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Cohn-Alperovich D, Rabner A, Kifer I, Mandel-Gutfreund Y, Yakhini Z. Mutual enrichment in aggregated ranked lists with applications to gene expression regulation. Bioinformatics 2017; 32:i464-i472. [PMID: 27587663 DOI: 10.1093/bioinformatics/btw435] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
MOTIVATION It is often the case in biological measurement data that results are given as a ranked list of quantities-for example, differential expression (DE) of genes as inferred from microarrays or RNA-seq. Recent years brought considerable progress in statistical tools for enrichment analysis in ranked lists. Several tools are now available that allow users to break the fixed set paradigm in assessing statistical enrichment of sets of genes. Continuing with the example, these tools identify factors that may be associated with measured differential expression. A drawback of existing tools is their focus on identifying single factors associated with the observed or measured ranks, failing to address relationships between these factors. For example, a scenario in which genes targeted by multiple miRNAs play a central role in the DE signal but the effect of each single miRNA is too subtle to be detected, as shown in our results. RESULTS We propose statistical and algorithmic approaches for selecting a sub-collection of factors that can be aggregated into one ranked list that is heuristically most associated with an input ranked list (pivot). We examine performance on simulated data and apply our approach to cancer datasets. We find small sub-collections of miRNA that are statistically associated with gene DE in several types of cancer, suggesting miRNA cooperativity in driving disease related processes. Many of our findings are consistent with known roles of miRNAs in cancer, while others suggest previously unknown roles for certain miRNAs. AVAILABILITY AND IMPLEMENTATION Code and instructions for our algorithmic framework, MULSEA, are in: https://github.com/YakhiniGroup/MULSEAContact:dalia.cohn@gmail.com SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Dalia Cohn-Alperovich
- Computer Science Department, Technion - Israel Institute of Technology, Haifa 3200003, Israel, Microsoft Research and Development Center, Haifa and Herzeliya, Israel
| | - Alona Rabner
- Department of Biology, Technion - Israel Institute of Technology, Haifa 3200003, Israel
| | - Ilona Kifer
- Microsoft Research and Development Center, Haifa and Herzeliya, Israel
| | - Yael Mandel-Gutfreund
- Department of Biology, Technion - Israel Institute of Technology, Haifa 3200003, Israel
| | - Zohar Yakhini
- Computer Science Department, Technion - Israel Institute of Technology, Haifa 3200003, Israel, School of Computer Science, The Interdisciplinary Center, Herzeliya 4610101, Israel
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2
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A Systems Genetics Approach Identified GPD1L and its Molecular Mechanism for Obesity in Human Adipose Tissue. Sci Rep 2017; 7:1799. [PMID: 28496128 PMCID: PMC5431993 DOI: 10.1038/s41598-017-01517-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Accepted: 03/27/2017] [Indexed: 01/14/2023] Open
Abstract
To explore novel molecular mechanisms underlying obesity, we applied a systems genetics framework to integrate risk genetic loci from the largest body mass index (BMI) genome-wide association studies (GWAS) meta-analysis with mRNA and microRNA profiling in adipose tissue from 200 subjects. One module was identified to be most significantly associated with obesity and other metabolic traits. We identified eight hub genes which likely play important roles in obesity metabolism and identified microRNAs that significantly negatively correlated with hub genes. This module was preserved in other three test gene expression datasets, and all hub genes were consistently downregulated in obese subjects through the meta-analysis. Gene GPD1L had the highest connectivity and was identified a key causal regulator in the module. Gene GPD1L was significantly negatively correlated with the expression of miR-210, which was experimentally validated that miR-210 regulated GPD1L protein level through direct interaction with its mRNA three prime untranslated region (3'-UTR). GPD1L was found to be upregulated during weight loss and weight maintenance induced by low calorie diet (LCD), while downregulated during weight gain induced by high-fat diet (HFD). The results indicated that increased GPD1L in adipose tissue may have a significant therapeutic potential in reducing obesity and insulin resistance.
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Kristensen MM, Davidsen PK, Vigelsø A, Hansen CN, Jensen LJ, Jessen N, Bruun JM, Dela F, Helge JW. miRNAs in human subcutaneous adipose tissue: Effects of weight loss induced by hypocaloric diet and exercise. Obesity (Silver Spring) 2017; 25:572-580. [PMID: 28158925 DOI: 10.1002/oby.21765] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/21/2016] [Revised: 11/29/2016] [Accepted: 12/09/2016] [Indexed: 12/20/2022]
Abstract
OBJECTIVE Obesity is central in the development of insulin resistance. However, the underlying mechanisms still need elucidation. Dysregulated microRNAs (miRNAs; post-transcriptional regulators) in adipose tissue may present an important link. METHODS The miRNA expression in subcutaneous adipose tissue from 19 individuals with severe obesity (10 women and 9 men) before and after a 15-week weight loss intervention was studied using genome-wide microarray analysis. The microarray results were validated with RT-qPCR, and pathway enrichment analysis of in silico predicted targets was performed to elucidate the biological consequences of the miRNA dysregulation. Lastly, the messenger RNA (mRNA) and/or protein expression of multiple predicted targets as well as several proteins involved in lipolysis were investigated. RESULTS The intervention led to upregulation of miR-29a-3p and miR-29a-5p and downregulation of miR-20b-5p. The mRNA and protein expression of predicted targets was not significantly affected by the intervention. However, negative correlations between miR-20b-5p and the protein levels of its predicted target, acyl-CoA synthetase long-chain family member 1, were observed. Several other miRNA-target relationships correlated negatively, indicating possible miRNA regulation, including miR-29a-3p and lipoprotein lipase mRNA levels. Proteins involved in lipolysis were not affected by the intervention. CONCLUSIONS Weight loss influenced several miRNAs, some of which were negatively correlated with predicted targets. These dysregulated miRNAs may affect adipocytokine signaling and forkhead box protein O signaling.
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Affiliation(s)
- Malene M Kristensen
- Xlab, Center for Healthy Aging, Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Peter K Davidsen
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Andreas Vigelsø
- Xlab, Center for Healthy Aging, Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Christina N Hansen
- Xlab, Center for Healthy Aging, Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Lars J Jensen
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Niels Jessen
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
| | - Jens M Bruun
- Randers Regional Hospital, Medical Department M, Randers, Denmark
- Department of Nutrition, Exercise, and Sports (NEXS), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Flemming Dela
- Xlab, Center for Healthy Aging, Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Geriatrics, Bispebjerg University Hospital, Copenhagen, Denmark
| | - Jørn W Helge
- Xlab, Center for Healthy Aging, Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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4
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Meerson A, Yehuda H. Leptin and insulin up-regulate miR-4443 to suppress NCOA1 and TRAF4, and decrease the invasiveness of human colon cancer cells. BMC Cancer 2016; 16:882. [PMID: 27842582 PMCID: PMC5109693 DOI: 10.1186/s12885-016-2938-1] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Accepted: 10/27/2016] [Indexed: 01/17/2023] Open
Abstract
Background Obesity is a risk factor for colorectal cancer (CRC). Normal and tumor cells respond to metabolic hormones, such as leptin and insulin. Thus, obesity-associated resistance to these hormones likely leads to changes in gene expression and behavior of tumor cells. However, the mechanisms affected by leptin and insulin signaling in CRC cells remain mostly unknown. Methods We hypothesized that microRNAs (miRNAs) are involved in the regulation of tumorigenesis-related gene expression in CRC cells by leptin and insulin. To test this hypothesis, miRNA levels in the CRC-derived cell lines HCT-116, HT-29 and DLD-1 were profiled, following leptin and insulin treatment. Candidate miRNAs were validated by RT-qPCR. Predicted miRNA targets with known roles in cancer, were validated by immunoblots and reporter assays in HCT-116 cells. Transfection of HCT-116 cells with candidate miRNA mimic was used to test in vitro effects on proliferation and invasion. Results Of ~800 miRNAs profiled, miR-4443 was consistently up-regulated by leptin and insulin in HCT-116 and HT-29, but not in DLD-1, which lacked normal leptin receptor expression. Dose response experiments showed that leptin at 100 ng/ml consistently up-regulated miR-4443 in HCT-116 cells, concomitantly with a significant decrease in cell invasion ability. Transfection with miR-4443 mimic decreased invasion and proliferation of HCT-116 cells. Moreover, leptin and miR-4443 transfection significantly down-regulated endogenous NCOA1 and TRAF4, both predicted targets of miR-4443 with known roles in cancer metastasis. miR-4443 was found to directly regulate TRAF4 and NCOA1, as validated by a reporter assay. The up-regulation of miR-4443 by leptin or insulin was attenuated by the inhibition of MEK1/2. Conclusions Our findings suggest that miR-4443 acts in a tumor-suppressive manner by down-regulating TRAF4 and NCOA1 downstream of MEK-C/EBP-mediated leptin and insulin signaling, and that insulin and/or leptin resistance (e.g. in obesity) may suppress this pathway and increase the risk of metastatic CRC. Electronic supplementary material The online version of this article (doi:10.1186/s12885-016-2938-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ari Meerson
- Molecular Biology of Chronic Diseases, MIGAL Galilee Research Institute, PO Box 831, Kiryat Shmona, 11016, Israel. .,Department of Biomedical Sciences, University of Copenhagen, Blegdamsvej 3, Copenhagen, DK-2200, Denmark.
| | - Hila Yehuda
- Molecular Biology of Chronic Diseases, MIGAL Galilee Research Institute, PO Box 831, Kiryat Shmona, 11016, Israel
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Amirkhah R, Farazmand A, Wolkenhauer O, Schmitz U. RNA Systems Biology for Cancer: From Diagnosis to Therapy. Methods Mol Biol 2016; 1386:305-30. [PMID: 26677189 DOI: 10.1007/978-1-4939-3283-2_14] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
It is due to the advances in high-throughput omics data generation that RNA species have re-entered the focus of biomedical research. International collaborate efforts, like the ENCODE and GENCODE projects, have spawned thousands of previously unknown functional non-coding RNAs (ncRNAs) with various but primarily regulatory roles. Many of these are linked to the emergence and progression of human diseases. In particular, interdisciplinary studies integrating bioinformatics, systems biology, and biotechnological approaches have successfully characterized the role of ncRNAs in different human cancers. These efforts led to the identification of a new tool-kit for cancer diagnosis, monitoring, and treatment, which is now starting to enter and impact on clinical practice. This chapter is to elaborate on the state of the art in RNA systems biology, including a review and perspective on clinical applications toward an integrative RNA systems medicine approach. The focus is on the role of ncRNAs in cancer.
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Affiliation(s)
- Raheleh Amirkhah
- Department of Cell and Molecular Biology, School of Biology, College of Science, University of Tehran, Tehran, Iran
| | - Ali Farazmand
- Department of Cell and Molecular Biology, School of Biology, College of Science, University of Tehran, Tehran, Iran
| | - Olaf Wolkenhauer
- Department of Systems Biology and Bioinformatics, University of Rostock, Rostock, Germany.,Stellenbosch Institute for Advanced Study (STIAS), Wallenberg Research Centre at Stellenbosch University, Stellenbosch, South Africa
| | - Ulf Schmitz
- Department of Systems Biology and Bioinformatics, University of Rostock, Rostock, Germany.
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6
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McDonald MK, Ramanathan S, Touati A, Zhou Y, Thanawala RU, Alexander GM, Sacan A, Ajit SK. Regulation of proinflammatory genes by the circulating microRNA hsa-miR-939. Sci Rep 2016; 6:30976. [PMID: 27498764 PMCID: PMC4976376 DOI: 10.1038/srep30976] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Accepted: 07/12/2016] [Indexed: 12/14/2022] Open
Abstract
Circulating microRNAs are beneficial biomarkers because of their stability and dysregulation in diseases. Here we sought to determine the role of miR-939, a miRNA downregulated in patients with complex regional pain syndrome (CRPS). Hsa-miR-939 is predicted to target several proinflammatory genes, including IL-6, VEGFA, TNFα, NFκB2, and nitric oxide synthase 2 (NOS2A). Binding of miR-939 to the 3' untranslated region of these genes was confirmed by reporter assay. Overexpression of miR-939 in vitro resulted in reduction of IL-6, NOS2A and NFκB2 mRNAs, IL-6, VEGFA, and NOS2 proteins and NFκB activation. We observed a significant decrease in the NOS substrate l-arginine in plasma from CRPS patients, suggesting reduced miR-939 levels may contribute to an increase in endogenous NOS2A levels and NO, and thereby to pain and inflammation. Pathway analysis showed that miR-939 represents a critical regulatory node in a network of inflammatory mediators. Collectively, our data suggest that miR-939 may regulate multiple proinflammatory genes and that downregulation of miR-939 in CRPS patients may increase expression of these genes, resulting in amplification of the inflammatory pain signal transduction cascade. Circulating miRNAs may function as crucial signaling nodes, and small changes in miRNA levels may influence target gene expression and thus disease.
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Affiliation(s)
- Marguerite K McDonald
- Pharmacology &Physiology, Drexel University College of Medicine, 245 North 15th Street, Philadelphia, PA 19102, USA.,Gene Therapy Program, Perelman School of Medicine, University of Pennsylvania, Suite 2000, Translational Research Laboratories (TRL), 125 S. 31st Street, Philadelphia, PA 19104-3403, USA
| | - Sujay Ramanathan
- Pharmacology &Physiology, Drexel University College of Medicine, 245 North 15th Street, Philadelphia, PA 19102, USA
| | - Andrew Touati
- Pharmacology &Physiology, Drexel University College of Medicine, 245 North 15th Street, Philadelphia, PA 19102, USA
| | - Yiqian Zhou
- School of Biomedical Engineering, Science &Health Systems, Drexel University, 3141 Chestnut Street, Philadelphia, PA 19104, USA
| | - Rushi U Thanawala
- Pharmacology &Physiology, Drexel University College of Medicine, 245 North 15th Street, Philadelphia, PA 19102, USA
| | - Guillermo M Alexander
- Neurology, Drexel University College of Medicine, 245 North 15th Street, Philadelphia, PA 19102, USA
| | - Ahmet Sacan
- School of Biomedical Engineering, Science &Health Systems, Drexel University, 3141 Chestnut Street, Philadelphia, PA 19104, USA
| | - Seena K Ajit
- Pharmacology &Physiology, Drexel University College of Medicine, 245 North 15th Street, Philadelphia, PA 19102, USA
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7
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Mal C, Deb A, Aftabuddin M, Kundu S. A network analysis of miRNA mediated gene regulation of rice: crosstalk among biological processes. MOLECULAR BIOSYSTEMS 2016; 11:2273-80. [PMID: 26066638 DOI: 10.1039/c5mb00222b] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
To understand the network architecture of miRNA mediated regulations at the genomic and functional levels of rice, we have made an unambiguous annotation of the experimentally verified miRNAs, predicted their targets and the possible biological functions they can affect. Some functions, namely translational and protein modifications and photosynthesis are targeted by higher percentage of miRNA. Using transformation procedures, we constructed a genome scale miRNA-miRNA functional synergistic network (MFSN). The analysis of MFSN modules help to identify miRNAs co-regulating target genes having several interrelated biological processes. Some of these target genes are also co-expressed under particular conditions. For example, the genes co-expressed under drought conditions as well as those targeted by miRNAs present in a MFSN module have interdependent biological processes namely, photosynthesis, cell-wall biogenesis, root development and xylan synthesis. The stress-induced miRNAs and their distributions, and the presence of transcription factors in the target set of MFSN modules were also analyzed.
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Affiliation(s)
- Chittabrata Mal
- Department of Biophysics, Molecular Biology & Bioinformatics, University of Calcutta, 92, A.P.C. Road, Kolkata 700009, India.
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8
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Kaller M, Hermeking H. Interplay Between Transcription Factors and MicroRNAs Regulating Epithelial-Mesenchymal Transitions in Colorectal Cancer. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 937:71-92. [DOI: 10.1007/978-3-319-42059-2_4] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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9
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Davey NE, Cyert MS, Moses AM. Short linear motifs - ex nihilo evolution of protein regulation. Cell Commun Signal 2015; 13:43. [PMID: 26589632 PMCID: PMC4654906 DOI: 10.1186/s12964-015-0120-z] [Citation(s) in RCA: 142] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2015] [Accepted: 11/13/2015] [Indexed: 12/12/2022] Open
Abstract
Short sequence motifs are ubiquitous across the three major types of biomolecules: hundreds of classes and thousands of instances of DNA regulatory elements, RNA motifs and protein short linear motifs (SLiMs) have been characterised. The increase in complexity of transcriptional, post-transcriptional and post-translational regulation in higher Eukaryotes has coincided with a significant expansion of motif use. But how did the eukaryotic cell acquire such a vast repertoire of motifs? In this review, we curate the available literature on protein motif evolution and discuss the evidence that suggests SLiMs can be acquired by mutations, insertions and deletions in disordered regions. We propose a mechanism of ex nihilo SLiM evolution – the evolution of a novel SLiM from “nothing” – adding a functional module to a previously non-functional region of protein sequence. In our model, hundreds of motif-binding domains in higher eukaryotic proteins connect simple motif specificities with useful functions to create a large functional motif space. Accessible peptides that match the specificity of these motif-binding domains are continuously created and destroyed by mutations in rapidly evolving disordered regions, creating a dynamic supply of new interactions that may have advantageous phenotypic novelty. This provides a reservoir of diversity to modify existing interaction networks. Evolutionary pressures will act on these motifs to retain beneficial instances. However, most will be lost on an evolutionary timescale as negative selection and genetic drift act on deleterious and neutral motifs respectively. In light of the parallels between the presented model and the evolution of motifs in the regulatory segments of genes and (pre-)mRNAs, we suggest our understanding of regulatory networks would benefit from the creation of a shared model describing the evolution of transcriptional, post-transcriptional and post-translational regulation.
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Affiliation(s)
- Norman E Davey
- Conway Institute of Biomolecular and Biomedical Sciences, University College Dublin, Dublin 4, Ireland.
| | - Martha S Cyert
- Department of Biology, Stanford University, Stanford, CA, 94305, USA.
| | - Alan M Moses
- Department of Cell & Systems Biology, University of Toronto, Toronto, Canada. .,Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, Canada.
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Stepicheva NA, Song JL. microRNA-31 modulates skeletal patterning in the sea urchin embryo. Development 2015; 142:3769-80. [PMID: 26400092 DOI: 10.1242/dev.127969] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Accepted: 09/03/2015] [Indexed: 01/25/2023]
Abstract
MicroRNAs (miRNAs) are small non-coding RNAs that repress the translation and reduce the stability of target mRNAs in animal cells. microRNA-31 (miR-31) is known to play a role in cancer, bone formation and lymphatic development. However, studies to understand the function of miR-31 in embryogenesis have been limited. We examined the regulatory role of miR-31 in early development using the sea urchin as a model. miR-31 is expressed at all stages of development and its knockdown (KD) disrupts the patterning and function of primary mesenchyme cells (PMCs), which form the embryonic skeleton spicules. We identified that miR-31 directly represses Pmar1, Alx1, Snail and VegfR7 within the PMC gene regulatory network using reporter constructs. Further, blocking the miR-31-mediated repression of Alx1 and/or VegfR7 in the developing embryo resulted in defects in PMC patterning and skeletogenesis. The majority of the mislocalized PMCs in miR-31 KD embryos did not express VegfR10, indicating that miR-31 regulates VegfR gene expression within PMCs. In addition, miR-31 indirectly suppresses Vegf3 expression in the ectoderm. These results indicate that miR-31 coordinately suppresses genes within the PMCs and in the ectoderm to impact PMC patterning and skeletogenesis. This study identifies the novel function and molecular mechanism of miR-31-mediated regulation in the developing embryo.
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Affiliation(s)
- Nadezda A Stepicheva
- Department of Biological Sciences, University of Delaware, Newark, DE 19716, USA
| | - Jia L Song
- Department of Biological Sciences, University of Delaware, Newark, DE 19716, USA
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11
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Mamdani M, Williamson V, McMichael GO, Blevins T, Aliev F, Adkins A, Hack L, Bigdeli T, D. van der Vaart A, Web BT, Bacanu SA, Kalsi G, Kendler KS, Miles MF, Dick D, Riley BP, Dumur C, Vladimirov VI. Integrating mRNA and miRNA Weighted Gene Co-Expression Networks with eQTLs in the Nucleus Accumbens of Subjects with Alcohol Dependence. PLoS One 2015; 10:e0137671. [PMID: 26381263 PMCID: PMC4575063 DOI: 10.1371/journal.pone.0137671] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2015] [Accepted: 08/05/2015] [Indexed: 11/18/2022] Open
Abstract
Alcohol consumption is known to lead to gene expression changes in the brain. After performing weighted gene co-expression network analyses (WGCNA) on genome-wide mRNA and microRNA (miRNA) expression in Nucleus Accumbens (NAc) of subjects with alcohol dependence (AD; N = 18) and of matched controls (N = 18), six mRNA and three miRNA modules significantly correlated with AD were identified (Bonferoni-adj. p≤ 0.05). Cell-type-specific transcriptome analyses revealed two of the mRNA modules to be enriched for neuronal specific marker genes and downregulated in AD, whereas the remaining four mRNA modules were enriched for astrocyte and microglial specific marker genes and upregulated in AD. Gene set enrichment analysis demonstrated that neuronal specific modules were enriched for genes involved in oxidative phosphorylation, mitochondrial dysfunction and MAPK signaling. Glial-specific modules were predominantly enriched for genes involved in processes related to immune functions, i.e. cytokine signaling (all adj. p≤ 0.05). In mRNA and miRNA modules, 461 and 25 candidate hub genes were identified, respectively. In contrast to the expected biological functions of miRNAs, correlation analyses between mRNA and miRNA hub genes revealed a higher number of positive than negative correlations (χ2 test p≤ 0.0001). Integration of hub gene expression with genome-wide genotypic data resulted in 591 mRNA cis-eQTLs and 62 miRNA cis-eQTLs. mRNA cis-eQTLs were significantly enriched for AD diagnosis and AD symptom counts (adj. p = 0.014 and p = 0.024, respectively) in AD GWAS signals in a large, independent genetic sample from the Collaborative Study on Genetics of Alcohol (COGA). In conclusion, our study identified putative gene network hubs coordinating mRNA and miRNA co-expression changes in the NAc of AD subjects, and our genetic (cis-eQTL) analysis provides novel insights into the etiological mechanisms of AD.
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Affiliation(s)
- Mohammed Mamdani
- Virginia Institute for Psychiatric and Behavioral Genetics, Virginia Commonwealth University, Richmond, VA, United States of America
| | - Vernell Williamson
- Virginia Institute for Psychiatric and Behavioral Genetics, Virginia Commonwealth University, Richmond, VA, United States of America
| | - Gowon O. McMichael
- Virginia Institute for Psychiatric and Behavioral Genetics, Virginia Commonwealth University, Richmond, VA, United States of America
| | - Tana Blevins
- Department of Pathology, Virginia Commonwealth University, Richmond, VA, United States of America
| | - Fazil Aliev
- Virginia Institute for Psychiatric and Behavioral Genetics, Virginia Commonwealth University, Richmond, VA, United States of America
- Department of Psychiatry, Virginia Commonwealth University, Richmond, VA, United States of America
| | - Amy Adkins
- Virginia Institute for Psychiatric and Behavioral Genetics, Virginia Commonwealth University, Richmond, VA, United States of America
| | - Laura Hack
- Virginia Institute for Psychiatric and Behavioral Genetics, Virginia Commonwealth University, Richmond, VA, United States of America
| | - Tim Bigdeli
- Virginia Institute for Psychiatric and Behavioral Genetics, Virginia Commonwealth University, Richmond, VA, United States of America
| | - Andrew D. van der Vaart
- Department of Pharmacology & Toxicology, Virginia Commonwealth University, Richmond, VA, United States of America
| | - Bradley Todd Web
- Virginia Institute for Psychiatric and Behavioral Genetics, Virginia Commonwealth University, Richmond, VA, United States of America
| | - Silviu-Alin Bacanu
- Virginia Institute for Psychiatric and Behavioral Genetics, Virginia Commonwealth University, Richmond, VA, United States of America
| | - Gursharan Kalsi
- Department of Social, Genetic and Developmental Psychiatry, Institute of Psychiatry, London SE5 8AF, United Kingdom
| | | | - Kenneth S. Kendler
- Virginia Institute for Psychiatric and Behavioral Genetics, Virginia Commonwealth University, Richmond, VA, United States of America
- Department of Psychiatry, Virginia Commonwealth University, Richmond, VA, United States of America
- Department of Human & Molecular Genetics, Virginia Commonwealth University, Richmond, VA, United States of America
| | - Michael F. Miles
- Virginia Institute for Psychiatric and Behavioral Genetics, Virginia Commonwealth University, Richmond, VA, United States of America
- Department of Pharmacology & Toxicology, Virginia Commonwealth University, Richmond, VA, United States of America
| | - Danielle Dick
- Virginia Institute for Psychiatric and Behavioral Genetics, Virginia Commonwealth University, Richmond, VA, United States of America
- Department of Psychiatry, Virginia Commonwealth University, Richmond, VA, United States of America
- Department of Human & Molecular Genetics, Virginia Commonwealth University, Richmond, VA, United States of America
- Department of Psychology, Virginia Commonwealth University, Richmond, VA, United States of America
| | - Brien P. Riley
- Virginia Institute for Psychiatric and Behavioral Genetics, Virginia Commonwealth University, Richmond, VA, United States of America
- Department of Psychiatry, Virginia Commonwealth University, Richmond, VA, United States of America
- Department of Human & Molecular Genetics, Virginia Commonwealth University, Richmond, VA, United States of America
| | - Catherine Dumur
- Department of Pathology, Virginia Commonwealth University, Richmond, VA, United States of America
| | - Vladimir I. Vladimirov
- Virginia Institute for Psychiatric and Behavioral Genetics, Virginia Commonwealth University, Richmond, VA, United States of America
- Department of Psychiatry, Virginia Commonwealth University, Richmond, VA, United States of America
- Center for Biomarker Research and Personalized Medicine, Virginia Commonwealth University, Richmond, VA, United States of America
- Lieber Institute for Brain Development, Johns Hopkins University, Baltimore, MD, United States of America
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Abstract
Spinal muscular atrophy (SMA) is a leading genetic cause of infant mortality. The disease originates from low levels of SMN protein due to deletion and/or mutations of SMN1 coupled with the inability of SMN2 to compensate for the loss of SMN1. While SMN1 and SMN2 are nearly identical, SMN2 predominantly generates a truncated protein (SMNΔ7) due to skipping of exon 7, the last coding exon. Several avenues for SMA therapy are being explored, including means to enhance SMN2 transcription, correct SMN2 exon 7 splicing, stabilize SMN/SMNΔ7 protein, manipulate SMN-regulated pathways and SMN1 gene delivery by viral vectors. This review focuses on the aspects of target discovery, validations and outcome measures for a promising therapy of SMA.
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13
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Wronska A, Kurkowska-Jastrzebska I, Santulli G. Application of microRNAs in diagnosis and treatment of cardiovascular disease. Acta Physiol (Oxf) 2015; 213:60-83. [PMID: 25362848 DOI: 10.1111/apha.12416] [Citation(s) in RCA: 124] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2014] [Revised: 10/08/2014] [Accepted: 10/24/2014] [Indexed: 12/13/2022]
Abstract
Cardiovascular disease (CVD) is a major cause of morbidity and mortality worldwide. Innovative, more stringent diagnostic and prognostic biomarkers and effective treatment options are needed to lessen its burden. In recent years, microRNAs have emerged as master regulators of gene expression - they bind to complementary sequences within the mRNAs of their target genes and inhibit their expression by either mRNA degradation or translational repression. microRNAs have been implicated in all major cellular processes, including cell cycle, differentiation and metabolism. Their unique mode of action, fine-tuning gene expression rather than turning genes on/off, and their ability to simultaneously regulate multiple elements of relevant pathways makes them enticing potential biomarkers and therapeutic targets. Indeed, cardiovascular patients have specific patterns of circulating microRNA levels, often early in the disease process. This article provides a systematic overview of the role of microRNAs in the pathophysiology, diagnosis and treatment of CVD.
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Affiliation(s)
- A. Wronska
- Helen and Clyde Wu Center for Molecular Cardiology; Department of Physiology and Cellular Biophysics; College of Physicians and Surgeons of Columbia University; New York NY USA
| | - I. Kurkowska-Jastrzebska
- Department of Experimental and Clinical Pharmacology; Medical University of Warsaw; Warsaw Poland
- 2nd Department of Neurology; National Institute of Psychiatry and Neurology; Warsaw Poland
| | - G. Santulli
- Helen and Clyde Wu Center for Molecular Cardiology; Department of Physiology and Cellular Biophysics; College of Physicians and Surgeons of Columbia University; New York NY USA
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14
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Schmitz U, Lai X, Winter F, Wolkenhauer O, Vera J, Gupta SK. Cooperative gene regulation by microRNA pairs and their identification using a computational workflow. Nucleic Acids Res 2014; 42:7539-52. [PMID: 24875477 PMCID: PMC4081082 DOI: 10.1093/nar/gku465] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
MicroRNAs (miRNAs) are an integral part of gene regulation at the post-transcriptional level. Recently, it has been shown that pairs of miRNAs can repress the translation of a target mRNA in a cooperative manner, which leads to an enhanced effectiveness and specificity in target repression. However, it remains unclear which miRNA pairs can synergize and which genes are target of cooperative miRNA regulation. In this paper, we present a computational workflow for the prediction and analysis of cooperating miRNAs and their mutual target genes, which we refer to as RNA triplexes. The workflow integrates methods of miRNA target prediction; triplex structure analysis; molecular dynamics simulations and mathematical modeling for a reliable prediction of functional RNA triplexes and target repression efficiency. In a case study we analyzed the human genome and identified several thousand targets of cooperative gene regulation. Our results suggest that miRNA cooperativity is a frequent mechanism for an enhanced target repression by pairs of miRNAs facilitating distinctive and fine-tuned target gene expression patterns. Human RNA triplexes predicted and characterized in this study are organized in a web resource at www.sbi.uni-rostock.de/triplexrna/.
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Affiliation(s)
- Ulf Schmitz
- Department of Systems Biology and Bioinformatics, University of Rostock, Rostock, Germany
| | - Xin Lai
- Laboratory of Systems Tumor Immunology, Department of Dermatology, University Hospital Erlangen, Friedrich-Alexander-University Erlangen-Nuremberg, Germany
| | - Felix Winter
- Department of Systems Biology and Bioinformatics, University of Rostock, Rostock, Germany
| | - Olaf Wolkenhauer
- Department of Systems Biology and Bioinformatics, University of Rostock, Rostock, Germany Stellenbosch Institute for Advanced Study (STIAS), Wallenberg Research Centre at Stellenbosch University, Stellenbosch, South Africa
| | - Julio Vera
- Laboratory of Systems Tumor Immunology, Department of Dermatology, University Hospital Erlangen, Friedrich-Alexander-University Erlangen-Nuremberg, Germany
| | - Shailendra K Gupta
- Department of Systems Biology and Bioinformatics, University of Rostock, Rostock, Germany Department of Bioinformatics, CSIR-Indian Institute of Toxicology Research, 226001 Lucknow, Uttar Pradesh, India
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15
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Aftabuddin M, Mal C, Deb A, Kundu S. C2Analyzer: Co-target-co-function analyzer. GENOMICS PROTEOMICS & BIOINFORMATICS 2014; 12:133-6. [PMID: 24862384 PMCID: PMC4411367 DOI: 10.1016/j.gpb.2014.03.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/23/2013] [Revised: 03/25/2014] [Accepted: 03/26/2014] [Indexed: 11/04/2022]
Abstract
MicroRNAs (miRNAs) interact with their target mRNAs and regulate biological processes at post-transcriptional level. While one miRNA can target many mRNAs, a single mRNA can also be targeted by a set of miRNAs. The targeted mRNAs may be involved in different biological processes that are described by gene ontology (GO) terms. The major challenges involved in analyzing these multitude regulations include identification of the combinatorial regulation of miRNAs as well as determination of the co-functionally-enriched miRNA pairs. The C2Analyzer: Co-target–Co-function Analyzer, is a Perl-based, versatile and user-friendly web tool with online instructions. Based on the hypergeometric analysis, this novel tool can determine whether given pairs of miRNAs are co-functionally enriched. For a given set of GO term(s), it can also identify the set of miRNAs whose targets are enriched in the given GO term(s). Moreover, C2Analyzer can also identify the co-targeting miRNA pairs, their targets and GO processes, which they are involved in. The miRNA–miRNA co-functional relationship can also be saved as a .txt file, which can be used to further visualize the co-functional network by using other software like Cytoscape. C2Analyzer is freely available at www.bioinformatics.org/c2analyzer.
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Affiliation(s)
- Md Aftabuddin
- West Bengal University of Technology, Kolkata 700064, India
| | - Chittabrata Mal
- Department of Biophysics, Molecular Biology & Bioinformatics, University of Calcutta, Kolkata 700009, India
| | - Arindam Deb
- Department of Biophysics, Molecular Biology & Bioinformatics, University of Calcutta, Kolkata 700009, India
| | - Sudip Kundu
- Department of Biophysics, Molecular Biology & Bioinformatics, University of Calcutta, Kolkata 700009, India.
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16
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Androsavich JR, Chau BN. Non-inhibited miRNAs shape the cellular response to anti-miR. Nucleic Acids Res 2014; 42:6945-55. [PMID: 24810853 PMCID: PMC4066772 DOI: 10.1093/nar/gku344] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Identification of primary microRNA (miRNA) gene targets is critical for developing miRNA-based therapeutics and understanding their mechanisms of action. However, disentangling primary target derepression induced by miRNA inhibition from secondary effects on the transcriptome remains a technical challenge. Here, we utilized RNA immunoprecipitation (RIP) combined with competitive binding assays to identify novel primary targets of miR-122. These transcripts physically dissociate from AGO2-miRNA complexes when anti-miR is spiked into liver lysates. mRNA target displacement strongly correlated with expression changes in these genes following in vivo anti-miR dosing, suggesting that derepression of these targets directly reflects changes in AGO2 target occupancy. Importantly, using a metric based on weighted miRNA expression, we found that the most responsive mRNA target candidates in both RIP competition assays and expression profiling experiments were those with fewer alternative seed sites for highly expressed non-inhibited miRNAs. These data strongly suggest that miRNA co-regulation modulates the transcriptomic response to anti-miR. We demonstrate the practical utility of this ‘miR-target impact’ model, and encourage its incorporation, together with the RIP competition assay, into existing target prediction and validation pipelines.
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Affiliation(s)
- John R Androsavich
- Regulus Therapeutics Inc., 3545 John Hopkins Ct, San Diego, CA 92121, USA
| | - B Nelson Chau
- Regulus Therapeutics Inc., 3545 John Hopkins Ct, San Diego, CA 92121, USA
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17
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Sala V, Bergerone S, Gatti S, Gallo S, Ponzetto A, Ponzetto C, Crepaldi T. MicroRNAs in myocardial ischemia: identifying new targets and tools for treating heart disease. New frontiers for miR-medicine. Cell Mol Life Sci 2014; 71:1439-52. [PMID: 24218009 PMCID: PMC11113160 DOI: 10.1007/s00018-013-1504-0] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2013] [Revised: 10/17/2013] [Accepted: 10/18/2013] [Indexed: 01/16/2023]
Abstract
MicroRNAs (miRNAs) are natural, single-stranded, small RNA molecules which subtly control gene expression. Several studies indicate that specific miRNAs can regulate heart function both in development and disease. Despite prevention programs and new therapeutic agents, cardiovascular disease remains the main cause of death in developed countries. The elevated number of heart failure episodes is mostly due to myocardial infarction (MI). An increasing number of studies have been carried out reporting changes in miRNAs gene expression and exploring their role in MI and heart failure. In this review, we furnish a critical analysis of where the frontier of knowledge has arrived in the fields of basic and translational research on miRNAs in cardiac ischemia. We first summarize the basal information on miRNA biology and regulation, especially concentrating on the feedback loops which control cardiac-enriched miRNAs. A focus on the role of miRNAs in the pathogenesis of myocardial ischemia and in the attenuation of injury is presented. Particular attention is given to cardiomyocyte death (apoptosis and necrosis), fibrosis, neovascularization, and heart failure. Then, we address the potential of miR-diagnosis (miRNAs as disease biomarkers) and miR-drugs (miRNAs as therapeutic targets) for cardiac ischemia and heart failure. Finally, we evaluate the use of miRNAs in the emerging field of regenerative medicine.
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Affiliation(s)
- V. Sala
- Department of Oncology, University of Turin, Turin, Italy
- Department of Medical Sciences, University of Turin, Turin, Italy
| | - S. Bergerone
- Azienda Ospedaliera Città della Salute e della Scienza di Torino, Turin, Italy
| | - S. Gatti
- Department of Oncology, University of Turin, Turin, Italy
| | - S. Gallo
- Department of Oncology, University of Turin, Turin, Italy
| | - A. Ponzetto
- Department of Medical Sciences, University of Turin, Turin, Italy
| | - C. Ponzetto
- Department of Oncology, University of Turin, Turin, Italy
| | - T. Crepaldi
- Department of Oncology, University of Turin, Turin, Italy
- Institute of Anatomy, Corso Massimo d’Azeglio 52, 10126 Turin, Italy
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18
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Iudicibus SD, Lucafò M, Martelossi S, Pierobon C, Ventura A, Decorti G. MicroRNAs as tools to predict glucocorticoid response in inflammatory bowel diseases. World J Gastroenterol 2013; 19:7947-54. [PMID: 24307788 PMCID: PMC3848142 DOI: 10.3748/wjg.v19.i44.7947] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/28/2013] [Revised: 10/16/2013] [Accepted: 10/19/2013] [Indexed: 02/06/2023] Open
Abstract
In spite of the introduction in therapy of highly effective biological agents, glucocorticoids (GCs) are still employed to induce remission in moderate to severe inflammatory bowel diseases (IBD), but considerable inter-individual differences in their efficacy and side effects have been reported. The effectiveness of these drugs is indeed very variable and side effects, particularly severe in pediatric patients, are common and often unpredictable: the understanding of the complex gene regulation mediated by GCs could shed light on the causes of this variability. In this context, microRNAs (miRNAs) represent a new and promising field of research. miRNAs are small non-coding RNA molecules that suppress gene expression at post-transcriptional level, and are fine-tuning regulators of diverse biological processes, including the development and function of the immune system, apoptosis, metabolism and inflammation. Emerging data have implicated the deregulated expression of certain miRNA networks in the pathogenesis of autoimmune and inflammatory diseases, such as IBD. There is a great interest in the identification of the role of miRNAs in the modulation of pharmacological response; however, the association between miRNA and GC response in patients with IBD has not yet been evaluated in a prospective clinical study. The identification of miRNAs differently expressed as a consequence of GC treatment in comparison to diagnosis, represents an important innovative approach that could be translated into clinical practice. In this review we highlight the altered regulation of proteins involved in GC molecular mechanism by miRNAs, and their potential role as molecular markers useful for predicting in advance GC response.
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