optimized RNA-Seq strategy. The data produced is highly reproducible in different sequencing locations and is able to detect the full length of imprinted macro ncRNAs such as Airn and Kcnq1ot1, whose length ranges between 80–118 kb. Transcripts show a more uniform read coverage when RNA is fragmented with RNA hydrolysis compared with cDNA fragmentation by shearing. Irrespective of the fragmentation method, all coding and non-coding transcripts longer than 8 kb show a gradual loss of sequencing tags towards the 3′ end. Comparisons to published RNA-Seq datasets show that the strategy presented here is more efficient in detecting known functional imprinted macro ncRNAs and also indicate that standardization of RNA preparation protocols would increase the comparability of the transcriptome between different RNA-Seq datasets.
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Affiliation(s)
- Ru Huang
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Markus Jaritz
- Research Institute of Molecular Pathology, Vienna, Austria
| | - Philipp Guenzl
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Irena Vlatkovic
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Andreas Sommer
- Research Institute of Molecular Pathology, Vienna, Austria
| | - Ido M. Tamir
- Research Institute of Molecular Pathology, Vienna, Austria
| | - Hendrik Marks
- Department of Molecular Biology, Faculty of Science, Nijmegen Center for Molecular Life Sciences (NCMLS), Radboud University Nijmegen, Nijmegen, The Netherlands
| | - Thorsten Klampfl
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Robert Kralovics
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Hendrik G. Stunnenberg
- Department of Molecular Biology, Faculty of Science, Nijmegen Center for Molecular Life Sciences (NCMLS), Radboud University Nijmegen, Nijmegen, The Netherlands
| | - Denise P. Barlow
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
- * E-mail: (DPB); (FMP)
| | - Florian M. Pauler
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
- * E-mail: (DPB); (FMP)
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40
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Abstract
The past 5 years have seen an explosion of knowledge about miRNAs and their roles in hematopoiesis, cancer, and other diseases. In myeloid development, there is a growing appreciation for both the importance of particular miRNAs and the unique features of myelopoiesis that are being uncovered by experimental manipulation of miRNAs. Here, we review in detail the roles played by 4 miRNAs, miR-125, miR-146, miR-155, and miR-223 in myeloid development and activation, and correlate these roles with their dysregulation in disease. All 4 miRNAs demonstrate effects on myelopoiesis, and their loss of function or overexpression leads to pathologic phenotypes in the myeloid lineage. We review their functions at distinct points in development, their targets, and the regulatory networks that they are embedded into in the myeloid lineage.
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41
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Watanabe Y, Kanai A. Systems Biology Reveals MicroRNA-Mediated Gene Regulation. Front Genet 2011; 2:29. [PMID: 22303325 PMCID: PMC3268584 DOI: 10.3389/fgene.2011.00029] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2011] [Accepted: 05/30/2011] [Indexed: 12/19/2022] Open
Abstract
MicroRNAs (miRNAs) are members of the small non-coding RNAs, which are principally known for their functions as post-transcriptional regulators of target genes. Regulation by miRNAs is triggered by the translational repression or degradation of their complementary target messenger RNAs (mRNAs). The growing number of reported miRNAs and the estimate that hundreds or thousands of genes are regulated by them suggest a magnificent gene regulatory network in which these molecules are embedded. Indeed, recent reports have suggested critical roles for miRNAs in various biological functions, such as cell differentiation, development, oncogenesis, and the immune responses, which are mediated by systems-wide changes in gene expression profiles. Therefore, it is essential to analyze this complex regulatory network at the transcriptome and proteome levels, which should be possible with approaches that include both high-throughput experiments and computational methodologies. Here, we introduce several systems-level approaches that have been applied to miRNA research, and discuss their potential to reveal miRNA-guided gene regulatory systems and their impacts on biological functions.
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Affiliation(s)
- Yuka Watanabe
- Institute for Advanced Biosciences, Keio University Tsuruoka, Japan
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Morgan RW, Burnside J. Roles of avian herpesvirus microRNAs in infection, latency, and oncogenesis. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2011; 1809:654-9. [PMID: 21683170 DOI: 10.1016/j.bbagrm.2011.06.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2011] [Revised: 06/01/2011] [Accepted: 06/02/2011] [Indexed: 01/24/2023]
Abstract
MicroRNAs have been reported for the avian herpesviruses Marek's disease virus 1 (MDV1; oncogenic), Marek's disease virus 2 (MDV2; non-oncogenic), herpesvirus of turkeys (HVT), and infectious laryngotracheitis virus (ILTV). No obvious phylogenetic relationships exist among the avian herpesvirus microRNAs, but the general genomic locations of microRNA clusters are conserved, with microRNAs being located in the repeat regions of the genomes. In some cases, microRNAs are antisense to open reading frames. Among MDV1 field isolates with different virulence properties, microRNAs are highly conserved, and variations that have been observed lie in putative promoter regions. One cluster of MDV1 microRNAs lies upstream of the meq gene, and this cluster is more highly expressed in tumors caused by an extremely virulent MDV1 isolate compared to tumors caused by a less virulent isolate. Several of the avian herpesvirus microRNAs are orthologs of microRNAs in other species. For example, mdv1-miR-M4 shares a seed sequence with gga-miR-155 (also shared with Kaposi sarcoma herpesvirus (KSHV) kshv-miR-K12), mdv2-miR-M21 shares a seed with miR-29b, and hvt-miR-H14 shares a seed sequence with miR-221. Functional analyses of avian herpesvirus microRNAs include a variety of in vitro assays to demonstrate potential function as well as the use of mutants that can exploit the ability to assess phenotypes experimentally in the natural host. This article is part of a Special Issue entitled:MicroRNA's in viral gene regulation.
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Affiliation(s)
- Robin W Morgan
- Department of Animal and Food Sciences, University of Delaware, Newark, DE, USA.
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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: 430] [Impact Index Per Article: 33.1] [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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Deng N, Puetter A, Zhang K, Johnson K, Zhao Z, Taylor C, Flemington EK, Zhu D. Isoform-level microRNA-155 target prediction using RNA-seq. Nucleic Acids Res 2011; 39:e61. [PMID: 21317189 PMCID: PMC3089486 DOI: 10.1093/nar/gkr042] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Computational prediction of microRNA targets remains a challenging problem. The existing rule-based, data-driven and expression profiling approaches to target prediction are mostly approached from the gene-level. The increasing availability of RNA-seq data provides a new perspective for microRNA target prediction on the isoform-level. We hypothesize that the splicing isoform is the ultimate effector in microRNA targeting and that the proposed isoform-level approach is capable of predicting non-dominant isoform targets as well as their targeting regions that are otherwise invisible to many existing approaches. To test the hypothesis, we used an iterative expectation maximization (EM) algorithm to quantify transcriptomes at the isoform-level. The performance of the EM algorithm in transcriptome quantification was examined in simulation studies using FluxSimulator. We used joint evidence from isoform-level down-regulation and seed enrichment to predict microRNA-155 targets. We validated our computational approach using results from 149 in-house performed in vitro 3′-UTR assays. We also augmented the splicing database using exon–exon junction evidence, and applied the EM algorithm to predict and quantify 1572 cell line specific novel isoforms. Combined with seed enrichment analysis, we predicted 51 novel microRNA-155 isoform targets. Our work is among the first computational studies advocating the isoform-level microRNA target prediction.
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Affiliation(s)
- Nan Deng
- Department of Computer Science, University of New Orleans, 2000 Lakeshore Drive, New Orleans, LA 70148, USA
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CULLUM R, ALDER O, HOODLESS PA. The next generation: Using new sequencing technologies to analyse gene regulation. Respirology 2011; 16:210-22. [DOI: 10.1111/j.1440-1843.2010.01899.x] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Xu G, Deng N, Zhao Z, Judeh T, Flemington E, Zhu D. SAMMate: a GUI tool for processing short read alignments in SAM/BAM format. SOURCE CODE FOR BIOLOGY AND MEDICINE 2011; 6:2. [PMID: 21232146 PMCID: PMC3027120 DOI: 10.1186/1751-0473-6-2] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/17/2010] [Accepted: 01/13/2011] [Indexed: 12/02/2022]
Abstract
Background Next Generation Sequencing (NGS) technology generates tens of millions of short reads for each DNA/RNA sample. A key step in NGS data analysis is the short read alignment of the generated sequences to a reference genome. Although storing alignment information in the Sequence Alignment/Map (SAM) or Binary SAM (BAM) format is now standard, biomedical researchers still have difficulty accessing this information. Results We have developed a Graphical User Interface (GUI) software tool named SAMMate. SAMMate allows biomedical researchers to quickly process SAM/BAM files and is compatible with both single-end and paired-end sequencing technologies. SAMMate also automates some standard procedures in DNA-seq and RNA-seq data analysis. Using either standard or customized annotation files, SAMMate allows users to accurately calculate the short read coverage of genomic intervals. In particular, for RNA-seq data SAMMate can accurately calculate the gene expression abundance scores for customized genomic intervals using short reads originating from both exons and exon-exon junctions. Furthermore, SAMMate can quickly calculate a whole-genome signal map at base-wise resolution allowing researchers to solve an array of bioinformatics problems. Finally, SAMMate can export both a wiggle file for alignment visualization in the UCSC genome browser and an alignment statistics report. The biological impact of these features is demonstrated via several case studies that predict miRNA targets using short read alignment information files. Conclusions With just a few mouse clicks, SAMMate will provide biomedical researchers easy access to important alignment information stored in SAM/BAM files. Our software is constantly updated and will greatly facilitate the downstream analysis of NGS data. Both the source code and the GUI executable are freely available under the GNU General Public License at http://sammate.sourceforge.net.
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Affiliation(s)
- Guorong Xu
- Department of Computer Science, University of New Orleans, 2000 Lakeshore Drive, New Orleans, LA 70148, USA.
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Quantitative and qualitative RNA-Seq-based evaluation of Epstein-Barr virus transcription in type I latency Burkitt's lymphoma cells. J Virol 2010; 84:13053-8. [PMID: 20943983 DOI: 10.1128/jvi.01521-10] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
RNA-seq provides a rich source of transcriptome information with high qualitative and quantitative value. Here, we provide a pipeline for Epstein-Barr virus (EBV) transcriptome analysis using RNA-seq and we apply it to two type I latency cell lines, Mutu I and Akata. This analysis revealed substantial average expression levels of many lytic genes in predominantly latent cell populations. The lytic transcripts BHLF1 and LF3 were expressed at levels greater than those for 98% of all cellular polyadenylated transcripts. Exon junction mapping accurately identified the Qp-derived EBNA1 splicing pattern, lytic gene splicing, and a complex splicing pattern within the BamHI A region.
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Lin Z, Flemington EK. miRNAs in the pathogenesis of oncogenic human viruses. Cancer Lett 2010; 305:186-99. [PMID: 20943311 DOI: 10.1016/j.canlet.2010.08.018] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2010] [Revised: 08/25/2010] [Accepted: 08/26/2010] [Indexed: 12/21/2022]
Abstract
Tumor viruses are a class of pathogens with well established roles in the development of malignant diseases. Numerous bodies of work have highlighted miRNAs (microRNAs) as critical regulators of tumor pathways and it is clear that the dysregulation of cellular miRNA expression can promote tumor formation. Tumor viruses encode their own miRNAs and/or manipulate the expression of cellular miRNAs to modulate their host cell environment, thereby facilitating their respective infection cycles. The modulation of these miRNA responsive pathways, however, often influences certain signal transduction cascades in ways that favor tumorigenesis. In this review, we discuss the roles of virally-encoded and virally-regulated cellular miRNAs in the respective viral life cycles and in virus associated pathogenesis.
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Affiliation(s)
- Zhen Lin
- Department of Pathology, SL-79, Tulane Health Sciences Center, 1430 Tulane Avenue, New Orleans, LA 70112, USA
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