1
|
Manna I, De Benedittis S, Porro D. A Comprehensive Examination of the Role of Epigenetic Factors in Multiple Sclerosis. Int J Mol Sci 2024; 25:8921. [PMID: 39201606 PMCID: PMC11355011 DOI: 10.3390/ijms25168921] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2024] [Revised: 08/05/2024] [Accepted: 08/14/2024] [Indexed: 09/02/2024] Open
Abstract
According to various research, the risk of multiple sclerosis (MS) is strongly influenced by genetic variations. Population, familial, and molecular studies provide strong empirical support for a polygenic pattern of inheritance, mainly due to relatively common allelic variants in the general population. The strongest MS susceptibility locus, which was unmistakably identified in tested populations, is the major histocompatibility complex on chromosome 6p21.3. However, the effect of a given predisposing variant remains modest, so there is the possibility that multiple gene-gene and/or gene-environment interactions could significantly increase the contribution of specific variants to the overall genetic risk. Furthermore, as is known, susceptibility genes can be subject to epigenetic modifications, which greatly increase the complexity of MS heritability. Investigating epigenetic and environmental factors can provide new opportunities for the molecular basis of the MS, which shows complicated pathogenesis. Although studies of epigenetic changes in MS only began in the last decade, a growing body of literature suggests that these may be involved in the development of MS. Here, we summarize recent studies regarding epigenetic changes related to MS initiation and progression. Furthermore, we discuss how current studies address important clinical questions and how future studies could be used in clinical practice.
Collapse
Affiliation(s)
- Ida Manna
- Institute of Bioimaging and Complex Biological Systems (IBSBC), National Research Council (CNR), Section of Catanzaro, 88100 Catanzaro, Italy
| | - Selene De Benedittis
- Institute for Biomedical Research and Innovation (IRIB), National Research Council (CNR) Cosenza, 88100 Catanzaro, Italy
| | - Danilo Porro
- Institute of Bioimaging and Complex Biological Systems (IBSBC), National Research Council (CNR), Segrate, 20054 Milan, Italy
| |
Collapse
|
2
|
MicroRNA-146: Biomarker and Mediator of Cardiovascular Disease. DISEASE MARKERS 2022. [DOI: 10.1155/2022/7767598] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Cardiovascular diseases (CVDs) are the prime cause of morbidity and mortality worldwide. Although noticeable progress has been made in the diagnosis, prognosis, and treatment, there is still a critical demand for new diagnostic biomarkers and novel therapeutic interventions to reduce this disease incidence. Many investigations have been conducted on the regulatory effects of microRNAs in cardiovascular diseases. miRNA circulating serum level changes are correlated with several CVDs. In addition, there is growing evidence representing the potential role of miRNAs as diagnostic biomarkers or potential therapeutic targets for CVD. Preliminary studies identified the prominent role of miR-146 in host defense, innate immunity, and different immunological diseases by regulating cytokine production and innate immunity modification in bacterial infections. However, more recently, it was also associated with CVD development. miR-146 has received much attention, with positive results in most studies. Research demonstrated the crucial role of this molecule in the pathogenesis of cardiac disease and related mechanisms. As a result, many potential applications of miR-146 are expected. In this paper, we provide an overview of recent studies highlighting the role of miR-146 in CVD, focusing on CAD (coronary artery disease), cardiomyopathy, and MI (myocardial infarction) in particular and discussing its current scientific state, and use a prognostic biomarker as a therapeutic agent for cardiovascular diseases.
Collapse
|
3
|
Kern F, Krammes L, Danz K, Diener C, Kehl T, Küchler O, Fehlmann T, Kahraman M, Rheinheimer S, Aparicio-Puerta E, Wagner S, Ludwig N, Backes C, Lenhof HP, von Briesen H, Hart M, Keller A, Meese E. Validation of human microRNA target pathways enables evaluation of target prediction tools. Nucleic Acids Res 2021; 49:127-144. [PMID: 33305319 PMCID: PMC7797041 DOI: 10.1093/nar/gkaa1161] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2020] [Revised: 10/20/2020] [Accepted: 11/13/2020] [Indexed: 12/17/2022] Open
Abstract
MicroRNAs are regulators of gene expression. A wide-spread, yet not validated, assumption is that the targetome of miRNAs is non-randomly distributed across the transcriptome and that targets share functional pathways. We developed a computational and experimental strategy termed high-throughput miRNA interaction reporter assay (HiTmIR) to facilitate the validation of target pathways. First, targets and target pathways are predicted and prioritized by computational means to increase the specificity and positive predictive value. Second, the novel webtool miRTaH facilitates guided designs of reporter assay constructs at scale. Third, automated and standardized reporter assays are performed. We evaluated HiTmIR using miR-34a-5p, for which TNF- and TGFB-signaling, and Parkinson's Disease (PD)-related categories were identified and repeated the pipeline for miR-7-5p. HiTmIR validated 58.9% of the target genes for miR-34a-5p and 46.7% for miR-7-5p. We confirmed the targeting by measuring the endogenous protein levels of targets in a neuronal cell model. The standardized positive and negative targets are collected in the new miRATBase database, representing a resource for training, or benchmarking new target predictors. Applied to 88 target predictors with different confidence scores, TargetScan 7.2 and miRanda outperformed other tools. Our experiments demonstrate the efficiency of HiTmIR and provide evidence for an orchestrated miRNA-gene targeting.
Collapse
Affiliation(s)
- Fabian Kern
- Chair for Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany
| | - Lena Krammes
- Institute of Human Genetics, Saarland University, 66421 Homburg, Germany
| | - Karin Danz
- Department of Bioprocessing & Bioanalytics, Fraunhofer Institute for Biomedical Engineering, 66280 Sulzbach, Germany
| | - Caroline Diener
- Institute of Human Genetics, Saarland University, 66421 Homburg, Germany
| | - Tim Kehl
- Center for Bioinformatics, Saarland Informatics Campus, Saarland University, 66123 Saarbrücken, Germany
| | - Oliver Küchler
- Chair for Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany
| | - Tobias Fehlmann
- Chair for Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany
| | - Mustafa Kahraman
- Chair for Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany
| | | | - Ernesto Aparicio-Puerta
- Chair for Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany.,Department of Genetics, Faculty of Science, University of Granada, 18071 Granada, Spain.,Instituto de Investigación Biosanitaria ibs. Granada, University of Granada, 18071 Granada, Spain
| | - Sylvia Wagner
- Department of Bioprocessing & Bioanalytics, Fraunhofer Institute for Biomedical Engineering, 66280 Sulzbach, Germany
| | - Nicole Ludwig
- Institute of Human Genetics, Saarland University, 66421 Homburg, Germany.,Center of Human and Molecular Biology, Saarland University, 66123 Saarbrücken, Germany
| | - Christina Backes
- Chair for Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany
| | - Hans-Peter Lenhof
- Center for Bioinformatics, Saarland Informatics Campus, Saarland University, 66123 Saarbrücken, Germany
| | - Hagen von Briesen
- Department of Bioprocessing & Bioanalytics, Fraunhofer Institute for Biomedical Engineering, 66280 Sulzbach, Germany
| | - Martin Hart
- Institute of Human Genetics, Saarland University, 66421 Homburg, Germany
| | - Andreas Keller
- Chair for Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany.,Center for Bioinformatics, Saarland Informatics Campus, Saarland University, 66123 Saarbrücken, Germany.,Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA
| | - Eckart Meese
- Institute of Human Genetics, Saarland University, 66421 Homburg, Germany
| |
Collapse
|
4
|
Solomon J, Kern F, Fehlmann T, Meese E, Keller A. HumiR: Web Services, Tools and Databases for Exploring Human microRNA Data. Biomolecules 2020; 10:biom10111576. [PMID: 33233537 PMCID: PMC7699549 DOI: 10.3390/biom10111576] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 11/13/2020] [Accepted: 11/17/2020] [Indexed: 12/29/2022] Open
Abstract
For many research aspects on small non-coding RNAs, especially microRNAs, computational tools and databases are developed. This includes quantification of miRNAs, piRNAs, tRNAs and tRNA fragments, circRNAs and others. Furthermore, the prediction of new miRNAs, isomiRs, arm switch events, target and target pathway prediction and miRNA pathway enrichment are common tasks. Additionally, databases and resources containing expression profiles, e.g., from different tissues, organs or cell types, are generated. This information in turn leads to improved miRNA repositories. While most of the respective tools are implemented in a species-independent manner, we focused on tools for human small non-coding RNAs. This includes four aspects: (1) miRNA analysis tools (2) databases on miRNAs and variations thereof (3) databases on expression profiles (4) miRNA helper tools facilitating frequent tasks such as naming conversion or reporter assay design. Although dependencies between the tools exist and several tools are jointly used in studies, the interoperability is limited. We present HumiR, a joint web presence for our tools. HumiR facilitates an entry in the world of miRNA research, supports the selection of the right tool for a research task and represents the very first step towards a fully integrated knowledge-base for human small non-coding RNA research. We demonstrate the utility of HumiR by performing a very comprehensive analysis of Alzheimer's miRNAs.
Collapse
Affiliation(s)
- Jeffrey Solomon
- Chair for Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany; (J.S.); (F.K.); (T.F.)
| | - Fabian Kern
- Chair for Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany; (J.S.); (F.K.); (T.F.)
| | - Tobias Fehlmann
- Chair for Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany; (J.S.); (F.K.); (T.F.)
| | - Eckart Meese
- Institute for Human Genetics, Saarland University, 66421 Homburg, Germany;
| | - Andreas Keller
- Chair for Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany; (J.S.); (F.K.); (T.F.)
- Center for Bioinformatics, Saarland University, 66123 Saarbrücken, Germany
- Department of Neurobiology, Stanford University, Palo Alto, CA 94305, USA
- Correspondence: ; Tel.: +49-681-30268611
| |
Collapse
|
5
|
Mallik S, Bandyopadhyay S. WeCoMXP: Weighted Connectivity Measure Integrating Co-Methylation, Co-Expression and Protein-Protein Interactions for Gene-Module Detection. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2020; 17:690-703. [PMID: 30183644 DOI: 10.1109/tcbb.2018.2868348] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The identification of modules (groups of several tightly interconnected genes) in gene interaction network is an essential task for better understanding of the architecture of the whole network. In this article, we develop a novel weighted connectivity measure integrating co-methylation, co-expression, and protein-protein interactions (called WeCoMXP) to detect gene-modules for multi-omics dataset. The proposed measure goes beyond the fundamental degree centrality measure through considering some formulation of higher-order connections. Thereafter, we apply the average linkage clustering method using the corresponding dissimilarity (distance) values of WeCoMXP scores, and utilize a dynamic tree cut method for identifying some gene-modules. We validate the modules through literature search, KEGG pathway, and gene-ontology analyses on the genes representing the modules. Furthermore, the top 10 TFs/miRNAs that are connected with the maximum number of gene-modules and that regulate/target the maximum number of genes from these connected gene-modules, are identified. Moreover, our proposed method provides a better performance than the existing methods in terms of several cluster-validity indices in maximum times.
Collapse
|
6
|
Kehl T, Kern F, Backes C, Fehlmann T, Stöckel D, Meese E, Lenhof HP, Keller A. miRPathDB 2.0: a novel release of the miRNA Pathway Dictionary Database. Nucleic Acids Res 2020; 48:D142-D147. [PMID: 31691816 PMCID: PMC7145528 DOI: 10.1093/nar/gkz1022] [Citation(s) in RCA: 118] [Impact Index Per Article: 29.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2019] [Revised: 10/17/2019] [Accepted: 10/19/2019] [Indexed: 12/13/2022] Open
Abstract
Since the initial release of miRPathDB, tremendous progress has been made in the field of microRNA (miRNA) research. New miRNA reference databases have emerged, a vast amount of new miRNA candidates has been discovered and the number of experimentally validated target genes has increased considerably. Hence, the demand for a major upgrade of miRPathDB, including extended analysis functionality and intuitive visualizations of query results has emerged. Here, we present the novel release 2.0 of the miRNA Pathway Dictionary Database (miRPathDB) that is freely accessible at https://mpd.bioinf.uni-sb.de/. miRPathDB 2.0 comes with a ten-fold increase of pre-processed data. In total, the updated database provides putative associations between 27 452 (candidate) miRNAs, 28 352 targets and 16 833 pathways for Homo sapiens, as well as interactions of 1978 miRNAs, 24 898 targets and 6511 functional categories for Mus musculus. Additionally, we analyzed publications citing miRPathDB to identify common use-cases and further extensions. Based on this evaluation, we added new functionality for interactive visualizations and down-stream analyses of bulk queries. In summary, the updated version of miRPathDB, with its new custom-tailored features, is one of the most comprehensive and advanced resources for miRNAs and their target pathways.
Collapse
Affiliation(s)
- Tim Kehl
- Chair for Bioinformatics, Saarland Informatics Campus, 66123 Saarbrücken, Germany
| | - Fabian Kern
- Chair for Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany
| | - Christina Backes
- Chair for Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany
| | - Tobias Fehlmann
- Chair for Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany
| | - Daniel Stöckel
- Chair for Bioinformatics, Saarland Informatics Campus, 66123 Saarbrücken, Germany
- EMD Digital, Merck KGaA, Darmstadt, Germany
| | - Eckart Meese
- Department of Human Genetics, Saarland University, 66421 Homburg, Germany
| | - Hans-Peter Lenhof
- Chair for Bioinformatics, Saarland Informatics Campus, 66123 Saarbrücken, Germany
| | - Andreas Keller
- Chair for Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany
- School of Medicine Office, Stanford University, Stanford, CA, USA
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, USA
| |
Collapse
|
7
|
Pham TT, Ban J, Lee K, Hong Y, Lee J, Truong AD, Lillehoj HS, Hong YH. MicroRNA gga-miR-10a-mediated transcriptional regulation of the immune genes in necrotic enteritis afflicted chickens. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2020; 102:103472. [PMID: 31437523 DOI: 10.1016/j.dci.2019.103472] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Revised: 08/18/2019] [Accepted: 08/18/2019] [Indexed: 06/10/2023]
Abstract
miRNAs are involved in both adaptive and innate immune systems of host animals; and play important roles in many immune-related pathways. The systemic biological roles of gga-miR-10a-5p chicken microRNA on immune response were investigated in two necrotic enteritis (NE) induced chicken lines, Marek's disease (MD) resistant (line 6.3) and susceptible (line 7.2). We determined the expression patterns of gga-miR-10a in the intestinal mucosal layer of chickens upon NE induction, and identified the target genes (MyD88, and SKP1) related to the host immune response to pathogens. We found that gga-miR-10a expression in the intestinal mucosal layer of MD-resistant chicken line 6.3 gga-miR-10a was significantly down-regulated (p < 0.01) during NE. Overexpression analysis of gga-miR-10a and reporter gene analysis using a wild- or mutant-type MyD88 3' untranslated region (3' UTR)-luciferase construct in chicken macrophage cell line HD11 and chicken fibroblast cell line OU2 showed that gga-miR-10a acted as a direct translational repressor of MyD88 by targeting the 3' UTR of this gene. Furthermore, miR-10a indirectly negatively influenced the expression of signaling molecules related to the MyD88-dependent pathway, including TRAF6, TAK1, and NF-κB1 at both transcriptional and translational levels. Downstream of the MyD88-dependent pathway, several proinflammatory cytokines such as IL-1β, IFN-γ, IL-12p40, TNFSF15, and LITAF were down-regulated by overexpression of gga-miR-10a. These results suggest that gga-miR-10a is an important regulator of the Toll-like receptor signaling pathway. The findings of this study improve our understanding of the biological functions of miR-10a and the mechanisms underlying the TLR signaling pathway upon NE afflicted chickens, as well improving the overall understanding of the immune system function in domestic animals.
Collapse
Affiliation(s)
- Thu Thao Pham
- Department of Animal Science and Technology, Chung-Ang University, Anseong, 17546, Republic of Korea
| | - Jihye Ban
- Department of Animal Science and Technology, Chung-Ang University, Anseong, 17546, Republic of Korea
| | - Kyungbaek Lee
- Department of Animal Science and Technology, Chung-Ang University, Anseong, 17546, Republic of Korea
| | - Yeojin Hong
- Department of Animal Science and Technology, Chung-Ang University, Anseong, 17546, Republic of Korea
| | - Jiae Lee
- Department of Animal Science and Technology, Chung-Ang University, Anseong, 17546, Republic of Korea
| | - Anh Duc Truong
- Department of Animal Science and Technology, Chung-Ang University, Anseong, 17546, Republic of Korea; Department of Biochemistry and Immunology, National Institute of Veterinary Research, 86 Truong Chinh, Dong Da, Hanoi, 100000, Viet Nam
| | - Hyun S Lillehoj
- Animal Biosciences and Biotechnology Laboratory, Agricultural Research Services, United States Department of Agriculture, Beltsville, MD, 20705, USA
| | - Yeong Ho Hong
- Department of Animal Science and Technology, Chung-Ang University, Anseong, 17546, Republic of Korea.
| |
Collapse
|
8
|
Kim EA, Jang JH, Sung EG, Song IH, Kim JY, Lee TJ. MiR-1208 Increases the Sensitivity to Cisplatin by Targeting TBCK in Renal Cancer Cells. Int J Mol Sci 2019; 20:ijms20143540. [PMID: 31331056 PMCID: PMC6679220 DOI: 10.3390/ijms20143540] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Revised: 07/17/2019] [Accepted: 07/17/2019] [Indexed: 02/07/2023] Open
Abstract
MicroRNAs (miRNAs) can be used to target a variety of human malignancies by targeting their oncogenes or tumor suppressor genes. Recent evidence has shown that miRNA-1208 (miR-1208) was rarely expressed in a variety of cancer cells, suggesting the possibility that miR-1208 functions as a tumor suppressor gene. Herein, ectopic expression of miR-1208 induced the accumulation of sub-G1 populations and the cleavage of procaspase-3 and PARP, which could be prevented by pre-treatment with the pan-caspase inhibitor, Z-VAD. In addition, miR-1208 increased the susceptibility to cisplatin and TRAIL in Caki-1 cells. Luciferase reporter assay results showed that miR-1208 negatively regulates TBC1 domain containing kinase (TBCK) expression by binding to the miR-1208 binding sites in the 3′-untranslated region of TBCK. In addition, miR-1208 specifically repressed TBCK expression at the transcriptional level. In contrast, inhibition of endogenous miR-1208 by anti-miRs resulted in an increase in TBCK expression. Downregulation of TBCK induced by TBCK-specific siRNAs increased susceptibility to cisplatin and TRAIL. These findings suggest that miR-1208 acts as a tumor suppressor and targets TBCK directly, thus possessing great potential for use in renal cancer therapy.
Collapse
Affiliation(s)
- Eun-Ae Kim
- Department of Anatomy, College of Medicine, Yeungnam University, 170 Hyeonchung-Ro, Nam-Gu, Daegu 42415, Korea
| | - Ji-Hoon Jang
- Department of Anatomy, College of Medicine, Yeungnam University, 170 Hyeonchung-Ro, Nam-Gu, Daegu 42415, Korea
| | - Eon-Gi Sung
- Department of Anatomy, College of Medicine, Yeungnam University, 170 Hyeonchung-Ro, Nam-Gu, Daegu 42415, Korea
| | - In-Hwan Song
- Department of Anatomy, College of Medicine, Yeungnam University, 170 Hyeonchung-Ro, Nam-Gu, Daegu 42415, Korea
| | - Joo-Young Kim
- Department of Anatomy, College of Medicine, Yeungnam University, 170 Hyeonchung-Ro, Nam-Gu, Daegu 42415, Korea
| | - Tae-Jin Lee
- Department of Anatomy, College of Medicine, Yeungnam University, 170 Hyeonchung-Ro, Nam-Gu, Daegu 42415, Korea.
| |
Collapse
|
9
|
Abdolvahabi Z, Nourbakhsh M, Hosseinkhani S, Hesari Z, Alipour M, Jafarzadeh M, Ghorbanhosseini SS, Seiri P, Yousefi Z, Yarahmadi S, Golpour P. MicroRNA-590-3P suppresses cell survival and triggers breast cancer cell apoptosis via targeting sirtuin-1 and deacetylation of p53. J Cell Biochem 2019; 120:9356-9368. [PMID: 30520099 DOI: 10.1002/jcb.28211] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Accepted: 11/15/2018] [Indexed: 12/29/2022]
Abstract
Downregulation of microRNA-590-3p (miR-590-3p) is a frequently occurring, nonphysiological event which is observed in several human cancers, especially breast cancer. However, the significance of miR-590-3p still remain unclear in the progression of this disease. This study explored the role of miR-590-3p in apoptosis of breast cancer cells. Gene expression of miR-590-3p, Sirtuin-1 (SIRT1), Bcl-2 associated X protein (BAX), and p21 was evaluated with real-time polymerase chain reaction (PCR) and SIRT1 protein expression was assessed by Western blot analysis in breast cancer cell lines. Bioinformatics analysis and luciferase reporter assay were used to evaluate targeting of SIRT1 messenger RNA (mRNA) by miR-590-3p. Cells were transfected with miR-590-3p mimic and inhibitor and their effects on the expression and activity of SIRT1 were evaluated. The effects of miR-590-3p upregulation on the acetylation of p53 as well as cell viability and apoptosis were assessed by Western blot analysis, WST-1 assay, and flow cytometry, respectively. miR-590-3p expression was considerably downregulated in breast cancer cells which was accompanied by upregulation of SIRT1 expression. SIRT1 was recognized as a direct target for miR-590-3p in breast cancer cells and its protein expression and activity was dramatically inhibited by the miR-590-3p. In addition, there was an increase in p53 and its acetylated form that ultimately led to upregulation of BAX and p21 expression, suppression of cell survival, and considerable induction of apoptosis in breast cancer cells. These findings suggest that miR-590-3p exerts tumor-suppressing effects through targeting SIRT1 in breast cancer cells, which makes it a potential therapeutic target for developing more efficient treatments for breast cancer.
Collapse
Affiliation(s)
- Zohreh Abdolvahabi
- Department of Biochemistry, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Mitra Nourbakhsh
- Department of Biochemistry, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Saman Hosseinkhani
- Department of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Zahra Hesari
- Department of Biochemistry, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Mohsen Alipour
- Department of Nano Biotechnology, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
- Department of Advanced Medical Sciences & Technologies, School of Medicine, Jahrom University of Medical Sciences, Jahrom, Iran
| | - Meisam Jafarzadeh
- Department of Molecular Genetics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | | | - Parvaneh Seiri
- Department of Biochemistry, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Zeynab Yousefi
- Department of Biochemistry, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Sahar Yarahmadi
- Department of Biochemistry, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Pegah Golpour
- Department of Biochemistry, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| |
Collapse
|
10
|
Piket E, Zheleznyakova GY, Kular L, Jagodic M. Small non-coding RNAs as important players, biomarkers and therapeutic targets in multiple sclerosis: A comprehensive overview. J Autoimmun 2019; 101:17-25. [PMID: 31014917 DOI: 10.1016/j.jaut.2019.04.002] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Revised: 04/02/2019] [Accepted: 04/04/2019] [Indexed: 10/27/2022]
Abstract
Multiple sclerosis (MS) is a leading cause of progressive disability among young adults caused by inflammation, demyelination and axonal loss in the central nervous system. Small non-coding RNAs (sncRNAs) are important regulators of various biological processes and could therefore play important roles in MS. Over the past decade, a large number of studies investigated sncRNAs in MS patients, focusing primarily on microRNAs (miRNAs). Overwhelming 500 miRNAs have been reported as dysregulated in MS. Nevertheless, owing to a large heterogeneity between studies it is challenging to evaluate the reproducibility of findings, in turn hampering our knowledge about the functional roles of miRNAs in disease. We systematically searched main databases and evaluated results from all studies that examined sncRNAs in MS to date (n = 61) and provided a detailed overview of experimental design and findings of these studies. We focused on the mechanisms of the most dysregulated sncRNAs and used predicted targets of the most dysregulated sncRNAs as input for functional enrichment analysis to highlight affected pathways. The prime affected pathway was TGF-β signaling. This multifunctional cytokine is important in the differentiation and function of T helper type 17 (Th17) and regulatory T (Treg) cells, with opposing functions in the disease. Recent studies demonstrate the importance of miRNAs in controlling the balance between Th17/Th1 cells and Tregs and, importantly, the potential to exploit this paradigm for therapeutic purposes. Additionally, some of the discussed miRNAs could potentially serve as biomarkers of disease. In order to assist researchers in evaluating the evidence of a particular sncRNA in the pathogenesis of MS, we provide a detailed overview of experimental design and findings of these studies to date.
Collapse
Affiliation(s)
- Eliane Piket
- Department of Clinical Neuroscience, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | | | - Lara Kular
- Department of Clinical Neuroscience, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Maja Jagodic
- Department of Clinical Neuroscience, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden.
| |
Collapse
|
11
|
Carlsson J, Christiansen J, Davidsson S, Giunchi F, Fiorentino M, Sundqvist P. The potential role of miR-126, miR-21 and miR-10b as prognostic biomarkers in renal cell carcinoma. Oncol Lett 2019; 17:4566-4574. [PMID: 30988818 PMCID: PMC6447904 DOI: 10.3892/ol.2019.10142] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Accepted: 02/04/2019] [Indexed: 12/19/2022] Open
Abstract
Renal cell carcinoma (RCC) is the most commonly diagnosed renal tumor, consisting of ~3% of all malignancies worldwide. The prognosis of RCC can vary widely, and detecting patients at risk of recurrence at an early stage of disease may improve patient outcome. The factors presently used in a clinical setting cannot reliably predict the natural history of the disease. Therefore, there is a requirement to identify novel biomarkers that can aid in predicting patient outcome. Previous studies have indicated that microRNAs (miRNAs/miRs) are potential candidates as prognostic biomarkers for patients suffering from RCC. Consequently, the aims of the present study were to validate the potential of 3 of these miRNAs to predict the prognosis of patients with RCC, and to investigate the stability of endogenous control genes for miRNA studies in RCC tissues. The expression of 7 endogenous controls was measured using reverse transcription-quantitative polymerase chain reaction (RT-qPCR) in formalin-fixed paraffin-embedded tumor and benign tissues from patients suffering from clear cell RCC (ccRCC). The analyses identified RNU48 and U47 as the most stable endogenous controls. The expression of miR-126, miR-21 and miR-10b was analyzed using RT-qPCR in renal tissues from 116 patients diagnosed with ccRCC. All three investigated miRNAs were differentially expressed between malignant and benign tissues. miR-126 and miR-10b were also differentially expressed between grades and stages of ccRCC. In a univariate, but not in a multivariate model, low expression of miR-126 was associated with shorter time to recurrence of the disease. The results of the present study indicate that of the 3 miRNAs investigated, the expression of miR-126 has the strongest potential as a prognostic biomarker for patients suffering from ccRCC.
Collapse
Affiliation(s)
- Jessica Carlsson
- Department of Urology, Faculty of Medicine and Health, Örebro University, 701 85 Örebro, Sweden
| | - Jesper Christiansen
- Department of Surgery, Faculty of Medicine and Health, Örebro University, 701 85 Örebro, Sweden
| | - Sabina Davidsson
- Department of Urology, Faculty of Medicine and Health, Örebro University, 701 85 Örebro, Sweden
| | - Francesca Giunchi
- Department of Pathology, F. Addari Institute of Oncology, S. Orsola Hospital, I-401 38 Bologna, Italy
| | - Michelangelo Fiorentino
- Department of Pathology, F. Addari Institute of Oncology, S. Orsola Hospital, I-401 38 Bologna, Italy
| | - Pernilla Sundqvist
- Department of Urology, Faculty of Medicine and Health, Örebro University, 701 85 Örebro, Sweden
| |
Collapse
|
12
|
Diener C, Galata V, Keller A, Meese E. MicroRNA profiling from dried blood samples. Crit Rev Clin Lab Sci 2019; 56:111-117. [DOI: 10.1080/10408363.2018.1561641] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Caroline Diener
- Institute of Human Genetics, Medical Faculty, Saarland University, Homburg, Germany
| | - Valentina Galata
- Chair for Clinical Bioinformatics, Medical Faculty, Saarland University, Center for Bioinformatics, Saarbrücken, Germany
| | - Andreas Keller
- Chair for Clinical Bioinformatics, Medical Faculty, Saarland University, Center for Bioinformatics, Saarbrücken, Germany
| | - Eckart Meese
- Institute of Human Genetics, Medical Faculty, Saarland University, Homburg, Germany
| |
Collapse
|
13
|
Pirritano M, Fehlmann T, Laufer T, Ludwig N, Gasparoni G, Li Y, Meese E, Keller A, Simon M. Next Generation Sequencing Analysis of Total Small Noncoding RNAs from Low Input RNA from Dried Blood Sampling. Anal Chem 2018; 90:11791-11796. [DOI: 10.1021/acs.analchem.8b03557] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Marcello Pirritano
- Molecular Cell Dynamics, Centre for Human and Molecular Biology, Campus A2.4, Saarland University, 66123 Saarbrücken, Germany
- Molecular Cell Biology and Microbiology, Wuppertal University, Building V12.070, 42097 Wuppertal, Germany
| | - Tobias Fehlmann
- Clinical Bioinformatics, Center for Bioinformatics, Campus E2.1, Saarland University, 66123 Saarbruecken, Germany
| | - Thomas Laufer
- Institute of Human Genetics, Medical School, Saarland University, Building 60, 66421 Homburg Germany
- Hummingbird Diagnostics GmbH, Im Neuenheimer Feld 583, 69120 Heidelberg, Germany
| | - Nicole Ludwig
- Institute of Human Genetics, Medical School, Saarland University, Building 60, 66421 Homburg Germany
| | - Gilles Gasparoni
- Epigenetics, Centere for Human and Molecular Biology, Campus A2.4, Saarland University, 66123 Saarbruecken, Germany
| | - Yongping Li
- Clinical Bioinformatics, Center for Bioinformatics, Campus E2.1, Saarland University, 66123 Saarbruecken, Germany
- BGI, Building No.7, BGI Park, No.12 Hongan Third Street, Yantian District, Shenzhen, 518083 China
| | - Eckart Meese
- Institute of Human Genetics, Medical School, Saarland University, Building 60, 66421 Homburg Germany
| | - Andreas Keller
- Clinical Bioinformatics, Center for Bioinformatics, Campus E2.1, Saarland University, 66123 Saarbruecken, Germany
- Hummingbird Diagnostics GmbH, Im Neuenheimer Feld 583, 69120 Heidelberg, Germany
| | - Martin Simon
- Molecular Cell Dynamics, Centre for Human and Molecular Biology, Campus A2.4, Saarland University, 66123 Saarbrücken, Germany
- Molecular Cell Biology and Microbiology, Wuppertal University, Building V12.070, 42097 Wuppertal, Germany
| |
Collapse
|
14
|
MicroRNA in diagnosis and therapy monitoring of early-stage triple-negative breast cancer. Sci Rep 2018; 8:11584. [PMID: 30072748 PMCID: PMC6072710 DOI: 10.1038/s41598-018-29917-2] [Citation(s) in RCA: 81] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Accepted: 07/09/2018] [Indexed: 11/12/2022] Open
Abstract
Breast cancer is a heterogeneous disease with distinct molecular subtypes including the aggressive subtype triple-negative breast cancer (TNBC). We compared blood-borne miRNA signatures of early-stage basal-like (cytokeratin-CK5-positive) TNBC patients to age-matched controls. The miRNAs of TNBC patients were assessed prior to and following platinum-based neoadjuvant chemotherapy (NCT). After an exploratory genome-wide study on 21 cases and 21 controls using microarrays, the identified signatures were verified independently in two laboratories on the same and a new cohort by RT-qPCR. We differentiated the blood of TNBC patients before NCT from controls with 84% sensitivity. The most significant miRNA for this diagnostic classification was miR-126-5p (two tailed t-test p-value of 1.4 × 10−5). Validation confirmed the microarray results for all tested miRNAs. Comparing cancer patients prior to and post NCT highlighted 321 significant miRNAs (among them miR-34a, p-value of 1.2 × 10−23). Our results also suggest that changes in miRNA expression during NCT may have predictive potential to predict pathological complete response (pCR). In conclusion we report that miRNA expression measured from blood facilitates early and minimally-invasive diagnosis of basal-like TNBC. We also demonstrate that NCT has a significant influence on miRNA expression. Finally, we show that blood-borne miRNA profiles monitored over time have potential to predict pCR.
Collapse
|
15
|
Zu C, Liu S, Cao W, Liu Z, Qiang H, Li Y, Cheng C, Ji L, Li J, Li J. MiR-590-3p suppresses epithelial-mesenchymal transition in intrahepatic cholangiocarcinoma by inhibiting SIP1 expression. Oncotarget 2018; 8:34698-34708. [PMID: 28423728 PMCID: PMC5471004 DOI: 10.18632/oncotarget.16150] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Accepted: 02/08/2017] [Indexed: 12/29/2022] Open
Abstract
The functional roles and clinical significances of miR-590-3p in ICC remain unclear. In the current study, we investigated the expression of miR-590-3p in tissues and sera of ICC by real-time quantitative polymerase chain reaction. We found miR-590-3p was significantly down-regulated in the sera and tissues of ICC patients, especially in those patients with lymph node metastasis or distant metastasis. AUC curves and Cox proportional hazards mode revealed serum miR-590-3p could be novel diagnostic and prognostic biomarker for ICC patients. MiR-590-3p dramatically suppressed epithelial-mesenchymal transition, cell migration, and invasion of ICC cells. SIP1 was identified as direct and functional target of miR-590-3p in ICC cells by luciferase assays. Finally, we found SIP1 expression was inversely correlated with miR-590-3p and closely related to diminished survival in ICC patients. These findings reveal functional and mechanistic roles of miR-590-3p and EMT activator SIP1 in the pathogenesis of ICC.
Collapse
Affiliation(s)
- Chao Zu
- Department of Surgical Oncology, Shaanxi Provincial People's Hospital, The Third Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710068, Shaanxi Province, P.R. China
| | - Shizhang Liu
- Department of Orthopaedics, Shaanxi Provincial People's Hospital, The Third Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710068, Shaanxi Province, P.R. China
| | - Wei Cao
- Department of Surgical Oncology, Shaanxi Provincial People's Hospital, The Third Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710068, Shaanxi Province, P.R. China
| | - Zongzhi Liu
- Department of Orthopaedics, Shaanxi Provincial People's Hospital, The Third Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710068, Shaanxi Province, P.R. China
| | - Hui Qiang
- Department of Orthopaedics, Shaanxi Provincial People's Hospital, The Third Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710068, Shaanxi Province, P.R. China
| | - Yong Li
- Department of Orthopaedics, Shaanxi Provincial People's Hospital, The Third Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710068, Shaanxi Province, P.R. China
| | - Chong Cheng
- Department of Surgical Oncology, Shaanxi Provincial People's Hospital, The Third Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710068, Shaanxi Province, P.R. China
| | - Le Ji
- Department of Orthopaedics, Shaanxi Provincial People's Hospital, The Third Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710068, Shaanxi Province, P.R. China
| | - Jianhui Li
- Department of Surgical Oncology, Shaanxi Provincial People's Hospital, The Third Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710068, Shaanxi Province, P.R. China
| | - Jingyuan Li
- Department of Orthopaedics, Shaanxi Provincial People's Hospital, The Third Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710068, Shaanxi Province, P.R. China
| |
Collapse
|
16
|
Dysregulation of Mir-196b in Head and Neck Cancers Leads to Pleiotropic Effects in the Tumor Cells and Surrounding Stromal Fibroblasts. Sci Rep 2017; 7:17785. [PMID: 29259267 PMCID: PMC5736577 DOI: 10.1038/s41598-017-18138-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Accepted: 11/24/2017] [Indexed: 02/07/2023] Open
Abstract
The miR-196 family members have been found dysregulated in different cancers. Therefore, they have been proposed as promising biomarkers and therapeutic targets. This study is the first to investigate the role of miR-196b in the development and progression of head and neck squamous cell carcinomas (HNSCC), and also the impact on the surrounding tumor microenvironment. Increased miR-196b levels were detected in 95% of primary tumors and precancerous lesions, although no significant differences were observed between non-progressing versus progressing dysplasias. Furthermore, increased levels of both miR-196a and miR-196b were successfully detected in saliva samples from HNSCC patients. The functional consequences of altered miR-196 expression were investigated in both HNSCC cell lines and cancer-associated fibroblasts (CAFs) by transfection with specific pre-miR precursors. Results showed that both miR-196a and miR-196b elicit cell-specific responses in target genes and downstream regulatory pathways, and have a distinctive impact on cell proliferation, migration and invasion. These data reveal the early occurrence and prevalence of miR-196b dysregulation in HNSCC tumorigenesis, suggesting its utility for early diagnosis and/or disease surveillance and also as a non-invasive biomarker in saliva. The pleiotropic effects of miR-196a/b in HNSCC cell subpopulations and surrounding CAFs may complicate a possible therapeutic application.
Collapse
|
17
|
Amri EZ, Scheideler M. Small non coding RNAs in adipocyte biology and obesity. Mol Cell Endocrinol 2017; 456:87-94. [PMID: 28412522 DOI: 10.1016/j.mce.2017.04.009] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/06/2017] [Revised: 04/10/2017] [Accepted: 04/10/2017] [Indexed: 12/12/2022]
Abstract
Obesity has reached epidemic proportions world-wide and constitutes a substantial risk factor for hypertension, type 2 diabetes, cardiovascular diseases and certain cancers. So far, regulation of energy intake by dietary and pharmacological treatments has met limited success. The main interest of current research is focused on understanding the role of different pathways involved in adipose tissue function and modulation of its mass. Whole-genome sequencing studies revealed that the majority of the human genome is transcribed, with thousands of non-protein-coding RNAs (ncRNA), which comprise small and long ncRNAs. ncRNAs regulate gene expression at the transcriptional and post-transcriptional level. Numerous studies described the involvement of ncRNAs in the pathogenesis of many diseases including obesity and associated metabolic disorders. ncRNAs represent potential diagnostic biomarkers and promising therapeutic targets. In this review, we focused on small ncRNAs involved in the formation and function of adipocytes and obesity.
Collapse
Affiliation(s)
| | - Marcel Scheideler
- Institute for Diabetes and Cancer (IDC), Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany; Joint Heidelberg-IDC Translational Diabetes Program, University Hospital Heidelberg, Germany; German Center for Diabetes Research (DZD), Neuherberg, Germany.
| |
Collapse
|
18
|
Kehl T, Backes C, Kern F, Fehlmann T, Ludwig N, Meese E, Lenhof HP, Keller A. About miRNAs, miRNA seeds, target genes and target pathways. Oncotarget 2017; 8:107167-107175. [PMID: 29291020 PMCID: PMC5739805 DOI: 10.18632/oncotarget.22363] [Citation(s) in RCA: 79] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Accepted: 09/21/2017] [Indexed: 11/25/2022] Open
Abstract
miRNAs are typically repressing gene expression by binding to the 3' UTR, leading to degradation of the mRNA. This process is dominated by the eight-base seed region of the miRNA. Further, miRNAs are known not only to target genes but also to target significant parts of pathways. A logical line of thoughts is: miRNAs with similar (seed) sequence target similar sets of genes and thus similar sets of pathways. By calculating similarity scores for all 3.25 million pairs of 2,550 human miRNAs, we found that this pattern frequently holds, while we also observed exceptions. Respective results were obtained for both, predicted target genes as well as experimentally validated targets. We note that miRNAs target gene set similarity follows a bimodal distribution, pointing at a set of 282 miRNAs that seems to target genes with very high specificity. Further, we discuss miRNAs with different (seed) sequences that nonetheless regulate similar gene sets or pathways. Most intriguingly, we found miRNA pairs that regulate different gene sets but similar pathways such as miR-6886-5p and miR-3529-5p. These are jointly targeting different parts of the MAPK signaling cascade. The main goal of this study is to provide a general overview on the results, to highlight a selection of relevant results on miRNAs, miRNA seeds, target genes and target pathways and to raise awareness for artifacts in respective comparisons. The full set of information that allows to infer detailed results on each miRNA has been included in miRPathDB, the miRNA target pathway database (https://mpd.bioinf.uni-sb.de).
Collapse
Affiliation(s)
- Tim Kehl
- Center for Bioinformatics, Saarland University, Saarland Informatics Campus, Saarbrücken, Germany
| | - Christina Backes
- Chair for Clinical Bioinformatics, Saarland University, Saarland Informatics Campus, Saarbrücken, Germany
| | - Fabian Kern
- Chair for Clinical Bioinformatics, Saarland University, Saarland Informatics Campus, Saarbrücken, Germany
| | - Tobias Fehlmann
- Chair for Clinical Bioinformatics, Saarland University, Saarland Informatics Campus, Saarbrücken, Germany
| | - Nicole Ludwig
- Department of Human Genetics, Saarland University, Homburg, Germany
| | - Eckart Meese
- Department of Human Genetics, Saarland University, Homburg, Germany
| | - Hans-Peter Lenhof
- Center for Bioinformatics, Saarland University, Saarland Informatics Campus, Saarbrücken, Germany
| | - Andreas Keller
- Chair for Clinical Bioinformatics, Saarland University, Saarland Informatics Campus, Saarbrücken, Germany
| |
Collapse
|
19
|
Micro-ribonucleic acids and extracellular vesicles repertoire in the spent culture media is altered in women undergoing In Vitro Fertilization. Sci Rep 2017; 7:13525. [PMID: 29051527 PMCID: PMC5648749 DOI: 10.1038/s41598-017-13683-8] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Accepted: 09/27/2017] [Indexed: 12/21/2022] Open
Abstract
MicroRNAs (miRNAs) are class of small RNA molecules with major impact on gene regulation. We analyzed the potential of miRNAs secreted from pre-implantation embryos into the embryonic culture media as biomarkers to predict successful pregnancy. Using microarray analysis, we profiled the miRNome of the 56 spent culture media (SCM) after embryos transfer and found a total of 621 miRNAs in the SCM. On average, we detected 163 miRNAs in SCM of samples with failed pregnancies, but only 149 SCM miRNAs of embryos leading to pregnancies. MiR-634 predicted an embryo transfer leading to a positive pregnancy with an accuracy of 71% and a sensitivity of 85%. Among the 621 miRNAs, 102 (16.4%) showed a differential expression between positive and negative outcome of pregnancy with miR-29c-3p as the most significantly differentially expressed miRNA. The number of extracellular vehicles was lower in SCM with positive outcomes (3.8 × 109/mL EVs), as compared to a negative outcome (7.35 × 109/mL EVs) possibly explaining the reduced number of miRNAs in the SCM associated with failed pregnancies. The analysis of the miRNome in the SCM of couples undergoing fertility treatment lays the ground towards development of biomarkers to predict successful pregnancy and towards understanding the role of embryonic miRNAs found in the SCM.
Collapse
|
20
|
Kahraman M, Laufer T, Backes C, Schrörs H, Fehlmann T, Ludwig N, Kohlhaas J, Meese E, Wehler T, Bals R, Keller A. Technical Stability and Biological Variability in MicroRNAs from Dried Blood Spots: A Lung Cancer Therapy-Monitoring Showcase. Clin Chem 2017; 63:1476-1488. [DOI: 10.1373/clinchem.2017.271619] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Accepted: 04/27/2017] [Indexed: 02/02/2023]
Abstract
Abstract
BACKGROUND
Different work flows have been proposed to use miRNAs as blood-borne biomarkers. In particular, the method used for collecting blood from patients can considerably influence the diagnostic results.
METHODS
We explored whether dried blood spots (DBSs) facilitate stable miRNA measurements and compared its technical stability with biological variability. First, we tested the stability of DBS samples by generating from 1 person 18 whole-genome-wide miRNA profiles of DBS samples that were exposed to different temperature and humidity conditions. Second, we investigated technical reproducibility by performing 7 replicates of DBS again from 1 person. Third, we investigated DBS samples from 53 patients with lung cancer undergoing different therapies. Across these 3 stages, 108 genome-wide miRNA profiles from DBS were generated and evaluated biostatistically.
RESULTS
In the stability analysis, we observed that temperature and humidity had an overall limited influence on the miRNomes (average correlation between the different conditions of 0.993). Usage of a silica gel slightly diminished DBS' technical reproducibility. The 7 technical replicates had an average correlation of 0.996. The correlation with whole-blood PAXGene miRNomes of the same individual was remarkable (correlation of 0.88). Finally, evaluation of the samples from the 53 patients with lung cancer exposed to different therapies showed that the biological variations exceeded the technical variability significantly (P < 0.0001), yielding 51 dysregulated miRNAs.
CONCLUSIONS
We present a stable work flow for profiling of whole miRNomes on the basis of samples collected from DBS. Biological variations exceeded technical variations significantly. DBS-based miRNA profiles will potentially further the translational character of miRNA biomarker studies.
Collapse
Affiliation(s)
- Mustafa Kahraman
- Clinical Bioinformatics, Saarland University, Homburg, Germany
- Hummingbird Diagnostics GmbH, Heidelberg, Germany
| | | | | | | | - Tobias Fehlmann
- Clinical Bioinformatics, Saarland University, Homburg, Germany
| | - Nicole Ludwig
- Department of Human Genetics, Saarland University, Homburg, Germany
| | | | - Eckart Meese
- Department of Human Genetics, Saarland University, Homburg, Germany
| | - Thomas Wehler
- Department of Internal Medicine V – Pulmonology, Allergology, Intensive Care Medicine, Saarland University, Homburg, Germany
| | - Robert Bals
- Department of Internal Medicine V – Pulmonology, Allergology, Intensive Care Medicine, Saarland University, Homburg, Germany
| | - Andreas Keller
- Clinical Bioinformatics, Saarland University, Homburg, Germany
| |
Collapse
|
21
|
Zheng B, Jeong S, Zhu Y, Chen L, Xia Q. miRNA and lncRNA as biomarkers in cholangiocarcinoma(CCA). Oncotarget 2017; 8:100819-100830. [PMID: 29246025 PMCID: PMC5725067 DOI: 10.18632/oncotarget.19044] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Accepted: 06/19/2017] [Indexed: 12/16/2022] Open
Abstract
The microRNAs are a group of 20 nucleotides-long non-coding RNAs. By binding to the 3'UTR region of target mRNA, microRNAs can perform extensive actions mediating gene expression at post-trancriptional stages. It makes microRNAs serve as very crucial regulators in various biological progress including carcinogenesis. Long non-coding RNAs, however, are a subgroup of RNA with the length of 200 nucleotides. Unlike microRNAs, long non-coding RNAs can form secondary of tertiary domain based on their length. With the ability of directly interacting with DNA, RNA, protein, long non-coding RNAs have promoting or inhibitive functions in gene expression regulation. Furthermore, the abnormal expression of certain long non-coding RNAs has roused people's interest in the role of long non-coding RNAs in tumorigenesis. Although the connection between microRNA/long non-coding RNA and CCA has been a hot field to researchers, the link between molecular mechanism and clinical outcome has been barely built. This review takes a retrospect at the latest researches on the link between microRNA/long non-coding RNA and cholangiocarcinoma and the potential of microRNA/long non-coding RNA serving as distinctive biomarkers for CCA in clinical practice.
Collapse
Affiliation(s)
- Bo Zheng
- International Cooperation Laboratory on Signal Transduction, Eastern Hepatobiliary Surgery Institute, Second Military Medical University, Shanghai 200438, P.R. China.,National Center for Liver Cancer, Shanghai 201805, P.R. China
| | - Seogsong Jeong
- Department of Liver Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, P.R. China
| | - Yanjing Zhu
- International Cooperation Laboratory on Signal Transduction, Eastern Hepatobiliary Surgery Institute, Second Military Medical University, Shanghai 200438, P.R. China.,National Center for Liver Cancer, Shanghai 201805, P.R. China
| | - Lei Chen
- International Cooperation Laboratory on Signal Transduction, Eastern Hepatobiliary Surgery Institute, Second Military Medical University, Shanghai 200438, P.R. China.,National Center for Liver Cancer, Shanghai 201805, P.R. China
| | - Qiang Xia
- Department of Liver Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, P.R. China
| |
Collapse
|
22
|
Alles J, Ludwig N, Rheinheimer S, Leidinger P, Grässer FA, Keller A, Meese E. MiR-148a impairs Ras/ERK signaling in B lymphocytes by targeting SOS proteins. Oncotarget 2017; 8:56417-56427. [PMID: 28915601 PMCID: PMC5593572 DOI: 10.18632/oncotarget.17662] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Accepted: 04/24/2017] [Indexed: 12/12/2022] Open
Abstract
Although microRNAs have been recognized as central cellular regulators, there is an evident lack of knowledge about their targets. Here, we analyzed potential target genes for miR-148a functioning in Ras signaling in B cells, including SOS1 and SOS2. A dual-luciferase reporter assay showed significantly decreased luciferase activity upon ectopic overexpression of miR-148a in HEK-293T cells that were co-transfected with the 3′UTR of either SOS1 or SOS2. Each of the 3′UTRs of SOS1 and SOS2 contained two binding sites for miR-148a both of which were necessary for the decreased luciferase activity. MiR-148a overexpression in HEK-293T lead to significantly reduced levels of both endogenous SOS1 and SOS2 proteins. Likewise, reduced levels of SOS proteins were found in two B cell lines that were transfected with miR-148a. The level of ERK1/2 phosphorylation as one of the most relevant downstream members of the Ras/ERK signaling pathway was also reduced in cells with miR-148a overexpression. The data show that miR-148a impairs the Ras/ERK signaling pathway via SOS1 and SOS2 proteins in B cells.
Collapse
Affiliation(s)
- Julia Alles
- Institute of Human Genetics, Saarland University, 66421 Homburg, Germany
| | - Nicole Ludwig
- Institute of Human Genetics, Saarland University, 66421 Homburg, Germany
| | | | - Petra Leidinger
- Institute of Human Genetics, Saarland University, 66421 Homburg, Germany
| | | | - Andreas Keller
- Chair for Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany
| | - Eckart Meese
- Institute of Human Genetics, Saarland University, 66421 Homburg, Germany
| |
Collapse
|
23
|
Abstract
MicroRNAs are small, noncoding, RNAs known for their powerful modulation of molecular processes, making them a major focus for studying pathological mechanisms. The human miR-146 family of microRNAs consists of two member genes, MIR146A and MIR146B These two microRNAs are located on different chromosomes and exhibit differential regulation in many cases. However, they are nearly identical in sequence, sharing a seed region, and are thus predicted to target the same set of genes. A large proportion of the microRNA (miR)-146 literature focuses on its role in regulating the innate immune response in the context of various pathologies by modulating two widely studied target genes in the toll-like receptor signaling cascade. A growing subset of the literature reports a role of miR-146 in cardiovascular and renal disease, and data suggest there is exciting potential for miR-146 as a diagnostic and therapeutic target. Nevertheless, the published literature is confounded by unclear and imprecise language concerning the specific effects of the two miR-146 family members. The present review will compare the genomic origin and regulation of miR-146a and miR-146b, discuss some approaches to overcome analytical and experimental challenges, and summarize findings in major areas of miR-146 research. Moving forward, careful evaluation of miR-146a/b specificity in analytical and experimental approaches will aid researchers in elucidating the functional relevance of differential regulation of the miR-146 family members in health and disease.
Collapse
Affiliation(s)
- Mark R Paterson
- Department of Physiology, Medical College of Wisconsin, Milwaukee, Wisconsin; and
| | - Alison J Kriegel
- Department of Physiology, Medical College of Wisconsin, Milwaukee, Wisconsin; and
- Center of Systems Molecular Medicine, Medical College of Wisconsin, Milwaukee, Wisconsin
| |
Collapse
|
24
|
Naga Prasad SV, Gupta MK, Duan ZH, Surampudi VSK, Liu CG, Kotwal A, Moravec CS, Starling RC, Perez DM, Sen S, Wu Q, Plow EF, Karnik S. A unique microRNA profile in end-stage heart failure indicates alterations in specific cardiovascular signaling networks. PLoS One 2017; 12:e0170456. [PMID: 28329018 PMCID: PMC5362047 DOI: 10.1371/journal.pone.0170456] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2016] [Accepted: 01/05/2017] [Indexed: 01/17/2023] Open
Abstract
It is well established that the gene expression patterns are substantially altered in cardiac hypertrophy and heart failure, however, less is known about the reasons behind such global differences. MicroRNAs (miRNAs) are short non-coding RNAs that can target multiple molecules to regulate wide array of proteins in diverse pathways. The goal of the study was to profile alterations in miRNA expression using end-stage human heart failure samples with an aim to build signaling network pathways using predicted targets for the altered miRNA and to determine nodal molecules regulating individual networks. Profiling of miRNAs using custom designed microarray and validation with an independent set of samples identified eight miRNAs that are altered in human heart failure including one novel miRNA yet to be implicated in cardiac pathology. To gain an unbiased perspective on global regulation by top eight altered miRNAs, functional relationship of predicted targets for these eight miRNAs were examined by network analysis. Ingenuity Pathways Analysis network algorithm was used to build global signaling networks based on the targets of altered miRNAs which allowed us to identify participating networks and nodal molecules that could contribute to cardiac pathophysiology. Majority of the nodal molecules identified in our analysis are targets of altered miRNAs and known regulators of cardiovascular signaling. Cardio-genomics heart failure gene expression public data base was used to analyze trends in expression pattern for target nodal molecules and indeed changes in expression of nodal molecules inversely correlated to miRNA alterations. We have used NF kappa B network as an example to show that targeting other molecules in the network could alter the nodal NF kappa B despite not being a miRNA target suggesting an integrated network response. Thus, using network analysis we show that altering key functional target proteins may regulate expression of the myriad signaling pathways underlying the cardiac pathology.
Collapse
Affiliation(s)
- Sathyamangla V. Naga Prasad
- Department of Molecular Cardiology, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, United States of America
| | - Manveen K. Gupta
- Department of Molecular Cardiology, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, United States of America
| | - Zhong-Hui Duan
- Department of Computer Sciences, University of Akron, Akron, Ohio, United States of America
| | - Venkata Suresh K. Surampudi
- Department of Molecular Cardiology, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, United States of America
| | - Chang-Gong Liu
- Department of Molecular Virology, Immunology and Medical Genetics and Comprehensive Cancer Center, Ohio State University, Columbus, Ohio, United States of America
| | - Ashwin Kotwal
- Department of Molecular Cardiology, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, United States of America
| | - Christine S. Moravec
- Department of Cardiovascular Medicine, Heart and Vascular Research Institute, Cleveland Clinic, Cleveland, Ohio, United States of America
| | - Randall C. Starling
- Department of Cardiovascular Medicine, Heart and Vascular Research Institute, Cleveland Clinic, Cleveland, Ohio, United States of America
| | - Dianne M. Perez
- Department of Molecular Cardiology, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, United States of America
| | - Subha Sen
- Department of Molecular Cardiology, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, United States of America
| | - Qingyu Wu
- Department of Molecular Cardiology, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, United States of America
| | - Edward F. Plow
- Department of Molecular Cardiology, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, United States of America
| | - Sadashiva Karnik
- Department of Molecular Cardiology, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, United States of America
| |
Collapse
|
25
|
Temporal changes of microRNA gga-let-7b and gga-let-7i expression in chickens challenged with subgroup J avian leukosis virus. Vet Res Commun 2017; 41:219-226. [PMID: 28190219 DOI: 10.1007/s11259-017-9681-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2016] [Accepted: 02/08/2017] [Indexed: 12/20/2022]
Abstract
Two important microRNAs, gga-let-7b and gga-let-7i were examined for the relative expression in liver and bone marrow tissues from specific pathogen free chickens that were challenged either with GD1109 or NX0101 strain of subgroup J avian leukosis virus (ALV-J). The GD1109 strain of ALV-J reportedly causes hemangioma (HE) and NX0101 reportedly causes myeloma (ML) in susceptible chickens. Temporal changes of both gga-let-7b and gga-let-7i expression in ALV-J infected chickens were observed in contrast to its counterpart of a non-infected negative control group of chickens (P < 0.05 or P < 0.01) during the first 120 days post infection. Use of the web-based computational DIANA-mirPath software (available at http://microrna.gr/mirpath ), it was predicted that both gga-let-7b and gga-let-7i were involved in multiple pathways including signaling pathways, such as MAPK, TGF-beta, Notch, Wnt, mTOR, Cell cycle, P53 and Jak-STAT. Combining our experimental data with reports on the microRNAs, we suggest that both gga-let-7i and gga-let-7b may also act as tumor suppressors in chicken, especially play a critical role in tumorigenesis induced by ALV-J.
Collapse
|
26
|
DIAZ DIANA, DONATO MICHELE, NGUYEN TIN, DRAGHICI SORIN. MICRORNA-AUGMENTED PATHWAYS (mirAP) AND THEIR APPLICATIONS TO PATHWAY ANALYSIS AND DISEASE SUBTYPING. PACIFIC SYMPOSIUM ON BIOCOMPUTING. PACIFIC SYMPOSIUM ON BIOCOMPUTING 2017; 22:390-401. [PMID: 27896992 PMCID: PMC5147738 DOI: 10.1142/9789813207813_0037] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
MicroRNAs play important roles in the development of many complex diseases. Because of their importance, the analysis of signaling pathways including miRNA interactions holds the potential for unveiling the mechanisms underlying such diseases. However, current signaling pathway databases are limited to interactions between genes and ignore miRNAs. Here, we use the information on miRNA targets to build a database of miRNA-augmented pathways (mirAP), and we show its application in the contexts of integrative pathway analysis and disease subtyping. Our miRNA-mRNA integrative pathway analysis pipeline incorporates a topology-aware approach that we previously implemented. Our integrative disease subtyping pipeline takes into account survival data, gene and miRNA expression, and knowledge of the interactions among genes. We demonstrate the advantages of our approach by analyzing nine sample-matched datasets that provide both miRNA and mRNA expression. We show that integrating miRNAs into pathway analysis results in greater statistical power, and provides a more comprehensive view of the underlying phenomena. We also compare our disease subtyping method with the state-of-the-art integrative analysis by analyzing a colorectal cancer database from TCGA. The colorectal cancer subtypes identified by our approach are significantly different in terms of their survival expectation. These miRNA-augmented pathways offer a more comprehensive view and a deeper understanding of biological pathways. A better understanding of the molecular processes associated with patients' survival can help to a better prognosis and an appropriate treatment for each subtype.
Collapse
Affiliation(s)
- DIANA DIAZ
- Department of Computer Science, Wayne State University, Detroit, MI 48202, U.S.A
| | - MICHELE DONATO
- Institute for Immunity, Transplantation and Infection, Stanford University Medical Center, Stanford, CA 94305, U.S.A
| | - TIN NGUYEN
- Department of Computer Science, Wayne State University, Detroit, MI 48202, U.S.A
| | - SORIN DRAGHICI
- Department of Computer Science, Wayne State University, Detroit, MI 48202, U.S.A
- Department of Obstetrics and Gynecology, Wayne State University, Detroit, MI 48202, U.S.A
| |
Collapse
|
27
|
Ma Z, Liu T, Huang W, Liu H, Zhang HM, Li Q, Chen Z, Guo AY. MicroRNA regulatory pathway analysis identifies miR-142-5p as a negative regulator of TGF-β pathway via targeting SMAD3. Oncotarget 2016; 7:71504-71513. [PMID: 27683030 PMCID: PMC5342096 DOI: 10.18632/oncotarget.12229] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Accepted: 09/12/2016] [Indexed: 02/06/2023] Open
Abstract
MicroRNAs (miRNAs) are non-coding RNAs with functions of posttranscriptional regulation. The abnormally expressed miRNAs have been shown to be crucial contributors and may serve as biomarkers in many diseases. However, determining the biological function of miRNAs is an ongoing challenge. By combining miRNA targets prediction, miRNA and mRNA expression profiles in TCGA cancers, and pathway data, we performed a miRNA-pathway regulation inference by Fisher's exact test for enrichment analysis. Then we constructed a database to show the cancer related miRNA-pathway regulatory network (http://bioinfo.life.hust.edu.cn/miR_path). As one of the miRNAs targeting many cancer related pathways, miR-142-5p potentially regulates the maximum number of genes in TGF-β signaling pathway. We experimentally confirmed that miR-142-5p directly targeted and suppressed SMAD3, a key component in TGF-β signaling. Ectopic overexpression of miR-142-5p significantly promoted tumor cell proliferation and inhibited apoptosis, while silencing of miR-142-5p inhibited the tumor cell proliferation and promoted apoptosis in vitro. These findings indicate that miR-142-5p plays as a negative regulator in TGF-β pathway by targeting SMAD3 and suppresses TGF-β-induced growth inhibition in cancer cells. Our study proved the feasibility of miRNA regulatory pathway analysis and shed light on combining bioinformatics with experiments in the research of complex diseases.
Collapse
Affiliation(s)
- Zhaowu Ma
- Hubei Bioinformatics and Molecular Imaging Key Laboratory, Department of Bioinformatics and Systems Biology, Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China.,Laboratory of Neuronal Network and Brain Diseases Modulation, School of Medicine, Yangtze University, Jingzhou, Hubei, 434023, China
| | - Teng Liu
- Hubei Bioinformatics and Molecular Imaging Key Laboratory, Department of Bioinformatics and Systems Biology, Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Wei Huang
- Hubei Bioinformatics and Molecular Imaging Key Laboratory, Department of Bioinformatics and Systems Biology, Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Hui Liu
- Hubei Bioinformatics and Molecular Imaging Key Laboratory, Department of Bioinformatics and Systems Biology, Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Hong-Mei Zhang
- Hubei Bioinformatics and Molecular Imaging Key Laboratory, Department of Bioinformatics and Systems Biology, Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Qiubai Li
- Institute of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Zhichao Chen
- Institute of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - An-Yuan Guo
- Hubei Bioinformatics and Molecular Imaging Key Laboratory, Department of Bioinformatics and Systems Biology, Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
| |
Collapse
|
28
|
Backes C, Kehl T, Stöckel D, Fehlmann T, Schneider L, Meese E, Lenhof HP, Keller A. miRPathDB: a new dictionary on microRNAs and target pathways. Nucleic Acids Res 2016; 45:D90-D96. [PMID: 27742822 PMCID: PMC5210630 DOI: 10.1093/nar/gkw926] [Citation(s) in RCA: 91] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Accepted: 10/10/2016] [Indexed: 12/22/2022] Open
Abstract
In the last decade, miRNAs and their regulatory mechanisms have been intensively studied and many tools for the analysis of miRNAs and their targets have been developed. We previously presented a dictionary on single miRNAs and their putative target pathways. Since then, the number of miRNAs has tripled and the knowledge on miRNAs and targets has grown substantially. This, along with changes in pathway resources such as KEGG, leads to an improved understanding of miRNAs, their target genes and related pathways. Here, we introduce the miRNA Pathway Dictionary Database (miRPathDB), freely accessible at https://mpd.bioinf.uni-sb.de/. With the database we aim to complement available target pathway web-servers by providing researchers easy access to the information which pathways are regulated by a miRNA, which miRNAs target a pathway and how specific these regulations are. The database contains a large number of miRNAs (2595 human miRNAs), different miRNA target sets (14 773 experimentally validated target genes as well as 19 281 predicted targets genes) and a broad selection of functional biochemical categories (KEGG-, WikiPathways-, BioCarta-, SMPDB-, PID-, Reactome pathways, functional categories from gene ontology (GO), protein families from Pfam and chromosomal locations totaling 12 875 categories). In addition to Homo sapiens, also Mus musculus data are stored and can be compared to human target pathways.
Collapse
Affiliation(s)
- Christina Backes
- Chair for Clinical Bioinformatics, Saarland Informatics Campus, Saarland University, D-66123 Saarbruecken, Germany
| | - Tim Kehl
- Chair for Bioinformatics, Saarland Informatics Campus, Saarland University, D-66123 Saarbruecken, Germany
| | - Daniel Stöckel
- Chair for Bioinformatics, Saarland Informatics Campus, Saarland University, D-66123 Saarbruecken, Germany
| | - Tobias Fehlmann
- Chair for Clinical Bioinformatics, Saarland Informatics Campus, Saarland University, D-66123 Saarbruecken, Germany
| | - Lara Schneider
- Chair for Bioinformatics, Saarland Informatics Campus, Saarland University, D-66123 Saarbruecken, Germany
| | - Eckart Meese
- Human Genetics, Saarland University, D-66421 Homburg, Germany
| | - Hans-Peter Lenhof
- Chair for Bioinformatics, Saarland Informatics Campus, Saarland University, D-66123 Saarbruecken, Germany
| | - Andreas Keller
- Chair for Clinical Bioinformatics, Saarland Informatics Campus, Saarland University, D-66123 Saarbruecken, Germany
| |
Collapse
|
29
|
Cossellu G, Motta V, Dioni L, Angelici L, Vigna L, Farronato G, Pesatori AC, Bollati V. Titanium and Zirconium Levels Are Associated with Changes in MicroRNAs Expression: Results from a Human Cross-Sectional Study on Obese Population. PLoS One 2016; 11:e0161916. [PMID: 27611787 PMCID: PMC5017677 DOI: 10.1371/journal.pone.0161916] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Accepted: 08/15/2016] [Indexed: 11/21/2022] Open
Abstract
Objectives In this study on 90 individuals we aimed at evaluating the microRNAs (miRNAs) expression profile associated with personal levels of Titanium (Ti) and Zirconium (Zr) traced in hair samples. Ti and Zr materials are broadly used for dental implants but the biological reactions triggered by a long term presence of these materials in the oral cavity still need to be assessed. MiRNAs are mechanisms that need to be investigated as they play a fundamental role in the control of gene expression following external stimuli and contribute to a wide range of pathophysiological processes. Methods Using the TaqMan® Low-Density Array, we assessed the expression levels of 377 human miRNAs in peripheral blood of 90 subjects. Hair samples were analyzed for Ti and Zr content using Inductively Coupled Plasma-Mass Spectrometry. We performed multivariable regression analysis to investigate the effects of Ti and Zr exposure on miRNA expression levels. We used the Ingenuity Pathway Analysis (IPA) software to explore the functional role of the investigated miRNAs and the related target genes. Results Seven miRNAs (miR-99b, miR-142-5p, miR-152, miR-193a-5p, miR-323-3p, miR-335, miR-494) resulted specifically associated with Zr levels. The functional target analysis showed that miRNAs are involved in mechanisms such as inflammation, skeletal and connective tissue disorders. Conclusions Our data suggest that Zr is more bioactive than Ti and show that miRNAs are relevant molecular mechanisms sensitive to Zr exposure.
Collapse
Affiliation(s)
- Gianguido Cossellu
- Department of Biomedical, Surgical and Dental Sciences, Fondazione IRCCS Cà Granda, Ospedale Maggiore Policlinico, Università degli Studi di Milano, Via della Commenda 10, 20122, Milan, Italy
- * E-mail:
| | - Valeria Motta
- EPIGET - Epidemiology, Epigenetics and Toxicology Lab, Department of Clinical Sciences and Community Health, Università degli Studi di Milano, Milan, Italy
| | - Laura Dioni
- EPIGET - Epidemiology, Epigenetics and Toxicology Lab, Department of Clinical Sciences and Community Health, Università degli Studi di Milano, Milan, Italy
| | - Laura Angelici
- EPIGET - Epidemiology, Epigenetics and Toxicology Lab, Department of Clinical Sciences and Community Health, Università degli Studi di Milano, Milan, Italy
| | - Luisella Vigna
- Worker’s Health Protection and Promotion Unit, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Giampietro Farronato
- Department of Biomedical, Surgical and Dental Sciences, Fondazione IRCCS Cà Granda, Ospedale Maggiore Policlinico, Università degli Studi di Milano, Via della Commenda 10, 20122, Milan, Italy
| | - Angela Cecilia Pesatori
- EPIGET - Epidemiology, Epigenetics and Toxicology Lab, Department of Clinical Sciences and Community Health, Università degli Studi di Milano, Milan, Italy
- Worker’s Health Protection and Promotion Unit, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Milan, Italy
- Epidemiology Unit, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Valentina Bollati
- EPIGET - Epidemiology, Epigenetics and Toxicology Lab, Department of Clinical Sciences and Community Health, Università degli Studi di Milano, Milan, Italy
| |
Collapse
|
30
|
Sigloch FC, Burk UC, Biniossek ML, Brabletz T, Schilling O. miR-200c dampens cancer cell migration via regulation of protein kinase A subunits. Oncotarget 2016. [PMID: 26203557 PMCID: PMC4695158 DOI: 10.18632/oncotarget.4381] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Expression of miR-200c is a molecular switch to determine cellular fate towards a mesenchymal or epithelial phenotype. miR-200c suppresses the early steps of tumor progression by preventing epithelial-mesenchymal transition (EMT) and intravasation of tumor cells. Unraveling the underlying molecular mechanisms might pinpoint to novel therapeutic options. To better understand these mechanisms it is crucial to identify targets of miR-200c. Here, we employ a combination of quantitative proteomic and bioinformatic strategies to identify novel miR-200c targets. We identify and confirm two subunits of the central cellular kinase protein kinase A (PKA), namely PRKAR1A and PRKACB, to be directly regulated by miR-200c. Notably, siRNA-mediated downregulation of both proteins phenocopies the migratory behavior of breast cancer cells after miR-200c overexpression. Patient data from publicly accessible databases supports a miR-200c-PKA axis. Thus, our study identifies the PKA heteroprotein as an important mediator of miR-200c induced repression of migration in breast cancer cells. By bioinformatics, we define a miRNA target cluster consisting of PRKAR1A, PRKAR2B, PRKACB, and COF2, which is targeted by a group of 14 miRNAs.
Collapse
Affiliation(s)
- Florian Christoph Sigloch
- Institute of Molecular Medicine and Cell Research, Albert-Ludwigs-University Freiburg, Freiburg, Germany.,Faculty of Biology, Albert-Ludwigs-University Freiburg, Freiburg, Germany
| | - Ulrike Christina Burk
- Institute of Molecular Medicine and Cell Research, Albert-Ludwigs-University Freiburg, Freiburg, Germany.,BIOSS Centre for Biological Signaling Studies, University of Freiburg, Freiburg, Germany
| | - Martin Lothar Biniossek
- Institute of Molecular Medicine and Cell Research, Albert-Ludwigs-University Freiburg, Freiburg, Germany
| | - Thomas Brabletz
- Experimental Medicine I, Nikolaus-Fiebiger-Center for Molecular Medicine, University Erlangen-Nürnberg, Erlangen, Germany
| | - Oliver Schilling
- Institute of Molecular Medicine and Cell Research, Albert-Ludwigs-University Freiburg, Freiburg, Germany.,BIOSS Centre for Biological Signaling Studies, University of Freiburg, Freiburg, Germany.,German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Heidelberg, Germany
| |
Collapse
|
31
|
Nguyen T, Diaz D, Tagett R, Draghici S. Overcoming the matched-sample bottleneck: an orthogonal approach to integrate omic data. Sci Rep 2016; 6:29251. [PMID: 27403564 PMCID: PMC4941544 DOI: 10.1038/srep29251] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Accepted: 06/14/2016] [Indexed: 01/22/2023] Open
Abstract
MicroRNAs (miRNAs) are small non-coding RNA molecules whose primary function is to regulate the expression of gene products via hybridization to mRNA transcripts, resulting in suppression of translation or mRNA degradation. Although miRNAs have been implicated in complex diseases, including cancer, their impact on distinct biological pathways and phenotypes is largely unknown. Current integration approaches require sample-matched miRNA/mRNA datasets, resulting in limited applicability in practice. Since these approaches cannot integrate heterogeneous information available across independent experiments, they neither account for bias inherent in individual studies, nor do they benefit from increased sample size. Here we present a novel framework able to integrate miRNA and mRNA data (vertical data integration) available in independent studies (horizontal meta-analysis) allowing for a comprehensive analysis of the given phenotypes. To demonstrate the utility of our method, we conducted a meta-analysis of pancreatic and colorectal cancer, using 1,471 samples from 15 mRNA and 14 miRNA expression datasets. Our two-dimensional data integration approach greatly increases the power of statistical analysis and correctly identifies pathways known to be implicated in the phenotypes. The proposed framework is sufficiently general to integrate other types of data obtained from high-throughput assays.
Collapse
Affiliation(s)
- Tin Nguyen
- Wayne State University, Department of Computer Science, Detroit, 48202, Michigan, USA
| | - Diana Diaz
- Wayne State University, Department of Computer Science, Detroit, 48202, Michigan, USA
| | - Rebecca Tagett
- Wayne State University, Department of Computer Science, Detroit, 48202, Michigan, USA
| | - Sorin Draghici
- Wayne State University, Department of Computer Science, Detroit, 48202, Michigan, USA.,Wayne State University, Department of Obstetrics and Gynecology, Detroit, 48202, Michigan, USA
| |
Collapse
|
32
|
Gururajan A, Clarke G, Dinan TG, Cryan JF. Molecular biomarkers of depression. Neurosci Biobehav Rev 2016; 64:101-33. [DOI: 10.1016/j.neubiorev.2016.02.011] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2015] [Revised: 01/11/2016] [Accepted: 02/12/2016] [Indexed: 12/22/2022]
|
33
|
Parafioriti A, Bason C, Armiraglio E, Calciano L, Daolio PA, Berardocco M, Di Bernardo A, Colosimo A, Luksch R, Berardi AC. Ewing's Sarcoma: An Analysis of miRNA Expression Profiles and Target Genes in Paraffin-Embedded Primary Tumor Tissue. Int J Mol Sci 2016; 17:ijms17050656. [PMID: 27144561 PMCID: PMC4881482 DOI: 10.3390/ijms17050656] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2016] [Revised: 04/15/2016] [Accepted: 04/25/2016] [Indexed: 12/19/2022] Open
Abstract
The molecular mechanism responsible for Ewing’s Sarcoma (ES) remains largely unknown. MicroRNAs (miRNAs), a class of small non-coding RNAs able to regulate gene expression, are deregulated in tumors and may serve as a tool for diagnosis and prediction. However, the status of miRNAs in ES has not yet been thoroughly investigated. This study compared global miRNAs expression in paraffin-embedded tumor tissue samples from 20 ES patients, affected by primary untreated tumors, with miRNAs expressed in normal human mesenchymal stromal cells (MSCs) by microarray analysis. A miRTarBase database was used to identify the predicted target genes for differentially expressed miRNAs. The miRNAs microarray analysis revealed distinct patterns of miRNAs expression between ES samples and normal MSCs. 58 of the 954 analyzed miRNAs were significantly differentially expressed in ES samples compared to MSCs. Moreover, the qRT-PCR analysis carried out on three selected miRNAs showed that miR-181b, miR-1915 and miR-1275 were significantly aberrantly regulated, confirming the microarray results. Bio-database analysis identified BCL-2 as a bona fide target gene of the miR-21, miR-181a, miR-181b, miR-29a, miR-29b, miR-497, miR-195, miR-let-7a, miR-34a and miR-1915. Using paraffin-embedded tissues from ES patients, this study has identified several potential target miRNAs and one gene that might be considered a novel critical biomarker for ES pathogenesis.
Collapse
Affiliation(s)
- Antonina Parafioriti
- Unità Operativa Complessa (U.O.C.) Azienda Socio Sanitaria Territoriale Centro Specialistico Ortopedico Traumatologico Gaetano Pini-CTO, Milano 20122, Italy.
| | - Caterina Bason
- Dipartimento di Medicina, Sezione di Medicina Interna B, Università di Verona, Verona 37134, Italy.
| | - Elisabetta Armiraglio
- Unità Operativa Complessa (U.O.C.) Azienda Socio Sanitaria Territoriale Centro Specialistico Ortopedico Traumatologico Gaetano Pini-CTO, Milano 20122, Italy.
| | - Lucia Calciano
- Dipartimento di Sanità Pubblica e Medicina di Comunità, Sezione di Epidemiologia e Statistica Medica, Università di Verona, Verona 37134, Italy.
| | - Primo Andrea Daolio
- Unità Operativa Complessa (U.O.C.) Chirurgia Ortopedica Oncologica, Azienda Socio Sanitaria Territoriale Centro Specialistico Ortopedico Traumatologico Gaetano Pini-CTO, Milano 20122, Italy.
| | - Martina Berardocco
- Unità Operativa Complessa (U.O.C.) Immunoematologia-Medicina Trasfusionale e Laboratorio di Ematologia, Laboratorio di Ricerca "Cellule Staminali" Azienda Unità Sanitaria Locale (AUSL)-Ospedale Santo Spirito, Pescara 65125, Italy.
| | - Andrea Di Bernardo
- Unità Operativa Complessa (U.O.C.) Azienda Socio Sanitaria Territoriale Centro Specialistico Ortopedico Traumatologico Gaetano Pini-CTO, Milano 20122, Italy.
| | - Alessia Colosimo
- Facoltà di Medicina Veterinaria, Università di Teramo, Teramo 64100, Italy.
| | - Roberto Luksch
- Dipartimento di Oncologia Pediatrica, Fondazione-Istituto di Ricovero e Cura a Carattere Scientifico-(IRCCS) Istituto Nazionale dei Tumori, Milano 20133, Italy.
| | - Anna C Berardi
- Unità Operativa Complessa (U.O.C.) Azienda Socio Sanitaria Territoriale Centro Specialistico Ortopedico Traumatologico Gaetano Pini-CTO, Milano 20122, Italy.
- Unità Operativa Complessa (U.O.C.) Immunoematologia-Medicina Trasfusionale e Laboratorio di Ematologia, Laboratorio di Ricerca "Cellule Staminali" Azienda Unità Sanitaria Locale (AUSL)-Ospedale Santo Spirito, Pescara 65125, Italy.
| |
Collapse
|
34
|
MiRTargetLink--miRNAs, Genes and Interaction Networks. Int J Mol Sci 2016; 17:564. [PMID: 27089332 PMCID: PMC4849020 DOI: 10.3390/ijms17040564] [Citation(s) in RCA: 88] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2016] [Revised: 04/06/2016] [Accepted: 04/07/2016] [Indexed: 01/22/2023] Open
Abstract
Information on miRNA targeting genes is growing rapidly. For high-throughput experiments, but also for targeted analyses of few genes or miRNAs, easy analysis with concise representation of results facilitates the work of life scientists. We developed miRTargetLink, a tool for automating respective analysis procedures that are frequently applied. Input of the web-based solution is either a single gene or single miRNA, but also sets of genes or miRNAs, can be entered. Validated and predicted targets are extracted from databases and an interaction network is presented. Users can select whether predicted targets, experimentally validated targets with strong or weak evidence, or combinations of those are considered. Central genes or miRNAs are highlighted and users can navigate through the network interactively. To discover the most relevant biochemical processes influenced by the target network, gene set analysis and miRNA set analysis are integrated. As a showcase for miRTargetLink, we analyze targets of five cardiac miRNAs. miRTargetLink is freely available without restrictions at www.ccb.uni-saarland.de/mirtargetlink.
Collapse
|
35
|
Quah S, Holland PWH. The Hox cluster microRNA miR-615: a case study of intronic microRNA evolution. EvoDevo 2015; 6:31. [PMID: 26451238 PMCID: PMC4597612 DOI: 10.1186/s13227-015-0027-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Accepted: 09/25/2015] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Introns represent a potentially rich source of existing transcription for the evolution of novel microRNAs (miRNAs). Within the Hox gene clusters, a miRNA gene, miR-615, is located within the intron of the Hoxc5 gene. This miRNA has a restricted phylogenetic distribution, providing an opportunity to examine the origin and evolution of a new miRNA within the intron of a developmentally-important homeobox gene. RESULTS Alignment and structural analyses show that the sequence is highly conserved across eutherian mammals and absent in non-mammalian tetrapods. Marsupials possess a similar sequence which we predict will not be efficiently processed as a miRNA. Our analyses suggest that transcription of HOXC5 in humans is accompanied by expression of miR-615 in all cases, but that the miRNA can also be transcribed independently of its host gene through the use of an intragenic promoter. We present scenarios for the evolution of miR-615 through intronic exaptation, and speculate on the acquisition of independent transcriptional regulation. Target prediction and transcriptomic analyses suggest that the dominant product of miR-615 is involved in the regulation of growth and a range of developmental processes. CONCLUSIONS The miR-615 gene evolved within the intron of Hoxc5 in the ancestor of placental mammals. Using miR-615 as a case study, we propose a model by which a functional miRNA can emerge within an intron gradually, by selection on secondary structure followed by evolution of an independent miRNA promoter. The location within a Hox gene intron is of particular interest as the miRNA is specific to placental mammals, is co-expressed with its host gene and may share complementary functions.
Collapse
Affiliation(s)
- Shan Quah
- Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3PS UK
| | - Peter W. H. Holland
- Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3PS UK
| |
Collapse
|
36
|
Lui PY, Jin DY, Stevenson NJ. MicroRNA: master controllers of intracellular signaling pathways. Cell Mol Life Sci 2015; 72:3531-42. [PMID: 26059472 PMCID: PMC11113591 DOI: 10.1007/s00018-015-1940-0] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2015] [Revised: 05/05/2015] [Accepted: 05/26/2015] [Indexed: 12/20/2022]
Abstract
Signaling pathways are essential intracellular networks that coordinate molecular outcomes to external stimuli. Tight regulation of these pathways is essential to ensure an appropriate response. MicroRNA (miRNA) is a class of small, non-coding RNA that regulates gene expression at a post-transcriptional level by binding to the complementary sequence on target mRNA, thus limiting protein translation. Intracellular pathways are controlled by protein regulators, such as suppressor of cytokine signaling and A20. Until recently, expression of these classical protein regulators was thought to be controlled solely by transcriptional induction and proteasomal degradation; however, there is a growing body of evidence describing their regulation by miRNA. This new information has transformed our understanding of cell signaling by adding a previously unknown layer of regulatory control. This review outlines the miRNA regulation of these classical protein regulators and describes their broad effects at both cellular and disease levels. We review the regulation of three important signaling pathways, including the JAK/STAT, NF-κB, and TGF-β pathways, and summarize an extensive catalog of their regulating miRNAs. This information highlights the importance of the miRNA regulon and reveals a previously unknown regulatory landscape that must be included in the identification and development of novel therapeutic targets for clinical disorders.
Collapse
Affiliation(s)
- Pak-Yin Lui
- Department of Biochemistry, The University of Hong Kong, Pokfulam, Hong Kong
| | - Dong-Yan Jin
- Department of Biochemistry, The University of Hong Kong, Pokfulam, Hong Kong
| | - Nigel J. Stevenson
- School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin, Ireland
| |
Collapse
|
37
|
Zafari S, Backes C, Leidinger P, Meese E, Keller A. Regulatory microRNA networks: complex patterns of target pathways for disease-related and housekeeping microRNAs. GENOMICS PROTEOMICS & BIOINFORMATICS 2015; 13:159-68. [PMID: 26169798 PMCID: PMC4563351 DOI: 10.1016/j.gpb.2015.02.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/28/2015] [Revised: 02/27/2015] [Accepted: 02/27/2015] [Indexed: 11/16/2022]
Abstract
Blood-based microRNA (miRNA) signatures as biomarkers have been reported for various pathologies, including cancer, neurological disorders, cardiovascular diseases, and also infections. The regulatory mechanism behind respective miRNA patterns is only partially understood. Moreover, “preserved” miRNAs, i.e., miRNAs that are not dysregulated in any disease, and their biological impact have been explored to a very limited extent. We set out to systematically determine their role in regulatory networks by defining groups of highly-dysregulated miRNAs that contribute to a disease signature as opposed to preserved housekeeping miRNAs. We further determined preferential targets and pathways of both dysregulated and preserved miRNAs by computing multi-layer networks, which were compared between housekeeping and dysregulated miRNAs. Of 848 miRNAs examined across 1049 blood samples, 8 potential housekeepers showed very limited expression variations, while 20 miRNAs showed highly-dysregulated expression throughout the investigated blood samples. Our approach provides important insights into miRNAs and their role in regulatory networks. The methodology can be applied to systematically investigate the differences in target genes and pathways of arbitrary miRNA sets.
Collapse
Affiliation(s)
- Sachli Zafari
- Chair for Clinical Bioinformatics, Saarland University, University Hospital, Saarbrücken 66123, Germany
| | - Christina Backes
- Chair for Clinical Bioinformatics, Saarland University, University Hospital, Saarbrücken 66123, Germany
| | - Petra Leidinger
- Department of Human Genetics, Saarland University, University Hospital, Homburg 66421, Germany
| | - Eckart Meese
- Department of Human Genetics, Saarland University, University Hospital, Homburg 66421, Germany
| | - Andreas Keller
- Chair for Clinical Bioinformatics, Saarland University, University Hospital, Saarbrücken 66123, Germany.
| |
Collapse
|
38
|
Keller A, Leidinger P, Vogel B, Backes C, ElSharawy A, Galata V, Mueller SC, Marquart S, Schrauder MG, Strick R, Bauer A, Wischhusen J, Beier M, Kohlhaas J, Katus HA, Hoheisel J, Franke A, Meder B, Meese E. miRNAs can be generally associated with human pathologies as exemplified for miR-144. BMC Med 2014; 12:224. [PMID: 25465851 PMCID: PMC4268797 DOI: 10.1186/s12916-014-0224-0] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/09/2014] [Accepted: 11/04/2014] [Indexed: 01/28/2023] Open
Abstract
BACKGROUND miRNA profiles are promising biomarker candidates for a manifold of human pathologies, opening new avenues for diagnosis and prognosis. Beyond studies that describe miRNAs frequently as markers for specific traits, we asked whether a general pattern for miRNAs across many diseases exists. METHODS We evaluated genome-wide circulating profiles of 1,049 patients suffering from 19 different cancer and non-cancer diseases as well as unaffected controls. The results were validated on 319 individuals using qRT-PCR. RESULTS We discovered 34 miRNAs with strong disease association. Among those, we found substantially decreased levels of hsa-miR-144* and hsa-miR-20b with AUC of 0.751 (95% CI: 0.703-0.799), respectively. We also discovered a set of miRNAs, including hsa-miR-155*, as rather stable markers, offering reasonable control miRNAs for future studies. The strong downregulation of hsa-miR-144* and the less variable pattern of hsa-miR-155* has been validated in a cohort of 319 samples in three different centers. Here, breast cancer as an additional disease phenotype not included in the screening phase has been included as the 20th trait. CONCLUSIONS Our study on 1,368 patients including 1,049 genome-wide miRNA profiles and 319 qRT-PCR validations further underscores the high potential of specific blood-borne miRNA patterns as molecular biomarkers. Importantly, we highlight 34 miRNAs that are generally dysregulated in human pathologies. Although these markers are not specific to certain diseases they may add to the diagnosis in combination with other markers, building a specific signature. Besides these dysregulated miRNAs, we propose a set of constant miRNAs that may be used as control markers.
Collapse
Affiliation(s)
- Andreas Keller
- Chair for Clinical Bioinformatics, Saarland University, Saarbrücken, Germany.
| | - Petra Leidinger
- Institute of Human Genetics, Saarland University, Homburg, Germany.
| | - Britta Vogel
- Department of Internal Medicine III, University of Heidelberg, Heidelberg, Germany.
| | - Christina Backes
- Chair for Clinical Bioinformatics, Saarland University, Saarbrücken, Germany.
| | - Abdou ElSharawy
- Institute of Clinical Molecular Biology, Christian-Albrechts-University Kiel, Kiel, Germany.
| | - Valentina Galata
- Chair for Clinical Bioinformatics, Saarland University, Saarbrücken, Germany.
| | - Sabine C Mueller
- Chair for Clinical Bioinformatics, Saarland University, Saarbrücken, Germany.
| | - Sabine Marquart
- Department of Internal Medicine III, University of Heidelberg, Heidelberg, Germany.
| | - Michael G Schrauder
- Department of Gynecology and Obstetrics, University Breast Center Franconia, University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nuremberg, Erlangen, Germany.
| | - Reiner Strick
- Department of Gynecology and Obstetrics, University Breast Center Franconia, University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nuremberg, Erlangen, Germany.
| | - Andrea Bauer
- German Cancer Research Center, Heidelberg, Germany.
| | | | - Markus Beier
- Comprehensive Biomarker Center, Heidelberg, Germany.
| | | | - Hugo A Katus
- Department of Internal Medicine III, University of Heidelberg, Heidelberg, Germany.
- German Center for Cardiovascular Research - DZHK, Germany, Heidelberg.
| | | | - Andre Franke
- Institute of Clinical Molecular Biology, Christian-Albrechts-University Kiel, Kiel, Germany.
| | - Benjamin Meder
- Department of Internal Medicine III, University of Heidelberg, Heidelberg, Germany.
- German Center for Cardiovascular Research - DZHK, Germany, Heidelberg.
| | - Eckart Meese
- Institute of Human Genetics, Saarland University, Homburg, Germany.
| |
Collapse
|
39
|
Targeted delivery of miRNA therapeutics for cardiovascular diseases: opportunities and challenges. Clin Sci (Lond) 2014; 127:351-65. [PMID: 24895056 DOI: 10.1042/cs20140005] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Dysregulation of miRNA expression has been associated with many cardiovascular diseases in animal models, as well as in patients. In the present review, we summarize recent findings on the role of miRNAs in cardiovascular diseases and discuss the opportunities, possibilities and challenges of using miRNAs as future therapeutic targets. Furthermore, we focus on the different approaches that can be used to deliver these newly developed miRNA therapeutics to their sites of action. Since siRNAs are structurally homologous with the miRNA therapeutics, important lessons learned from siRNA delivery strategies are discussed that might be applicable to targeted delivery of miRNA therapeutics, thereby reducing costs and potential side effects, and improving efficacy.
Collapse
|
40
|
Friedman Y, Karsenty S, Linial M. miRror-Suite: decoding coordinated regulation by microRNAs. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2014; 2014:bau043. [PMID: 24907353 PMCID: PMC4051442 DOI: 10.1093/database/bau043] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
MicroRNAs (miRNAs) are short, non-coding RNAs that negatively regulate post-transcriptional mRNA levels. Recent data from cross-linking and immunoprecipitation technologies confirmed the combinatorial nature of the miRNA regulation. We present the miRror-Suite platform, developed to yield a robust and concise explanation for miRNA regulation from a large collection of differentially expressed transcripts and miRNAs. The miRror-Suite platform includes the miRror2.0 and Probability Supported Iterative miRror (PSI-miRror) tools. Researchers who performed large-scale transcriptomics or miRNA profiling experiments from cells and tissues will benefit from miRror-Suite. Our platform provides a concise, plausible explanation for the regulation of miRNAs in such complex settings. The input for miRror2.0 may include hundreds of differentially expressed genes or miRNAs. In the case of miRNAs as input, the algorithm seeks the statistically most likely set of genes regulated by this input. Alternatively, for a set of genes, the miRror algorithm seeks a collection of miRNAs that best explains their regulation. The miRror-Suite algorithm designates statistical criteria that were uniformly applied to a dozen miRNA-target prediction databases. Users select the preferred databases for predictions and numerous optional filters/parameters that restrict the search to the desired tissues, cell lines, level of expression and predictor scores. PSI-miRror is an advanced application for refining the input set by gradually enhancing the degree of pairing of the sets of miRNAs with the sets of targets. The iterations of PSI-miRror probe the interlinked nature of miRNAs and targets within cells. miRror-Suite serves experimentalists in facilitating the understanding of miRNA regulation through combinatorial– cooperative activity. The platform applies to human, mouse, rat, fly, worm and zebrafish. Database URL:http://www.mirrorsuite.cs.huji.ac.il.
Collapse
Affiliation(s)
- Yitzhak Friedman
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, Sudarsky Center for Computational Biology and The Selim and Rachel Benin School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Solange Karsenty
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, Sudarsky Center for Computational Biology and The Selim and Rachel Benin School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Michal Linial
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, Sudarsky Center for Computational Biology and The Selim and Rachel Benin School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| |
Collapse
|
41
|
Abstract
MicroRNAs (miRNAs) have attracted ever-increasing interest in recent years. Since experimental approaches for determining miRNAs are nontrivial in their application, computational methods for the prediction of miRNAs have gained popularity. Such methods can be grouped into two broad categories (1) performing ab initio predictions of miRNAs from primary sequence alone and (2) additionally employing phylogenetic conservation. Most methods acknowledge the importance of hairpin or stem-loop structures and employ various methods for the prediction of RNA secondary structure. Machine learning has been employed in both categories with classification being the predominant method. In most cases, positive and negative examples are necessary for performing classification. Since it is currently elusive to experimentally determine all possible miRNAs for an organism, true negative examples are hard to come by, and therefore the accuracy assessment of algorithms is hampered. In this chapter, first RNA secondary structure prediction is introduced since it provides a basis for miRNA prediction. This is followed by an assessment of homology and then ab initio miRNA prediction methods.
Collapse
Affiliation(s)
- Jens Allmer
- Molecular Biology and Genetics, Izmir Institute of Technology, Izmir, Turkey
| |
Collapse
|
42
|
ElHefnawi M, Soliman B, Abu-Shahba N, Amer M. An integrative meta-analysis of microRNAs in hepatocellular carcinoma. GENOMICS PROTEOMICS & BIOINFORMATICS 2013; 11:354-67. [PMID: 24287119 PMCID: PMC4357785 DOI: 10.1016/j.gpb.2013.05.007] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/12/2012] [Revised: 09/14/2013] [Accepted: 11/14/2013] [Indexed: 02/08/2023]
Abstract
We aimed to shed new light on the roles of microRNAs (miRNAs) in liver cancer using an integrative in silico bioinformatics analysis. A new protocol for target prediction and functional analysis is presented and applied to the 26 highly differentially deregulated miRNAs in hepatocellular carcinoma. This framework comprises: (1) the overlap of prediction results by four out of five target prediction tools, including TargetScan, PicTar, miRanda, DIANA-microT and miRDB (combining machine-learning, alignment, interaction energy and statistical tests in order to minimize false positives), (2) evidence from previous microarray analysis on the expression of these targets, (3) gene ontology (GO) and pathway enrichment analysis of the miRNA targets and their pathways and (4) linking these results to oncogenesis and cancer hallmarks. This yielded new insights into the roles of miRNAs in cancer hallmarks. Here we presented several key targets and hundreds of new targets that are significantly enriched in many new cancer-related hallmarks. In addition, we also revealed some known and new oncogenic pathways for liver cancer. These included the famous MAPK, TGFβ and cell cycle pathways. New insights were also provided into Wnt signaling, prostate cancer, axon guidance and oocyte meiosis pathways. These signaling and developmental pathways crosstalk to regulate stem cell transformation and implicate a role of miRNAs in hepatic stem cell deregulation and cancer development. By analyzing their complete interactome, we proposed new categorization for some of these miRNAs as either tumor-suppressors or oncomiRs with dual roles. Therefore some of these miRNAs may be addressed as therapeutic targets or used as therapeutic agents. Such dual roles thus expand the view of miRNAs as active maintainers of cellular homeostasis.
Collapse
Affiliation(s)
- Mahmoud ElHefnawi
- Centre of Excellence for Advanced Sciences, Informatics and Systems Department, National Research Centre, Cairo 12622, Egypt.
| | - Bangli Soliman
- Centre of Excellence for Advanced Sciences, Informatics and Systems Department, National Research Centre, Cairo 12622, Egypt
| | - Nourhan Abu-Shahba
- Stem Cells Research Group, Centre of Excellence for Advanced Sciences, Medical Molecular Genetics Department, National Research Centre, Cairo 12622, Egypt
| | - Marwa Amer
- Biology Department, American University in Cairo (AUC), New Cairo 11211, Egypt; Faculty of Biotechnology, Misr University for Science and Technology (MUST), 6th of October City 16432, Egypt
| |
Collapse
|
43
|
Guruceaga E, Segura V. Functional interpretation of microRNA-mRNA association in biological systems using R. Comput Biol Med 2013; 44:124-31. [PMID: 24377695 DOI: 10.1016/j.compbiomed.2013.11.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2013] [Revised: 10/30/2013] [Accepted: 11/03/2013] [Indexed: 12/24/2022]
Abstract
The prediction of microRNA targets is a challenging task that has given rise to several prediction algorithms. Databases of predicted targets can be used in a microRNA target enrichment analysis, enhancing our capacity to extract functional information from gene lists. However, the available tools in this field analyze gene sets one by one limiting their use in a meta-analysis. Here, we present an R system for miRNA enrichment analysis that is suitable for systems biology. These collection of R scripts and embedded data allow using predicted targets of public databases or a custom integration of them. As a proof-of-principle, we have successfully performed the challenging analysis of 2158 tumoral samples at a time. The obtained results have been summarized in a network where each cancer disease is linked to enriched miRNAs and overrepresented functions. These network connections have proven to be an invaluable resource for the study of biological and pathological causes and effects of the expression of miRNAs.
Collapse
Affiliation(s)
- Elizabeth Guruceaga
- Unit of Proteomics, Genomics and Bioinformatics, Center for Applied Medical Research (CIMA), University of Navarra, Pamplona, Spain.
| | - Victor Segura
- Unit of Proteomics, Genomics and Bioinformatics, Center for Applied Medical Research (CIMA), University of Navarra, Pamplona, Spain.
| |
Collapse
|
44
|
Zhang Y, Wang R, Du W, Wang S, Yang L, Pan Z, Li X, Xiong X, He H, Shi Y, Liu X, Yu S, Bi Z, Lu Y, Shan H. Downregulation of miR-151-5p contributes to increased susceptibility to arrhythmogenesis during myocardial infarction with estrogen deprivation. PLoS One 2013; 8:e72985. [PMID: 24039836 PMCID: PMC3767733 DOI: 10.1371/journal.pone.0072985] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2013] [Accepted: 07/23/2013] [Indexed: 12/04/2022] Open
Abstract
Estrogen deficiency is associated with increased incidence of cardiovascular diseases. But merely estrogen supplementary treatment can induce many severe complications such as breast cancer. The present study was designed to elucidate molecular mechanisms underlying increased susceptibility of arrhythmogenesis during myocardial infarction with estrogen deprivation, which provides us a new target to cure cardiac disease accompanied with estrogen deprivation. We successfully established a rat model of myocardial ischemia (MI) accompanied with estrogen deprivation by coronary artery ligation and ovariectomy (OVX). Vulnerability and mortality of ventricular arrhythmias increased in estrogen deficiency rats compared to non estrogen deficiency rats when suffered MI, which was associated with down-regulation of microRNA-151-5p (miR-151-5p). Luciferase Reporter Assay demonstrated that miR-151-5p can bind to the 3′-UTR of FXYD1 (coding gene of phospholemman, PLM) and inhibit its expression. We found that the expression of PLM was increased in (OVX+MI) group compared with MI group. More changes such as down-regulation of Kir2.1/IK1, calcium overload had emerged in (OVX+MI) group compared to MI group merely. Transfection of miR-151-5p into primary cultured myocytes decreased PLM levels and [Ca2+]i, however, increased Kir2.1 levels. These effects were abolished by the antisense oligonucleotides against miR-151-5p. Co-immunoprecipitation and immunofluorescent experiments confirmed the co-localization between Kir2.1 and PLM in rat ventricular tissue. We conclude that the increased ventricular arrhythmias vulnerability in response to acute myocardial ischemia in rat is critically dependent upon down-regulation of miR-151-5p. These findings support the proposal that miR-151-5p could be a potential therapeutic target for the prevention of ischemic arrhythmias in the subjects with estrogen deficiency.
Collapse
Affiliation(s)
- Ying Zhang
- Department of Pharmacology (State-Province Key Laboratories of Biomedicine- Pharmaceutics of China, Key Laboratory of Cardiovascular Research, Ministry of Education), Harbin Medical University, Harbin, China
| | - Renjun Wang
- Department of Pharmacology (State-Province Key Laboratories of Biomedicine- Pharmaceutics of China, Key Laboratory of Cardiovascular Research, Ministry of Education), Harbin Medical University, Harbin, China
| | - Weijie Du
- Department of Pharmacology (State-Province Key Laboratories of Biomedicine- Pharmaceutics of China, Key Laboratory of Cardiovascular Research, Ministry of Education), Harbin Medical University, Harbin, China
| | - Shuxuan Wang
- Department of Pharmacology (State-Province Key Laboratories of Biomedicine- Pharmaceutics of China, Key Laboratory of Cardiovascular Research, Ministry of Education), Harbin Medical University, Harbin, China
| | - Lei Yang
- Department of Orthopedics, the First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Zhenwei Pan
- Department of Pharmacology (State-Province Key Laboratories of Biomedicine- Pharmaceutics of China, Key Laboratory of Cardiovascular Research, Ministry of Education), Harbin Medical University, Harbin, China
| | - Xuelian Li
- Department of Pharmacology (State-Province Key Laboratories of Biomedicine- Pharmaceutics of China, Key Laboratory of Cardiovascular Research, Ministry of Education), Harbin Medical University, Harbin, China
| | - Xuehui Xiong
- Department of Pharmacology (State-Province Key Laboratories of Biomedicine- Pharmaceutics of China, Key Laboratory of Cardiovascular Research, Ministry of Education), Harbin Medical University, Harbin, China
| | - Hua He
- Department of Pharmacology (State-Province Key Laboratories of Biomedicine- Pharmaceutics of China, Key Laboratory of Cardiovascular Research, Ministry of Education), Harbin Medical University, Harbin, China
| | - Yongfang Shi
- Department of Pharmacology (State-Province Key Laboratories of Biomedicine- Pharmaceutics of China, Key Laboratory of Cardiovascular Research, Ministry of Education), Harbin Medical University, Harbin, China
| | - Xue Liu
- Department of Pharmacology (State-Province Key Laboratories of Biomedicine- Pharmaceutics of China, Key Laboratory of Cardiovascular Research, Ministry of Education), Harbin Medical University, Harbin, China
| | - Shaonan Yu
- Department of Pharmacology (State-Province Key Laboratories of Biomedicine- Pharmaceutics of China, Key Laboratory of Cardiovascular Research, Ministry of Education), Harbin Medical University, Harbin, China
| | - Zhengang Bi
- Department of Orthopedics, the First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Yanjie Lu
- Department of Pharmacology (State-Province Key Laboratories of Biomedicine- Pharmaceutics of China, Key Laboratory of Cardiovascular Research, Ministry of Education), Harbin Medical University, Harbin, China
- * E-mail: (HS); (YL)
| | - Hongli Shan
- Department of Pharmacology (State-Province Key Laboratories of Biomedicine- Pharmaceutics of China, Key Laboratory of Cardiovascular Research, Ministry of Education), Harbin Medical University, Harbin, China
- * E-mail: (HS); (YL)
| |
Collapse
|
45
|
Vogel B, Keller A, Frese KS, Leidinger P, Sedaghat-Hamedani F, Kayvanpour E, Kloos W, Backe C, Thanaraj A, Brefort T, Beier M, Hardt S, Meese E, Katus HA, Meder B. Multivariate miRNA signatures as biomarkers for non-ischaemic systolic heart failure. Eur Heart J 2013; 34:2812-22. [PMID: 23864135 DOI: 10.1093/eurheartj/eht256] [Citation(s) in RCA: 87] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
AIMS Non-ischaemic heart failure is one of the today's most prevalent cardiovascular disorders. Since modern pharmacotherapy has proved to be very effective in delaying disease progression and preventing death, imaging modalities and molecular biomarkers play an important role in early identification and clinical management as well as risk assessment of patients. The present study evaluated for the first time whole peripheral blood miRNAs as novel biomarker candidates for non-ischaemic heart failure with reduced ejection fraction (HF-REF). METHODS AND RESULTS We assessed genome-wide miRNA expression profiles in 53 HF-REF patients and 39 controls. We could identify and validate several miRNAs that show altered expression levels in non-ischaemic HF-REF, discriminating cases from controls both as single markers or when combined in a multivariate signature. In addition, we demonstrate that the miRNAs of this signature significantly correlate with disease severity as indicated by left ventricular ejection fraction. CONCLUSION Our data further denote that miRNAs are potential biomarkers for systolic heart failure. Since their detection levels in whole blood are also related to the degree of left ventricular dysfunction, they may serve as objective molecular tools to assess disease severity and prognosis.
Collapse
Affiliation(s)
- Britta Vogel
- Department of Internal Medicine III, University of Heidelberg, Im Neuenheimer Feld 410, 69120 Heidelberg, Germany
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
46
|
Duskova K, Nagilla P, Le HS, Iyer P, Thalamuthu A, Martinson J, Bar-Joseph Z, Buchanan W, Rinaldo C, Ayyavoo V. MicroRNA regulation and its effects on cellular transcriptome in human immunodeficiency virus-1 (HIV-1) infected individuals with distinct viral load and CD4 cell counts. BMC Infect Dis 2013; 13:250. [PMID: 23721325 PMCID: PMC3680326 DOI: 10.1186/1471-2334-13-250] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2012] [Accepted: 05/16/2013] [Indexed: 12/13/2022] Open
Abstract
Background Disease progression in the absence of therapy varies significantly in HIV-1 infected individuals. Both viral and host cellular molecules are implicated; however, the exact role of these factors and/or the mechanism involved remains elusive. To understand how microRNAs (miRNAs), which are regulators of transcription and translation, influence host cellular gene expression (mRNA) during HIV-1 infection, we performed a comparative miRNA and mRNA microarray analysis using PBMCs obtained from infected individuals with distinct viral load and CD4 counts. Methods RNA isolated from PBMCs obtained from HIV-1 seronegative and HIV-1 positive individuals with distinct viral load and CD4 counts were assessed for miRNA and mRNA profile. Selected miRNA and mRNA transcripts were validated using in vivo and in vitro infection model. Results Our results indicate that HIV-1 positive individuals with high viral load (HVL) showed a dysregulation of 191 miRNAs and 309 mRNA transcripts compared to the uninfected age and sex matched controls. The miRNAs miR-19b, 146a, 615-3p, 382, 34a, 144 and 155, that are known to target innate and inflammatory factors, were significantly upregulated in PBMCs with high viral load, as were the inflammatory molecules CXCL5, CCL2, IL6 and IL8, whereas defensin, CD4, ALDH1, and Neurogranin (NRGN) were significantly downregulated. Using the transcriptome profile and predicted target genes, we constructed the regulatory networks of miRNA-mRNA pairs that were differentially expressed between control, LVL and HVL subjects. The regulatory network revealed an inverse correlation of several miRNA-mRNA pair expression patterns, suggesting HIV-1 mediated transcriptional regulation is in part likely through miRNA regulation. Conclusions Results from our studies indicate that gene expression is significantly altered in PBMCs in response to virus replication. It is interesting to note that the infected individuals with low or undetectable viral load exhibit a gene expression profile very similar to control or uninfected subjects. Importantly, we identified several new mRNA targets (Defensin, Neurogranin, AIF) as well as the miRNAs that could be involved in regulating their expression through the miRNA-mRNA interaction.
Collapse
Affiliation(s)
- Karolina Duskova
- Department of Infectious Diseases and Microbiology, Graduate School of Public Health, University of Pittsburgh, 425 Parran Hall, 130 Desoto Street, Pittsburgh, PA 15261, USA
| | | | | | | | | | | | | | | | | | | |
Collapse
|
47
|
McCracken AN, Edinger AL. Nutrient transporters: the Achilles' heel of anabolism. Trends Endocrinol Metab 2013; 24:200-8. [PMID: 23402769 PMCID: PMC3617053 DOI: 10.1016/j.tem.2013.01.002] [Citation(s) in RCA: 87] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/08/2012] [Revised: 01/03/2013] [Accepted: 01/04/2013] [Indexed: 01/08/2023]
Abstract
Highly proliferative cells, including cancer cells, require a constant supply of molecular building blocks to support their growth. To acquire substrates such as glucose and amino acids from the extracellular space, dividing cells rely on transporter proteins in the plasma membrane. Numerous studies link transcriptional and post-translational control of nutrient transporter expression with proliferation, highlighting the importance of nutrient transporters in both physiologic and pathologic growth. Here we review recent work that spotlights the crucial role of nutrient transporters in cell growth and proliferation, discuss post-translational mechanisms for coordinating expression of different transporters, and consider the therapeutic potential of targeting these proteins in cancer and other diseases characterized by inappropriate cell division.
Collapse
Affiliation(s)
| | - Aimee L. Edinger
- Corresponding Author: Aimee L. Edinger 2128 Natural Sciences 1 University of California, Irvine Irvine, CA 92697-2300 Tel: 949-824-1921 FAX: 949-824-4709
| |
Collapse
|
48
|
Frese KS, Katus HA, Meder B. Next-generation sequencing: from understanding biology to personalized medicine. BIOLOGY 2013; 2:378-98. [PMID: 24832667 PMCID: PMC4009863 DOI: 10.3390/biology2010378] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/21/2013] [Revised: 01/21/2013] [Accepted: 02/04/2013] [Indexed: 12/11/2022]
Abstract
Within just a few years, the new methods for high-throughput next-generation sequencing have generated completely novel insights into the heritability and pathophysiology of human disease. In this review, we wish to highlight the benefits of the current state-of-the-art sequencing technologies for genetic and epigenetic research. We illustrate how these technologies help to constantly improve our understanding of genetic mechanisms in biological systems and summarize the progress made so far. This can be exemplified by the case of heritable heart muscle diseases, so-called cardiomyopathies. Here, next-generation sequencing is able to identify novel disease genes, and first clinical applications demonstrate the successful translation of this technology into personalized patient care.
Collapse
Affiliation(s)
- Karen S Frese
- Department of Internal Medicine III, University of Heidelberg, Heidelberg 69120, Germany.
| | - Hugo A Katus
- Department of Internal Medicine III, University of Heidelberg, Heidelberg 69120, Germany.
| | - Benjamin Meder
- Department of Internal Medicine III, University of Heidelberg, Heidelberg 69120, Germany.
| |
Collapse
|
49
|
Genomic and Epigenomic Cross-talks in the Regulatory Landscape of miRNAs in Breast Cancer. Mol Cancer Res 2013; 11:315-28. [DOI: 10.1158/1541-7786.mcr-12-0649] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
|
50
|
Friedman Y, Balaga O, Linial M. Working together: combinatorial regulation by microRNAs. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2013; 774:317-37. [PMID: 23377980 DOI: 10.1007/978-94-007-5590-1_16] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
MicroRNAs (miRNAs) negatively regulate gene expression level of mRNA post-transcriptionally. Deep sequencing and large-scale screening methods have yielded about 1,500 miRNA sequences in human. Each miRNA contains a seed sequence that is required, but not sufficient, for the correct matching with its targets. Recent technological advances make it possible to capture the miRNAs with their cognate mRNAs at the RISC complex. These experiments have revealed thousands of validated mRNA-miRNA pairing events. In the context of human stem cells, 90% of the identified transcripts appear to be paired with at least two different miRNAs.In this chapter, we present a comprehensive outline for a combinatorial regulation mode by miRNAs. Initially, we summarize the computational and experimental evidence that support a combined effect of multiple miRNAs. Then, we describe miRror2.0, a platform specifically convened to consider the likelihood of miRNAs cooperativity in view of the targets, tissues and cell lines. We show that results from miRror2.0 can be further refined by an iterative procedure, calls Psi-miRror that gauges the robustness of the regulation. We illustrate the combinatorial regulation projected onto graphs of human pathways and show that these pathways are amenable to disruption by a small set of miRNAs. Finally, we propose that miRNA combinatorial regulation is an attractive regulatory strategy not only at the level of single target, but also at the level of pathways and cellular homeostasis. The joint operation of miRNAs is a powerful means to overcome the low specificity inherent in each individual miRNA.
Collapse
Affiliation(s)
- Yitzhak Friedman
- Department of Biological Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel
| | | | | |
Collapse
|