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Stein-O'Brien G, Kagohara LT, Li S, Thakar M, Ranaweera R, Ozawa H, Cheng H, Considine M, Schmitz S, Favorov AV, Danilova LV, Califano JA, Izumchenko E, Gaykalova DA, Chung CH, Fertig EJ. Integrated time course omics analysis distinguishes immediate therapeutic response from acquired resistance. Genome Med 2018; 10:37. [PMID: 29792227 PMCID: PMC5966898 DOI: 10.1186/s13073-018-0545-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Accepted: 05/01/2018] [Indexed: 02/06/2023] Open
Abstract
Background Targeted therapies specifically act by blocking the activity of proteins that are encoded by genes critical for tumorigenesis. However, most cancers acquire resistance and long-term disease remission is rarely observed. Understanding the time course of molecular changes responsible for the development of acquired resistance could enable optimization of patients’ treatment options. Clinically, acquired therapeutic resistance can only be studied at a single time point in resistant tumors. Methods To determine the dynamics of these molecular changes, we obtained high throughput omics data (RNA-sequencing and DNA methylation) weekly during the development of cetuximab resistance in a head and neck cancer in vitro model. The CoGAPS unsupervised algorithm was used to determine the dynamics of the molecular changes associated with resistance during the time course of resistance development. Results CoGAPS was used to quantify the evolving transcriptional and epigenetic changes. Applying a PatternMarker statistic to the results from CoGAPS enabled novel heatmap-based visualization of the dynamics in these time course omics data. We demonstrate that transcriptional changes result from immediate therapeutic response or resistance, whereas epigenetic alterations only occur with resistance. Integrated analysis demonstrates delayed onset of changes in DNA methylation relative to transcription, suggesting that resistance is stabilized epigenetically. Conclusions Genes with epigenetic alterations associated with resistance that have concordant expression changes are hypothesized to stabilize the resistant phenotype. These genes include FGFR1, which was associated with EGFR inhibitors resistance previously. Thus, integrated omics analysis distinguishes the timing of molecular drivers of resistance. This understanding of the time course progression of molecular changes in acquired resistance is important for the development of alternative treatment strategies that would introduce appropriate selection of new drugs to treat cancer before the resistant phenotype develops. Electronic supplementary material The online version of this article (10.1186/s13073-018-0545-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Genevieve Stein-O'Brien
- Institute of Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA.,Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA
| | - Luciane T Kagohara
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA
| | - Sijia Li
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA
| | - Manjusha Thakar
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA
| | - Ruchira Ranaweera
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA.,Department of Head and Neck-Endocrine Oncology, Moffitt Cancer Center, Tampa, FL, USA
| | - Hiroyuki Ozawa
- Department of Otorhinolaryngology-Head and Neck Surgery, Keio University School of Medicine, Tokyo, Japan
| | - Haixia Cheng
- Department of Surgery - Otolaryngology-Head and Neck Surgery, University of Utah,
- Salt Lake City, UT, USA
| | - Michael Considine
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA
| | - Sandra Schmitz
- Head and Neck Surgery Unit, St Luc University Hospital, Brussels, Belgium
| | - Alexander V Favorov
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA.,Laboratory of Systems Biology and Computational Genetics, Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia
| | - Ludmila V Danilova
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA.,Laboratory of Systems Biology and Computational Genetics, Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia
| | - Joseph A Califano
- Department of Surgery, UC San Diego Moores Cancer Center, La Jolla, CA, USA
| | - Evgeny Izumchenko
- Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins University, Baltimore, MD, USA
| | - Daria A Gaykalova
- Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins University, Baltimore, MD, USA
| | - Christine H Chung
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA. .,Department of Head and Neck-Endocrine Oncology, Moffitt Cancer Center, Tampa, FL, USA.
| | - Elana J Fertig
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA.
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Holtman IR, Bsibsi M, Gerritsen WH, Boddeke HWGM, Eggen BJL, van der Valk P, Kipp M, van Noort JM, Amor S. Identification of highly connected hub genes in the protective response program of human macrophages and microglia activated by alpha B-crystallin. Glia 2017; 65:460-473. [DOI: 10.1002/glia.23104] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Revised: 11/15/2016] [Accepted: 11/18/2016] [Indexed: 12/22/2022]
Affiliation(s)
- Inge R. Holtman
- Department of Medical Physiology; University of Groningen, University Medical Center Groningen; Groningen AV the Netherlands
| | | | - Wouter H. Gerritsen
- Department of Pathology; VU University Medical Center; Amsterdam HV the Netherlands
| | - Hendrikus W. G. M. Boddeke
- Department of Medical Physiology; University of Groningen, University Medical Center Groningen; Groningen AV the Netherlands
| | - Bart J. L. Eggen
- Department of Medical Physiology; University of Groningen, University Medical Center Groningen; Groningen AV the Netherlands
| | - Paul van der Valk
- Department of Pathology; VU University Medical Center; Amsterdam HV the Netherlands
| | - Markus Kipp
- Department of Neuroanatomy; University of Munich; Munich Germany
| | - Johannes M. van Noort
- Delta Crystallon BV; Beverwijk ED the Netherlands
- Department of Pathology; VU University Medical Center; Amsterdam HV the Netherlands
| | - Sandra Amor
- Department of Pathology; VU University Medical Center; Amsterdam HV the Netherlands
- Department of Neuroscience and Trauma, Blizard Institute, Barts and the London School of Medicine & Dentistry; Queen Mary University of London; London United Kingdom
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Thiébaut R, Esmiol S, Lecine P, Mahfouz B, Hermant A, Nicoletti C, Parnis S, Perroy J, Borg JP, Pascoe L, Hugot JP, Ollendorff V. Characterization and Genetic Analyses of New Genes Coding for NOD2 Interacting Proteins. PLoS One 2016; 11:e0165420. [PMID: 27812135 PMCID: PMC5094585 DOI: 10.1371/journal.pone.0165420] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Accepted: 10/11/2016] [Indexed: 01/26/2023] Open
Abstract
NOD2 contributes to the innate immune response and to the homeostasis of the intestinal mucosa. In response to its bacterial ligand, NOD2 interacts with RICK and activates the NF-κB and MAPK pathways, inducing gene transcription and synthesis of proteins required to initiate a balanced immune response. Mutations in NOD2 have been associated with an increased risk of Crohn’s Disease (CD), a disabling inflammatory bowel disease (IBD). Because NOD2 signaling plays a key role in CD, it is important to further characterize the network of protein interacting with NOD2. Using yeast two hybrid (Y2H) screens, we identified new NOD2 interacting proteins (NIP). The primary interaction was confirmed by coimmunoprecipitation and/or bioluminescence resonance energy transfer (BRET) experiments for 11 of these proteins (ANKHD1, CHMP5, SDCCAG3, TRIM41, LDOC1, PPP1R12C, DOCK7, VIM, KRT15, PPP2R3B, and C10Orf67). These proteins are involved in diverse functions, including endosomal sorting complexes required for transport (ESCRT), cytoskeletal architecture and signaling regulation. Additionally, we show that the interaction of 8 NIPs is compromised with the 3 main CD associated NOD2 mutants (R702W, G908R and 1007fs). Furthermore, to determine whether these NOD2 protein partners could be encoded by IBD susceptibility genes, a transmission disequilibrium test (TDT) was performed on 101 single nucleotide polymorphisms (SNPs) and the main corresponding haplotypes in genes coding for 15 NIPs using a set of 343 IBD families with 556 patients. Overall this work did not increase the number of IBD susceptibility genes but extends the NOD2 protein interaction network and suggests that NOD2 interactome and signaling depend upon the NOD2 mutation profile in CD.
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Affiliation(s)
- Raphaële Thiébaut
- UMR1149, INSERM et Université Paris Diderot-Sorbonne Paris-Cité, 75018, Paris, France
| | - Sophie Esmiol
- INRA, UMR866, DMEM, Université de Montpellier, Montpellier, France
| | - Patrick Lecine
- Aix Marseille Univ, CNRS, INSERM, Institut Paoli-Calmettes, CRCM, "Cell Polarity, Cell signaling and Cancer - Equipe labellisée Ligue Contre le Cancer", Marseille, France
| | - Batoul Mahfouz
- UMR1149, INSERM et Université Paris Diderot-Sorbonne Paris-Cité, 75018, Paris, France
| | - Aurelie Hermant
- Aix Marseille Univ, CNRS, INSERM, Institut Paoli-Calmettes, CRCM, "Cell Polarity, Cell signaling and Cancer - Equipe labellisée Ligue Contre le Cancer", Marseille, France
| | - Cendrine Nicoletti
- Aix Marseille Université, Centrale Marseille, CNRS, ISM2 UMR7313, 13397, Marseille, France
| | - Stephane Parnis
- Aix Marseille Université, Centrale Marseille, CNRS, ISM2 UMR7313, 13397, Marseille, France
| | - Julie Perroy
- CNRS, UMR-5203, Institut de Génomique Fonctionnelle, Montpellier, F-34094, France
- INSERM, U1191, Montpellier, F-34094, France
- Université de Montpellier, UMR-5203, Montpellier, F-34094, France
| | - Jean-Paul Borg
- Aix Marseille Univ, CNRS, INSERM, Institut Paoli-Calmettes, CRCM, "Cell Polarity, Cell signaling and Cancer - Equipe labellisée Ligue Contre le Cancer", Marseille, France
| | | | - Jean-Pierre Hugot
- UMR1149, INSERM et Université Paris Diderot-Sorbonne Paris-Cité, 75018, Paris, France
- Assistance Publique Hôpitaux de Paris, service de gastroentérologie pédiatrique, Hôpital Robert Debré, 75019, Paris, France
| | - Vincent Ollendorff
- INRA, UMR866, DMEM, Université de Montpellier, Montpellier, France
- * E-mail:
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Reconstruction of temporal activity of microRNAs from gene expression data in breast cancer cell line. BMC Genomics 2015; 16:1077. [PMID: 26763900 PMCID: PMC4712512 DOI: 10.1186/s12864-015-2260-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2015] [Accepted: 11/30/2015] [Indexed: 12/20/2022] Open
Abstract
Background MicroRNAs (miRNAs) are small non-coding RNAs that regulate genes at the post-transcriptional level in spatiotemporal manner. Several miRNAs are identified as prognostic and diagnostic markers in many human cancers. Estimation of the temporal activities of the miRNAs is an important step in the way to understand the complex interactions of these important regulatory elements with transcription factors (TFs) and target genes (TGs). However, current research on miRNA activities excludes network dynamics from the studies, disregarding the important element of time in the regulatory network analysis. Results In the current study, we combined experimentally verified miRNA-TG interactions with breast cancer microarray TG expression data to identify key miRNAs and compute their temporal activity using network component analysis (NCA). The computed activities showed that miRNAs were regulated in a time dependent manner. Our results allowed constructing a synergistic network of miRNAs using the computed miRNA activities and their shared regulation of TGs. We further extended this network by incorporating miRNA-TG, miRNA-TF, TF-miRNA and TF-TG regulations in the context of breast cancer. Our integrated network identified several miRNAs known to be involved in breast cancer regulation and revealed several novel miRNAs. Our further analysis detected substantial involvement of the miRNAs miR-324, miR-93, miR-615 and miR-1 in breast cancer, which was not known previously. Next, combining our integrated networks with functional annotation of differentially expressed genes resulted in new sub-networks. These sub-networks allowed us to identify the key miRNAs and their interactions with TFs and TGs of several biological processes involved in breast cancer. The identified markers are validated for their potential as prognostic markers for breast cancer through survival analysis. Conclusions Our dynamical analysis of the miRNA interactions greatly helps to discover new network based markers, and is highly applicable (but not limited) to cancer research. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-2260-3) contains supplementary material, which is available to authorized users.
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Walters KA, Olsufka R, Kuestner RE, Wu X, Wang K, Skerrett SJ, Ozinsky A. Prior infection with Type A Francisella tularensis antagonizes the pulmonary transcriptional response to an aerosolized Toll-like receptor 4 agonist. BMC Genomics 2015; 16:874. [PMID: 26510639 PMCID: PMC4625460 DOI: 10.1186/s12864-015-2022-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2015] [Accepted: 10/07/2015] [Indexed: 12/21/2022] Open
Abstract
Background Francisella infection attenuates immune cell infiltration and expression of selected pro-inflammatory cytokines in response to endogenous LPS, suggesting the bacteria is actively antagonizing at least some part of the response to Toll-like receptor 4 (TLR4) engagement. The ability of different Francisella strains to inhibit the ability of E. coli LPS to induce a pulmonary inflammatory response, as measured by gene expression profiling, was examined to define the scope of modulation and identify of inflammatory genes/pathways that are specifically antagonized by a virulent F. tularensis infection. Results Prior aerosol exposure to F. tularensis subsp. tularensis, but not the live attenuated strain (LVS) of F. tularensis subsp. holarctica or F. novicida, significantly antagonized the transcriptional response in the lungs of infected mice exposed to aerosolized E. coli LPS. The response to E. coli LPS was not completely inhibited, suggesting that the bacteria is targeting further downstream of the TLR4 molecule. Analysis of the promotors of LPS-responsive genes that were perturbed by Type A Francisella infection identified candidate transcription factors that were potentially modulated by the bacteria, including multiple members of the forkhead transcription factor family (FoxA1, Foxa2, FoxD1, Foxd3, Foxf2, FoxI1, Fox03, Foxq1), IRF1, CEBPA, and Mef2. The annotated functional roles of the affected genes suggested that virulent Francisella infection suppressed cellular processes including mRNA processing, antiviral responses, intracellular trafficking, and regulation of the actin cytoskeleton. Surprisingly, despite the broad overall suppression of LPS-induced genes by virulent Francisella, and contrary to what was anticipated from prior studies, Type A Francisella did not inhibit the expression of the majority of LPS-induced cytokines, nor the expression of many classic annotated inflammatory genes. Conclusions Collectively, this analysis demonstrates clear differences in the ability of different Francisella strains to modulate TLR4 signaling and identifies genes/pathways that are specifically targeted by virulent Type A Francisella. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-2022-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | - Rachael Olsufka
- Division of Pulmonary and Critical Care Medicine, University of Washington, Seattle, WA, 98104, USA.
| | - Rolf E Kuestner
- Institute for Systems Biology, 401 Terry Ave. N, Seattle, WA, 98109, USA.
| | - Xiagang Wu
- Institute for Systems Biology, 401 Terry Ave. N, Seattle, WA, 98109, USA.
| | - Kai Wang
- Institute for Systems Biology, 401 Terry Ave. N, Seattle, WA, 98109, USA.
| | - Shawn J Skerrett
- Division of Pulmonary and Critical Care Medicine, University of Washington, Seattle, WA, 98104, USA.
| | - Adrian Ozinsky
- Institute for Systems Biology, 401 Terry Ave. N, Seattle, WA, 98109, USA.
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Seok J, Davis RW, Xiao W. A hybrid approach of gene sets and single genes for the prediction of survival risks with gene expression data. PLoS One 2015; 10:e0122103. [PMID: 25933378 PMCID: PMC4416884 DOI: 10.1371/journal.pone.0122103] [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: 01/04/2015] [Accepted: 02/21/2015] [Indexed: 12/04/2022] Open
Abstract
Accumulated biological knowledge is often encoded as gene sets, collections of genes associated with similar biological functions or pathways. The use of gene sets in the analyses of high-throughput gene expression data has been intensively studied and applied in clinical research. However, the main interest remains in finding modules of biological knowledge, or corresponding gene sets, significantly associated with disease conditions. Risk prediction from censored survival times using gene sets hasn’t been well studied. In this work, we propose a hybrid method that uses both single gene and gene set information together to predict patient survival risks from gene expression profiles. In the proposed method, gene sets provide context-level information that is poorly reflected by single genes. Complementarily, single genes help to supplement incomplete information of gene sets due to our imperfect biomedical knowledge. Through the tests over multiple data sets of cancer and trauma injury, the proposed method showed robust and improved performance compared with the conventional approaches with only single genes or gene sets solely. Additionally, we examined the prediction result in the trauma injury data, and showed that the modules of biological knowledge used in the prediction by the proposed method were highly interpretable in biology. A wide range of survival prediction problems in clinical genomics is expected to benefit from the use of biological knowledge.
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Affiliation(s)
- Junhee Seok
- School of Electrical Engineering, Korea University, Seoul 136-713, Republic of Korea
- * E-mail: (JS); (WX)
| | - Ronald W. Davis
- Stanford Genome Technology Center, Palo Alto, California, United States of America
| | - Wenzhong Xiao
- Stanford Genome Technology Center, Palo Alto, California, United States of America
- Massachusetts General Hospital and Shriners Hospital for Children, Boston, Massachusetts, United States of America
- * E-mail: (JS); (WX)
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Dual RNA sequencing reveals the expression of unique transcriptomic signatures in lipopolysaccharide-induced BV-2 microglial cells. PLoS One 2015; 10:e0121117. [PMID: 25811458 PMCID: PMC4374676 DOI: 10.1371/journal.pone.0121117] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2014] [Accepted: 01/28/2015] [Indexed: 11/26/2022] Open
Abstract
Microglial cells become rapidly activated through interactions with pathogens, and the persistent activation of these cells is associated with various neurodegenerative diseases. Previous studies have investigated the transcriptomic signatures in microglia or macrophages using microarray technologies. However, this method has numerous restrictions, such as spatial biases, uneven probe properties, low sensitivity, and dependency on the probes spotted. To overcome this limitation and identify novel transcribed genes in response to LPS, we used RNA Sequencing (RNA-Seq) to determine the novel transcriptomic signatures in BV-2 microglial cells. Sequencing assessment and quality evaluation showed that approximately 263 and 319 genes (≥ 1.5 log2-fold), such as cytokines and chemokines, were strongly induced after 2 and 4 h, respectively, and the induction of several genes with unknown immunological functions was also observed. Importantly, we observed that previously unidentified transcription factors (TFs) (irf1, irf7, and irf9), histone demethylases (kdm4a) and DNA methyltransferases (dnmt3l) were significantly and selectively expressed in BV-2 microglial cells. The gene expression levels, transcription start sites (TSS), isoforms, and differential promoter usage revealed a complex pattern of transcriptional and post-transcriptional gene regulation upon infection with LPS. In addition, gene ontology, molecular networks and pathway analyses identified the top significantly regulated functional classification, canonical pathways and network functions at each activation status. Moreover, we further analyzed differentially expressed genes to identify transcription factor (TF) motifs (−950 to +50 bp of the 5’ upstream promoters) and epigenetic mechanisms. Furthermore, we confirmed that the expressions of key inflammatory genes as well as pro-inflammatory mediators in the supernatants were significantly induced in LPS treated primary microglial cells. This transcriptomic analysis is the first to show a comparison of the family-wide differential expression of most known immune genes and also reveal transcription evidence of multiple gene families in BV-2 microglial cells. Collectively, these findings reveal unique transcriptomic signatures in BV-2 microglial cells required for homeostasis and effective immune responses.
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Subramanian N, Torabi-Parizi P, Gottschalk RA, Germain RN, Dutta B. Network representations of immune system complexity. WILEY INTERDISCIPLINARY REVIEWS-SYSTEMS BIOLOGY AND MEDICINE 2015; 7:13-38. [PMID: 25625853 PMCID: PMC4339634 DOI: 10.1002/wsbm.1288] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/25/2014] [Revised: 12/09/2014] [Accepted: 12/11/2014] [Indexed: 12/25/2022]
Abstract
The mammalian immune system is a dynamic multiscale system composed of a hierarchically organized set of molecular, cellular, and organismal networks that act in concert to promote effective host defense. These networks range from those involving gene regulatory and protein–protein interactions underlying intracellular signaling pathways and single‐cell responses to increasingly complex networks of in vivo cellular interaction, positioning, and migration that determine the overall immune response of an organism. Immunity is thus not the product of simple signaling events but rather nonlinear behaviors arising from dynamic, feedback‐regulated interactions among many components. One of the major goals of systems immunology is to quantitatively measure these complex multiscale spatial and temporal interactions, permitting development of computational models that can be used to predict responses to perturbation. Recent technological advances permit collection of comprehensive datasets at multiple molecular and cellular levels, while advances in network biology support representation of the relationships of components at each level as physical or functional interaction networks. The latter facilitate effective visualization of patterns and recognition of emergent properties arising from the many interactions of genes, molecules, and cells of the immune system. We illustrate the power of integrating ‘omics’ and network modeling approaches for unbiased reconstruction of signaling and transcriptional networks with a focus on applications involving the innate immune system. We further discuss future possibilities for reconstruction of increasingly complex cellular‐ and organism‐level networks and development of sophisticated computational tools for prediction of emergent immune behavior arising from the concerted action of these networks. WIREs Syst Biol Med 2015, 7:13–38. doi: 10.1002/wsbm.1288 This article is categorized under:
Analytical and Computational Methods > Computational Methods Laboratory Methods and Technologies > Macromolecular Interactions, Methods
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Affiliation(s)
- Naeha Subramanian
- Institute for Systems Biology, Seattle, WA, USA; Laboratory of Systems Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
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Hu H, Dai Y. A model-based approach to transcription regulatory network reconstruction from time-course gene expression data. ANNUAL INTERNATIONAL CONFERENCE OF THE IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. ANNUAL INTERNATIONAL CONFERENCE 2015; 2014:4767-70. [PMID: 25571058 DOI: 10.1109/embc.2014.6944690] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Time-course gene expression profiling provides valuable data on dynamic behavior of cellular responses to external stimulation. Investigation of transcription factors (TFs) that regulate co-expressed genes in a dynamic process can reveal insights on the underlying molecular mechanisms. As the ChIP-seq technology is only suitable for a fraction of TFs in mammalian organisms, the computational identification of relevant TFs remains to be critical. We propose a regression-based model to infer the functional binding sites of TFs from time-course gene expression profiles. Our approach incorporates an association strength for each potential TF and target gene pair based on computational analysis of binding sites in promoter sequences of co-expressed genes. Our model further uses the Lasso-penalized technique to search for the most informative TF-target pairs. The application of our method to a gene expression study on E2-induced apoptosis in a variant of MCF-7 cells revealed that the findings are biologically meaningful.
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Chen Y, Wang Z, Wang Y. Spatiotemporal positioning of multipotent modules in diverse biological networks. Cell Mol Life Sci 2014; 71:2605-24. [PMID: 24413666 PMCID: PMC11113103 DOI: 10.1007/s00018-013-1547-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2013] [Revised: 12/05/2013] [Accepted: 12/19/2013] [Indexed: 02/06/2023]
Abstract
A biological network exhibits a modular organization. The modular structure dependent on functional module is of great significance in understanding the organization and dynamics of network functions. A huge variety of module identification methods as well as approaches to analyze modularity and dynamics of the inter- and intra-module interactions have emerged recently, but they are facing unexpected challenges in further practical applications. Here, we discuss recent progress in understanding how such a modular network can be deconstructed spatiotemporally. We focus particularly on elucidating how various deciphering mechanisms operate to ensure precise module identification and assembly. In this case, a system-level understanding of the entire mechanism of module construction is within reach, with important implications for reasonable perspectives in both constructing a modular analysis framework and deconstructing different modular hierarchical structures.
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Affiliation(s)
- Yinying Chen
- Institute of Basic Research in Clinical Medicine, China Academy of Chinese Medical Sciences, Dongzhimen, Beijing, 100700 China
- Guang’anmen Hospital, China Academy of Chinese Medical Sciences, Beijing, 100053 China
| | - Zhong Wang
- Institute of Basic Research in Clinical Medicine, China Academy of Chinese Medical Sciences, Dongzhimen, Beijing, 100700 China
| | - Yongyan Wang
- Institute of Basic Research in Clinical Medicine, China Academy of Chinese Medical Sciences, Dongzhimen, Beijing, 100700 China
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A systems biology approach to the analysis of subset-specific responses to lipopolysaccharide in dendritic cells. PLoS One 2014; 9:e100613. [PMID: 24949855 PMCID: PMC4065045 DOI: 10.1371/journal.pone.0100613] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2013] [Accepted: 05/28/2014] [Indexed: 12/24/2022] Open
Abstract
Dendritic cells (DCs) are critical for regulating CD4 and CD8 T cell immunity, controlling Th1, Th2, and Th17 commitment, generating inducible Tregs, and mediating tolerance. It is believed that distinct DC subsets have evolved to control these different immune outcomes. However, how DC subsets mount different responses to inflammatory and/or tolerogenic signals in order to accomplish their divergent functions remains unclear. Lipopolysaccharide (LPS) provides an excellent model for investigating responses in closely related splenic DC subsets, as all subsets express the LPS receptor TLR4 and respond to LPS in vitro. However, previous studies of the LPS-induced DC transcriptome have been performed only on mixed DC populations. Moreover, comparisons of the in vivo response of two closely related DC subsets to LPS stimulation have not been reported in the literature to date. We compared the transcriptomes of murine splenic CD8 and CD11b DC subsets after in vivo LPS stimulation, using RNA-Seq and systems biology approaches. We identified subset-specific gene signatures, which included multiple functional immune mediators unique to each subset. To explain the observed subset-specific differences, we used a network analysis approach. While both DC subsets used a conserved set of transcription factors and major signalling pathways, the subsets showed differential regulation of sets of genes that ‘fine-tune’ the network Hubs expressed in common. We propose a model in which signalling through common pathway components is ‘fine-tuned’ by transcriptional control of subset-specific modulators, thus allowing for distinct functional outcomes in closely related DC subsets. We extend this analysis to comparable datasets from the literature and confirm that our model can account for cell subset-specific responses to LPS stimulation in multiple subpopulations in mouse and man.
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12
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Dynamic regulatory network reconstruction for Alzheimer's disease based on matrix decomposition techniques. COMPUTATIONAL AND MATHEMATICAL METHODS IN MEDICINE 2014; 2014:891761. [PMID: 25024739 PMCID: PMC4082865 DOI: 10.1155/2014/891761] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/18/2014] [Revised: 05/19/2014] [Accepted: 05/26/2014] [Indexed: 11/18/2022]
Abstract
Alzheimer's disease (AD) is the most common form of dementia and leads to irreversible neurodegenerative damage of the brain. Finding the dynamic responses of genes, signaling proteins, transcription factor (TF) activities, and regulatory networks of the progressively deteriorative progress of AD would represent a significant advance in discovering the pathogenesis of AD. However, the high throughput technologies of measuring TF activities are not yet available on a genome-wide scale. In this study, based on DNA microarray gene expression data and a priori information of TFs, network component analysis (NCA) algorithm is applied to determining the TF activities and regulatory influences on TGs of incipient, moderate, and severe AD. Based on that, the dynamical gene regulatory networks of the deteriorative courses of AD were reconstructed. To select significant genes which are differentially expressed in different courses of AD, independent component analysis (ICA), which is better than the traditional clustering methods and can successfully group one gene in different meaningful biological processes, was used. The molecular biological analysis showed that the changes of TF activities and interactions of signaling proteins in mitosis, cell cycle, immune response, and inflammation play an important role in the deterioration of AD.
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Blankley S, Graham CM, Howes A, Bloom CI, Berry MPR, Chaussabel D, Pascual V, Banchereau J, Lipman M, O’Garra A. Identification of the key differential transcriptional responses of human whole blood following TLR2 or TLR4 ligation in-vitro. PLoS One 2014; 9:e97702. [PMID: 24842522 PMCID: PMC4026482 DOI: 10.1371/journal.pone.0097702] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2013] [Accepted: 04/23/2014] [Indexed: 01/01/2023] Open
Abstract
The use of human whole blood for transcriptomic analysis has potential advantages over the use of isolated immune cells for studying the transcriptional response to pathogens and their products. Whole blood stimulation can be carried out in a laboratory without the expertise or equipment to isolate immune cells from blood, with the added advantage of being able to undertake experiments using very small volumes of blood. Toll like receptors (TLRs) are a family of pattern recognition receptors which recognise highly conserved microbial products. Using the TLR2 ligand (Pam3CSK4) and the TLR4 ligand (LPS), human whole blood was stimulated for 0, 1, 3, 6, 12 or 24 hours at which times mRNA was isolated and a comparative microarray was undertaken. A common NFκB transcriptional programme was identified following both TLR2 and TLR4 ligation which peaked at between 3 to 6 hours including upregulation of many of the NFκB family members. In contrast an interferon transcriptional response was observed following TLR4 but not TLR2 ligation as early as 1 hour post stimulation and peaking at 6 hours. These results recapitulate the findings observed in previously published studies using isolated murine and human myeloid cells indicating that in vitro stimulated human whole blood can be used to interrogate the early transcriptional kinetic response of innate cells to TLR ligands. Our study demonstrates that a transcriptomic analysis of mRNA isolated from human whole blood can delineate both the temporal response and the key transcriptional differences following TLR2 and TLR4 ligation.
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Affiliation(s)
- Simon Blankley
- Division of Immunoregulation, MRC National Institute for Medical Research, London, United Kingdom
- * E-mail:
| | - Christine M. Graham
- Division of Immunoregulation, MRC National Institute for Medical Research, London, United Kingdom
| | - Ashleigh Howes
- Division of Immunoregulation, MRC National Institute for Medical Research, London, United Kingdom
| | - Chloe I. Bloom
- Division of Immunoregulation, MRC National Institute for Medical Research, London, United Kingdom
| | - Matthew P. R. Berry
- Division of Immunoregulation, MRC National Institute for Medical Research, London, United Kingdom
- Department of Respiratory Medicine, Imperial College Healthcare NHS trust, London, United Kingdom
| | - Damien Chaussabel
- Baylor Institute for Immunology Research/ANRS Center for Human Vaccines, INSERM, Dallas, Texas, United States of America
- Systems Immunology, Benaroya Research Institute, Seattle, Washington, United States of America
| | - Virginia Pascual
- Baylor Institute for Immunology Research/ANRS Center for Human Vaccines, INSERM, Dallas, Texas, United States of America
| | - Jacques Banchereau
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut, United States of America
| | - Marc Lipman
- Department of Respiratory Medicine, Royal Free London NHS Foundation Trust, University College London, London, United Kingdom
| | - Anne O’Garra
- Division of Immunoregulation, MRC National Institute for Medical Research, London, United Kingdom
- Department of Medicine, National Heart and Lung Institute, Imperial College, London, United Kingdom
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14
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Modeling the transcriptional regulatory network that controls the early hypoxic response in Candida albicans. EUKARYOTIC CELL 2014; 13:675-90. [PMID: 24681685 DOI: 10.1128/ec.00292-13] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
We determined the changes in transcriptional profiles that occur in the first hour following the transfer of Candida albicans to hypoxic growth conditions. The impressive speed of this response is not compatible with current models of fungal adaptation to hypoxia that depend on the depletion of sterol and heme. Functional analysis using Gene Set Enrichment Analysis (GSEA) identified the Sit4 phosphatase, Ccr4 mRNA deacetylase, and Sko1 transcription factor (TF) as potential regulators of the early hypoxic response. Cells mutated in these and other regulators exhibit a delay in their transcriptional responses to hypoxia. Promoter occupancy data for 29 TFs were combined with the transcriptional profiles of 3,111 in vivo target genes in a Network Component Analysis (NCA) to produce a model of the dynamic and highly interconnected TF network that controls this process. With data from the TF network obtained from a variety of sources, we generated an edge and node model that was capable of separating many of the hypoxia-upregulated and -downregulated genes. Upregulated genes are centered on Tye7, Upc2, and Mrr1, which are associated with many of the gene promoters that exhibit the strongest activations. The connectivity of the model illustrates the high redundancy of this response system and the challenges that lie in determining the individual contributions of specific TFs. Finally, treating cells with an inhibitor of the oxidative phosphorylation chain mimics most of the early hypoxic profile, which suggests that this response may be initiated by a drop in ATP production.
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15
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Doni Jayavelu N, Bar N. Dynamics of regulatory networks in gastrin-treated adenocarcinoma cells. PLoS One 2014; 9:e78349. [PMID: 24416123 PMCID: PMC3885390 DOI: 10.1371/journal.pone.0078349] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2013] [Accepted: 09/20/2013] [Indexed: 12/29/2022] Open
Abstract
Understanding gene transcription regulatory networks is critical to deciphering the molecular mechanisms of different cellular states. Most studies focus on static transcriptional networks. In the current study, we used the gastrin-regulated system as a model to understand the dynamics of transcriptional networks composed of transcription factors (TFs) and target genes (TGs). The hormone gastrin activates and stimulates signaling pathways leading to various cellular states through transcriptional programs. Dysregulation of gastrin can result in cancerous tumors, for example. However, the regulatory networks involving gastrin are highly complex, and the roles of most of the components of these networks are unknown. We used time series microarray data of AR42J adenocarcinoma cells treated with gastrin combined with static TF-TG relationships integrated from different sources, and we reconstructed the dynamic activities of TFs using network component analysis (NCA). Based on the peak expression of TGs and activity of TFs, we created active sub-networks at four time ranges after gastrin treatment, namely immediate-early (IE), mid-early (ME), mid-late (ML) and very late (VL). Network analysis revealed that the active sub-networks were topologically different at the early and late time ranges. Gene ontology analysis unveiled that each active sub-network was highly enriched in a particular biological process. Interestingly, network motif patterns were also distinct between the sub-networks. This analysis can be applied to other time series microarray datasets, focusing on smaller sub-networks that are activated in a cascade, allowing better overview of the mechanisms involved at each time range.
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Affiliation(s)
- Naresh Doni Jayavelu
- Department of Chemical Engineering, Norwegian University of Science and Technology, Trondheim, Norway
- * E-mail:
| | - Nadav Bar
- Department of Chemical Engineering, Norwegian University of Science and Technology, Trondheim, Norway
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16
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Freilich RW, Woodbury ME, Ikezu T. Integrated expression profiles of mRNA and miRNA in polarized primary murine microglia. PLoS One 2013; 8:e79416. [PMID: 24244499 PMCID: PMC3823621 DOI: 10.1371/journal.pone.0079416] [Citation(s) in RCA: 127] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2012] [Accepted: 09/23/2013] [Indexed: 12/21/2022] Open
Abstract
Neuroinflammation contributes to many neurologic disorders including Alzheimer’s disease, multiple sclerosis, and stroke. Microglia is brain resident myeloid cells and have emerged as a key driver of the neuroinflammatory responses. MicroRNAs (miRNAs) provide a novel layer of gene regulation and play a critical role in regulating the inflammatory response of peripheral macrophages. However, little is known about the miRNA in inflammatory activation of microglia. To elucidate the role that miRNAs have on microglial phenotypes under classical (M1) or alternative (M2) activation under lipopolysaccharide (‘M1’-skewing) and interleukin-4 (‘M2a’-skewing) stimulation conditions, we performed microarray expression profiling and bioinformatics analysis of both mRNA and miRNA using primary cultured murine microglia. miR-689, miR-124, and miR-155 were the most strongly associated miRNAs predicted to mediate pro-inflammatory pathways and M1-like activation phenotype. miR-155, the most strongly up-regulated miRNA, regulates the signal transducer and activator of transcription 3 signaling pathway enabling the late phase response to M1-skewing stimulation. Reduced expression in miR-689 and miR-124 are associated with dis-inhibition of many canonical inflammatory pathways. miR-124, miR-711, miR-145 are the strongly associated miRNAs predicted to mediate anti-inflammatory pathways and M2-like activation phenotype. Reductions in miR-711 and miR-124 may regulate inflammatory signaling pathways and peroxisome proliferator-activated receptor-gamma pathway. miR-145 potentially regulate peripheral monocyte/macrophage differentiation and faciliate the M2-skewing phenotype. Overall, through combined miRNA and mRNA expression profiling and bioinformatics analysis we have identified six miRNAs and their putative roles in M1 and M2-skewing of microglial activation through different signaling pathways.
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Affiliation(s)
- Robert W. Freilich
- Laboratory of Molecular NeuroTherapeutics, Department of Pharmacology and Experimental Therapeutics, Boston University School of Medicine, Boston, Massachusetts, United States of America
| | - Maya E. Woodbury
- Laboratory of Molecular NeuroTherapeutics, Department of Pharmacology and Experimental Therapeutics, Boston University School of Medicine, Boston, Massachusetts, United States of America
- Graduate Program in Neuroscience, Boston University, Boston, Massachusetts, United States of America
| | - Tsuneya Ikezu
- Laboratory of Molecular NeuroTherapeutics, Department of Pharmacology and Experimental Therapeutics, Boston University School of Medicine, Boston, Massachusetts, United States of America
- Department of Neurology and Alzheimer’s Disease Center, Boston University School of Medicine, Boston, Massachusetts, United States of America
- * E-mail:
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17
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Patil A, Kumagai Y, Liang KC, Suzuki Y, Nakai K. Linking transcriptional changes over time in stimulated dendritic cells to identify gene networks activated during the innate immune response. PLoS Comput Biol 2013; 9:e1003323. [PMID: 24244133 PMCID: PMC3820512 DOI: 10.1371/journal.pcbi.1003323] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2013] [Accepted: 09/21/2013] [Indexed: 01/09/2023] Open
Abstract
The innate immune response is primarily mediated by the Toll-like receptors functioning through the MyD88-dependent and TRIF-dependent pathways. Despite being widely studied, it is not yet completely understood and systems-level analyses have been lacking. In this study, we identified a high-probability network of genes activated during the innate immune response using a novel approach to analyze time-course gene expression profiles of activated immune cells in combination with a large gene regulatory and protein-protein interaction network. We classified the immune response into three consecutive time-dependent stages and identified the most probable paths between genes showing a significant change in expression at each stage. The resultant network contained several novel and known regulators of the innate immune response, many of which did not show any observable change in expression at the sampled time points. The response network shows the dominance of genes from specific functional classes during different stages of the immune response. It also suggests a role for the protein phosphatase 2a catalytic subunit α in the regulation of the immunoproteasome during the late phase of the response. In order to clarify the differences between the MyD88-dependent and TRIF-dependent pathways in the innate immune response, time-course gene expression profiles from MyD88-knockout and TRIF-knockout dendritic cells were analyzed. Their response networks suggest the dominance of the MyD88-dependent pathway in the innate immune response, and an association of the circadian regulators and immunoproteasomal degradation with the TRIF-dependent pathway. The response network presented here provides the most probable associations between genes expressed in the early and the late phases of the innate immune response, while taking into account the intermediate regulators. We propose that the method described here can also be used in the identification of time-dependent gene sub-networks in other biological systems.
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Affiliation(s)
- Ashwini Patil
- The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Yutaro Kumagai
- WPI Immunology Frontier Research Center, Osaka University, Osaka, Japan
| | - Kuo-ching Liang
- The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Yutaka Suzuki
- Department of Medical Genome Sciences, The University of Tokyo, Tokyo, Japan
| | - Kenta Nakai
- The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
- * E-mail:
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18
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St. Laurent G, Shtokalo D, Tackett MR, Yang Z, Vyatkin Y, Milos PM, Seilheimer B, McCaffrey TA, Kapranov P. On the importance of small changes in RNA expression. Methods 2013; 63:18-24. [DOI: 10.1016/j.ymeth.2013.03.027] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2012] [Revised: 02/26/2013] [Accepted: 03/22/2013] [Indexed: 01/09/2023] Open
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Westra JW, Schlage WK, Hengstermann A, Gebel S, Mathis C, Thomson T, Wong B, Hoang V, Veljkovic E, Peck M, Lichtner RB, Weisensee D, Talikka M, Deehan R, Hoeng J, Peitsch MC. A modular cell-type focused inflammatory process network model for non-diseased pulmonary tissue. Bioinform Biol Insights 2013; 7:167-92. [PMID: 23843693 PMCID: PMC3700945 DOI: 10.4137/bbi.s11509] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Exposure to environmental stressors such as cigarette smoke (CS) elicits a variety of biological responses in humans, including the induction of inflammatory responses. These responses are especially pronounced in the lung, where pulmonary cells sit at the interface between the body’s internal and external environments. We combined a literature survey with a computational analysis of multiple transcriptomic data sets to construct a computable causal network model (the Inflammatory Process Network (IPN)) of the main pulmonary inflammatory processes. The IPN model predicted decreased epithelial cell barrier defenses and increased mucus hypersecretion in human bronchial epithelial cells, and an attenuated pro-inflammatory (M1) profile in alveolar macrophages following exposure to CS, consistent with prior results. The IPN provides a comprehensive framework of experimentally supported pathways related to CS-induced pulmonary inflammation. The IPN is freely available to the scientific community as a resource with broad applicability to study the pathogenesis of pulmonary disease.
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20
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Walpole J, Papin JA, Peirce SM. Multiscale computational models of complex biological systems. Annu Rev Biomed Eng 2013; 15:137-54. [PMID: 23642247 DOI: 10.1146/annurev-bioeng-071811-150104] [Citation(s) in RCA: 121] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Integration of data across spatial, temporal, and functional scales is a primary focus of biomedical engineering efforts. The advent of powerful computing platforms, coupled with quantitative data from high-throughput experimental methodologies, has allowed multiscale modeling to expand as a means to more comprehensively investigate biological phenomena in experimentally relevant ways. This review aims to highlight recently published multiscale models of biological systems, using their successes to propose the best practices for future model development. We demonstrate that coupling continuous and discrete systems best captures biological information across spatial scales by selecting modeling techniques that are suited to the task. Further, we suggest how to leverage these multiscale models to gain insight into biological systems using quantitative biomedical engineering methods to analyze data in nonintuitive ways. These topics are discussed with a focus on the future of the field, current challenges encountered, and opportunities yet to be realized.
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Affiliation(s)
- Joseph Walpole
- Department of Biomedical Engineering, University of Virginia, Charlottesville, VA 22908, USA
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21
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Greenfield A, Hafemeister C, Bonneau R. Robust data-driven incorporation of prior knowledge into the inference of dynamic regulatory networks. ACTA ACUST UNITED AC 2013; 29:1060-7. [PMID: 23525069 PMCID: PMC3624811 DOI: 10.1093/bioinformatics/btt099] [Citation(s) in RCA: 118] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
MOTIVATION Inferring global regulatory networks (GRNs) from genome-wide data is a computational challenge central to the field of systems biology. Although the primary data currently used to infer GRNs consist of gene expression and proteomics measurements, there is a growing abundance of alternate data types that can reveal regulatory interactions, e.g. ChIP-Chip, literature-derived interactions, protein-protein interactions. GRN inference requires the development of integrative methods capable of using these alternate data as priors on the GRN structure. Each source of structure priors has its unique biases and inherent potential errors; thus, GRN methods using these data must be robust to noisy inputs. RESULTS We developed two methods for incorporating structure priors into GRN inference. Both methods [Modified Elastic Net (MEN) and Bayesian Best Subset Regression (BBSR)] extend the previously described Inferelator framework, enabling the use of prior information. We test our methods on one synthetic and two bacterial datasets, and show that both MEN and BBSR infer accurate GRNs even when the structure prior used has significant amounts of error (>90% erroneous interactions). We find that BBSR outperforms MEN at inferring GRNs from expression data and noisy structure priors. AVAILABILITY AND IMPLEMENTATION Code, datasets and networks presented in this article are available at http://bonneaulab.bio.nyu.edu/software.html. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Alex Greenfield
- Computational Biology Program, New York University Sackler School of Medicine, New York, NY 10065, USA
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22
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Bengmark S. Nutrition of the critically ill — a 21st-century perspective. Nutrients 2013; 5:162-207. [PMID: 23344250 PMCID: PMC3571643 DOI: 10.3390/nu5010162] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2012] [Revised: 12/17/2012] [Accepted: 12/24/2012] [Indexed: 02/07/2023] Open
Abstract
Health care-induced diseases constitute a fast-increasing problem. Just one type of these health care-associated infections (HCAI) constitutes the fourth leading cause of death in Western countries. About 25 million individuals worldwide are estimated each year to undergo major surgery, of which approximately 3 million will never return home from the hospital. Furthermore, the quality of life is reported to be significantly impaired for the rest of the lives of those who, during their hospital stay, suffered life-threatening infections/sepsis. Severe infections are strongly associated with a high degree of systemic inflammation in the body, and intimately associated with significantly reduced and malfunctioning GI microbiota, a condition called dysbiosis. Deranged composition and function of the gastrointestinal microbiota, occurring from the mouth to the anus, has been found to cause impaired ability to maintain intact mucosal membrane functions and prevent leakage of toxins - bacterial endotoxins, as well as whole bacteria or debris of bacteria, the DNA of which are commonly found in most cells of the body, often in adipocytes of obese individuals or in arteriosclerotic plaques. Foods rich in proteotoxins such as gluten, casein and zein, and proteins, have been observed to have endotoxin-like effects that can contribute to dysbiosis. About 75% of the food in the Western diet is of limited or no benefit to the microbiota in the lower gut. Most of it, comprised specifically of refined carbohydrates, is already absorbed in the upper part of the GI tract, and what eventually reaches the large intestine is of limited value, as it contains only small amounts of the minerals, vitamins and other nutrients necessary for maintenance of the microbiota. The consequence is that the microbiota of modern humans is greatly reduced, both in terms of numbers and diversity when compared to the diets of our paleolithic forebears and the individuals living a rural lifestyle today. It is the artificial treatment provided in modern medical care - unfortunately often the only alternative provided - which constitute the main contributors to a poor outcome. These treatments include artificial ventilation, artificial nutrition, hygienic measures, use of skin-penetrating devices, tubes and catheters, frequent use of pharmaceuticals; they are all known to severely impair the microbiomes in various locations of the body, which, to a large extent, are ultimately responsible for a poor outcome. Attempts to reconstitute a normal microbiome by supply of probiotics have often failed as they are almost always undertaken as a complement to - and not as an alternative to - existing treatment schemes, especially those based on antibiotics, but also other pharmaceuticals.
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Affiliation(s)
- Stig Bengmark
- Division of Surgery & Interventional Science, University College London, 4th floor, 74 Huntley Street, London, WC1E 6AU, UK.
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23
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Gottschalk RA, Martins AJ, Sjoelund V, Angermann BR, Lin B, Germain RN. Recent progress using systems biology approaches to better understand molecular mechanisms of immunity. Semin Immunol 2012; 25:201-8. [PMID: 23238271 DOI: 10.1016/j.smim.2012.11.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/24/2012] [Accepted: 11/08/2012] [Indexed: 01/06/2023]
Abstract
The immune system is composed of multiple dynamic molecular and cellular networks, the complexity of which has been revealed by decades of exacting reductionist research. However, understanding of the immune system sufficient to anticipate its response to novel perturbations requires a more integrative or systems approach to immunology. While methods for unbiased high-throughput data acquisition and computational integration of the resulting datasets are still relatively new, they have begun to substantially enhance our understanding of immunological phenomena. Such approaches have expanded our view of interconnected signaling and transcriptional networks and have highlighted the function of non-linear processes such as spatial regulation and feedback loops. In addition, advances in single cell measurement technology have demonstrated potential sources and functions of response heterogeneity in system behavior. The success of the studies reviewed here often depended upon integration of one or more systems biology approaches with more traditional methods. We hope these examples will inspire a broader range of immunologists to probe questions in a quantitative and integrated manner, advancing collective efforts to understand the immune "system".
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Affiliation(s)
- Rachel A Gottschalk
- Laboratory of Systems Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892 USA
| | - Andrew J Martins
- Laboratory of Systems Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892 USA
| | - Virginie Sjoelund
- Laboratory of Systems Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892 USA
| | - Bastian R Angermann
- Laboratory of Systems Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892 USA
| | - Bin Lin
- Laboratory of Systems Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892 USA
| | - Ronald N Germain
- Laboratory of Systems Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892 USA
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24
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Bengmark S. Nutrition of the critically ill - emphasis on liver and pancreas. Hepatobiliary Surg Nutr 2012; 1:25-52. [PMID: 24570901 PMCID: PMC3924628 DOI: 10.3978/j.issn.2304-3881.2012.10.14] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/22/2012] [Accepted: 10/25/2012] [Indexed: 12/13/2022]
Abstract
About 25 million individuals undergo high risk surgery each year. Of these about 3 million will never return home from hospital, and the quality of life for many of those who return is often significantly impaired. Furthermore, many of those who manage to leave hospital have undergone severe life-threatening complications, mostly infections/sepsis. The development is strongly associated with the level of systemic inflammation in the body, which again is entirely a result of malfunctioning GI microbiota, a condition called dysbiosis, with deranged composition and function of the gastrointestinal microbiota from the mouth to the anus and impaired ability to maintain intact mucosal membrane functions and prevent leakage of toxins-bacterial endotoxins and whole or debris of bacteria, but also foods containing proteotoxins gluten, casein and zein and heat-induced molecules such as advanced glycation end products (AGEs) and advanced lipoxidation end products (ALEs). Markedly lower total anaerobic bacterial counts, particularly of the beneficial Bifidobacterium and Lactobacillus and higher counts of total facultative anaerobes such as Staphylococcus and Pseudomonas are often observed when analyzing the colonic microbiota. In addition Gram-negative facultative anaerobes are commonly identified microbial organisms in mesenteric lymph nodes and at serosal "scrapings" at laparotomy in patients suffering what is called "Systemic inflammation response system" (SIRS). Clearly the outcome is influenced by preexisting conditions in those undergoing surgery, but not to the extent as one could expect. Several studies have for example been unable to find significant influence of pre-existing obesity. The outcome seems much more to be related to the life-style of the individual and her/his "maintenance" of the microbiota e.g., size and diversity of microbiota, normal microbiota, eubiosis, being highly preventive. About 75% of the food Westerners consume does not benefit microbiota in the lower gut. Most of it, refined carbohydrates, is already absorbed in the upper part of the GI tract, and of what reaches the large intestine is of limited value containing less minerals, less vitamins and other nutrients important for maintenance of the microbiota. The consequence is that the microbiota of modern man has a much reduced size and diversity in comparison to what our Palelithic forefathers had, and individuals living a rural life have today. It is the artificial treatment provided by modern care, unfortunately often the only alternative, which belongs to the main contributor to poor outcome, among them; artificial ventilation, artificial nutrition, hygienic measures, use of skin penetrating devices, tubes and catheters, frequent use of pharmaceuticals, all known to significantly impair the total microbiome of the body and dramatically contribute to poor outcome. Attempts to reconstitute a normal microbiome have often failed as they have always been undertaken as a complement to and not an alternative to existing treatment schemes, especially treatments with antibiotics. Modern nutrition formulas are clearly too artificial as they are based on mixture of a variety of chemicals, which alone or together induce inflammation. Alternative formulas, based on regular food ingredients, especially rich in raw fresh greens, vegetables and fruits and with them healthy bacteria are suggested to be developed and tried.
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Affiliation(s)
- Stig Bengmark
- Division of Surgery & Interventional Science, University College London, London, WC1E 6AU, United Kingdom
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25
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St Laurent G, Shtokalo D, Tackett MR, Yang Z, Eremina T, Wahlestedt C, Urcuqui-Inchima S, Seilheimer B, McCaffrey TA, Kapranov P. Intronic RNAs constitute the major fraction of the non-coding RNA in mammalian cells. BMC Genomics 2012; 13:504. [PMID: 23006825 PMCID: PMC3507791 DOI: 10.1186/1471-2164-13-504] [Citation(s) in RCA: 92] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2012] [Accepted: 09/14/2012] [Indexed: 01/24/2023] Open
Abstract
BACKGROUND The function of RNA from the non-coding (the so called "dark matter") regions of the genome has been a subject of considerable recent debate. Perhaps the most controversy is regarding the function of RNAs found in introns of annotated transcripts, where most of the reads that map outside of exons are usually found. However, it has been reported that the levels of RNA in introns are minor relative to those of the corresponding exons, and that changes in the levels of intronic RNAs correlate tightly with that of adjacent exons. This would suggest that RNAs produced from the vast expanse of intronic space are just pieces of pre-mRNAs or excised introns en route to degradation. RESULTS We present data that challenges the notion that intronic RNAs are mere by-standers in the cell. By performing a highly quantitative RNAseq analysis of transcriptome changes during an inflammation time course, we show that intronic RNAs have a number of features that would be expected from functional, standalone RNA species. We show that there are thousands of introns in the mouse genome that generate RNAs whose overall abundance, which changes throughout the inflammation timecourse, and other properties suggest that they function in yet unknown ways. CONCLUSIONS So far, the focus of non-coding RNA discovery has shied away from intronic regions as those were believed to simply encode parts of pre-mRNAs. Results presented here suggest a very different situation--the sequences encoded in the introns appear to harbor a yet unexplored reservoir of novel, functional RNAs. As such, they should not be ignored in surveys of functional transcripts or other genomic studies.
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Affiliation(s)
- Georges St Laurent
- Immunovirology-Biogenisis Group, University of Antioquia, Medellin A.A. 1226, Colombia.
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26
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Bengmark S. Gut microbiota, immune development and function. Pharmacol Res 2012; 69:87-113. [PMID: 22989504 DOI: 10.1016/j.phrs.2012.09.002] [Citation(s) in RCA: 140] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/29/2012] [Accepted: 09/01/2012] [Indexed: 02/08/2023]
Abstract
The microbiota of Westerners is significantly reduced in comparison to rural individuals living a similar lifestyle to our Paleolithic forefathers but also to that of other free-living primates such as the chimpanzee. The great majority of ingredients in the industrially produced foods consumed in the West are absorbed in the upper part of small intestine and thus of limited benefit to the microbiota. Lack of proper nutrition for microbiota is a major factor under-pinning dysfunctional microbiota, dysbiosis, chronically elevated inflammation, and the production and leakage of endotoxins through the various tissue barriers. Furthermore, the over-comsumption of insulinogenic foods and proteotoxins, such as advanced glycation and lipoxidation molecules, gluten and zein, and a reduced intake of fruit and vegetables, are key factors behind the commonly observed elevated inflammation and the endemic of obesity and chronic diseases, factors which are also likely to be detrimental to microbiota. As a consequence of this lifestyle and the associated eating habits, most barriers, including the gut, the airways, the skin, the oral cavity, the vagina, the placenta, the blood-brain barrier, etc., are increasingly permeable. Attempts to recondition these barriers through the use of so called 'probiotics', normally applied to the gut, are rarely successful, and sometimes fail, as they are usually applied as adjunctive treatments, e.g. in parallel with heavy pharmaceutical treatment, not rarely consisting in antibiotics and chemotherapy. It is increasingly observed that the majority of pharmaceutical drugs, even those believed to have minimal adverse effects, such as proton pump inhibitors and anti-hypertensives, in fact adversely affect immune development and functions and are most likely also deleterious to microbiota. Equally, it appears that probiotic treatment is not compatible with pharmacological treatments. Eco-biological treatments, with plant-derived substances, or phytochemicals, e.g. curcumin and resveratrol, and pre-, pro- and syn-biotics offers similar effects as use of biologicals, although milder but also free from adverse effects. Such treatments should be tried as alternative therapies; mainly, to begin with, for disease prevention but also in early cases of chronic diseases. Pharmaceutical treatment has, thus far, failed to inhibit the tsunami of endemic diseases spreading around the world, and no new tools are in sight. Dramatic alterations, in direction of a paleolithic-like lifestyle and food habits, seem to be the only alternatives with the potential to control the present escalating crisis. The present review focuses on human studies, especially those of clinical relevance.
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Affiliation(s)
- Stig Bengmark
- Division of Surgery & Interventional Science, University College London, 4th floor, 74 Huntley Street, London WC1E 6AU, United Kingdom.
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Schulz MH, Devanny WE, Gitter A, Zhong S, Ernst J, Bar-Joseph Z. DREM 2.0: Improved reconstruction of dynamic regulatory networks from time-series expression data. BMC SYSTEMS BIOLOGY 2012; 6:104. [PMID: 22897824 PMCID: PMC3464930 DOI: 10.1186/1752-0509-6-104] [Citation(s) in RCA: 90] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/28/2012] [Accepted: 07/18/2012] [Indexed: 12/28/2022]
Abstract
Background Modeling dynamic regulatory networks is a major challenge since much of the protein-DNA interaction data available is static. The Dynamic Regulatory Events Miner (DREM) uses a Hidden Markov Model-based approach to integrate this static interaction data with time series gene expression leading to models that can determine when transcription factors (TFs) activate genes and what genes they regulate. DREM has been used successfully in diverse areas of biological research. However, several issues were not addressed by the original version. Results DREM 2.0 is a comprehensive software for reconstructing dynamic regulatory networks that supports interactive graphical or batch mode. With version 2.0 a set of new features that are unique in comparison with other softwares are introduced. First, we provide static interaction data for additional species. Second, DREM 2.0 now accepts continuous binding values and we added a new method to utilize TF expression levels when searching for dynamic models. Third, we added support for discriminative motif discovery, which is particularly powerful for species with limited experimental interaction data. Finally, we improved the visualization to support the new features. Combined, these changes improve the ability of DREM 2.0 to accurately recover dynamic regulatory networks and make it much easier to use it for analyzing such networks in several species with varying degrees of interaction information. Conclusions DREM 2.0 provides a unique framework for constructing and visualizing dynamic regulatory networks. DREM 2.0 can be downloaded from: www.sb.cs.cmu.edu/drem.
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Affiliation(s)
- Marcel H Schulz
- Ray and Stephanie Lane Center for Computational Biology, Carnegie Mellon University, 5000 Forbes Avenue, Pittsburgh, PA 15213, USA.
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Bar-Joseph Z, Gitter A, Simon I. Studying and modelling dynamic biological processes using time-series gene expression data. Nat Rev Genet 2012; 13:552-64. [PMID: 22805708 DOI: 10.1038/nrg3244] [Citation(s) in RCA: 291] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Biological processes are often dynamic, thus researchers must monitor their activity at multiple time points. The most abundant source of information regarding such dynamic activity is time-series gene expression data. These data are used to identify the complete set of activated genes in a biological process, to infer their rates of change, their order and their causal effects and to model dynamic systems in the cell. In this Review we discuss the basic patterns that have been observed in time-series experiments, how these patterns are combined to form expression programs, and the computational analysis, visualization and integration of these data to infer models of dynamic biological systems.
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Affiliation(s)
- Ziv Bar-Joseph
- Lane Center for Computational Biology and Machine Learning Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, Pennsylvania, USA.
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Wang J, Qiu X, Li Y, Deng Y, Shi T. A transcriptional dynamic network during Arabidopsis thaliana pollen development. BMC SYSTEMS BIOLOGY 2011; 5 Suppl 3:S8. [PMID: 22784627 PMCID: PMC3287576 DOI: 10.1186/1752-0509-5-s3-s8] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Background To understand transcriptional regulatory networks (TRNs), especially the coordinated dynamic regulation between transcription factors (TFs) and their corresponding target genes during development, computational approaches would represent significant advances in the genome-wide expression analysis. The major challenges for the experiments include monitoring the time-specific TFs' activities and identifying the dynamic regulatory relationships between TFs and their target genes, both of which are currently not yet available at the large scale. However, various methods have been proposed to computationally estimate those activities and regulations. During the past decade, significant progresses have been made towards understanding pollen development at each development stage under the molecular level, yet the regulatory mechanisms that control the dynamic pollen development processes remain largely unknown. Here, we adopt Networks Component Analysis (NCA) to identify TF activities over time couse, and infer their regulatory relationships based on the coexpression of TFs and their target genes during pollen development. Results We carried out meta-analysis by integrating several sets of gene expression data related to Arabidopsis thaliana pollen development (stages range from UNM, BCP, TCP, HP to 0.5 hr pollen tube and 4 hr pollen tube). We constructed a regulatory network, including 19 TFs, 101 target genes and 319 regulatory interactions. The computationally estimated TF activities were well correlated to their coordinated genes' expressions during the development process. We clustered the expression of their target genes in the context of regulatory influences, and inferred new regulatory relationships between those TFs and their target genes, such as transcription factor WRKY34, which was identified that specifically expressed in pollen, and regulated several new target genes. Our finding facilitates the interpretation of the expression patterns with more biological relevancy, since the clusters corresponding to the activity of specific TF or the combination of TFs suggest the coordinated regulation of TFs to their target genes. Conclusions Through integrating different resources, we constructed a dynamic regulatory network of Arabidopsis thaliana during pollen development with gene coexpression and NCA. The network illustrated the relationships between the TFs' activities and their target genes' expression, as well as the interactions between TFs, which provide new insight into the molecular mechanisms that control the pollen development.
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Affiliation(s)
- Jigang Wang
- College of Life Sciences, Northeast Forestry University, Heilongjiang, Harbin 150040, China
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Nguyen TT, Foteinou PT, Calvano SE, Lowry SF, Androulakis IP. Computational identification of transcriptional regulators in human endotoxemia. PLoS One 2011; 6:e18889. [PMID: 21637747 PMCID: PMC3103499 DOI: 10.1371/journal.pone.0018889] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2010] [Accepted: 03/23/2011] [Indexed: 12/21/2022] Open
Abstract
One of the great challenges in the post-genomic era is to decipher the underlying principles governing the dynamics of biological responses. As modulating gene expression levels is among the key regulatory responses of an organism to changes in its environment, identifying biologically relevant transcriptional regulators and their putative regulatory interactions with target genes is an essential step towards studying the complex dynamics of transcriptional regulation. We present an analysis that integrates various computational and biological aspects to explore the transcriptional regulation of systemic inflammatory responses through a human endotoxemia model. Given a high-dimensional transcriptional profiling dataset from human blood leukocytes, an elementary set of temporal dynamic responses which capture the essence of a pro-inflammatory phase, a counter-regulatory response and a dysregulation in leukocyte bioenergetics has been extracted. Upon identification of these expression patterns, fourteen inflammation-specific gene batteries that represent groups of hypothetically ‘coregulated’ genes are proposed. Subsequently, statistically significant cis-regulatory modules (CRMs) are identified and decomposed into a list of critical transcription factors (34) that are validated largely on primary literature. Finally, our analysis further allows for the construction of a dynamic representation of the temporal transcriptional regulatory program across the host, deciphering possible combinatorial interactions among factors under which they might be active. Although much remains to be explored, this study has computationally identified key transcription factors and proposed a putative time-dependent transcriptional regulatory program associated with critical transcriptional inflammatory responses. These results provide a solid foundation for future investigations to elucidate the underlying transcriptional regulatory mechanisms under the host inflammatory response. Also, the assumption that coexpressed genes that are functionally relevant are more likely to share some common transcriptional regulatory mechanism seems to be promising, making the proposed framework become essential in unravelling context-specific transcriptional regulatory interactions underlying diverse mammalian biological processes.
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Affiliation(s)
- Tung T. Nguyen
- BioMaPS Institute for Quantitative Biology, Rutgers University, Piscataway, New Jersey, United States of America
| | - Panagiota T. Foteinou
- Department of Biomedical Engineering, Rutgers University, Piscataway, New Jersey, United States of America
| | - Steven E. Calvano
- Department of Surgery, Robert Wood Johnson Medical School, University of Medicine and Dentistry, New Jersey, New Brunswick, New Jersey, United States of America
| | - Stephen F. Lowry
- Department of Surgery, Robert Wood Johnson Medical School, University of Medicine and Dentistry, New Jersey, New Brunswick, New Jersey, United States of America
| | - Ioannis P. Androulakis
- Department of Biomedical Engineering, Rutgers University, Piscataway, New Jersey, United States of America
- Department of Surgery, Robert Wood Johnson Medical School, University of Medicine and Dentistry, New Jersey, New Brunswick, New Jersey, United States of America
- * E-mail:
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Haimovich B, Reddell MT, Calvano JE, Calvano SE, Macor MA, Coyle SM, Lowry SF. A novel model of common Toll-like receptor 4- and injury-induced transcriptional themes in human leukocytes. CRITICAL CARE : THE OFFICIAL JOURNAL OF THE CRITICAL CARE FORUM 2010; 14:R177. [PMID: 20929567 PMCID: PMC3219281 DOI: 10.1186/cc9283] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/08/2010] [Revised: 07/29/2010] [Accepted: 10/07/2010] [Indexed: 12/16/2022]
Abstract
Introduction An endotoxin challenge, sepsis, and injury/trauma, trigger significant changes in human peripheral blood leukocytes (PBL) gene expression. In this study, we have sought to test the hypothesis that the Toll-like receptor 4 (TLR4) induced transcription patterns elicited in humans exposed to in vivo endotoxin would parallel gene expression patterns observed in trauma patients with initial non-infectious injury. In addition, we sought to identify functional modules that are commonly affected by these two insults of differing magnitude and duration. Methods PBL were obtained from seven adult human subject experimental groups. The groups included a group of healthy, hospitalized volunteers (n = 15), that comprised four study groups of subjects challenged with intravenous endotoxin, without or with cortisol, and two serial samplings of trauma patients (n = 5). The PBL were analyzed for gene expression using a 8,793 probe microarray platform (Gene Chip® Focus, Affymetrix). The expression of a subset of genes was determined using qPCR. Results We describe sequential selection criteria of gene expression data that identifies 445 genes that are significantly differentially expressed (both P ≤ 0.05 and >1.2 fold-change) in PBL derived from human subjects during the peak of systemic inflammatory responses induced by in vivo endotoxin, as well as in PBL obtained from trauma patients at 1 to 12 days after admission. We identified two functional modules that are commonly represented by this analysis. The first module includes more than 50 suppressed genes that encode ribosomal proteins or translation regulators. The second module includes up-regulated genes encoding key enzymes associated with glycolysis. Finally, we show that several circadian clock genes are also suppressed in PBL of surgical ICU patients. Conclusions We identified a group of >400 genes that exhibit similar expression trends in PBL derived from either endotoxin-challenged subjects or trauma patients. The suppressed translational and circadian clock modules, and the upregulated glycolytic module, constitute a robust and long lasting PBL gene expression signature that may provide a tool for monitoring systemic inflammation and injury.
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Affiliation(s)
- Beatrice Haimovich
- Department of Surgery, Division of Surgical Sciences, UMDNJ-Robert Wood Johnson Medical School, New Brunswick, New Jersey, USA.
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Lee TK, Covert MW. High-throughput, single-cell NF-κB dynamics. Curr Opin Genet Dev 2010; 20:677-83. [PMID: 20846851 DOI: 10.1016/j.gde.2010.08.005] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2010] [Revised: 07/23/2010] [Accepted: 08/19/2010] [Indexed: 01/08/2023]
Abstract
Single cells in a population often respond differently to perturbations in the environment. Live-cell microscopy has enabled scientists to observe these differences at the single-cell level. Some advantages of live-cell imaging over population-based methods include better time resolution, higher sensitivity, automation, and richer datasets. One specific area where live-cell microscopy has made a significant impact is the field of NF-κB signaling dynamics, and recent efforts have focused on making live-cell imaging of these dynamics more high-throughput. We highlight the major aspects of increasing throughput and describe a current system that can monitor, image and analyze the NF-κB activation of thousands of single cells in parallel.
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Affiliation(s)
- Timothy K Lee
- Department of Bioengineering, Stanford University, 318 Campus Drive, Stanford, CA 94305, United States
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Przytycka TM, Singh M, Slonim DK. Toward the dynamic interactome: it's about time. Brief Bioinform 2010; 11:15-29. [PMID: 20061351 PMCID: PMC2810115 DOI: 10.1093/bib/bbp057] [Citation(s) in RCA: 144] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2009] [Revised: 11/01/2009] [Indexed: 11/14/2022] Open
Abstract
Dynamic molecular interactions play a central role in regulating the functioning of cells and organisms. The availability of experimentally determined large-scale cellular networks, along with other high-throughput experimental data sets that provide snapshots of biological systems at different times and conditions, is increasingly helpful in elucidating interaction dynamics. Here we review the beginnings of a new subfield within computational biology, one focused on the global inference and analysis of the dynamic interactome. This burgeoning research area, which entails a shift from static to dynamic network analysis, promises to be a major step forward in our ability to model and reason about cellular function and behavior.
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Affiliation(s)
- Teresa M Przytycka
- National Center of Biotechnology Information, NLM, NIH, 8000 Rockville Pike, Bethesda MD 20814, USA.
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