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Buddham R, Chauhan S, Narad P, Mathur P. Reconstruction and Exploratory Analysis of mTORC1 Signaling Pathway and Its Applications to Various Diseases Using Network-Based Approach. J Microbiol Biotechnol 2022; 32:365-377. [PMID: 35001007 PMCID: PMC9628786 DOI: 10.4014/jmb.2108.08007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 01/04/2022] [Accepted: 01/06/2022] [Indexed: 12/15/2022]
Abstract
Mammalian target of rapamycin (mTOR) is a serine-threonine kinase member of the cellular phosphatidylinositol 3-kinase (PI3K) pathway, which is involved in multiple biological functions by transcriptional and translational control. mTOR is a downstream mediator in the PI3K/Akt signaling pathway and plays a critical role in cell survival. In cancer, this pathway can be activated by membrane receptors, including the HER (or ErbB) family of growth factor receptors, the insulin-like growth factor receptor, and the estrogen receptor. In the present work, we congregated an electronic network of mTORC1 built on an assembly of data using natural language processing, consisting of 470 edges (activations/interactions and/or inhibitions) and 206 nodes representing genes/proteins, using the Cytoscape 3.6.0 editor and its plugins for analysis. The experimental design included the extraction of gene expression data related to five distinct types of cancers, namely, pancreatic ductal adenocarcinoma, hepatic cirrhosis, cervical cancer, glioblastoma, and anaplastic thyroid cancer from Gene Expression Omnibus (NCBI GEO) followed by pre-processing and normalization of the data using R & Bioconductor. ExprEssence plugin was used for network condensation to identify differentially expressed genes across the gene expression samples. Gene Ontology (GO) analysis was performed to find out the over-represented GO terms in the network. In addition, pathway enrichment and functional module analysis of the protein-protein interaction (PPI) network were also conducted. Our results indicated NOTCH1, NOTCH3, FLCN, SOD1, SOD2, NF1, and TLR4 as upregulated proteins in different cancer types highlighting their role in cancer progression. The MCODE analysis identified gene clusters for each cancer type with MYC, PCNA, PARP1, IDH1, FGF10, PTEN, and CCND1 as hub genes with high connectivity. MYC for cervical cancer, IDH1 for hepatic cirrhosis, MGMT for glioblastoma and CCND1 for anaplastic thyroid cancer were identified as genes with prognostic importance using survival analysis.
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Affiliation(s)
- Richa Buddham
- Centre for Computational Biology and Bioinformatics, Amity Institute of Biotechnology, Amity University Uttar Pradesh Noida-201313, India
| | - Sweety Chauhan
- Centre for Computational Biology and Bioinformatics, Amity Institute of Biotechnology, Amity University Uttar Pradesh Noida-201313, India
| | - Priyanka Narad
- Centre for Computational Biology and Bioinformatics, Amity Institute of Biotechnology, Amity University Uttar Pradesh Noida-201313, India
| | - Puniti Mathur
- Centre for Computational Biology and Bioinformatics, Amity Institute of Biotechnology, Amity University Uttar Pradesh Noida-201313, India,Corresponding author Phone: +91-120-4392204 E-mail:
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Henze L, Walter U, Murua Escobar H, Junghanss C, Jaster R, Köhling R, Lange F, Salehzadeh-Yazdi A, Wolkenhauer O, Hamed M, Barrantes I, Palmer D, Möller S, Kowald A, Heussen N, Fuellen G. Towards biomarkers for outcomes after pancreatic ductal adenocarcinoma and ischaemic stroke, with focus on (co)-morbidity and ageing/cellular senescence (SASKit): protocol for a prospective cohort study. BMJ Open 2020; 10:e039560. [PMID: 33334830 PMCID: PMC7747584 DOI: 10.1136/bmjopen-2020-039560] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
INTRODUCTION Ageing-related processes such as cellular senescence are believed to underlie the accumulation of diseases in time, causing (co)morbidity, including cancer, thromboembolism and stroke. Interfering with these processes may delay, stop or reverse morbidity. The aim of this study is to investigate the link between (co)morbidity and ageing by exploring biomarkers and molecular mechanisms of disease-triggered deterioration in patients with pancreatic ductal adenocarcinoma (PDAC) and (thromboembolic) ischaemic stroke (IS). METHODS AND ANALYSIS We will recruit 50 patients with PDAC, 50 patients with (thromboembolic) IS and 50 controls at Rostock University Medical Center, Germany. We will gather routine blood data, clinical performance measurements and patient-reported outcomes at up to seven points in time, alongside in-depth transcriptomics and proteomics at two of the early time points. Aiming for clinically relevant biomarkers, the primary outcome is a composite of probable sarcopenia, clinical performance (described by ECOG Performance Status for patients with PDAC and the Modified Rankin Scale for patients with stroke) and quality of life. Further outcomes cover other aspects of morbidity such as cognitive decline and of comorbidity such as vascular or cancerous events. The data analysis is comprehensive in that it includes biostatistics and machine learning, both following standard role models and additional explorative approaches. Prognostic and predictive biomarkers for interventions addressing senescence may become available if the biomarkers that we find are specifically related to ageing/cellular senescence. Similarly, diagnostic biomarkers will be explored. Our findings will require validation in independent studies, and our dataset shall be useful to validate the findings of other studies. In some of the explorative analyses, we shall include insights from systems biology modelling as well as insights from preclinical animal models. We anticipate that our detailed study protocol and data analysis plan may also guide other biomarker exploration trials. ETHICS AND DISSEMINATION The study was approved by the local ethics committee (Ethikkommission an der Medizinischen Fakultät der Universität Rostock, A2019-0174), registered at the German Clinical Trials Register (DRKS00021184), and results will be published following standard guidelines.
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Affiliation(s)
- Larissa Henze
- Department of Medicine, Clinic III, Hematology, Oncology, Palliative Medicine, Rostock University Medical Center and Research Focus Oncology, Rostock, Germany
| | - Uwe Walter
- Department of Neurology, Rostock University Medical Center and Centre for Transdisciplinary Neurosciences Rostock, Rostock, Germany
| | - Hugo Murua Escobar
- Department of Medicine, Clinic III, Hematology, Oncology, Palliative Medicine, Rostock University Medical Center and Research Focus Oncology, Rostock, Germany
| | - Christian Junghanss
- Department of Medicine, Clinic III, Hematology, Oncology, Palliative Medicine, Rostock University Medical Center and Research Focus Oncology, Rostock, Germany
| | - Robert Jaster
- Department of Gastroenterology, Rostock University Medical Center and Research Focus Oncology, Rostock, Germany
| | - Rüdiger Köhling
- Oscar Langendorff Institute of Physiology, Rostock University Medical Center and Centre for Transdisciplinary Neurosciences Rostock and Ageing of Individuals and Society, Interdisciplinary Faculty, Rostock University, Rostock, Germany
| | - Falko Lange
- Oscar Langendorff Institute of Physiology, Rostock University Medical Center, Rostock, Germany
| | - Ali Salehzadeh-Yazdi
- Department of Systems Biology and Bioinformatics, University of Rostock, Rostock, Germany
| | - Olaf Wolkenhauer
- Department of Systems Biology and Bioinformatics, University of Rostock and Centre for Transdisciplinary Neurosciences Rostock, Rostock University Medical Center, Rostock, Germany
| | - Mohamed Hamed
- Institute for Biostatistics and Informatics in Medicine and Ageing Research, Rostock University Medical Center and Research Focus Oncology, Rostock, Germany
| | - Israel Barrantes
- Institute for Biostatistics and Informatics in Medicine and Ageing Research, Rostock University Medical Center and Research Focus Oncology, Rostock, Germany
| | - Daniel Palmer
- Institute for Biostatistics and Informatics in Medicine and Ageing Research, Rostock University Medical Center, Rostock, Germany
| | - Steffen Möller
- Institute for Biostatistics and Informatics in Medicine and Ageing Research, Rostock University Medical Center, Rostock, Germany
| | - Axel Kowald
- Institute for Biostatistics and Informatics in Medicine and Ageing Research, Rostock University Medical Center, Rostock, Germany
| | - Nicole Heussen
- Department of Medical Statistics, RWTH Aachen, Aachen, Germany
| | - Georg Fuellen
- Institute for Biostatistics and Informatics in Medicine and Ageing Research, Rostock University Medical Center and Centre for Transdisciplinary Neurosciences Rostock and Research Focus Oncology, Rostock and Ageing of Individuals and Society, Interdisciplinary Faculty, Rostock University, Rostock, Germany
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Stahnke T, Gajda-Deryło B, Jünemann AG, Stachs O, Sterenczak KA, Rejdak R, Beck J, Schütz E, Möller S, Barrantes I, Warsow G, Struckmann S, Fuellen G. Suppression of the TGF-β pathway by a macrolide antibiotic decreases fibrotic responses by ocular fibroblasts in vitro. ROYAL SOCIETY OPEN SCIENCE 2020; 7:200441. [PMID: 33047019 PMCID: PMC7540802 DOI: 10.1098/rsos.200441] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Accepted: 08/19/2020] [Indexed: 05/12/2023]
Abstract
To elucidate and to inhibit post-surgical fibrotic processes after trabeculectomy in glaucoma therapy, we measured gene expression in a fibrotic cell culture model, based on transforming growth factor TGF-β induction in primary human tenon fibroblasts (hTFs), and used Connectivity Map (CMap) data for drug repositioning. We found that specific molecular mechanisms behind fibrosis are the upregulation of actins, the downregulation of CD34, and the upregulation of inflammatory cytokines such as IL6, IL11 and BMP6. The macrolide antibiotic Josamycin (JM) reverses these molecular mechanisms according to data from the CMap, and we thus tested JM as an inhibitor of fibrosis. JM was first tested for its toxic effects on hTFs, where it showed no influence on cell viability, but inhibited hTF proliferation in a concentration-dependent manner. We then demonstrated that JM suppresses the synthesis of extracellular matrix (ECM) components. In hTFs stimulated with TGF-β1, JM specifically inhibited α-smooth muslce actin expression, suggesting that it inhibits the transformation of fibroblasts into fibrotic myofibroblasts. In addition, a decrease of components of the ECM such as fibronectin, which is involved in in vivo scarring, was observed. We conclude that JM may be a promising candidate for the treatment of fibrosis after glaucoma filtration surgery or drainage device implantation in vivo.
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Affiliation(s)
- Thomas Stahnke
- Department of Ophthalmology, Rostock University Medical Center, Rostock, Germany
| | - Beata Gajda-Deryło
- Institute for Biostatistics and Informatics in Medicine and Ageing Research, Rostock University Medical Center, Rostock, Germany
| | - Anselm G. Jünemann
- Department of Ophthalmology, Rostock University Medical Center, Rostock, Germany
| | - Oliver Stachs
- Department of Ophthalmology, Rostock University Medical Center, Rostock, Germany
| | | | - Robert Rejdak
- Department of General Ophthalmology, Medical University in Lublin, Poland
| | - Julia Beck
- Chronix Biomedical GmbH, Göttingen, Germany
| | | | - Steffen Möller
- Institute for Biostatistics and Informatics in Medicine and Ageing Research, Rostock University Medical Center, Rostock, Germany
| | - Israel Barrantes
- Institute for Biostatistics and Informatics in Medicine and Ageing Research, Rostock University Medical Center, Rostock, Germany
| | - Gregor Warsow
- Institute for Biostatistics and Informatics in Medicine and Ageing Research, Rostock University Medical Center, Rostock, Germany
| | - Stephan Struckmann
- Institute for Biostatistics and Informatics in Medicine and Ageing Research, Rostock University Medical Center, Rostock, Germany
- SHIP-KEF, Institute for Community Medicine, Greifswald University Medical Center, Greifswald, Germany
- Authors for correspondence: Stephan Struckmann e-mail:
| | - Georg Fuellen
- Institute for Biostatistics and Informatics in Medicine and Ageing Research, Rostock University Medical Center, Rostock, Germany
- Authors for correspondence: Georg Fuellen e-mail:
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Rush STA, Repsilber D. Capturing context-specific regulation in molecular interaction networks. BMC Bioinformatics 2018; 19:539. [PMID: 30577761 PMCID: PMC6303932 DOI: 10.1186/s12859-018-2513-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Accepted: 11/20/2018] [Indexed: 01/20/2023] Open
Abstract
BACKGROUND Molecular profiles change in response to perturbations. These changes are coordinated into functional modules via regulatory interactions. The genes and their products within a functional module are expected to be differentially expressed in a manner coherent with their regulatory network. This perspective presents a promising approach to increase precision in detecting differential signals as well as for describing differential regulatory signals within the framework of a priori knowledge about the underlying network, and so from a mechanistic point of view. RESULTS We present Coherent Network Expression (CoNE), an effective procedure for identifying differentially activated functional modules in molecular interaction networks. Differential gene expression is chosen as example, and differential signals coherent with the regulatory nature of the network are identified. We apply our procedure to systematically simulated data, comparing its performance to alternative methods. We then take the example case of a transcription regulatory network in the context of particle-induced pulmonary inflammation, recapitulating and proposing additional candidates to previously obtained results. CoNE is conveniently implemented in an R-package along with simulation utilities. CONCLUSION Combining coherent interactions with error control on differential gene expression results in uniformly greater specificity in inference than error control alone, ensuring that captured functional modules constitute real findings.
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Affiliation(s)
- Stephen T. A. Rush
- School of Medical Sciences, Örebro University, Södra Grev Rosengatan, Örebro, Sweden
| | - Dirk Repsilber
- School of Medical Sciences, Örebro University, Södra Grev Rosengatan, Örebro, Sweden
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5
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Legeay M, Aubourg S, Renou JP, Duval B. Large scale study of anti-sense regulation by differential network analysis. BMC SYSTEMS BIOLOGY 2018; 12:95. [PMID: 30458828 PMCID: PMC6245689 DOI: 10.1186/s12918-018-0613-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Background Systems biology aims to analyse regulation mechanisms into the cell. By mapping interactions observed in different situations, differential network analysis has shown its power to reveal specific cellular responses or specific dysfunctional regulations. In this work, we propose to explore on a large scale the role of natural anti-sense transcription on gene regulation mechanisms, and we focus our study on apple (Malus domestica) in the context of fruit ripening in cold storage. Results We present a differential functional analysis of the sense and anti-sense transcriptomic data that reveals functional terms linked to the ripening process. To develop our differential network analysis, we introduce our inference method of an Extended Core Network; this method is inspired by C3NET, but extends the notion of significant interactions. By comparing two extended core networks, one inferred with sense data and the other one inferred with sense and anti-sense data, our differential analysis is first performed on a local view and reveals AS-impacted genes, genes that have important interactions impacted by anti-sense transcription. The motifs surrounding AS-impacted genes gather transcripts with functions mostly consistent with the biological context of the data used and the method allows us to identify new actors involved in ripening and cold acclimation pathways and to decipher their interactions. Then from a more global view, we compute minimal sub-networks that connect the AS-impacted genes using Steiner trees. Those Steiner trees allow us to study the rewiring of the AS-impacted genes in the network with anti-sense actors. Conclusion Anti-sense transcription is usually ignored in transcriptomic studies. The large-scale differential analysis of apple data that we propose reveals that anti-sense regulation may have an important impact in several cellular stress response mechanisms. Our data mining process enables to highlight specific interactions that deserve further experimental investigations. Electronic supplementary material The online version of this article (10.1186/s12918-018-0613-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Marc Legeay
- LERIA, Université d'Angers, 2 bd Lavoisier, Angers, 49045, France.,IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, Beaucouzé, 49071, France
| | - Sébastien Aubourg
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, Beaucouzé, 49071, France
| | - Jean-Pierre Renou
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, Beaucouzé, 49071, France
| | - Béatrice Duval
- LERIA, Université d'Angers, 2 bd Lavoisier, Angers, 49045, France.
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Salvador M, Argandoña M, Naranjo E, Piubeli F, Nieto JJ, Csonka LN, Vargas C. Quantitative RNA-seq Analysis Unveils Osmotic and Thermal Adaptation Mechanisms Relevant for Ectoine Production in Chromohalobacter salexigens. Front Microbiol 2018; 9:1845. [PMID: 30158907 PMCID: PMC6104435 DOI: 10.3389/fmicb.2018.01845] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Accepted: 07/24/2018] [Indexed: 01/18/2023] Open
Abstract
Quantitative RNA sequencing (RNA-seq) and the complementary phenotypic assays were implemented to investigate the transcriptional responses of Chromohalobacter salexigens to osmotic and heat stress. These conditions trigger the synthesis of ectoine and hydroxyectoine, two compatible solutes of biotechnological interest. Our findings revealed that both stresses make a significant impact on C. salexigens global physiology. Apart from compatible solute metabolism, the most relevant adaptation mechanisms were related to “oxidative- and protein-folding- stress responses,” “modulation of respiratory chain and related components,” and “ion homeostasis.” A general salt-dependent induction of genes related to the metabolism of ectoines, as well as repression of ectoine degradation genes by temperature, was observed. Different oxidative stress response mechanisms, secondary or primary, were induced at low and high salinity, respectively, and repressed by temperature. A higher sensitivity to H2O2 was observed at high salinity, regardless of temperature. Low salinity induced genes involved in “protein-folding-stress response,” suggesting disturbance of protein homeostasis. Transcriptional shift of genes encoding three types of respiratory NADH dehydrogenases, ATP synthase, quinone pool, Na+/H+ antiporters, and sodium-solute symporters, was observed depending on salinity and temperature, suggesting modulation of the components of the respiratory chain and additional systems involved in the generation of H+ and/or Na+ gradients. Remarkably, the Na+ intracellular content remained constant regardless of salinity and temperature. Disturbance of Na+- and H+-gradients with specific ionophores suggested that both gradients influence ectoine production, but with differences depending on the solute, salinity, and temperature conditions. Flagellum genes were strongly induced by salinity, and further induced by temperature. However, salt-induced cell motility was reduced at high temperature, possibly caused by an alteration of Na+ permeability by temperature, as dependence of motility on Na+-gradient was observed. The transcriptional induction of genes related to the synthesis and transport of siderophores correlated with a higher siderophore production and intracellular iron content only at low salinity. An excess of iron increased hydroxyectoine accumulation by 20% at high salinity. Conversely, it reduced the intracellular content of ectoines by 50% at high salinity plus high temperature. These findings support the relevance of iron homeostasis for osmoadaptation, thermoadaptation and accumulation of ectoines, in C. salexigens.
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Affiliation(s)
- Manuel Salvador
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Seville, Seville, Spain.,Faculty of Health and Medical Sciences, University of Surrey, Guildford, United Kingdom
| | - Montserrat Argandoña
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Seville, Seville, Spain
| | - Emilia Naranjo
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Seville, Seville, Spain
| | - Francine Piubeli
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Seville, Seville, Spain
| | - Joaquín J Nieto
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Seville, Seville, Spain
| | - Lazslo N Csonka
- Department of Biological Sciences, Purdue University, West Lafayette, IN, United States
| | - Carmen Vargas
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Seville, Seville, Spain
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Avey S, Mohanty S, Wilson J, Zapata H, Joshi SR, Siconolfi B, Tsang S, Shaw AC, Kleinstein SH. Multiple network-constrained regressions expand insights into influenza vaccination responses. Bioinformatics 2018; 33:i208-i216. [PMID: 28881994 PMCID: PMC5870750 DOI: 10.1093/bioinformatics/btx260] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Motivation Systems immunology leverages recent technological advancements that enable broad profiling of the immune system to better understand the response to infection and vaccination, as well as the dysregulation that occurs in disease. An increasingly common approach to gain insights from these large-scale profiling experiments involves the application of statistical learning methods to predict disease states or the immune response to perturbations. However, the goal of many systems studies is not to maximize accuracy, but rather to gain biological insights. The predictors identified using current approaches can be biologically uninterpretable or present only one of many equally predictive models, leading to a narrow understanding of the underlying biology. Results Here we show that incorporating prior biological knowledge within a logistic modeling framework by using network-level constraints on transcriptional profiling data significantly improves interpretability. Moreover, incorporating different types of biological knowledge produces models that highlight distinct aspects of the underlying biology, while maintaining predictive accuracy. We propose a new framework, Logistic Multiple Network-constrained Regression (LogMiNeR), and apply it to understand the mechanisms underlying differential responses to influenza vaccination. Although standard logistic regression approaches were predictive, they were minimally interpretable. Incorporating prior knowledge using LogMiNeR led to models that were equally predictive yet highly interpretable. In this context, B cell-specific genes and mTOR signaling were associated with an effective vaccination response in young adults. Overall, our results demonstrate a new paradigm for analyzing high-dimensional immune profiling data in which multiple networks encoding prior knowledge are incorporated to improve model interpretability. Availability and implementation The R source code described in this article is publicly available at https://bitbucket.org/kleinstein/logminer . Contact steven.kleinstein@yale.edu or stefan.avey@yale.edu. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Stefan Avey
- Interdepartmental Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA
| | - Subhasis Mohanty
- Section of Infectious Diseases, Department of Internal Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Jean Wilson
- Section of Infectious Diseases, Department of Internal Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Heidi Zapata
- Section of Infectious Diseases, Department of Internal Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Samit R Joshi
- Section of Infectious Diseases, Department of Internal Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Barbara Siconolfi
- Section of Infectious Diseases, Department of Internal Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Sui Tsang
- Department of Internal Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Albert C Shaw
- Section of Infectious Diseases, Department of Internal Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Steven H Kleinstein
- Interdepartmental Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA.,Departments of Pathology and Immunobiology, Yale School of Medicine, New Haven, CT, USA
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Liu D, Yu X, Wang S, Dai E, Jiang L, Wang J, Yang Q, Yang F, Zhou S, Jiang W. The gain and loss of long noncoding RNA associated-competing endogenous RNAs in prostate cancer. Oncotarget 2018; 7:57228-57238. [PMID: 27528026 PMCID: PMC5302985 DOI: 10.18632/oncotarget.11128] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Accepted: 07/27/2016] [Indexed: 12/11/2022] Open
Abstract
Prostate cancer (PC) is one of the most common solid tumors in men. However, the molecular mechanism of PC remains unclear. Numerous studies have demonstrated that long noncoding RNA (lncRNA) can act as microRNA (miRNA) sponge, one type of competing endogenous RNAs (ceRNAs), which offers a novel viewpoint to elucidate the mechanisms of PC. Here, we proposed an integrative systems biology approach to infer the gain and loss of ceRNAs in PC. First, we re-annotated exon microarray data to obtain lncRNA expression profiles of PC. Second, by integrating mRNA and miRNA expression, as well as miRNA targets, we constructed lncRNA-miRNA-mRNA ceRNA networks in cancer and normal samples. The lncRNAs in these two ceRNA networks tended to have a longer transcript length and cover more exons than the lncRNAs not involved in ceRNA networks. Next, we further extracted the gain and loss ceRNA networks in PC. We found that the gain ceRNAs in PC participated in cell cycle, and the loss ceRNAs in PC were associated with metabolism. We also identified potential prognostic ceRNA pairs such as MALAT1-EGR2 and MEG3-AQP3. Finally, we inferred a novel mechanism of known drugs, such as cisplatin, for the treatment of PC through gain and loss ceRNA networks. The potential drugs such as 1,2,6-tri-O-galloyl-beta-D-glucopyranose (TGGP) could modulate lncRNA-mRNA competing relationships, which may uncover new strategy for treating PC. In summary, we systematically investigated the gain and loss of ceRNAs in PC, which may prove useful for identifying potential biomarkers and therapeutics for PC.
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Affiliation(s)
- Dianming Liu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Xuexin Yu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Shuyuan Wang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Enyu Dai
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Leiming Jiang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Jing Wang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Qian Yang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Feng Yang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Shunheng Zhou
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Wei Jiang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
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Exome Sequencing Landscape Analysis in Ovarian Clear Cell Carcinoma Shed Light on Key Chromosomal Regions and Mutation Gene Networks. THE AMERICAN JOURNAL OF PATHOLOGY 2017; 187:2246-2258. [PMID: 28888422 DOI: 10.1016/j.ajpath.2017.06.012] [Citation(s) in RCA: 74] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Accepted: 06/08/2017] [Indexed: 12/18/2022]
Abstract
Previous studies have reported genome-wide mutation profile analyses in ovarian clear cell carcinomas (OCCCs). This study aims to identify specific novel molecular alterations by combined analyses of somatic mutation and copy number variation. We performed whole exome sequencing of 39 OCCC samples with 16 matching blood tissue samples. Four hundred twenty-six genes had recurrent somatic mutations. Among the 39 samples, ARID1A (62%) and PIK3CA (51%) were frequently mutated, as were genes such as KRAS (10%), PPP2R1A (10%), and PTEN (5%), that have been reported in previous OCCC studies. We also detected mutations in MLL3 (15%), ARID1B (10%), and PIK3R1 (8%), which are associations not previously reported. Gene interaction analysis and functional assessment revealed that mutated genes were clustered into groups pertaining to chromatin remodeling, cell proliferation, DNA repair and cell cycle checkpointing, and cytoskeletal organization. Copy number variation analysis identified frequent amplification in chr8q (64%), chr20q (54%), and chr17q (46%) loci as well as deletion in chr19p (41%), chr13q (28%), chr9q (21%), and chr18q (21%) loci. Integration of the analyses uncovered that frequently mutated or amplified/deleted genes were involved in the KRAS/phosphatidylinositol 3-kinase (82%) and MYC/retinoblastoma (75%) pathways as well as the critical chromatin remodeling complex switch/sucrose nonfermentable (85%). The individual and integrated analyses contribute details about the OCCC genomic landscape, which could lead to enhanced diagnostics and therapeutic options.
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Neuditschko M, Raadsma HW, Khatkar MS, Jonas E, Steinig EJ, Flury C, Signer-Hasler H, Frischknecht M, von Niederhäusern R, Leeb T, Rieder S. Identification of key contributors in complex population structures. PLoS One 2017; 12:e0177638. [PMID: 28520805 PMCID: PMC5433729 DOI: 10.1371/journal.pone.0177638] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Accepted: 05/01/2017] [Indexed: 11/18/2022] Open
Abstract
Evaluating the genetic contribution of individuals to population structure is essential to select informative individuals for genome sequencing, genotype imputation and to ascertain complex population structures. Existing methods for the selection of informative individuals for genomic imputation solely focus on the identification of key ancestors, which can lead to a loss of phasing accuracy of the reference population. Currently many methods are independently applied to investigate complex population structures. Based on the Eigenvalue Decomposition (EVD) of a genomic relationship matrix we describe a novel approach to evaluate the genetic contribution of individuals to population structure. We combined the identification of key contributors with model-based clustering and population network visualization into an integrated three-step approach, which allows identification of high-resolution population structures and substructures around such key contributors. The approach was applied and validated in four disparate datasets including a simulated population (5,100 individuals and 10,000 SNPs), a highly structured experimental sheep population (1,421 individuals and 44,693 SNPs) and two large complex pedigree populations namely horse (1,077 individuals and 38,124 SNPs) and cattle (2,457 individuals and 45,765 SNPs). In the simulated and experimental sheep dataset, our method, which is unsupervised, successfully identified all known key contributors. Applying our three-step approach to the horse and cattle populations, we observed high-resolution population substructures including the absence of obvious important key contributors. Furthermore, we show that compared to commonly applied strategies to select informative individuals for genotype imputation including the computation of marginal gene contributions (Pedig) and the optimization of genetic relatedness (Rel), the selection of key contributors provided the highest phasing accuracies within the selected reference populations. The presented approach opens new perspectives in the characterization and informed management of populations in general, and in areas such as conservation genetics and selective animal breeding in particular, where assessing the genetic contribution of influential and admixed individuals is crucial for research and management applications. As such, this method provides a valuable complement to common applied tools to visualize complex population structures and to select individuals for re-sequencing.
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Affiliation(s)
- Markus Neuditschko
- Agroscope, Swiss National Stud Farm, Avenches, Switzerland
- Reprogen – Animal Bioscience Group, Faculty of Veterinary Science, University of Sydney, Camden, Australia
- * E-mail:
| | - Herman W. Raadsma
- Reprogen – Animal Bioscience Group, Faculty of Veterinary Science, University of Sydney, Camden, Australia
| | - Mehar S. Khatkar
- Reprogen – Animal Bioscience Group, Faculty of Veterinary Science, University of Sydney, Camden, Australia
| | - Elisabeth Jonas
- Reprogen – Animal Bioscience Group, Faculty of Veterinary Science, University of Sydney, Camden, Australia
- SLU, Department of Animal Breeding and Genetics, Uppsala, Sweden
| | - Eike J. Steinig
- College of Marine and Environmental Sciences, James Cook University, Townsville, Australia
| | - Christine Flury
- School of Agricultural Forest and Food Sciences, Bern University of Applied Sciences, Zollikofen, Switzerland
| | - Heidi Signer-Hasler
- School of Agricultural Forest and Food Sciences, Bern University of Applied Sciences, Zollikofen, Switzerland
| | - Mirjam Frischknecht
- Agroscope, Swiss National Stud Farm, Avenches, Switzerland
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | | | - Tosso Leeb
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Stefan Rieder
- Agroscope, Swiss National Stud Farm, Avenches, Switzerland
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11
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Dietary restriction protects against diethylnitrosamine-induced hepatocellular tumorigenesis by restoring the disturbed gene expression profile. Sci Rep 2017; 7:43745. [PMID: 28262799 PMCID: PMC5338348 DOI: 10.1038/srep43745] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2016] [Accepted: 01/30/2017] [Indexed: 02/08/2023] Open
Abstract
Hepatocellular carcinoma (HCC) is one of the most lethal and prevalent malignancies, worse still, there are very limited therapeutic measures with poor clinical outcomes. Dietary restriction (DR) has been known to inhibit spontaneous and induced tumors in several species, but the mechanisms are little known. In the current study, by using a diethylnitrosamine (DEN)-induced HCC mice model, we found that DR significantly reduced the hepatic tumor number and size, delayed tumor development, suppressed proliferation and promoted apoptosis. Further transcriptome sequencing of liver tissues from the DEN and the DEN accompanied with DR (DEN+DR) mice showed that DEN induced profound changes in the gene expression profile, especially in cancer-related pathways while DR treatment reversed most of the disturbed gene expression induced by DEN. Finally, transcription factor enrichment analysis uncovered the transcription factor specificity protein 1 (SP1) probably functioned as the main regulator of gene changes, orchestrating the protective effects of DR on DEN induced HCC. Taken together, by the first comprehensive transcriptome analysis, we elucidate that DR protects aginst DEN-induced HCC by restoring the disturbed gene expression profile, which holds the promise to provide effective molecular targets for cancer therapies.
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12
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Paul S, Lakatos P, Hartmann A, Schneider-Stock R, Vera J. Identification of miRNA-mRNA Modules in Colorectal Cancer Using Rough Hypercuboid Based Supervised Clustering. Sci Rep 2017; 7:42809. [PMID: 28220871 PMCID: PMC5318911 DOI: 10.1038/srep42809] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2016] [Accepted: 01/13/2017] [Indexed: 02/06/2023] Open
Abstract
Differences in the expression profiles of miRNAs and mRNAs have been reported in colorectal cancer. Nevertheless, information on important miRNA-mRNA regulatory modules in colorectal cancer is still lacking. In this regard, this study presents an application of the RH-SAC algorithm on miRNA and mRNA expression data for identification of potential miRNA-mRNA modules. First, a set of miRNA rules was generated using the RH-SAC algorithm. The mRNA targets of the selected miRNAs were identified using the miRTarBase database. Next, the expression values of target mRNAs were used to generate mRNA rules using the RH-SAC. Then all miRNA-mRNA rules have been integrated for generating networks. The RH-SAC algorithm unlike other existing methods selects a group of co-expressed miRNAs and mRNAs that are also differentially expressed. In total 17 miRNAs and 141 mRNAs were selected. The enrichment analysis of selected mRNAs revealed that our method selected mRNAs that are significantly associated with colorectal cancer. We identified novel miRNA/mRNA interactions in colorectal cancer. Through experiment, we could confirm that one of our discovered miRNAs, hsa-miR-93-5p, was significantly up-regulated in 75.8% CRC in comparison to their corresponding non-tumor samples. It could have the potential to examine colorectal cancer subtype specific unique miRNA/mRNA interactions.
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Affiliation(s)
- Sushmita Paul
- Department of Bioscience & Bioengineering, Indian Institute of Technology Jodhpur, India
| | - Petra Lakatos
- Experimental Tumorpathology, Institute of Pathology, University Hospital of Friedrich-Alexander-University Erlangen-Nürnberg, Germany
| | - Arndt Hartmann
- Institute of Pathology, University Hospital of Friedrich-Alexander-University Erlangen-Nürnberg, Germany
| | - Regine Schneider-Stock
- Experimental Tumorpathology, Institute of Pathology, University Hospital of Friedrich-Alexander-University Erlangen-Nürnberg, Germany
| | - Julio Vera
- Laboratory of Systems Tumor Immunology, Department of Dermatology, Erlangen University Hospital and Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
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13
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FocusHeuristics - expression-data-driven network optimization and disease gene prediction. Sci Rep 2017; 7:42638. [PMID: 28205611 PMCID: PMC5311990 DOI: 10.1038/srep42638] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Accepted: 01/10/2017] [Indexed: 12/27/2022] Open
Abstract
To identify genes contributing to disease phenotypes remains a challenge for bioinformatics. Static knowledge on biological networks is often combined with the dynamics observed in gene expression levels over disease development, to find markers for diagnostics and therapy, and also putative disease-modulatory drug targets and drugs. The basis of current methods ranges from a focus on expression-levels (Limma) to concentrating on network characteristics (PageRank, HITS/Authority Score), and both (DeMAND, Local Radiality). We present an integrative approach (the FocusHeuristics) that is thoroughly evaluated based on public expression data and molecular disease characteristics provided by DisGeNet. The FocusHeuristics combines three scores, i.e. the log fold change and another two, based on the sum and difference of log fold changes of genes/proteins linked in a network. A gene is kept when one of the scores to which it contributes is above a threshold. Our FocusHeuristics is both, a predictor for gene-disease-association and a bioinformatics method to reduce biological networks to their disease-relevant parts, by highlighting the dynamics observed in expression data. The FocusHeuristics is slightly, but significantly better than other methods by its more successful identification of disease-associated genes measured by AUC, and it delivers mechanistic explanations for its choice of genes.
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14
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Parejo M, Wragg D, Gauthier L, Vignal A, Neumann P, Neuditschko M. Using Whole-Genome Sequence Information to Foster Conservation Efforts for the European Dark Honey Bee, Apis mellifera mellifera. Front Ecol Evol 2016. [DOI: 10.3389/fevo.2016.00140] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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15
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Singh NK, Ernst M, Liebscher V, Fuellen G, Taher L. Revealing complex function, process and pathway interactions with high-throughput expression and biological annotation data. MOLECULAR BIOSYSTEMS 2016; 12:3196-208. [PMID: 27507577 DOI: 10.1039/c6mb00280c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The biological relationships both between and within the functions, processes and pathways that operate within complex biological systems are only poorly characterized, making the interpretation of large scale gene expression datasets extremely challenging. Here, we present an approach that integrates gene expression and biological annotation data to identify and describe the interactions between biological functions, processes and pathways that govern a phenotype of interest. The product is a global, interconnected network, not of genes but of functions, processes and pathways, that represents the biological relationships within the system. We validated our approach on two high-throughput expression datasets describing organismal and organ development. Our findings are well supported by the available literature, confirming that developmental processes and apoptosis play key roles in cell differentiation. Furthermore, our results suggest that processes related to pluripotency and lineage commitment, which are known to be critical for development, interact mainly indirectly, through genes implicated in more general biological processes. Moreover, we provide evidence that supports the relevance of cell spatial organization in the developing liver for proper liver function. Our strategy can be viewed as an abstraction that is useful to interpret high-throughput data and devise further experiments.
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Affiliation(s)
- Nitesh Kumar Singh
- Institute for Biostatistics and Informatics in Medicine and Ageing Research, Rostock University Medical Center, Ernst-Heydemann-Str. 8, 18057 Rostock, Germany.
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16
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Pir P, Le Novère N. Mathematical Models of Pluripotent Stem Cells: At the Dawn of Predictive Regenerative Medicine. Methods Mol Biol 2016; 1386:331-50. [PMID: 26677190 DOI: 10.1007/978-1-4939-3283-2_15] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Regenerative medicine, ranging from stem cell therapy to organ regeneration, is promising to revolutionize treatments of diseases and aging. These approaches require a perfect understanding of cell reprogramming and differentiation. Predictive modeling of cellular systems has the potential to provide insights about the dynamics of cellular processes, and guide their control. Moreover in many cases, it provides alternative to experimental tests, difficult to perform for practical or ethical reasons. The variety and accuracy of biological processes represented in mathematical models grew in-line with the discovery of underlying molecular mechanisms. High-throughput data generation led to the development of models based on data analysis, as an alternative to more established modeling based on prior mechanistic knowledge. In this chapter, we give an overview of existing mathematical models of pluripotency and cell fate, to illustrate the variety of methods and questions. We conclude that current approaches are yet to overcome a number of limitations: Most of the computational models have so far focused solely on understanding the regulation of pluripotency, and the differentiation of selected cell lineages. In addition, models generally interrogate only a few biological processes. However, a better understanding of the reprogramming process leading to ESCs and iPSCs is required to improve stem-cell therapies. One also needs to understand the links between signaling, metabolism, regulation of gene expression, and the epigenetics machinery.
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Affiliation(s)
- Pınar Pir
- Babraham Institute, Babraham Research Campus, Cambridge, CB22 3AT, UK.
| | - Nicolas Le Novère
- Babraham Institute, Babraham Research Campus, Cambridge, CB22 3AT, UK.
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17
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Luyten W, Antal P, Braeckman BP, Bundy J, Cirulli F, Fang-Yen C, Fuellen G, Leroi A, Liu Q, Martorell P, Metspalu A, Perola M, Ristow M, Saul N, Schoofs L, Siems K, Temmerman L, Smets T, Wolk A, Rattan SIS. Ageing with elegans: a research proposal to map healthspan pathways. Biogerontology 2016; 17:771-82. [DOI: 10.1007/s10522-016-9644-x] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2015] [Accepted: 03/13/2016] [Indexed: 12/18/2022]
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18
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Kiran M, Nagarajaram HA. Interaction and localization diversities of global and local hubs in human protein–protein interaction networks. MOLECULAR BIOSYSTEMS 2016; 12:2875-82. [DOI: 10.1039/c6mb00104a] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Hubs, the highly connected nodes in protein–protein interaction networks (PPINs), are associated with several characteristic properties and are known to perform vital roles in cells.
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Affiliation(s)
- M. Kiran
- Laboratory of Computational Biology
- Centre for DNA Fingerprinting and Diagnostics
- Gruhakalpa
- Hyderabad 500 001
- India
| | - H. A. Nagarajaram
- Laboratory of Computational Biology
- Centre for DNA Fingerprinting and Diagnostics
- Gruhakalpa
- Hyderabad 500 001
- India
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19
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White CH, Johnston HE, Moesker B, Manousopoulou A, Margolis DM, Richman DD, Spina CA, Garbis SD, Woelk CH, Beliakova-Bethell N. Mixed effects of suberoylanilide hydroxamic acid (SAHA) on the host transcriptome and proteome and their implications for HIV reactivation from latency. Antiviral Res 2015; 123:78-85. [PMID: 26343910 PMCID: PMC5606336 DOI: 10.1016/j.antiviral.2015.09.002] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2015] [Revised: 08/22/2015] [Accepted: 09/03/2015] [Indexed: 02/06/2023]
Abstract
Suberoylanilide hydroxamic acid (SAHA) has been assessed in clinical trials as part of a "shock and kill" strategy to cure HIV-infected patients. While it was effective at inducing expression of HIV RNA ("shock"), treatment with SAHA did not result in a reduction of reservoir size ("kill"). We therefore utilized a combined analysis of effects of SAHA on the host transcriptome and proteome to dissect its mechanisms of action that may explain its limited success in "shock and kill" strategies. CD4+ T cells from HIV seronegative donors were treated with 1μM SAHA or its solvent dimethyl sulfoxide (DMSO) for 24h. Protein expression and post-translational modifications were measured with iTRAQ proteomics using ultra high-precision two-dimensional liquid chromatography-tandem mass spectrometry. Gene expression was assessed by Illumina microarrays. Using limma package in the R computing environment, we identified 185 proteins, 18 phosphorylated forms, 4 acetylated forms and 2982 genes, whose expression was modulated by SAHA. A protein interaction network integrating these 4 data types identified the HIV transcriptional repressor HMGA1 to be upregulated by SAHA at the transcript, protein and acetylated protein levels. Further functional category assessment of proteins and genes modulated by SAHA identified gene ontology terms related to NFκB signaling, protein folding and autophagy, which are all relevant to HIV reactivation. In summary, SAHA modulated numerous host cell transcripts, proteins and post-translational modifications of proteins, which would be expected to have very mixed effects on the induction of HIV-specific transcription and protein function. Proteome profiling highlighted a number of potential counter-regulatory effects of SAHA with respect to viral induction, which transcriptome profiling alone would not have identified. These observations could lead to a more informed selection and design of other HDACi with a more refined targeting profile, and prioritization of latency reversing agents of other classes to be used in combination with SAHA to achieve more potent induction of HIV expression.
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Affiliation(s)
- Cory H White
- Graduate Program in Bioinformatics and Systems Biology, University of California San Diego, La Jolla, CA 92093, USA; San Diego VA Medical Center and Veterans Medical Research Foundation, San Diego, CA 92161, USA
| | - Harvey E Johnston
- Cancer Sciences Faculty of Medicine, University of Southampton, Southampton, Hants SO16 6YD, UK; Centre for Proteomic Research, Institute for Life Sciences, University of Southampton, Highfield Campus, Southampton, UK
| | - Bastiaan Moesker
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, Hants SO16 6YD, UK
| | - Antigoni Manousopoulou
- Centre for Proteomic Research, Institute for Life Sciences, University of Southampton, Highfield Campus, Southampton, UK; Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, Hants SO16 6YD, UK
| | - David M Margolis
- Departments of Medicine, Microbiology and Immunology, Epidemiology, University of North Carolina, Chapel Hill, NC, USA
| | - Douglas D Richman
- San Diego VA Medical Center and Veterans Medical Research Foundation, San Diego, CA 92161, USA; Department of Pathology, University of California San Diego, La Jolla, CA 92093, USA; Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Celsa A Spina
- San Diego VA Medical Center and Veterans Medical Research Foundation, San Diego, CA 92161, USA; Department of Pathology, University of California San Diego, La Jolla, CA 92093, USA
| | - Spiros D Garbis
- Cancer Sciences Faculty of Medicine, University of Southampton, Southampton, Hants SO16 6YD, UK; Centre for Proteomic Research, Institute for Life Sciences, University of Southampton, Highfield Campus, Southampton, UK; Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, Hants SO16 6YD, UK.
| | - Christopher H Woelk
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, Hants SO16 6YD, UK.
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20
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Proteomic Study to Survey the CIGB-552 Antitumor Effect. BIOMED RESEARCH INTERNATIONAL 2015; 2015:124082. [PMID: 26576414 PMCID: PMC4630370 DOI: 10.1155/2015/124082] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/11/2015] [Accepted: 08/26/2015] [Indexed: 11/17/2022]
Abstract
CIGB-552 is a cell-penetrating peptide that exerts in vitro and in vivo antitumor effect on cancer cells. In the present work, the mechanism involved in such anticancer activity was studied using chemical proteomics and expression-based proteomics in culture cancer cell lines. CIGB-552 interacts with at least 55 proteins, as determined by chemical proteomics. A temporal differential proteomics based on iTRAQ quantification method was performed to identify CIGB-552 modulated proteins. The proteomic profile includes 72 differentially expressed proteins in response to CIGB-552 treatment. Proteins related to cell proliferation and apoptosis were identified by both approaches. In line with previous findings, proteomic data revealed that CIGB-552 triggers the inhibition of NF-κB signaling pathway. Furthermore, proteins related to cell invasion were differentially modulated by CIGB-552 treatment suggesting new potentialities of CIGB-552 as anticancer agent. Overall, the current study contributes to a better understanding of the antitumor action mechanism of CIGB-552.
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21
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Matone A, O'Grada CM, Dillon ET, Morris C, Ryan MF, Walsh M, Gibney ER, Brennan L, Gibney MJ, Morine MJ, Roche HM. Body mass index mediates inflammatory response to acute dietary challenges. Mol Nutr Food Res 2015; 59:2279-92. [DOI: 10.1002/mnfr.201500184] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2015] [Revised: 07/27/2015] [Accepted: 08/06/2015] [Indexed: 01/08/2023]
Affiliation(s)
- Alice Matone
- The Microsoft Research; University of Trento Centre for Computational Systems Biology (COSBI); Rovereto Italy
| | - Colm M. O'Grada
- Nutrigenomics Research Group; UCD Conway Institute of Biomolecular and Biomedical Research; School of Public Health and Population Science; University College Dublin; Belfield Dublin Ireland
- Institute of Food and Health; University College Dublin; Belfield Dublin Ireland
| | - Eugene T. Dillon
- Nutrigenomics Research Group; UCD Conway Institute of Biomolecular and Biomedical Research; School of Public Health and Population Science; University College Dublin; Belfield Dublin Ireland
- Institute of Food and Health; University College Dublin; Belfield Dublin Ireland
| | - Ciara Morris
- Institute of Food and Health; University College Dublin; Belfield Dublin Ireland
| | - Miriam F. Ryan
- Institute of Food and Health; University College Dublin; Belfield Dublin Ireland
| | - Marianne Walsh
- Institute of Food and Health; University College Dublin; Belfield Dublin Ireland
| | - Eileen R. Gibney
- Institute of Food and Health; University College Dublin; Belfield Dublin Ireland
| | - Lorraine Brennan
- Institute of Food and Health; University College Dublin; Belfield Dublin Ireland
- UCD Conway Institute of Biomolecular and Biomedical Research; University College Dublin; Belfield Dublin Ireland
| | - Michael J. Gibney
- Institute of Food and Health; University College Dublin; Belfield Dublin Ireland
| | - Melissa J. Morine
- The Microsoft Research; University of Trento Centre for Computational Systems Biology (COSBI); Rovereto Italy
- Department of Mathematics; University of Trento; Trento Italy
| | - Helen M. Roche
- Nutrigenomics Research Group; UCD Conway Institute of Biomolecular and Biomedical Research; School of Public Health and Population Science; University College Dublin; Belfield Dublin Ireland
- Institute of Food and Health; University College Dublin; Belfield Dublin Ireland
- UCD Conway Institute of Biomolecular and Biomedical Research; University College Dublin; Belfield Dublin Ireland
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22
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Yalcin D, Hakguder ZM, Otu HH. Bioinformatics approaches to single-cell analysis in developmental biology. Mol Hum Reprod 2015; 22:182-92. [PMID: 26358759 DOI: 10.1093/molehr/gav050] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2015] [Accepted: 09/04/2015] [Indexed: 12/17/2022] Open
Abstract
Individual cells within the same population show various degrees of heterogeneity, which may be better handled with single-cell analysis to address biological and clinical questions. Single-cell analysis is especially important in developmental biology as subtle spatial and temporal differences in cells have significant associations with cell fate decisions during differentiation and with the description of a particular state of a cell exhibiting an aberrant phenotype. Biotechnological advances, especially in the area of microfluidics, have led to a robust, massively parallel and multi-dimensional capturing, sorting, and lysis of single-cells and amplification of related macromolecules, which have enabled the use of imaging and omics techniques on single cells. There have been improvements in computational single-cell image analysis in developmental biology regarding feature extraction, segmentation, image enhancement and machine learning, handling limitations of optical resolution to gain new perspectives from the raw microscopy images. Omics approaches, such as transcriptomics, genomics and epigenomics, targeting gene and small RNA expression, single nucleotide and structural variations and methylation and histone modifications, rely heavily on high-throughput sequencing technologies. Although there are well-established bioinformatics methods for analysis of sequence data, there are limited bioinformatics approaches which address experimental design, sample size considerations, amplification bias, normalization, differential expression, coverage, clustering and classification issues, specifically applied at the single-cell level. In this review, we summarize biological and technological advancements, discuss challenges faced in the aforementioned data acquisition and analysis issues and present future prospects for application of single-cell analyses to developmental biology.
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Affiliation(s)
- Dicle Yalcin
- Department of Electrical and Computer Engineering, University of Nebraska-Lincoln, Lincoln, NE 68588-0511, USA
| | - Zeynep M Hakguder
- Department of Electrical and Computer Engineering, University of Nebraska-Lincoln, Lincoln, NE 68588-0511, USA
| | - Hasan H Otu
- Department of Electrical and Computer Engineering, University of Nebraska-Lincoln, Lincoln, NE 68588-0511, USA
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23
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Karr JR, Guturu H, Chen EY, Blair SL, Irish JM, Kotecha N, Covert MW. NetworkPainter: dynamic intracellular pathway animation in Cytobank. BMC Bioinformatics 2015; 16:172. [PMID: 26003204 PMCID: PMC4491883 DOI: 10.1186/s12859-015-0602-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2014] [Accepted: 04/28/2015] [Indexed: 02/02/2023] Open
Abstract
BACKGROUND High-throughput technologies such as flow and mass cytometry have the potential to illuminate cellular networks. However, analyzing the data produced by these technologies is challenging. Visualization is needed to help researchers explore this data. RESULTS We developed a web-based software program, NetworkPainter, to enable researchers to analyze dynamic cytometry data in the context of pathway diagrams. NetworkPainter provides researchers a graphical interface to draw and "paint" pathway diagrams with experimental data, producing animated diagrams which display the activity of each network node at each time point. CONCLUSION NetworkPainter enables researchers to more fully explore multi-parameter, dynamical cytometry data.
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Affiliation(s)
- Jonathan R Karr
- Graduate Program in Biophysics, Stanford University, 443 Via Ortega, MC 4245, Stanford, CA, 94305, USA.
- Department of Genetics & Genomic Sciences, Mount Sinai School of Medicine, One Gustave L Levy Place, New York, NY, 10029, USA.
| | - Harendra Guturu
- Department of Electrical Engineering, Stanford University, 279 Campus Drive West, MC 5329, Stanford, CA, 94305, USA.
| | - Edward Y Chen
- Department of Bioengineering, Stanford University, 443 Via Ortega, MC 4245, Stanford, CA, 94305, USA.
| | - Stuart L Blair
- Cytobank Inc, 821 West El Camino Real, Mountain View, CA, 94040, USA.
| | - Jonathan M Irish
- Department of Medicine, Stanford University, 269 Campus Drive West, MC 5175, Stanford, CA, 94305, USA.
- Department of Microbiology & Immunology, Stanford University, 269 Campus Drive West, MC 5175, Stanford, CA, 94305, USA.
- Cytobank Inc, 821 West El Camino Real, Mountain View, CA, 94040, USA.
- Department of Cancer Biology, Vanderbilt University, 740B Preston Building, 2220 Pierce Avenue, Nashville, TN, 37232, USA.
| | - Nikesh Kotecha
- Graduate Program in Biomedical Informatics, Stanford University, 269 Campus Drive West, MC 5175, Stanford, CA, 94305, USA.
- Cytobank Inc, 821 West El Camino Real, Mountain View, CA, 94040, USA.
| | - Markus W Covert
- Department of Bioengineering, Stanford University, 443 Via Ortega, MC 4245, Stanford, CA, 94305, USA.
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24
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Andreassen OA, Desikan RS, Wang Y, Thompson WK, Schork AJ, Zuber V, Doncheva NT, Ellinghaus E, Albrecht M, Mattingsdal M, Franke A, Lie BA, Mills I, Aukrust P, McEvoy LK, Djurovic S, Karlsen TH, Dale AM. Abundant genetic overlap between blood lipids and immune-mediated diseases indicates shared molecular genetic mechanisms. PLoS One 2015; 10:e0123057. [PMID: 25853426 PMCID: PMC4390360 DOI: 10.1371/journal.pone.0123057] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Accepted: 01/16/2015] [Indexed: 12/29/2022] Open
Abstract
Epidemiological studies suggest a relationship between blood lipids and immune-mediated diseases, but the nature of these associations is not well understood. We used genome-wide association studies (GWAS) to investigate shared single nucleotide polymorphisms (SNPs) between blood lipids and immune-mediated diseases. We analyzed data from GWAS (n~200,000 individuals), applying new False Discovery Rate (FDR) methods, to investigate genetic overlap between blood lipid levels [triglycerides (TG), low density lipoproteins (LDL), high density lipoproteins (HDL)] and a selection of archetypal immune-mediated diseases (Crohn’s disease, ulcerative colitis, rheumatoid arthritis, type 1 diabetes, celiac disease, psoriasis and sarcoidosis). We found significant polygenic pleiotropy between the blood lipids and all the investigated immune-mediated diseases. We discovered several shared risk loci between the immune-mediated diseases and TG (n = 88), LDL (n = 87) and HDL (n = 52). Three-way analyses differentiated the pattern of pleiotropy among the immune-mediated diseases. The new pleiotropic loci increased the number of functional gene network nodes representing blood lipid loci by 40%. Pathway analyses implicated several novel shared mechanisms for immune pathogenesis and lipid biology, including glycosphingolipid synthesis (e.g. FUT2) and intestinal host-microbe interactions (e.g. ATG16L1). We demonstrate a shared genetic basis for blood lipids and immune-mediated diseases independent of environmental factors. Our findings provide novel mechanistic insights into dyslipidemia and immune-mediated diseases and may have implications for therapeutic trials involving lipid-lowering and anti-inflammatory agents.
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Affiliation(s)
- Ole A. Andreassen
- NORMENT, KG Jebsen Centre for Psychosis Research, Institute of Clinical Medicine, University of Oslo and Division of Mental Health and Addiction, Oslo University Hospital, 0407 Oslo, Norway
- Department of Psychiatry, University of California San Diego, La Jolla, CA 92093, United States of America
- * E-mail: (AMD); (OAA)
| | - Rahul S. Desikan
- Multimodal Imaging Laboratory, University of California San Diego, La Jolla, CA 92093, United States of America
- Department of Radiology, University of California San Diego, La Jolla, CA 92093, United States of America
| | - Yunpeng Wang
- NORMENT, KG Jebsen Centre for Psychosis Research, Institute of Clinical Medicine, University of Oslo and Division of Mental Health and Addiction, Oslo University Hospital, 0407 Oslo, Norway
- Multimodal Imaging Laboratory, University of California San Diego, La Jolla, CA 92093, United States of America
- Department of Neurosciences, University of California San Diego, La Jolla, CA 92093, United States of America
| | - Wesley K. Thompson
- Department of Psychiatry, University of California San Diego, La Jolla, CA 92093, United States of America
| | - Andrew J. Schork
- Multimodal Imaging Laboratory, University of California San Diego, La Jolla, CA 92093, United States of America
- Cognitive Sciences Graduate Program, University of California San Diego, La Jolla, CA 92093, United States of America
- Center for Human Development, University of California San Diego, La Jolla, CA 92093, United States of America
| | - Verena Zuber
- NORMENT, KG Jebsen Centre for Psychosis Research, Institute of Clinical Medicine, University of Oslo and Division of Mental Health and Addiction, Oslo University Hospital, 0407 Oslo, Norway
- Centre for Molecular Medicine Norway, Nordic EMBL Partnership, University of Oslo and Oslo University Hospital, 0407 Oslo, Norway
| | | | - Eva Ellinghaus
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, 24118 Kiel, Germany
| | - Mario Albrecht
- Max Planck Institute for Informatics, 66123 Saarbrücken, Germany
- Department of Bioinformatics, Institute of Biometrics and Medical Informatics, University Medicine Greifswald, 17475 Greifswald, Germany
- Institute for Knowledge Discovery, Graz University of Technology, 8010 Graz, Austria
- BioTechMed-Graz, 8010 Graz, Austria
| | - Morten Mattingsdal
- NORMENT, KG Jebsen Centre for Psychosis Research, Institute of Clinical Medicine, University of Oslo and Division of Mental Health and Addiction, Oslo University Hospital, 0407 Oslo, Norway
- Sørlandet Hospital, 3000 Kristiansand, Norway
| | - Andre Franke
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, 24118 Kiel, Germany
| | | | - Ian Mills
- Centre for Molecular Medicine Norway, Nordic EMBL Partnership, University of Oslo and Oslo University Hospital, 0407 Oslo, Norway
- Department of Cancer Prevention, Institute of Cancer Research and Department of Urology, Oslo University Hospital, 0407 Oslo, Norway
| | - Pål Aukrust
- Department of Medical Genetics, University of Oslo and Oslo University Hospital, 0407 Oslo, Norway
- Section of Clinical Immunology and Infectious Diseases, Oslo University Hospital, 0407 Oslo Norway
| | - Linda K. McEvoy
- Multimodal Imaging Laboratory, University of California San Diego, La Jolla, CA 92093, United States of America
- Department of Radiology, University of California San Diego, La Jolla, CA 92093, United States of America
| | - Srdjan Djurovic
- NORMENT, KG Jebsen Centre for Psychosis Research, Institute of Clinical Medicine, University of Oslo and Division of Mental Health and Addiction, Oslo University Hospital, 0407 Oslo, Norway
- Department of Medical Genetics, University of Oslo and Oslo University Hospital, 0407 Oslo, Norway
| | - Tom H. Karlsen
- K.G.Jebsen Inflammation Research Centre, Research Institute of Internal Medicine, Division of Cancer Medicine, Surgery and Transplantation, Oslo University Hospital Rikshospitalet, 0407 Oslo, Norway
- Division of Gastroenterology, Institute of Medicine, University of Bergen, 5000 Bergen, Norway
- Norwegian PSC Research Center, Department of Transplantation Medicine, Division of Cancer Medicine, Surgery and Transplantation, Oslo University Hospital Rikshospitalet, 0407 Oslo, Norway
| | - Anders M. Dale
- Department of Psychiatry, University of California San Diego, La Jolla, CA 92093, United States of America
- Multimodal Imaging Laboratory, University of California San Diego, La Jolla, CA 92093, United States of America
- Department of Radiology, University of California San Diego, La Jolla, CA 92093, United States of America
- Department of Neurosciences, University of California San Diego, La Jolla, CA 92093, United States of America
- * E-mail: (AMD); (OAA)
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Increased expression of interferon signaling genes in the bone marrow microenvironment of myelodysplastic syndromes. PLoS One 2015; 10:e0120602. [PMID: 25803272 PMCID: PMC4372597 DOI: 10.1371/journal.pone.0120602] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2014] [Accepted: 01/24/2015] [Indexed: 11/19/2022] Open
Abstract
Introduction The bone marrow (BM) microenvironment plays an important role in the pathogenesis of myelodysplastic syndromes (MDS) through a reciprocal interaction with resident BM hematopoietic cells. We investigated the differences between BM mesenchymal stromal cells (MSCs) in MDS and normal individuals and identified genes involved in such differences. Materials and Methods BM-derived MSCs from 7 MDS patients (3 RCMD, 3 RAEB-1, and 1 RAEB-2) and 7 controls were cultured. Global gene expression was analyzed using a microarray. Result We found 314 differentially expressed genes (DEGs) in RCMD vs. control, 68 in RAEB vs. control, and 51 in RAEB vs. RCMD. All comparisons were clearly separated from one another by hierarchical clustering. The overall similarity between differential expression signatures from the RCMD vs. control comparison and the RAEB vs. control comparison was highly significant (p = 0), which indicates a common transcriptomic response in these two MDS subtypes. RCMD and RAEB simultaneously showed an up-regulation of interferon alpha/beta signaling and the ISG15 antiviral mechanism, and a significant fraction of the RAEB vs. control DEGs were also putative targets of transcription factors IRF and ICSBP. Pathways that involved RNA polymerases I and III and mitochondrial transcription were down-regulated in RAEB compared to RCMD. Conclusion Gene expression in the MDS BM microenvironment was different from that in normal BM and exhibited altered expression according to disease progression. The present study provides genetic evidence that inflammation and immune dysregulation responses that involve the interferon signaling pathway in the BM microenvironment are associated with MDS pathogenesis, which suggests BM MSCs as a possible therapeutic target in MDS.
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Dimitrakopoulou K, Vrahatis AG, Bezerianos A. Integromics network meta-analysis on cardiac aging offers robust multi-layer modular signatures and reveals micronome synergism. BMC Genomics 2015; 16:147. [PMID: 25887273 PMCID: PMC4367845 DOI: 10.1186/s12864-015-1256-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2014] [Accepted: 01/19/2015] [Indexed: 02/02/2023] Open
Abstract
Background The avalanche of integromics and panomics approaches shifted the deciphering of aging mechanisms from single molecular entities to communities of them. In this orientation, we explore the cardiac aging mechanisms – risk factor for multiple cardiovascular diseases - by capturing the micronome synergism and detecting longevity signatures in the form of communities (modules). For this, we developed a meta-analysis scheme that integrates transcriptome expression data from multiple cardiac-specific independent studies in mouse and human along with proteome and micronome interaction data in the form of multiple independent weighted networks. Modularization of each weighted network produced modules, which in turn were further analyzed so as to define consensus modules across datasets that change substantially during lifespan. Also, we established a metric that determines - from the modular perspective - the synergism of microRNA-microRNA interactions as defined by significantly functionally associated targets. Results The meta-analysis provided 40 consensus integromics modules across mouse datasets and revealed microRNA relations with substantial collective action during aging. Three modules were reproducible, based on homology, when mapped against human-derived modules. The respective homologs mainly represent NADH dehydrogenases, ATP synthases, cytochrome oxidases, Ras GTPases and ribosomal proteins. Among various observations, we corroborate to the involvement of miR-34a (included in consensus modules) as proposed recently; yet we report that has no synergistic effect. Moving forward, we determined its age-related neighborhood in which HCN3, a known heart pacemaker channel, was included. Also, miR-125a-5p/-351, miR-200c/-429, miR-106b/-17, miR-363/-92b, miR-181b/-181d, miR-19a/-19b, let-7d/-7f, miR-18a/-18b, miR-128/-27b and miR-106a/-291a-3p pairs exhibited significant synergy and their association to aging and/or cardiovascular diseases is supported in many cases by a disease database and previous studies. On the contrary, we suggest that miR-22 has not substantial impact on heart longevity as proposed recently. Conclusions We revised several proteins and microRNAs recently implicated in cardiac aging and proposed for the first time modules as signatures. The integromics meta-analysis approach can serve as an efficient subvening signature tool for more-oriented better-designed experiments. It can also promote the combinational multi-target microRNA therapy of age-related cardiovascular diseases along the continuum from prevention to detection, diagnosis, treatment and outcome. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1256-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | - Aristidis G Vrahatis
- Department of Medical Physics, School of Medicine, University of Patras, Patras, 26500, Greece. .,Department of Computer Engineering and Informatics, University of Patras, Patras, 26500, Greece.
| | - Anastasios Bezerianos
- Department of Medical Physics, School of Medicine, University of Patras, Patras, 26500, Greece. .,Singapore Institute for Neurotechnology (SINAPSE), Center of Life Sciences, National University of Singapore, Singapore, 117456, Singapore.
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Ernst M, Abu Dawud R, Kurtz A, Schotta G, Taher L, Fuellen G. Comparative computational analysis of pluripotency in human and mouse stem cells. Sci Rep 2015; 5:7927. [PMID: 25604210 PMCID: PMC4300513 DOI: 10.1038/srep07927] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2014] [Accepted: 12/18/2014] [Indexed: 12/22/2022] Open
Abstract
Pluripotent cells can be subdivided into two distinct states, the naïve and the primed state, the latter being further advanced on the path of differentiation. There are substantial differences in the regulation of pluripotency between human and mouse, and in humans only stem cells that resemble the primed state in mouse are readily available. Reprogramming of human stem cells into a more naïve-like state is an important research focus. Here, we developed a pipeline to reanalyze transcriptomics data sets that describe both states, naïve and primed pluripotency, in human and mouse. The pipeline consists of identifying regulated start-ups/shut-downs in terms of molecular interactions, followed by functional annotation of the genes involved and aggregation of results across conditions, yielding sets of mechanisms that are consistently regulated in transitions towards similar states of pluripotency. Our results suggest that one published protocol for naïve human cells gave rise to human cells that indeed share putative mechanisms with the prototypical naïve mouse pluripotent cells, such as DNA damage response and histone acetylation. However, cellular response and differentiation-related mechanisms are similar between the naïvehuman state and the primedmouse state, so the naïvehuman state did not fully reflect the naïvemouse state.
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Affiliation(s)
- Mathias Ernst
- Institute for Biostatistics and Informatics in Medicine and Ageing Research, Rostock University Medical Center, Rostock, Germany
| | - Raed Abu Dawud
- Berlin-Brandenburg Center for Regenerative Therapies (BCRT), Charité, Berlin, Germany
| | - Andreas Kurtz
- 1] Berlin-Brandenburg Center for Regenerative Therapies (BCRT), Charité, Berlin, Germany [2] College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul, Republic of Korea
| | - Gunnar Schotta
- Ludwig Maximilians University and Munich Center for Integrated Protein Science (CiPSM), Adolf-Butenandt-Institute, Munich, Germany
| | - Leila Taher
- Institute for Biostatistics and Informatics in Medicine and Ageing Research, Rostock University Medical Center, Rostock, Germany
| | - Georg Fuellen
- Institute for Biostatistics and Informatics in Medicine and Ageing Research, Rostock University Medical Center, Rostock, Germany
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28
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Capurro A, Bodea LG, Schaefer P, Luthi-Carter R, Perreau VM. Computational deconvolution of genome wide expression data from Parkinson's and Huntington's disease brain tissues using population-specific expression analysis. Front Neurosci 2015; 8:441. [PMID: 25620908 PMCID: PMC4288238 DOI: 10.3389/fnins.2014.00441] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2014] [Accepted: 12/15/2014] [Indexed: 01/09/2023] Open
Abstract
The characterization of molecular changes in diseased tissues gives insight into pathophysiological mechanisms and is important for therapeutic development. Genome-wide gene expression analysis has proven valuable for identifying biological processes in neurodegenerative diseases using post mortem human brain tissue and numerous datasets are publically available. However, many studies utilize heterogeneous tissue samples consisting of multiple cell types, all of which contribute to global gene expression values, confounding biological interpretation of the data. In particular, changes in numbers of neuronal and glial cells occurring in neurodegeneration confound transcriptomic analyses, particularly in human brain tissues where sample availability and controls are limited. To identify cell specific gene expression changes in neurodegenerative disease, we have applied our recently published computational deconvolution method, population specific expression analysis (PSEA). PSEA estimates cell-type-specific expression values using reference expression measures, which in the case of brain tissue comprises mRNAs with cell-type-specific expression in neurons, astrocytes, oligodendrocytes and microglia. As an exercise in PSEA implementation and hypothesis development regarding neurodegenerative diseases, we applied PSEA to Parkinson's and Huntington's disease (PD, HD) datasets. Genes identified as differentially expressed in substantia nigra pars compacta neurons by PSEA were validated using external laser capture microdissection data. Network analysis and Annotation Clustering (DAVID) identified molecular processes implicated by differential gene expression in specific cell types. The results of these analyses provided new insights into the implementation of PSEA in brain tissues and additional refinement of molecular signatures in human HD and PD.
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Affiliation(s)
- Alberto Capurro
- Department of Cell Physiology and Pharmacology, University of Leicester Leicester, UK
| | - Liviu-Gabriel Bodea
- Neural Regeneration Unit, Institute of Reconstructive Neurobiology, University of Bonn Bonn, Germany ; Clem Jones Centre for Ageing Dementia Research, Queensland Brain Institute, The University of Queensland St Lucia, QLD, Australia
| | | | - Ruth Luthi-Carter
- Department of Cell Physiology and Pharmacology, University of Leicester Leicester, UK
| | - Victoria M Perreau
- The Bioinformatics Core and The Synaptic Neurobiology Laboratory, The Florey Institute of Neuroscience and Mental Health Parkville, VIC, Australia
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29
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Bundalovic-Torma C, Parkinson J. Comparative Genomics and Evolutionary Modularity of Prokaryotes. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2015; 883:77-96. [PMID: 26621462 DOI: 10.1007/978-3-319-23603-2_4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The soaring number of high-quality genomic sequences has ushered in the era of post-genomic research where our understanding of organisms has dramatically shifted towards defining the function of genes within their larger biological contexts. As a result, novel high-throughput experimental technologies are being increasingly employed to uncover physical and functional associations of genes and proteins in complex biological processes. Through the construction and analysis of physical, genetic and metabolic networks generated for the model organisms, such as Escherichia coli, organizational principles of the genome have been deduced, such as modularity, which has important implications toward understanding prokaryotic evolution and adaptation to novel lifestyles.
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Affiliation(s)
- Cedoljub Bundalovic-Torma
- Department of Molecular Structure and Function, The Peter Gilgan Centre for Research and Learning, Hospital for Sick Children, 686 Bay St. Rm 21-9830, Toronto, ON, Canada, M5G 0A4.
| | - John Parkinson
- Department of Molecular Structure and Function, The Peter Gilgan Centre for Research and Learning, Hospital for Sick Children, 686 Bay St. Rm 20-9709, Toronto, ON, Canada, M5G 0A4.
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30
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Tan F, Yang R, Xu X, Chen X, Wang Y, Ma H, Liu X, Wu X, Chen Y, Liu L, Jia X. Drug repositioning by applying 'expression profiles' generated by integrating chemical structure similarity and gene semantic similarity. MOLECULAR BIOSYSTEMS 2014; 10:1126-38. [PMID: 24603772 DOI: 10.1039/c3mb70554d] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Drug repositioning, also known as drug repurposing or reprofiling, is the process of finding new indications for established drugs. Because drug repositioning can reduce costs and enhance the efficiency of drug development, it is of paramount importance in medical research. Here, we present a systematic computational method to identify potential novel indications for a given drug. This method utilizes some prior knowledge such as 3D drug chemical structure information, drug-target interactions and gene semantic similarity information. Its prediction is based on another form of 'expression profile', which contains scores ranging from -1 to 1, reflecting the consensus response scores (CRSs) between each drug of 965 and 1560 proteins. The CRS integrates chemical structure similarity and gene semantic similarity information. We define the degree of similarity between two drugs as the absolute value of their correlation coefficients. Finally, we establish a drug similarity network (DSN) and obtain 33 modules of drugs with similar modes of action, determining their common indications. Using these modules, we predict new indications for 143 drugs and identify previously unknown indications for 42 drugs without ATC codes. This method overcomes the instability of gene expression profiling derived from experiments due to experimental conditions, and predicts indications for a new compound feasibly, requiring only the 3D structure of the compound. In addition, the high literature validation rate of 71.8% also suggests that our method has the potential to discover novel drug indications for existing drugs.
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Affiliation(s)
- Fujian Tan
- College of Bioinformatics Science and Technology, Harbin Medical University, 194 Xuefu Road, Harbin, Heilongjiang 150081, PR China.
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31
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Truman AW, Kristjansdottir K, Wolfgeher D, Ricco N, Mayampurath A, Volchenboum SL, Clotet J, Kron SJ. Quantitative proteomics of the yeast Hsp70/Hsp90 interactomes during DNA damage reveal chaperone-dependent regulation of ribonucleotide reductase. J Proteomics 2014; 112:285-300. [PMID: 25452130 DOI: 10.1016/j.jprot.2014.09.028] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2014] [Revised: 09/05/2014] [Accepted: 09/27/2014] [Indexed: 12/11/2022]
Abstract
UNLABELLED The highly conserved molecular chaperones Hsp90 and Hsp70 are indispensible for folding and maturation of a significant fraction of the proteome, including many proteins involved in signal transduction and stress response. To examine the dynamics of chaperone-client interactions after DNA damage, we applied quantitative affinity-purification mass spectrometry (AP-MS) proteomics to characterize interactomes of the yeast Hsp70 isoform Ssa1 and Hsp90 isoform Hsp82 before and after exposure to methyl methanesulfonate. Of 256 proteins identified and quantified via (16)O(/18)O labeling and LC-MS/MS, 142 are novel Hsp70/90 interactors. Nearly all interactions remained unchanged or decreased after DNA damage, but 5 proteins increased interactions with Ssa1 and/or Hsp82, including the ribonucleotide reductase (RNR) subunit Rnr4. Inhibiting Hsp70 or 90 chaperone activity destabilized Rnr4 in yeast and its vertebrate homolog hRMM2 in breast cancer cells. In turn, pre-treatment of cancer cells with chaperone inhibitors sensitized cells to the RNR inhibitor gemcitabine, suggesting a novel chemotherapy strategy. All MS data have been deposited in the ProteomeXchange with identifier PXD001284. BIOLOGICAL SIGNIFICANCE This study provides the dynamic interactome of the yeast Hsp70 and Hsp90 under DNA damage which suggest key roles for the chaperones in a variety of signaling cascades. Importantly, the cancer drug target ribonucleotide reductase was shown to be a client of Hsp70 and Hsp90 in both yeast and breast cancer cells. As such, this study highlights the potential of a novel cancer therapeutic strategy that exploits the synergy of chaperone and ribonucleotide reductase inhibitors.
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Affiliation(s)
- Andrew W Truman
- Department of Molecular Genetics and Cell Biology, The University of Chicago, Chicago, IL 60637, USA
| | | | - Donald Wolfgeher
- Department of Molecular Genetics and Cell Biology, The University of Chicago, Chicago, IL 60637, USA
| | - Natalia Ricco
- Departament de Ciències Bàsiques, Universitat Internacional de Catalunya, Barcelona, Catalunya, Spain
| | - Anoop Mayampurath
- Computation Institute, The University of Chicago, Chicago, IL 60637, USA
| | - Samuel L Volchenboum
- Computation Institute, The University of Chicago, Chicago, IL 60637, USA; Department of Pediatrics, The University of Chicago, Chicago, IL 60637, USA
| | - Josep Clotet
- Departament de Ciències Bàsiques, Universitat Internacional de Catalunya, Barcelona, Catalunya, Spain
| | - Stephen J Kron
- Department of Molecular Genetics and Cell Biology, The University of Chicago, Chicago, IL 60637, USA.
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32
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Taher L, Pfeiffer MJ, Fuellen G. Bioinformatics approaches to single-blastomere transcriptomics. ACTA ACUST UNITED AC 2014; 21:115-25. [DOI: 10.1093/molehr/gau083] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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33
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Morris JH, Kuchinsky A, Ferrin TE, Pico AR. enhancedGraphics: a Cytoscape app for enhanced node graphics. F1000Res 2014; 3:147. [PMID: 25285206 PMCID: PMC4176421 DOI: 10.12688/f1000research.4460.1] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 06/17/2014] [Indexed: 11/20/2022] Open
Abstract
enhancedGraphics ( http://apps.cytoscape.org/apps/enhancedGraphics) is a Cytoscape app that implements a series of enhanced charts and graphics that may be added to Cytoscape nodes. It enables users and other app developers to create pie, line, bar, and circle plots that are driven by columns in the Cytoscape Node Table. Charts are drawn using vector graphics to allow full-resolution scaling.
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Affiliation(s)
- John H Morris
- Resource for Biocomputing, Visualization and Informatics, University of California, San Francisco, CA 94143, USA
| | | | - Thomas E Ferrin
- Resource for Biocomputing, Visualization and Informatics, University of California, San Francisco, CA 94143, USA
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34
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Genz B, Thomas M, Pützer BM, Siatkowski M, Fuellen G, Vollmar B, Abshagen K. Adenoviral overexpression of Lhx2 attenuates cell viability but does not preserve the stem cell like phenotype of hepatic stellate cells. Exp Cell Res 2014; 328:429-43. [PMID: 24995995 DOI: 10.1016/j.yexcr.2014.06.019] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2014] [Revised: 06/13/2014] [Accepted: 06/14/2014] [Indexed: 01/04/2023]
Abstract
Hepatic stellate cells (HSC) are well known initiators of hepatic fibrosis. After liver cell damage, HSC transdifferentiate into proliferative myofibroblasts, representing the major source of extracellular matrix in the fibrotic organ. Recent studies also demonstrate a role of HSC as progenitor or stem cell like cells in liver regeneration. Lhx2 is described as stem cell maintaining factor in different organs and as an inhibitory transcription factor in HSC activation. Here we examined whether a continuous expression of Lhx2 in HSC could attenuate their activation and whether Lhx2 could serve as a potential target for antifibrotic gene therapy. Therefore, we evaluated an adenoviral mediated overexpression of Lhx2 in primary HSC and investigated mRNA expression patterns by qRT-PCR as well as the activation status by different in vitro assays. HSC revealed a marked increase in activation markers like smooth muscle actin alpha (αSMA) and collagen 1α independent from adenoviral transduction. Lhx2 overexpression resulted in attenuated cell viability as shown by a slightly hampered migratory and contractile phenotype of HSC. Expression of stem cell factors or signaling components was also unaffected by Lhx2. Summarizing these results, we found no antifibrotic or stem cell maintaining effect of Lhx2 overexpression in primary HSC.
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Affiliation(s)
- Berit Genz
- Institute for Experimental Surgery, Rostock University Medical Center, Rostock, Germany
| | - Maria Thomas
- Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart, Germany
| | - Brigitte M Pützer
- Institute of Experimental Gene Therapy and Cancer Research, Rostock University Medical Center, Rostock, Germany
| | - Marcin Siatkowski
- Institute for Biostatistics and Informatics in Medicine and Ageing Research, Rostock University Medical Center, Rostock, Germany
| | - Georg Fuellen
- Institute for Biostatistics and Informatics in Medicine and Ageing Research, Rostock University Medical Center, Rostock, Germany
| | - Brigitte Vollmar
- Institute for Experimental Surgery, Rostock University Medical Center, Rostock, Germany
| | - Kerstin Abshagen
- Institute for Experimental Surgery, Rostock University Medical Center, Rostock, Germany.
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Wisniewska M, Happonen L, Kahn F, Varjosalo M, Malmström L, Rosenberger G, Karlsson C, Cazzamali G, Pozdnyakova I, Frick IM, Björck L, Streicher W, Malmström J, Wikström M. Functional and structural properties of a novel protein and virulence factor (Protein sHIP) in Streptococcus pyogenes. J Biol Chem 2014; 289:18175-88. [PMID: 24825900 DOI: 10.1074/jbc.m114.565978] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Streptococcus pyogenes is a significant bacterial pathogen in the human population. The importance of virulence factors for the survival and colonization of S. pyogenes is well established, and many of these factors are exposed to the extracellular environment, enabling bacterial interactions with the host. In the present study, we quantitatively analyzed and compared S. pyogenes proteins in the growth medium of a strain that is virulent to mice with a non-virulent strain. Particularly, one of these proteins was present at significantly higher levels in stationary growth medium from the virulent strain. We determined the three-dimensional structure of the protein that showed a unique tetrameric organization composed of four helix-loop-helix motifs. Affinity pull-down mass spectrometry analysis in human plasma demonstrated that the protein interacts with histidine-rich glycoprotein (HRG), and the name sHIP (streptococcal histidine-rich glycoprotein-interacting protein) is therefore proposed. HRG has antibacterial activity, and when challenged by HRG, sHIP was found to rescue S. pyogenes bacteria. This and the finding that patients with invasive S. pyogenes infection respond with antibody production against sHIP suggest a role for the protein in S. pyogenes pathogenesis.
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Affiliation(s)
- Magdalena Wisniewska
- From the Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, DK-2200 Copenhagen, Denmark
| | - Lotta Happonen
- the Department of Clinical Sciences, Lund University, SE-221 84 Lund, Sweden
| | - Fredrik Kahn
- the Department of Clinical Sciences, Lund University, SE-221 84 Lund, Sweden
| | - Markku Varjosalo
- the Institute of Biotechnology, Viikinkaari 1, University of Helsinki, FI-00014 Helsinki, Finland, and
| | - Lars Malmström
- the Department of Biology, ETH Zürich, 8093 Zürich, Switzerland
| | | | - Christofer Karlsson
- the Department of Clinical Sciences, Lund University, SE-221 84 Lund, Sweden
| | - Giuseppe Cazzamali
- From the Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, DK-2200 Copenhagen, Denmark
| | - Irina Pozdnyakova
- From the Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, DK-2200 Copenhagen, Denmark
| | - Inga-Maria Frick
- the Department of Clinical Sciences, Lund University, SE-221 84 Lund, Sweden
| | - Lars Björck
- the Department of Clinical Sciences, Lund University, SE-221 84 Lund, Sweden
| | - Werner Streicher
- From the Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, DK-2200 Copenhagen, Denmark
| | - Johan Malmström
- the Department of Clinical Sciences, Lund University, SE-221 84 Lund, Sweden
| | - Mats Wikström
- From the Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, DK-2200 Copenhagen, Denmark,
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Kristensen VN, Lingjærde OC, Russnes HG, Vollan HKM, Frigessi A, Børresen-Dale AL. Principles and methods of integrative genomic analyses in cancer. Nat Rev Cancer 2014; 14:299-313. [PMID: 24759209 DOI: 10.1038/nrc3721] [Citation(s) in RCA: 235] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Combined analyses of molecular data, such as DNA copy-number alteration, mRNA and protein expression, point to biological functions and molecular pathways being deregulated in multiple cancers. Genomic, metabolomic and clinical data from various solid cancers and model systems are emerging and can be used to identify novel patient subgroups for tailored therapy and monitoring. The integrative genomics methodologies that are used to interpret these data require expertise in different disciplines, such as biology, medicine, mathematics, statistics and bioinformatics, and they can seem daunting. The objectives, methods and computational tools of integrative genomics that are available to date are reviewed here, as is their implementation in cancer research.
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Affiliation(s)
- Vessela N Kristensen
- 1] Department of Genetics, Institute for Cancer Research, Oslo University Hospital, The Norwegian Radium Hospital, Montebello, 0310 Oslo, Norway. [2] K.G. Jebsen Centre for Breast Cancer Research, Institute for Clinical Medicine, Faculty of Medicine, University of Oslo, 0313 Oslo, Norway. [3] Department of Clinical Molecular Oncology, Division of Medicine, Akershus University Hospital, 1478 Ahus, Norway
| | - Ole Christian Lingjærde
- 1] K.G. Jebsen Centre for Breast Cancer Research, Institute for Clinical Medicine, Faculty of Medicine, University of Oslo, 0313 Oslo, Norway. [2] Division for Biomedical Informatics, Department of Computer Science, University of Oslo, 0316 Oslo, Norway
| | - Hege G Russnes
- 1] Department of Genetics, Institute for Cancer Research, Oslo University Hospital, The Norwegian Radium Hospital, Montebello, 0310 Oslo, Norway. [2] K.G. Jebsen Centre for Breast Cancer Research, Institute for Clinical Medicine, Faculty of Medicine, University of Oslo, 0313 Oslo, Norway. [3] Department of Pathology, Oslo University Hospital, 0450 Oslo, Norway
| | - Hans Kristian M Vollan
- 1] Department of Genetics, Institute for Cancer Research, Oslo University Hospital, The Norwegian Radium Hospital, Montebello, 0310 Oslo, Norway. [2] K.G. Jebsen Centre for Breast Cancer Research, Institute for Clinical Medicine, Faculty of Medicine, University of Oslo, 0313 Oslo, Norway. [3] Department of Oncology, Division of Cancer, Surgery and Transplantation, Oslo University Hospital, 0450 Oslo, Norway
| | - Arnoldo Frigessi
- 1] Statistics for Innovation, Norwegian Computing Center, 0314 Oslo, Norway. [2] Department of Biostatistics, Institute of Basic Medical Sciences, University of Oslo, PO Box 1122 Blindern, 0317 Oslo, Norway
| | - Anne-Lise Børresen-Dale
- 1] Department of Genetics, Institute for Cancer Research, Oslo University Hospital, The Norwegian Radium Hospital, Montebello, 0310 Oslo, Norway. [2] K.G. Jebsen Centre for Breast Cancer Research, Institute for Clinical Medicine, Faculty of Medicine, University of Oslo, 0313 Oslo, Norway
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Xue J, Schmidt SV, Sander J, Draffehn A, Krebs W, Quester I, De Nardo D, Gohel TD, Emde M, Schmidleithner L, Ganesan H, Nino-Castro A, Mallmann MR, Labzin L, Theis H, Kraut M, Beyer M, Latz E, Freeman TC, Ulas T, Schultze JL. Transcriptome-based network analysis reveals a spectrum model of human macrophage activation. Immunity 2014; 40:274-88. [PMID: 24530056 PMCID: PMC3991396 DOI: 10.1016/j.immuni.2014.01.006] [Citation(s) in RCA: 1461] [Impact Index Per Article: 146.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2013] [Accepted: 01/02/2014] [Indexed: 12/14/2022]
Abstract
Macrophage activation is associated with profound transcriptional reprogramming. Although much progress has been made in the understanding of macrophage activation, polarization, and function, the transcriptional programs regulating these processes remain poorly characterized. We stimulated human macrophages with diverse activation signals, acquiring a data set of 299 macrophage transcriptomes. Analysis of this data set revealed a spectrum of macrophage activation states extending the current M1 versus M2-polarization model. Network analyses identified central transcriptional regulators associated with all macrophage activation complemented by regulators related to stimulus-specific programs. Applying these transcriptional programs to human alveolar macrophages from smokers and patients with chronic obstructive pulmonary disease (COPD) revealed an unexpected loss of inflammatory signatures in COPD patients. Finally, by integrating murine data from the ImmGen project we propose a refined, activation-independent core signature for human and murine macrophages. This resource serves as a framework for future research into regulation of macrophage activation in health and disease. Macrophages react with specific transcriptional programming upon distinct signals Activation by TNF, PGE2, and P3C activates a STAT4-associated transcriptional program NFKB1, JUNB, and CREB1 are central transcription factors of macrophage activation Inflammatory signatures are lost in alveolar macrophages from COPD patients
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Affiliation(s)
- Jia Xue
- Genomics and Immunoregulation, LIMES-Institute, University of Bonn, 53115 Bonn, Germany
| | - Susanne V Schmidt
- Genomics and Immunoregulation, LIMES-Institute, University of Bonn, 53115 Bonn, Germany
| | - Jil Sander
- Genomics and Immunoregulation, LIMES-Institute, University of Bonn, 53115 Bonn, Germany
| | - Astrid Draffehn
- Genomics and Immunoregulation, LIMES-Institute, University of Bonn, 53115 Bonn, Germany
| | - Wolfgang Krebs
- Genomics and Immunoregulation, LIMES-Institute, University of Bonn, 53115 Bonn, Germany
| | - Inga Quester
- Genomics and Immunoregulation, LIMES-Institute, University of Bonn, 53115 Bonn, Germany
| | - Dominic De Nardo
- Institute of Innate Immunity, University Hospitals, University of Bonn, 53127 Bonn, Germany
| | - Trupti D Gohel
- Genomics and Immunoregulation, LIMES-Institute, University of Bonn, 53115 Bonn, Germany
| | - Martina Emde
- Genomics and Immunoregulation, LIMES-Institute, University of Bonn, 53115 Bonn, Germany
| | - Lisa Schmidleithner
- Genomics and Immunoregulation, LIMES-Institute, University of Bonn, 53115 Bonn, Germany
| | - Hariharasudan Ganesan
- Genomics and Immunoregulation, LIMES-Institute, University of Bonn, 53115 Bonn, Germany
| | - Andrea Nino-Castro
- Genomics and Immunoregulation, LIMES-Institute, University of Bonn, 53115 Bonn, Germany
| | - Michael R Mallmann
- Genomics and Immunoregulation, LIMES-Institute, University of Bonn, 53115 Bonn, Germany
| | - Larisa Labzin
- Institute of Innate Immunity, University Hospitals, University of Bonn, 53127 Bonn, Germany
| | - Heidi Theis
- Genomics and Immunoregulation, LIMES-Institute, University of Bonn, 53115 Bonn, Germany
| | - Michael Kraut
- Genomics and Immunoregulation, LIMES-Institute, University of Bonn, 53115 Bonn, Germany
| | - Marc Beyer
- Genomics and Immunoregulation, LIMES-Institute, University of Bonn, 53115 Bonn, Germany
| | - Eicke Latz
- Institute of Innate Immunity, University Hospitals, University of Bonn, 53127 Bonn, Germany; Division of Infectious Diseases and Immunology, UMass Medical School, Worcester, MA 01605, USA; German Center of Neurodegenerative Diseases (DZNE), 53127 Bonn, Germany
| | - Tom C Freeman
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Edinburgh, Midlothian EH25 9RG, Scotland, UK
| | - Thomas Ulas
- Genomics and Immunoregulation, LIMES-Institute, University of Bonn, 53115 Bonn, Germany
| | - Joachim L Schultze
- Genomics and Immunoregulation, LIMES-Institute, University of Bonn, 53115 Bonn, Germany.
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38
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Dimitrakopoulou K, Dimitrakopoulos GN, Wilk E, Tsimpouris C, Sgarbas KN, Schughart K, Bezerianos A. Influenza A immunomics and public health omics: the dynamic pathway interplay in host response to H1N1 infection. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2014; 18:167-83. [PMID: 24512282 DOI: 10.1089/omi.2013.0062] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Towards unraveling the influenza A (H1N1) immunome, this work aims at constructing the murine host response pathway interactome. To accomplish that, an ensemble of dynamic and time-varying Gene Regulatory Network Inference methodologies was recruited to set a confident interactome based on mouse time series transcriptome data (day 1-day 60). The proposed H1N1 interactome demonstrated significant transformations among activated and suppressed pathways in time. Enhanced interplay was observed at day 1, while the maximal network complexity was reached at day 8 (correlated with viral clearance and iBALT tissue formation) and one interaction was present at day 40. Next, we searched for common interactivity features between the murine-adapted PR8 strain and other influenza A subtypes/strains. For this, two other interactomes, describing the murine host response against H5N1 and H1N1pdm, were constructed, which in turn validated many of the observed interactions (in the period day 1-day 7). The H1N1 interactome revealed the role of cell cycle both in innate and adaptive immunity (day 1-day 14). Also, pathogen sensory pathways (e.g., RIG-I) displayed long-lasting association with cytokine/chemokine signaling (until day 8). Interestingly, the above observations were also supported by the H5N1 and H1N1pdm models. It also elucidated the enhanced coupling of the activated innate pathways with the suppressed PPAR signaling to keep low inflammation until viral clearance (until day 14). Further, it showed that interactions reflecting phagocytosis processes continued long after the viral clearance and the establishment of adaptive immunity (day 8-day 40). Additionally, interactions involving B cell receptor pathway were evident since day 1. These results collectively inform the emerging field of public health omics and future clinical studies aimed at deciphering dynamic host responses to infectious agents.
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Van den Hof WFPM, Coonen MLJ, van Herwijnen M, Brauers K, Wodzig WKWH, van Delft JHM, Kleinjans JCS. Classification of Hepatotoxicants Using HepG2 Cells: A Proof of Principle Study. Chem Res Toxicol 2014; 27:433-42. [DOI: 10.1021/tx4004165] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Wim F. P. M. Van den Hof
- Department
of Toxicogenomics, Maastricht University, Maastricht, The Netherlands
- Netherlands Toxicogenomics
Centre, Maastricht, The Netherlands
| | - Maarten L. J. Coonen
- Department
of Toxicogenomics, Maastricht University, Maastricht, The Netherlands
- Netherlands Toxicogenomics
Centre, Maastricht, The Netherlands
| | - Marcel van Herwijnen
- Department
of Toxicogenomics, Maastricht University, Maastricht, The Netherlands
| | - Karen Brauers
- Department
of Toxicogenomics, Maastricht University, Maastricht, The Netherlands
| | - Will K. W. H. Wodzig
- Department
of Clinical Chemistry, Maastricht University Medical Center, Maastricht, The Netherlands
- Netherlands Toxicogenomics
Centre, Maastricht, The Netherlands
| | - Joost H. M. van Delft
- Department
of Toxicogenomics, Maastricht University, Maastricht, The Netherlands
- Netherlands Toxicogenomics
Centre, Maastricht, The Netherlands
| | - Jos C. S. Kleinjans
- Department
of Toxicogenomics, Maastricht University, Maastricht, The Netherlands
- Netherlands Toxicogenomics
Centre, Maastricht, The Netherlands
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40
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Differential network analysis applied to preoperative breast cancer chemotherapy response. PLoS One 2013; 8:e81784. [PMID: 24349128 PMCID: PMC3857210 DOI: 10.1371/journal.pone.0081784] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2013] [Accepted: 10/16/2013] [Indexed: 12/31/2022] Open
Abstract
In silico approaches are increasingly considered to improve breast cancer treatment. One of these treatments, neoadjuvant TFAC chemotherapy, is used in cases where application of preoperative systemic therapy is indicated. Estimating response to treatment allows or improves clinical decision-making and this, in turn, may be based on a good understanding of the underlying molecular mechanisms. Ever increasing amounts of high throughput data become available for integration into functional networks. In this study, we applied our software tool ExprEssence to identify specific mechanisms relevant for TFAC therapy response, from a gene/protein interaction network. We contrasted the resulting active subnetwork to the subnetworks of two other such methods, OptDis and KeyPathwayMiner. We could show that the ExprEssence subnetwork is more related to the mechanistic functional principles of TFAC therapy than the subnetworks of the other two methods despite the simplicity of ExprEssence. We were able to validate our method by recovering known mechanisms and as an application example of our method, we identified a mechanism that may further explain the synergism between paclitaxel and doxorubicin in TFAC treatment: Paclitaxel may attenuate MELK gene expression, resulting in lower levels of its target MYBL2, already associated with doxorubicin synergism in hepatocellular carcinoma cell lines. We tested our hypothesis in three breast cancer cell lines, confirming it in part. In particular, the predicted effect on MYBL2 could be validated, and a synergistic effect of paclitaxel and doxorubicin could be demonstrated in the breast cancer cell lines SKBR3 and MCF-7.
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41
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Dimitrakopoulou K, Dimitrakopoulos GN, Sgarbas KN, Bezerianos A. Tamoxifen integromics and personalized medicine: dynamic modular transformations underpinning response to tamoxifen in breast cancer treatment. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2013; 18:15-33. [PMID: 24299457 DOI: 10.1089/omi.2013.0055] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Recent advances in pharmacogenomics technologies allow bold steps to be taken towards personalized medicine, more accurate health planning, and personalized drug development. In this framework, systems pharmacology network-based approaches offer an appealing way for integrating multi-omics data and set the basis for defining systems-level drug response biomarkers. On the road to individualized tamoxifen treatment in estrogen receptor-positive breast cancer patients, we examine the dynamics of the attendant pharmacological response mechanisms. By means of an "integromics" network approach, we assessed the tamoxifen effect through the way the high-order organization of interactome (i.e., the modules) is perturbed. To accomplish that, first we integrated the time series transcriptome data with the human protein interaction data, and second, an efficient module-detecting algorithm was applied onto the composite graphs. Our findings show that tamoxifen induces severe modular transformations on specific areas of the interactome. Our modular biomarkers in response to tamoxifen attest to the immunomodulatory role of tamoxifen, and further reveal that it deregulates cell cycle and apoptosis pathways, while coordinating the proteasome and basal transcription factors. To the best of our knowledge, this is the first report that informs the fields of personalized medicine and clinical pharmacology about the actual dynamic interactome response to tamoxifen administration.
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Siatkowski M, Liebscher V, Fuellen G. CellFateScout - a bioinformatics tool for elucidating small molecule signaling pathways that drive cells in a specific direction. Cell Commun Signal 2013; 11:85. [PMID: 24206562 PMCID: PMC3833265 DOI: 10.1186/1478-811x-11-85] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2013] [Accepted: 10/29/2013] [Indexed: 12/12/2022] Open
Abstract
Background Small molecule effects can be represented by active signaling pathways within functional networks. Identifying these can help to design new strategies to utilize known small molecules, e.g. to trigger specific cellular transformations or to reposition known drugs. Results We developed CellFateScout that uses the method of Latent Variables to turn differential high-throughput expression data and a functional network into a list of active signaling pathways. Applying it to Connectivity Map data, i.e., differential expression data describing small molecule effects, we then generated a Human Small Molecule Mechanisms Database. Finally, using a list of active signaling pathways as query, a similarity search can identify small molecules from the database that may trigger these pathways. We validated our approach systematically, using expression data of small molecule perturbations, yielding better predictions than popular bioinformatics tools. Conclusions CellFateScout can be used to select small molecules for their desired effects. The CellFateScout Cytoscape plugin, a tutorial and the Human Small Molecule Mechanisms Database are available at https://sourceforge.net/projects/cellfatescout/ under LGPLv2 license.
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Affiliation(s)
| | | | - Georg Fuellen
- Institute for Biostatistics and Informatics in Medicine and Ageing Research, University of Rostock, Ernst Heydemann Strasse 8, D-18057 Rostock, Germany.
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Xie B, Wang D, Duan Y, Yu J, Lei H. Functional networking of human divergently paired genes (DPGs). PLoS One 2013; 8:e78896. [PMID: 24205343 PMCID: PMC3815023 DOI: 10.1371/journal.pone.0078896] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2013] [Accepted: 09/17/2013] [Indexed: 11/18/2022] Open
Abstract
Divergently paired genes (DPGs), also known as bidirectional (head-to-head positioned) genes, are conserved across species and lineages, and thus deemed to be exceptional in genomic organization and functional regulation. Despite previous investigations on the features of their conservation and gene organization, the functional relationship among DPGs in a given species and lineage has not been thoroughly clarified. Here we report a network-based comprehensive analysis on human DPGs and our results indicate that the two members of the DPGs tend to participate in different biological processes while enforcing related functions as modules. Comparing to randomly paired genes as a control, the DPG pairs have a tendency to be clustered in similar “cellular components” and involved in similar “molecular functions”. The functional network bridged by DPGs consists of three major modules. The largest module includes many house-keeping genes involved in core cellular activities. This module also shows low variation in expression in both CNS (central nervous system) and non-CNS tissues. Based on analyses of disease transcriptome data, we further suggest that this particular module may play crucial roles in HIV infection and its disease mechanism.
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Affiliation(s)
- Bin Xie
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Dapeng Wang
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Yong Duan
- UC Davis Genome Center and Department of Biomedical Engineering, Davis, California, United States of America
| | - Jun Yu
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
- * E-mail: (JY); (HL)
| | - Hongxing Lei
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
- UC Davis Genome Center and Department of Biomedical Engineering, Davis, California, United States of America
- * E-mail: (JY); (HL)
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Human intellectual disability genes form conserved functional modules in Drosophila. PLoS Genet 2013; 9:e1003911. [PMID: 24204314 PMCID: PMC3814316 DOI: 10.1371/journal.pgen.1003911] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2013] [Accepted: 09/08/2013] [Indexed: 12/15/2022] Open
Abstract
Intellectual Disability (ID) disorders, defined by an IQ below 70, are genetically and phenotypically highly heterogeneous. Identification of common molecular pathways underlying these disorders is crucial for understanding the molecular basis of cognition and for the development of therapeutic intervention strategies. To systematically establish their functional connectivity, we used transgenic RNAi to target 270 ID gene orthologs in the Drosophila eye. Assessment of neuronal function in behavioral and electrophysiological assays and multiparametric morphological analysis identified phenotypes associated with knockdown of 180 ID gene orthologs. Most of these genotype-phenotype associations were novel. For example, we uncovered 16 genes that are required for basal neurotransmission and have not previously been implicated in this process in any system or organism. ID gene orthologs with morphological eye phenotypes, in contrast to genes without phenotypes, are relatively highly expressed in the human nervous system and are enriched for neuronal functions, suggesting that eye phenotyping can distinguish different classes of ID genes. Indeed, grouping genes by Drosophila phenotype uncovered 26 connected functional modules. Novel links between ID genes successfully predicted that MYCN, PIGV and UPF3B regulate synapse development. Drosophila phenotype groups show, in addition to ID, significant phenotypic similarity also in humans, indicating that functional modules are conserved. The combined data indicate that ID disorders, despite their extreme genetic diversity, are caused by disruption of a limited number of highly connected functional modules. Intellectual Disability (ID) affects 2% of our population and is associated with many different disorders. Although more than 400 causative genes (‘ID genes’) have been identified, their function remains poorly understood and the degree to which these disorders share a common molecular basis is unknown. Here, we systematically characterized behavioral and morphological phenotypes associated with 270 conserved ID genes, using the Drosophila eye and photoreceptor neurons as a model. These and follow up approaches generated previously undescribed genotype-phenotype associations for the majority (180) of ID gene orthologs, and identified, among others, 16 novel regulators of basal neurotransmission. Importantly, groups of genes that show the same phenotype in Drosophila are highly enriched in known connectivity, also share increased phenotypic similarity in humans and successfully predicted novel gene functions. In total, we mapped 26 conserved functional modules that together comprise 100 ID gene orthologs. Our findings provide unbiased evidence for the long suspected but never experimentally demonstrated functional coherence among ID disorders. The identified conserved functional modules may aid to develop therapeutic strategies that target genetically heterogeneous ID patients with a common treatment.
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Identifying genes relevant to specific biological conditions in time course microarray experiments. PLoS One 2013; 8:e76561. [PMID: 24146889 PMCID: PMC3795718 DOI: 10.1371/journal.pone.0076561] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2013] [Accepted: 08/28/2013] [Indexed: 11/19/2022] Open
Abstract
Microarrays have been useful in understanding various biological processes by allowing the simultaneous study of the expression of thousands of genes. However, the analysis of microarray data is a challenging task. One of the key problems in microarray analysis is the classification of unknown expression profiles. Specifically, the often large number of non-informative genes on the microarray adversely affects the performance and efficiency of classification algorithms. Furthermore, the skewed ratio of sample to variable poses a risk of overfitting. Thus, in this context, feature selection methods become crucial to select relevant genes and, hence, improve classification accuracy. In this study, we investigated feature selection methods based on gene expression profiles and protein interactions. We found that in our setup, the addition of protein interaction information did not contribute to any significant improvement of the classification results. Furthermore, we developed a novel feature selection method that relies exclusively on observed gene expression changes in microarray experiments, which we call "relative Signal-to-Noise ratio" (rSNR). More precisely, the rSNR ranks genes based on their specificity to an experimental condition, by comparing intrinsic variation, i.e. variation in gene expression within an experimental condition, with extrinsic variation, i.e. variation in gene expression across experimental conditions. Genes with low variation within an experimental condition of interest and high variation across experimental conditions are ranked higher, and help in improving classification accuracy. We compared different feature selection methods on two time-series microarray datasets and one static microarray dataset. We found that the rSNR performed generally better than the other methods.
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46
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Fuellen G, Jansen L, Leser U, Kurtz A. Using ontologies to study cell transitions. J Biomed Semantics 2013; 4:25. [PMID: 24103098 PMCID: PMC4128511 DOI: 10.1186/2041-1480-4-25] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2013] [Accepted: 08/19/2013] [Indexed: 11/29/2022] Open
Abstract
Background Understanding, modelling and influencing the transition between different states of cells, be it reprogramming of somatic cells to pluripotency or trans-differentiation between cells, is a hot topic in current biomedical and cell-biological research. Nevertheless, the large body of published knowledge in this area is underused, as most results are only represented in natural language, impeding their finding, comparison, aggregation, and usage. Scientific understanding of the complex molecular mechanisms underlying cell transitions could be improved by making essential pieces of knowledge available in a formal (and thus computable) manner. Results We describe the outline of two ontologies for cell phenotypes and for cellular mechanisms which together enable the representation of data curated from the literature or obtained by bioinformatics analyses and thus for building a knowledge base on mechanisms involved in cellular reprogramming. In particular, we discuss how comprehensive ontologies of cell phenotypes and of changes in mechanisms can be designed using the entity-quality (EQ) model. Conclusions We show that the principles for building cellular ontologies published in this work allow deeper insights into the relations between the continuants (cell phenotypes) and the occurrents (cell mechanism changes) involved in cellular reprogramming, although implementation remains for future work. Further, our design principles lead to ontologies that allow the meaningful application of similarity searches in the spaces of cell phenotypes and of mechanisms, and, especially, of changes of mechanisms during cellular transitions.
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Affiliation(s)
- Georg Fuellen
- Institute for Biostatistics and Informatics in Medicine and Ageing Research, Rostock Medical School, Ernst-Heydemann-Str, 8, 18057 Rostock, Germany.
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Foerster S, Kacprowski T, Dhople VM, Hammer E, Herzog S, Saafan H, Bien-Möller S, Albrecht M, Völker U, Ritter CA. Characterization of the EGFR interactome reveals associated protein complex networks and intracellular receptor dynamics. Proteomics 2013; 13:3131-44. [PMID: 23956138 DOI: 10.1002/pmic.201300154] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2013] [Revised: 07/21/2013] [Accepted: 07/26/2013] [Indexed: 11/05/2022]
Abstract
Growth factor receptor mediated signaling is meanwhile recognized as a complex signaling network, which is initiated by recruiting specific patterns of adaptor proteins to the intracellular domain of epidermal growth factor receptor (EGFR). Approaches to globally identify EGFR-binding proteins are required to elucidate this network. We affinity-purified EGFR with its interacting proteins by coprecipitation from lysates of A431 cells. A total of 183 proteins were repeatedly detected in high-resolution MS measurements. For 15 of these, direct interactions with EGFR were listed in the iRefIndex interaction database, including Grb2, shc-1, SOS1 and 2, STAT 1 and 3, AP2, UBS3B, and ERRFI. The newly developed Cytoscape plugin ModuleGraph allowed retrieving and visualizing 93 well-described protein complexes that contained at least one of the proteins found to interact with EGFR in our experiments. Abundances of 14 proteins were modulated more than twofold upon EGFR activation whereof clathrin-associated adaptor complex AP-2 showed 4.6-fold enrichment. These proteins were further annotated with different cellular compartments. Finally, interactions of AP-2 proteins and the newly discovered interaction of CIP2A could be verified. In conclusion, a powerful technique is presented that allowed identification and quantitative assessment of the EGFR interactome to provide further insight into EGFR signaling.
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Affiliation(s)
- Sarah Foerster
- Department of Clinical Pharmacy, Institute of Pharmacy, Ernst-Moritz-Arndt-University Greifswald, Greifswald, Germany
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Hekmat O, Munk S, Fogh L, Yadav R, Francavilla C, Horn H, Würtz SØ, Schrohl AS, Damsgaard B, Rømer MU, Belling KC, Jensen NF, Gromova I, Bekker-Jensen DB, Moreira JM, Jensen LJ, Gupta R, Lademann U, Brünner N, Olsen JV, Stenvang J. TIMP-1 increases expression and phosphorylation of proteins associated with drug resistance in breast cancer cells. J Proteome Res 2013; 12:4136-51. [PMID: 23909892 DOI: 10.1021/pr400457u] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Tissue inhibitor of metalloproteinase 1 (TIMP-1) is a protein with a potential biological role in drug resistance. To elucidate the unknown molecular mechanisms underlying the association between high TIMP-1 levels and increased chemotherapy resistance, we employed SILAC-based quantitative mass spectrometry to analyze global proteome and phosphoproteome differences of MCF-7 breast cancer cells expressing high or low levels of TIMP-1. In TIMP-1 high expressing cells, 312 proteins and 452 phosphorylation sites were up-regulated. Among these were the cancer drug targets topoisomerase 1, 2A, and 2B, which may explain the resistance phenotype to topoisomerase inhibitors that was observed in cells with high TIMP-1 levels. Pathway analysis showed an enrichment of proteins from functional categories such as apoptosis, cell cycle, DNA repair, transcription factors, drug targets and proteins associated with drug resistance or sensitivity, and drug transportation. The NetworKIN algorithm predicted the protein kinases CK2a, CDK1, PLK1, and ATM as likely candidates involved in the hyperphosphorylation of the topoisomerases. Up-regulation of protein and/or phosphorylation levels of topoisomerases in TIMP-1 high expressing cells may be part of the mechanisms by which TIMP-1 confers resistance to treatment with the widely used topoisomerase inhibitors in breast and colorectal cancer.
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Affiliation(s)
- Omid Hekmat
- Institute of Veterinary Disease Biology, Faculty of Health and Medical Sciences and Sino-Danish Breast Cancer Research Centre, University of Copenhagen, Dyrlægevej 88, 1., 1870 Frederiksberg C, Denmark
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Abstract
Time is of the essence in biology as in so much else. For example, monitoring disease progression or the timing of developmental defects is important for the processes of drug discovery and therapy trials. Furthermore, an understanding of the basic dynamics of biological phenomena that are often strictly time regulated (e.g. circadian rhythms) is needed to make accurate inferences about the evolution of biological processes. Recent advances in technologies have enabled us to measure timing effects more accurately and in more detail. This has driven related advances in visualization and analysis tools that try to effectively exploit this data. Beyond timeline plots, notable attempts at more involved temporal interpretation have been made in recent years, but awareness of the available resources is still limited within the scientific community. Here, we review some advances in biological visualization of time-driven processes and consider how they aid data analysis and interpretation.
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50
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PodNet, a protein-protein interaction network of the podocyte. Kidney Int 2013; 84:104-15. [PMID: 23552858 DOI: 10.1038/ki.2013.64] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2012] [Revised: 12/10/2012] [Accepted: 12/13/2012] [Indexed: 02/06/2023]
Abstract
Interactions between proteins crucially determine cellular structure and function. Differential analysis of the interactome may help elucidate molecular mechanisms during disease development; however, this analysis necessitates mapping of expression data on protein-protein interaction networks. These networks do not exist for the podocyte; therefore, we built PodNet, a literature-based mouse podocyte network in Cytoscape format. Using database protein-protein interactions, we expanded PodNet to XPodNet with enhanced connectivity. In order to test the performance of XPodNet in differential interactome analysis, we examined podocyte developmental differentiation and the effect of cell culture. Transcriptomes of podocytes in 10 different states were mapped on XPodNet and analyzed with the Cytoscape plugin ExprEssence, based on the law of mass action. Interactions between slit diaphragm proteins are most significantly upregulated during podocyte development and most significantly downregulated in culture. On the other hand, our analysis revealed that interactions lost during podocyte differentiation are not regained in culture, suggesting a loss rather than a reversal of differentiation for podocytes in culture. Thus, we have developed PodNet as a valuable tool for differential interactome analysis in podocytes, and we have identified established and unexplored regulated interactions in developing and cultured podocytes.
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