1
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Pavlicev M, Wagner GP. Reading the palimpsest of cell interactions: What questions may we ask of the data? iScience 2024; 27:109670. [PMID: 38665209 PMCID: PMC11043885 DOI: 10.1016/j.isci.2024.109670] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/28/2024] Open
Abstract
Biological function depends on the composition and structure of the organism, the latter describing the organization of interactions between parts. While cells in multicellular organisms are capable of a remarkable degree of autonomy, most functions do require cell communication: the coordination of functions (growth, differentiation, and apoptosis), the compartmentalization of cellular processes, and the integration of cells into higher levels of structural organization. A wealth of data on putative cell interactions has become available, yet its biological interpretation depends on our expectations about the structure of interaction networks. Here, we attempt to formulate basic questions to ask when interpreting cell interaction data. We build on the understanding that cells fulfill two general functions: the integrity-maintaining and the organismal service function. We derive the expected patterns of cell interactions considering two intertwined aspects: the functional and the evolutionary. Based on these, we propose guidelines for analysis and interpretation of transcriptional cell-interactome data.
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Affiliation(s)
- Mihaela Pavlicev
- Unit for Theoretical Biology, Department for Evolutionary Biology, University of Vienna, Vienna 1030, Austria
- Complexity Science Hub, Vienna 1090, Austria
| | - Günter P. Wagner
- Unit for Theoretical Biology, Department for Evolutionary Biology, University of Vienna, Vienna 1030, Austria
- Yale University, New Haven, CT 06520, USA
- Texas A&M University, College Station, TX 77843, USA
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2
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Pasqualotto A, da Silva V, Pellenz FM, Schuh AFS, Schwartz IVD, Siebert M. Identification of metabolic pathways and key genes associated with atypical parkinsonism using a systems biology approach. Metab Brain Dis 2024; 39:577-587. [PMID: 38305999 DOI: 10.1007/s11011-024-01342-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Accepted: 12/23/2023] [Indexed: 02/03/2024]
Abstract
Atypical parkinsonism (AP) is a group of complex neurodegenerative disorders with marked clinical and pathophysiological heterogeneity. The use of systems biology tools may contribute to the characterization of hub-bottleneck genes, and the identification of its biological pathways to broaden the understanding of the bases of these disorders. A systematic search was performed on the DisGeNET database, which integrates data from expert curated repositories, GWAS catalogues, animal models and the scientific literature. The tools STRING 11.0 and Cytoscape 3.8.2 were used for analysis of protein-protein interaction (PPI) network. The PPI network topography analyses were performed using the CytoHubba 0.1 plugin for Cytoscape. The hub and bottleneck genes were inserted into 4 different sets on the InteractiveVenn. Additional functional enrichment analyses were performed to identify Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways and gene ontology for a described set of genes. The systematic search in the DisGeNET database identified 485 genes involved with Atypical Parkinsonism. Superimposing these genes, we detected a total of 31 hub-bottleneck genes. Moreover, our functional enrichment analyses demonstrated the involvement of these hub-bottleneck genes in 3 major KEGG pathways. We identified 31 highly interconnected hub-bottleneck genes through a systems biology approach, which may play a key role in the pathogenesis of atypical parkinsonism. The functional enrichment analyses showed that these genes are involved in several biological processes and pathways, such as the glial cell development, glial cell activation and cognition, pathways were related to Alzheimer disease and Parkinson disease. As a hypothesis, we highlight as possible key genes for AP the MAPT (microtubule associated protein tau), APOE (apolipoprotein E), SNCA (synuclein alpha) and APP (amyloid beta precursor protein) genes.
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Affiliation(s)
- Amanda Pasqualotto
- Programa de Pós-graduação em Genética e Biologia Molecular, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
- BRAIN Laboratory, Hospital de Clínicas de Porto Alegre, Porto Alegre, RS, Brazil
| | | | - Felipe Mateus Pellenz
- Serviço de Endocrinologia, -Hospital de Clinicas de Porto Alegre, Porto Alegre, RS, Brazil
- Graduate Program in Medical Sciences: Endocrinology, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Artur Francisco Schumacher Schuh
- Serviço de Neurologia, Hospital de Clínicas de Porto Alegre, Porto Alegre, RS, Brazil
- Departatamento de Farmacologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Ida Vanessa Doederlein Schwartz
- Programa de Pós-graduação em Genética e Biologia Molecular, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil.
- BRAIN Laboratory, Hospital de Clínicas de Porto Alegre, Porto Alegre, RS, Brazil.
- Medical Genetics Service, Hospital de Clínicas de Porto Alegre, Porto Alegre, RS, Brazil.
- Department of Genetics, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil.
| | - Marina Siebert
- BRAIN Laboratory, Hospital de Clínicas de Porto Alegre, Porto Alegre, RS, Brazil
- Unit of Laboratorial Research, Experimental Research Center, Hospital de Clínicas de Porto Alegre, Porto Alegre, RS, Brazil
- Programa de Pós Graduação em Hepatologia e Gastroenterologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
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3
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Flowers S, Holder KH, Rump GK, Gardner SM. Missed connections: Exploring features of undergraduate biology students' knowledge networks relating gene regulation, cell-cell communication, and phenotypic expression. CBE LIFE SCIENCES EDUCATION 2023; 22:ar44. [PMID: 37751503 PMCID: PMC10756040 DOI: 10.1187/cbe.22-03-0041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 08/09/2023] [Accepted: 08/16/2023] [Indexed: 09/28/2023]
Abstract
Explaining biological phenomena requires understanding how different processes function and describing interactions between components at various levels of organization over time and space in biological systems. This is a desired competency yet is a complicated and often challenging task for undergraduate biology students. Therefore, we need a better understanding of their integrated knowledge regarding important biological concepts. Informed by the theory of knowledge integration and mechanistic reasoning, in this qualitative case study, we elicited and characterized knowledge networks of nine undergraduate biology students. We investigated students' conceptions of and the various ways they connect three fundamental subsystems in biology: 1) gene regulation, 2) cell-cell communication, and 3) phenotypic expression. We found that only half of the conceptual questions regarding the three subsystems were answered correctly by the majority of students. Knowledge networks tended to be linear and unidirectional, with little variation in the types of relationships displayed. Students did not spontaneously express mechanistic connections, mainly described undefined, cellular, and macromolecular levels of organization, and mainly discussed unspecified and intracellular localizations. These results emphasize the need to support students' understanding of fundamental concepts, and promoting knowledge integration in the classroom could assist students' ability to understand biological systems.
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Affiliation(s)
- Sharleen Flowers
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907
| | - Kal H. Holder
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907
| | - Gabrielle K. Rump
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907
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4
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Fernandez ME, Martinez-Romero J, Aon MA, Bernier M, Price NL, de Cabo R. How is Big Data reshaping preclinical aging research? Lab Anim (NY) 2023; 52:289-314. [PMID: 38017182 DOI: 10.1038/s41684-023-01286-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Accepted: 10/10/2023] [Indexed: 11/30/2023]
Abstract
The exponential scientific and technological progress during the past 30 years has favored the comprehensive characterization of aging processes with their multivariate nature, leading to the advent of Big Data in preclinical aging research. Spanning from molecular omics to organism-level deep phenotyping, Big Data demands large computational resources for storage and analysis, as well as new analytical tools and conceptual frameworks to gain novel insights leading to discovery. Systems biology has emerged as a paradigm that utilizes Big Data to gain insightful information enabling a better understanding of living organisms, visualized as multilayered networks of interacting molecules, cells, tissues and organs at different spatiotemporal scales. In this framework, where aging, health and disease represent emergent states from an evolving dynamic complex system, context given by, for example, strain, sex and feeding times, becomes paramount for defining the biological trajectory of an organism. Using bioinformatics and artificial intelligence, the systems biology approach is leading to remarkable advances in our understanding of the underlying mechanism of aging biology and assisting in creative experimental study designs in animal models. Future in-depth knowledge acquisition will depend on the ability to fully integrate information from different spatiotemporal scales in organisms, which will probably require the adoption of theories and methods from the field of complex systems. Here we review state-of-the-art approaches in preclinical research, with a focus on rodent models, that are leading to conceptual and/or technical advances in leveraging Big Data to understand basic aging biology and its full translational potential.
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Affiliation(s)
- Maria Emilia Fernandez
- Experimental Gerontology Section, Translational Gerontology Branch, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
| | - Jorge Martinez-Romero
- Experimental Gerontology Section, Translational Gerontology Branch, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
- Laboratory of Epidemiology and Population Science, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
| | - Miguel A Aon
- Experimental Gerontology Section, Translational Gerontology Branch, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
- Laboratory of Cardiovascular Science, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
| | - Michel Bernier
- Experimental Gerontology Section, Translational Gerontology Branch, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
| | - Nathan L Price
- Experimental Gerontology Section, Translational Gerontology Branch, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
| | - Rafael de Cabo
- Experimental Gerontology Section, Translational Gerontology Branch, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA.
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5
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A 3D structural SARS-CoV-2-human interactome to explore genetic and drug perturbations. Nat Methods 2021; 18:1477-1488. [PMID: 34845387 PMCID: PMC8665054 DOI: 10.1038/s41592-021-01318-w] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Accepted: 10/05/2021] [Indexed: 01/08/2023]
Abstract
Emergence of new viral agents is driven by evolution of interactions between viral proteins and host targets. For instance, increased infectivity of SARS-CoV-2 compared to SARS-CoV-1 arose in part through rapid evolution along the interface between the spike protein and its human receptor ACE2, leading to increased binding affinity. To facilitate broader exploration of how pathogen-host interactions might impact transmission and virulence in the ongoing COVID-19 pandemic, we performed state-of-the-art interface prediction followed by molecular docking to construct a three-dimensional structural interactome between SARS-CoV-2 and human. We additionally carried out downstream meta-analyses to investigate enrichment of sequence divergence between SARS-CoV-1 and SARS-CoV-2 or human population variants along viral-human protein-interaction interfaces, predict changes in binding affinity by these mutations/variants and further prioritize drug repurposing candidates predicted to competitively bind human targets. We believe this resource ( http://3D-SARS2.yulab.org ) will aid in development and testing of informed hypotheses for SARS-CoV-2 etiology and treatments.
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6
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Emmert-Streib F, Dehmer M. Data-Driven Computational Social Network Science: Predictive and Inferential Models for Web-Enabled Scientific Discoveries. Front Big Data 2021; 4:591749. [PMID: 33969290 PMCID: PMC8100320 DOI: 10.3389/fdata.2021.591749] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Accepted: 02/18/2021] [Indexed: 12/13/2022] Open
Abstract
The ultimate goal of the social sciences is to find a general social theory encompassing all aspects of social and collective phenomena. The traditional approach to this is very stringent by trying to find causal explanations and models. However, this approach has been recently criticized for preventing progress due to neglecting prediction abilities of models that support more problem-oriented approaches. The latter models would be enabled by the surge of big Web-data currently available. Interestingly, this problem cannot be overcome with methods from computational social science (CSS) alone because this field is dominated by simulation-based approaches and descriptive models. In this article, we address this issue and argue that the combination of big social data with social networks is needed for creating prediction models. We will argue that this alliance has the potential for gradually establishing a causal social theory. In order to emphasize the importance of integrating big social data with social networks, we call this approach data-driven computational social network science (DD-CSNS).
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Affiliation(s)
- Frank Emmert-Streib
- Predictive Society and Data Analytics Lab, Faculty of Information Technology and Communication Sciences, Tampere University, Tampere, Finland.,Institute of Biosciences and Medical Technology, Tampere, Finland
| | - Matthias Dehmer
- Department of Computer Science, Swiss Distance University of Applied Sciences, Brig, Switzerland.,School of Science, Xian Technological University, Xian, China.,College of Artificial Intelligence, Nankai University, Tianjin, China.,Department of Biomedical Computer Science and Mechatronics, The Health and Life Science University, UMIT, Hall in Tyrol, Austria
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7
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Manjang K, Tripathi S, Yli-Harja O, Dehmer M, Glazko G, Emmert-Streib F. Prognostic gene expression signatures of breast cancer are lacking a sensible biological meaning. Sci Rep 2021; 11:156. [PMID: 33420139 PMCID: PMC7794581 DOI: 10.1038/s41598-020-79375-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 12/03/2020] [Indexed: 12/28/2022] Open
Abstract
The identification of prognostic biomarkers for predicting cancer progression is an important problem for two reasons. First, such biomarkers find practical application in a clinical context for the treatment of patients. Second, interrogation of the biomarkers themselves is assumed to lead to novel insights of disease mechanisms and the underlying molecular processes that cause the pathological behavior. For breast cancer, many signatures based on gene expression values have been reported to be associated with overall survival. Consequently, such signatures have been used for suggesting biological explanations of breast cancer and drug mechanisms. In this paper, we demonstrate for a large number of breast cancer signatures that such an implication is not justified. Our approach eliminates systematically all traces of biological meaning of signature genes and shows that among the remaining genes, surrogate gene sets can be formed with indistinguishable prognostic prediction capabilities and opposite biological meaning. Hence, our results demonstrate that none of the studied signatures has a sensible biological interpretation or meaning with respect to disease etiology. Overall, this shows that prognostic signatures are black-box models with sensible predictions of breast cancer outcome but no value for revealing causal connections. Furthermore, we show that the number of such surrogate gene sets is not small but very large.
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Affiliation(s)
- Kalifa Manjang
- Predictive Society and Data Analytics Lab, Tampere University, Tampere, Korkeakoulunkatu 10, 33720, Tampere, Finland
| | - Shailesh Tripathi
- Predictive Society and Data Analytics Lab, Tampere University, Tampere, Korkeakoulunkatu 10, 33720, Tampere, Finland
| | - Olli Yli-Harja
- Computational Systems Biology, Tampere University, Tampere, Korkeakoulunkatu 10, 33720, Tampere, Finland
- Institute for Systems Biology, Seattle, WA, USA
- Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, USA
| | - Matthias Dehmer
- Steyr School of Management, University of Applied Sciences Upper Austria, 4400 Steyr Campus, Wels, Austria
- College of Artificial Intelligence, Nankai University, Tianjin, 300350, China
- Department of Biomedical Computer Science and Mechatronics, UMIT-The Health and Life Science University, 6060 Hall in Tyrol, Innsbruck, Austria
| | - Galina Glazko
- Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, USA
| | - Frank Emmert-Streib
- Predictive Society and Data Analytics Lab, Tampere University, Tampere, Korkeakoulunkatu 10, 33720, Tampere, Finland.
- Institute of Biosciences and Medical Technology, Tampere University, Tampere, Korkeakoulunkatu 10, 33720, Tampere, Finland.
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8
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Klann K, Tascher G, Münch C. Virus systems biology: Proteomics profiling of dynamic protein networks during infection. Adv Virus Res 2021; 109:1-29. [PMID: 33934824 DOI: 10.1016/bs.aivir.2020.12.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The host cell proteome undergoes a variety of dynamic changes during viral infection, elicited by the virus itself or host cell defense mechanisms. Studying these changes on a global scale by integrating functional and physical interactions within protein networks during infection is an important tool to understand pathology. Indeed, proteomics studies dissecting protein signaling cascades and interaction networks upon infection showed how global information can significantly improve understanding of disease mechanisms of diverse viral infections. Here, we summarize and give examples of different experimental designs, proteomics approaches and bioinformatics analyses that allow profiling proteome changes and host-pathogen interactions to gain a molecular systems view of viral infection.
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Affiliation(s)
- Kevin Klann
- Institute of Biochemistry II, Faculty of Medicine, Goethe University, Frankfurt am Main, Germany
| | - Georg Tascher
- Institute of Biochemistry II, Faculty of Medicine, Goethe University, Frankfurt am Main, Germany
| | - Christian Münch
- Institute of Biochemistry II, Faculty of Medicine, Goethe University, Frankfurt am Main, Germany; Frankfurt Cancer Institute, Frankfurt am Main, Germany; Cardio-Pulmonary Institute, Frankfurt am Main, Germany.
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9
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Manjang K, Tripathi S, Yli-Harja O, Dehmer M, Emmert-Streib F. Graph-based exploitation of gene ontology using GOxploreR for scrutinizing biological significance. Sci Rep 2020; 10:16672. [PMID: 33028846 PMCID: PMC7542435 DOI: 10.1038/s41598-020-73326-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Accepted: 08/17/2020] [Indexed: 12/12/2022] Open
Abstract
Gene ontology (GO) is an eminent knowledge base frequently used for providing biological interpretations for the analysis of genes or gene sets from biological, medical and clinical problems. Unfortunately, the interpretation of such results is challenging due to the large number of GO terms, their hierarchical and connected organization as directed acyclic graphs (DAGs) and the lack of tools allowing to exploit this structural information explicitly. For this reason, we developed the R package GOxploreR. The main features of GOxploreR are (I) easy and direct access to structural features of GO, (II) structure-based ranking of GO-terms, (III) mapping to reduced GO-DAGs including visualization capabilities and (IV) prioritizing of GO-terms. The underlying idea of GOxploreR is to exploit a graph-theoretical perspective of GO as manifested by its DAG-structure and the containing hierarchy levels for cumulating semantic information. That means all these features enhance the utilization of structural information of GO and complement existing analysis tools. Overall, GOxploreR provides exploratory as well as confirmatory tools for complementing any kind of analysis resulting in a list of GO-terms, e.g., from differentially expressed genes or gene sets, GWAS or biomarkers. Our R package GOxploreR is freely available from CRAN.
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Affiliation(s)
- Kalifa Manjang
- Predictive Society and Data Analytics Lab, Tampere University, Tampere, Korkeakoulunkatu 10, 33720, Tampere, Finland
| | - Shailesh Tripathi
- Predictive Society and Data Analytics Lab, Tampere University, Tampere, Korkeakoulunkatu 10, 33720, Tampere, Finland
| | - Olli Yli-Harja
- Computational Systems Biology, Tampere University, Tampere, Korkeakoulunkatu 10, 33720, Tampere, Finland.,Institute for Systems Biology, Seattle, WA, USA.,Institute of Biosciences and Medical Technology, Tampere University, Tampere, Korkeakoulunkatu 10, 33720, Tampere, Finland
| | - Matthias Dehmer
- Department of Biomedical Computer Science and Mechatronics, UMIT-The Health and Life Science University, 6060, Hall in Tyrol, Austria.,College of Artificial Intelligence, Nankai University, Tianjin, 300350, China
| | - Frank Emmert-Streib
- Predictive Society and Data Analytics Lab, Tampere University, Tampere, Korkeakoulunkatu 10, 33720, Tampere, Finland. .,Institute of Biosciences and Medical Technology, Tampere University, Tampere, Korkeakoulunkatu 10, 33720, Tampere, Finland.
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10
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Abstract
Network theory provides one of the most potent analysis tools for the study of complex systems. In this paper, we illustrate the network-based perspective in drug research and how it is coherent with the new paradigm of drug discovery. We first present data sources from which networks are built, then show some examples of how the networks can be used to investigate drug-related systems. A section is devoted to network-based inference applications, i.e., prediction methods based on interactomes, that can be used to identify putative drug-target interactions without resorting to 3D modeling. Finally, we present some aspects of Boolean networks dynamics, anticipating that it might become a very potent modeling framework to develop in silico screening protocols able to simulate phenotypic screening experiments. We conclude that network applications integrated with machine learning and 3D modeling methods will become an indispensable tool for computational drug discovery in the next years.
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Affiliation(s)
- Maurizio Recanatini
- Department of Pharmacy and
Biotechnology, Alma Mater Studiorum—University of Bologna, Via Belmeloro 6, I-40126 Bologna, Italy
| | - Chiara Cabrelle
- Department of Pharmacy and
Biotechnology, Alma Mater Studiorum—University of Bologna, Via Belmeloro 6, I-40126 Bologna, Italy
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11
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A massively parallel barcoded sequencing pipeline enables generation of the first ORFeome and interactome map for rice. Proc Natl Acad Sci U S A 2020; 117:11836-11842. [PMID: 32398372 DOI: 10.1073/pnas.1918068117] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Systematic mappings of protein interactome networks have provided invaluable functional information for numerous model organisms. Here we develop PCR-mediated Linkage of barcoded Adapters To nucleic acid Elements for sequencing (PLATE-seq) that serves as a general tool to rapidly sequence thousands of DNA elements. We validate its utility by generating the ORFeome for Oryza sativa covering 2,300 genes and constructing a high-quality protein-protein interactome map consisting of 322 interactions between 289 proteins, expanding the known interactions in rice by roughly 50%. Our work paves the way for high-throughput profiling of protein-protein interactions in a wide range of organisms.
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12
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Bozhilova LV, Whitmore AV, Wray J, Reinert G, Deane CM. Measuring rank robustness in scored protein interaction networks. BMC Bioinformatics 2019; 20:446. [PMID: 31462221 PMCID: PMC6714100 DOI: 10.1186/s12859-019-3036-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Accepted: 08/19/2019] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Protein interaction databases often provide confidence scores for each recorded interaction based on the available experimental evidence. Protein interaction networks (PINs) are then built by thresholding on these scores, so that only interactions of sufficiently high quality are included. These networks are used to identify biologically relevant motifs or nodes using metrics such as degree or betweenness centrality. This type of analysis can be sensitive to the choice of threshold. If a node metric is to be useful for extracting biological signal, it should induce similar node rankings across PINs obtained at different reasonable confidence score thresholds. RESULTS We propose three measures-rank continuity, identifiability, and instability-to evaluate how robust a node metric is to changes in the score threshold. We apply our measures to twenty-five metrics and identify four as the most robust: the number of edges in the step-1 ego network, as well as the leave-one-out differences in average redundancy, average number of edges in the step-1 ego network, and natural connectivity. Our measures show good agreement across PINs from different species and data sources. Analysis of synthetically generated scored networks shows that robustness results are context-specific, and depend both on network topology and on how scores are placed across network edges. CONCLUSION Due to the uncertainty associated with protein interaction detection, and therefore network structure, for PIN analysis to be reproducible, it should yield similar results across different confidence score thresholds. We demonstrate that while certain node metrics are robust with respect to threshold choice, this is not always the case. Promisingly, our results suggest that there are some metrics that are robust across networks constructed from different databases, and different scoring procedures.
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Affiliation(s)
- Lyuba V Bozhilova
- Department of Statistics, University of Oxford, 24-29 St Giles', Oxford, OX1 3LB, UK
| | - Alan V Whitmore
- e-Therapeutics Plc, 17 Fenlock Rd, Long Hanborough, OX29 8LN, UK
| | - Jonny Wray
- e-Therapeutics Plc, 17 Fenlock Rd, Long Hanborough, OX29 8LN, UK
| | - Gesine Reinert
- Department of Statistics, University of Oxford, 24-29 St Giles', Oxford, OX1 3LB, UK
| | - Charlotte M Deane
- Department of Statistics, University of Oxford, 24-29 St Giles', Oxford, OX1 3LB, UK.
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13
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Smolander J, Dehmer M, Emmert-Streib F. Comparing deep belief networks with support vector machines for classifying gene expression data from complex disorders. FEBS Open Bio 2019; 9:1232-1248. [PMID: 31074948 PMCID: PMC6609581 DOI: 10.1002/2211-5463.12652] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Revised: 04/25/2019] [Accepted: 05/08/2019] [Indexed: 12/24/2022] Open
Abstract
Genomics data provide great opportunities for translational research and the clinical practice, for example, for predicting disease stages. However, the classification of such data is a challenging task due to their high dimensionality, noise, and heterogeneity. In recent years, deep learning classifiers generated much interest, but due to their complexity, so far, little is known about the utility of this method for genomics. In this paper, we address this problem by studying a computational diagnostics task by classification of breast cancer and inflammatory bowel disease patients based on high‐dimensional gene expression data. We provide a comprehensive analysis of the classification performance of deep belief networks (DBNs) in dependence on its multiple model parameters and in comparison with support vector machines (SVMs). Furthermore, we investigate combined classifiers that integrate DBNs with SVMs. Such a classifier utilizes a DBN as representation learner forming the input for a SVM. Overall, our results provide guidelines for the complex usage of DBN for classifying gene expression data from complex diseases.
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Affiliation(s)
- Johannes Smolander
- Predictive Society and Data Analytics Lab, Faculty of Information Technology and Communication Sciences, Tampere University, Finland.,Turku Centre for Biotechnology, University of Turku, Finland
| | - Matthias Dehmer
- Institute for Intelligent Production, Faculty for Management, University of Applied Sciences Upper Austria, Steyr, Austria.,Department of Mechatronics and Biomedical Computer Science, UMIT, Hall in Tyrol, Austria.,College of Computer and Control Engineering, Nankai University, Tianjin, China
| | - Frank Emmert-Streib
- Predictive Society and Data Analytics Lab, Faculty of Information Technology and Communication Sciences, Tampere University, Finland.,Institute of Biosciences and Medical Technology, Tampere, Finland
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14
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Musa A, Tripathi S, Dehmer M, Yli-Harja O, Kauffman SA, Emmert-Streib F. Systems Pharmacogenomic Landscape of Drug Similarities from LINCS data: Drug Association Networks. Sci Rep 2019; 9:7849. [PMID: 31127155 PMCID: PMC6534546 DOI: 10.1038/s41598-019-44291-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Accepted: 05/08/2019] [Indexed: 02/01/2023] Open
Abstract
Modern research in the biomedical sciences is data-driven utilizing high-throughput technologies to generate big genomic data. The Library of Integrated Network-based Cellular Signatures (LINCS) is an example for a large-scale genomic data repository providing hundred thousands of high-dimensional gene expression measurements for thousands of drugs and dozens of cell lines. However, the remaining challenge is how to use these data effectively for pharmacogenomics. In this paper, we use LINCS data to construct drug association networks (DANs) representing the relationships between drugs. By using the Anatomical Therapeutic Chemical (ATC) classification of drugs we demonstrate that the DANs represent a systems pharmacogenomic landscape of drugs summarizing the entire LINCS repository on a genomic scale meaningfully. Here we identify the modules of the DANs as therapeutic attractors of the ATC drug classes.
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Affiliation(s)
- Aliyu Musa
- Predictive Society and Data Analytics Lab, Tampere University, Tampere, Korkeakoulunkatu 10, 33720, Tampere, Finland
- Institute of Biosciences and Medical Technology, Tampere University, Tampere, Korkeakoulunkatu 10, 33720, Tampere, Finland
| | - Shailesh Tripathi
- Predictive Society and Data Analytics Lab, Tampere University, Tampere, Korkeakoulunkatu 10, 33720, Tampere, Finland
- Institute for Intelligent Production, Faculty for Management, University of Applied Sciences Upper Austria, Wehrgrabengasse 1-3, 4400, Steyr, Austria
| | - Matthias Dehmer
- Department for Biomedical Computer Science and Mechatronics, UMIT - The Health and Lifesciences University, Eduard Wallnoefer Zentrum 1, 6060, Hall in Tyrol, Austria
- College of Computer and Control Engineering, Nankai University, Tianjin, 300350, P.R. China
- Institute for Intelligent Production, Faculty for Management, University of Applied Sciences Upper Austria, Wehrgrabengasse 1-3, 4400, Steyr, Austria
| | - Olli Yli-Harja
- Institute of Biosciences and Medical Technology, Tampere University, Tampere, Korkeakoulunkatu 10, 33720, Tampere, Finland
- Computational Systems Biology Lab, Tampere University of Technology, Korkeakoulunkatu 10, 33720, Tampere, Finland
- Institute for Systems Biology, Seattle, WA, 98109, USA
| | | | - Frank Emmert-Streib
- Predictive Society and Data Analytics Lab, Tampere University, Tampere, Korkeakoulunkatu 10, 33720, Tampere, Finland.
- Institute of Biosciences and Medical Technology, Tampere University, Tampere, Korkeakoulunkatu 10, 33720, Tampere, Finland.
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15
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Joseph JA, Akkermans S, Nimmegeers P, Van Impe JFM. Bioproduction of the Recombinant Sweet Protein Thaumatin: Current State of the Art and Perspectives. Front Microbiol 2019; 10:695. [PMID: 31024485 PMCID: PMC6463758 DOI: 10.3389/fmicb.2019.00695] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Accepted: 03/19/2019] [Indexed: 12/12/2022] Open
Abstract
There is currently a worldwide trend to reduce sugar consumption. This trend is mostly met by the use of artificial non-nutritive sweeteners. However, these sweeteners have also been proven to have adverse health effects such as dizziness, headaches, gastrointestinal issues, and mood changes for aspartame. One of the solutions lies in the commercialization of sweet proteins, which are not associated with adverse health effects. Of these proteins, thaumatin is one of the most studied and most promising alternatives for sugars and artificial sweeteners. Since the natural production of these proteins is often too expensive, biochemical production methods are currently under investigation. With these methods, recombinant DNA technology is used for the production of sweet proteins in a host organism. The most promising host known today is the methylotrophic yeast, Pichia pastoris. This yeast has a tightly regulated methanol-induced promotor, allowing a good control over the recombinant protein production. Great efforts have been undertaken for improving the yields and purities of thaumatin productions, but a further optimization is still desired. This review focuses on (i) the motivation for using and producing sweet proteins, (ii) the properties and history of thaumatin, (iii) the production of recombinant sweet proteins, and (iv) future possibilities for process optimization based on a systems biology approach.
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Affiliation(s)
- Jewel Ann Joseph
- BioTeC+, Chemical and Biochemical Process Technology and Control, Department of Chemical Engineering, KU Leuven, Leuven, Belgium
- Optimization in Engineering Center-of-Excellence, KU Leuven, Leuven, Belgium
- CPMF, Flemish Cluster Predictive Microbiology in Foods, Leuven, Belgium
| | - Simen Akkermans
- BioTeC+, Chemical and Biochemical Process Technology and Control, Department of Chemical Engineering, KU Leuven, Leuven, Belgium
- Optimization in Engineering Center-of-Excellence, KU Leuven, Leuven, Belgium
- CPMF, Flemish Cluster Predictive Microbiology in Foods, Leuven, Belgium
| | - Philippe Nimmegeers
- BioTeC+, Chemical and Biochemical Process Technology and Control, Department of Chemical Engineering, KU Leuven, Leuven, Belgium
- Optimization in Engineering Center-of-Excellence, KU Leuven, Leuven, Belgium
- CPMF, Flemish Cluster Predictive Microbiology in Foods, Leuven, Belgium
| | - Jan F. M. Van Impe
- BioTeC+, Chemical and Biochemical Process Technology and Control, Department of Chemical Engineering, KU Leuven, Leuven, Belgium
- Optimization in Engineering Center-of-Excellence, KU Leuven, Leuven, Belgium
- CPMF, Flemish Cluster Predictive Microbiology in Foods, Leuven, Belgium
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16
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Jiang M, Pei Z, Fan X, Jiang J, Wang Q, Zhang Z. Function Analysis of Human Protein Interactions Based on a Novel Minimal Loop Algorithm. Curr Bioinform 2019. [DOI: 10.2174/1574893613666180906103946] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Background:
Various properties of Protein-Protein Interaction (PPI) network have been
widely exploited to discover the topological organizing principle and the crucial function motifs
involving specific biological pathway or disease process. The current motifs of PPI network are
either detected by the topology-based coarse grain algorithms, i.e. community discovering, or
depended on the limited-accessible protein annotation data derived precise algorithms. However,
the identified network motifs are hardly compatible with the well-defined biological functions
according to those two types of methods.
Method:
In this paper, we proposed a minimal protein loop finding method to explore the
elementary structural motifs of human PPI network. Initially, an improved article exchange model
was designed to search all the independent shortest protein loops of PPI network. Furthermore,
Gene Ontology (GO) based function clustering analysis was implemented to identify the biological
functions of the shortest protein loops. Additionally, the disease process associated shortest protein
loops were considered as the potential drug targets.
</P><P>
Result: Our proposed method presents the lowest computational complexity and the highest
functional consistency, compared to the three other methods. The functional enrichment and
clustering analysis for the identified minimal protein loops revealed the high correlation between
the protein loops and the corresponding biological functions, particularly, statistical analysis
presenting the protein loops with the length less than 4 is closely connected with some disease
process, suggesting the potential drug target.
Conclusion:
Our minimal protein loop method provides a novel manner to precisely define the
functional motif of PPI network, which extends the current knowledge about the cooperating
mechanisms and topological properties of protein modules composed of the short loops.
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Affiliation(s)
- Mingyang Jiang
- Inner Mongolia Engineering Research Center of Personalized Medicine, College of Computer Science and Technology, Inner Mongolia University for the Nationalities, Tongliao, China
| | - Zhili Pei
- Inner Mongolia Engineering Research Center of Personalized Medicine, College of Computer Science and Technology, Inner Mongolia University for the Nationalities, Tongliao, China
| | - Xiaojing Fan
- College of Mechanical Engineering, Inner Mongolia University for the Nationalities, Tongliao, China
| | - Jingqing Jiang
- Inner Mongolia Engineering Research Center of Personalized Medicine, College of Computer Science and Technology, Inner Mongolia University for the Nationalities, Tongliao, China
| | - Qinghu Wang
- Inner Mongolia Engineering Research Center of Personalized Medicine, College of Computer Science and Technology, Inner Mongolia University for the Nationalities, Tongliao, China
| | - Zhifeng Zhang
- Inner Mongolia Engineering Research Center of Personalized Medicine, College of Computer Science and Technology, Inner Mongolia University for the Nationalities, Tongliao, China
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17
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Erdmann J, Preusse M, Khaledi A, Pich A, Häussler S. Environment-driven changes of mRNA and protein levels in Pseudomonas aeruginosa. Environ Microbiol 2018; 20:3952-3963. [DOI: 10.1111/1462-2920.14419] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Revised: 09/13/2018] [Accepted: 09/15/2018] [Indexed: 12/27/2022]
Affiliation(s)
- Jelena Erdmann
- Centre for Experimental and Clinical Infection Research, a joint venture of the Hannover Medical School and the Helmholtz Centre for Infection Research; Institute for Molecular Bacteriology, TWINCORE GmbH; Hannover Germany
- Centre for Pharmacology and Toxicology; Research Core Unit Proteomics and Institute of Toxicology, Hannover Medical School; Hannover Germany
| | - Matthias Preusse
- Centre for Experimental and Clinical Infection Research, a joint venture of the Hannover Medical School and the Helmholtz Centre for Infection Research; Institute for Molecular Bacteriology, TWINCORE GmbH; Hannover Germany
- Department of Molecular Bacteriology, Helmholtz Center for Infection Research; Braunschweig Germany
| | - Ariane Khaledi
- Department of Molecular Bacteriology, Helmholtz Center for Infection Research; Braunschweig Germany
| | - Andreas Pich
- Centre for Pharmacology and Toxicology; Research Core Unit Proteomics and Institute of Toxicology, Hannover Medical School; Hannover Germany
| | - Susanne Häussler
- Centre for Experimental and Clinical Infection Research, a joint venture of the Hannover Medical School and the Helmholtz Centre for Infection Research; Institute for Molecular Bacteriology, TWINCORE GmbH; Hannover Germany
- Department of Molecular Bacteriology, Helmholtz Center for Infection Research; Braunschweig Germany
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18
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Hampel H, Toschi N, Babiloni C, Baldacci F, Black KL, Bokde AL, Bun RS, Cacciola F, Cavedo E, Chiesa PA, Colliot O, Coman CM, Dubois B, Duggento A, Durrleman S, Ferretti MT, George N, Genthon R, Habert MO, Herholz K, Koronyo Y, Koronyo-Hamaoui M, Lamari F, Langevin T, Lehéricy S, Lorenceau J, Neri C, Nisticò R, Nyasse-Messene F, Ritchie C, Rossi S, Santarnecchi E, Sporns O, Verdooner SR, Vergallo A, Villain N, Younesi E, Garaci F, Lista S. Revolution of Alzheimer Precision Neurology. Passageway of Systems Biology and Neurophysiology. J Alzheimers Dis 2018; 64:S47-S105. [PMID: 29562524 PMCID: PMC6008221 DOI: 10.3233/jad-179932] [Citation(s) in RCA: 95] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
The Precision Neurology development process implements systems theory with system biology and neurophysiology in a parallel, bidirectional research path: a combined hypothesis-driven investigation of systems dysfunction within distinct molecular, cellular, and large-scale neural network systems in both animal models as well as through tests for the usefulness of these candidate dynamic systems biomarkers in different diseases and subgroups at different stages of pathophysiological progression. This translational research path is paralleled by an "omics"-based, hypothesis-free, exploratory research pathway, which will collect multimodal data from progressing asymptomatic, preclinical, and clinical neurodegenerative disease (ND) populations, within the wide continuous biological and clinical spectrum of ND, applying high-throughput and high-content technologies combined with powerful computational and statistical modeling tools, aimed at identifying novel dysfunctional systems and predictive marker signatures associated with ND. The goals are to identify common biological denominators or differentiating classifiers across the continuum of ND during detectable stages of pathophysiological progression, characterize systems-based intermediate endophenotypes, validate multi-modal novel diagnostic systems biomarkers, and advance clinical intervention trial designs by utilizing systems-based intermediate endophenotypes and candidate surrogate markers. Achieving these goals is key to the ultimate development of early and effective individualized treatment of ND, such as Alzheimer's disease. The Alzheimer Precision Medicine Initiative (APMI) and cohort program (APMI-CP), as well as the Paris based core of the Sorbonne University Clinical Research Group "Alzheimer Precision Medicine" (GRC-APM) were recently launched to facilitate the passageway from conventional clinical diagnostic and drug development toward breakthrough innovation based on the investigation of the comprehensive biological nature of aging individuals. The APMI movement is gaining momentum to systematically apply both systems neurophysiology and systems biology in exploratory translational neuroscience research on ND.
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Affiliation(s)
- Harald Hampel
- AXA Research Fund & Sorbonne Université Chair, Paris, France
- Sorbonne Université, AP-HP, GRC n° 21, Alzheimer Precision Medicine (APM), Hôpital de la Pitié-Salpêtrière, Boulevard de l’hôpital, F-75013, Paris, France
- Institut du Cerveau et de la Moelle Épinière (ICM), INSERM U 1127, CNRS UMR 7225, Boulevard de l’hôpital, F-75013, Paris, France
- Institut de la Mémoire et de la Maladie d’Alzheimer (IM2A), Département de Neurologie, Hôpital de la Pitié-Salpêtrière, AP-HP, Boulevard de l’hôpital, F-75013, Paris, France
| | - Nicola Toschi
- Department of Biomedicine and Prevention, University of Rome “Tor Vergata”, Rome, Italy
- Department of Radiology, “Athinoula A. Martinos” Center for Biomedical Imaging, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Claudio Babiloni
- Department of Physiology and Pharmacology “Vittorio Erspamer”, University of Rome “La Sapienza”, Rome, Italy
- Institute for Research and Medical Care, IRCCS “San Raffaele Pisana”, Rome, Italy
| | - Filippo Baldacci
- AXA Research Fund & Sorbonne Université Chair, Paris, France
- Sorbonne Université, AP-HP, GRC n° 21, Alzheimer Precision Medicine (APM), Hôpital de la Pitié-Salpêtrière, Boulevard de l’hôpital, F-75013, Paris, France
- Institut du Cerveau et de la Moelle Épinière (ICM), INSERM U 1127, CNRS UMR 7225, Boulevard de l’hôpital, F-75013, Paris, France
- Institut de la Mémoire et de la Maladie d’Alzheimer (IM2A), Département de Neurologie, Hôpital de la Pitié-Salpêtrière, AP-HP, Boulevard de l’hôpital, F-75013, Paris, France
- Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| | - Keith L. Black
- Department of Neurosurgery, Maxine Dunitz Neurosurgical Research Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Arun L.W. Bokde
- Discipline of Psychiatry, School of Medicine and Trinity College Institute of Neuroscience (TCIN), Trinity College Dublin, Dublin, Ireland
| | - René S. Bun
- AXA Research Fund & Sorbonne Université Chair, Paris, France
- Sorbonne Université, AP-HP, GRC n° 21, Alzheimer Precision Medicine (APM), Hôpital de la Pitié-Salpêtrière, Boulevard de l’hôpital, F-75013, Paris, France
- Institut du Cerveau et de la Moelle Épinière (ICM), INSERM U 1127, CNRS UMR 7225, Boulevard de l’hôpital, F-75013, Paris, France
- Institut de la Mémoire et de la Maladie d’Alzheimer (IM2A), Département de Neurologie, Hôpital de la Pitié-Salpêtrière, AP-HP, Boulevard de l’hôpital, F-75013, Paris, France
| | - Francesco Cacciola
- Unit of Neurosurgery, Azienda Ospedaliera Universitaria Senese, Siena, Italy
| | - Enrica Cavedo
- AXA Research Fund & Sorbonne Université Chair, Paris, France
- Sorbonne Université, AP-HP, GRC n° 21, Alzheimer Precision Medicine (APM), Hôpital de la Pitié-Salpêtrière, Boulevard de l’hôpital, F-75013, Paris, France
- Institut du Cerveau et de la Moelle Épinière (ICM), INSERM U 1127, CNRS UMR 7225, Boulevard de l’hôpital, F-75013, Paris, France
- Institut de la Mémoire et de la Maladie d’Alzheimer (IM2A), Département de Neurologie, Hôpital de la Pitié-Salpêtrière, AP-HP, Boulevard de l’hôpital, F-75013, Paris, France
- IRCCS “San Giovanni di Dio-Fatebenefratelli”, Brescia, Italy
| | - Patrizia A. Chiesa
- AXA Research Fund & Sorbonne Université Chair, Paris, France
- Sorbonne Université, AP-HP, GRC n° 21, Alzheimer Precision Medicine (APM), Hôpital de la Pitié-Salpêtrière, Boulevard de l’hôpital, F-75013, Paris, France
- Institut du Cerveau et de la Moelle Épinière (ICM), INSERM U 1127, CNRS UMR 7225, Boulevard de l’hôpital, F-75013, Paris, France
- Institut de la Mémoire et de la Maladie d’Alzheimer (IM2A), Département de Neurologie, Hôpital de la Pitié-Salpêtrière, AP-HP, Boulevard de l’hôpital, F-75013, Paris, France
| | - Olivier Colliot
- Inserm, U1127, Paris, France; CNRS, UMR 7225 ICM, Paris, France; Sorbonne Universités, UPMC Univ Paris 06, UMR S 1127, Paris, France; Institut du Cerveau et de la Moelle Épinière (ICM) Paris, France; Inria, Aramis project-team, Centre de Recherche de Paris, France; Department of Neuroradiology, AP-HP, Hôpital de la Pitié-Salpêtrière, Paris, France; Department of Neurology, AP-HP, Hôpital de la Pitié-Salpêtrière, Institut de la Mémoire et de la Maladie d’Alzheimer (IM2A), Paris, France
| | - Cristina-Maria Coman
- AXA Research Fund & Sorbonne Université Chair, Paris, France
- Sorbonne Université, AP-HP, GRC n° 21, Alzheimer Precision Medicine (APM), Hôpital de la Pitié-Salpêtrière, Boulevard de l’hôpital, F-75013, Paris, France
- Institut du Cerveau et de la Moelle Épinière (ICM), INSERM U 1127, CNRS UMR 7225, Boulevard de l’hôpital, F-75013, Paris, France
- Institut de la Mémoire et de la Maladie d’Alzheimer (IM2A), Département de Neurologie, Hôpital de la Pitié-Salpêtrière, AP-HP, Boulevard de l’hôpital, F-75013, Paris, France
| | - Bruno Dubois
- Sorbonne Université, Inserm, CNRS, Institut du Cerveau et de la Moelle Épinière (ICM), Département de Neurologie, Institut de la Mémoire et de la Maladie d’Alzheimer (IM2A), Hôpital Pitié-Salpêtrière, Boulevard de l’hôpital, F-75013, Paris, France
| | - Andrea Duggento
- Department of Biomedicine and Prevention, University of Rome “Tor Vergata”, Rome, Italy
| | - Stanley Durrleman
- Inserm, U1127, Paris, France; CNRS, UMR 7225 ICM, Paris, France; Sorbonne Universités, UPMC Univ Paris 06, UMR S 1127, Paris, France; Institut du Cerveau et de la Moelle Épinière (ICM) Paris, France; Inria, Aramis project-team, Centre de Recherche de Paris, France
| | - Maria-Teresa Ferretti
- IREM, Institute for Regenerative Medicine, University of Zurich, Zürich, Switzerland
- ZNZ Neuroscience Center Zurich, Zürich, Switzerland
| | - Nathalie George
- Sorbonne Universités, UPMC Univ Paris 06 UMR S 1127, Inserm U 1127, CNRS UMR 7225, Institut du Cerveau et de la Moelle Épinière, ICM, Ecole Normale Supérieure, ENS, Centre MEG-EEG, F-75013, Paris, France
| | - Remy Genthon
- Sorbonne Université, Inserm, CNRS, Institut du Cerveau et de la Moelle Épinière (ICM), Département de Neurologie, Institut de la Mémoire et de la Maladie d’Alzheimer (IM2A), Hôpital Pitié-Salpêtrière, Boulevard de l’hôpital, F-75013, Paris, France
| | - Marie-Odile Habert
- Département de Médecine Nucléaire, Hôpital de la Pitié-Salpêtrière, AP-HP, Paris, France
- Laboratoire d’Imagerie Biomédicale, Sorbonne Universités, UPMC Univ Paris 06, Inserm U 1146, CNRS UMR 7371, Paris, France
| | - Karl Herholz
- Division of Neuroscience and Experimental Psychology, University of Manchester, Manchester, UK
- Division of Informatics, Imaging and Data Sciences, University of Manchester, Wolfson Molecular Imaging Centre, Manchester, UK
| | - Yosef Koronyo
- Department of Neurosurgery, Maxine Dunitz Neurosurgical Research Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Maya Koronyo-Hamaoui
- Department of Neurosurgery, Maxine Dunitz Neurosurgical Research Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
- Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Foudil Lamari
- AP-HP, UF Biochimie des Maladies Neuro-métaboliques, Service de Biochimie Métabolique, Groupe Hospitalier Pitié-Salpêtrière, Paris, France
| | | | - Stéphane Lehéricy
- Centre de NeuroImagerie de Recherche - CENIR, Institut du Cerveau et de la Moelle Épinière - ICM, F-75013, Paris, France
- Sorbonne Universités, UPMC Univ Paris 06 UMR S 1127, Inserm U 1127, CNRS UMR 7225, ICM, F-75013, Paris, France
| | - Jean Lorenceau
- Institut de la Vision, INSERM, Sorbonne Universités, UPMC Univ Paris 06, UMR_S968, CNRS UMR7210, Paris, France
| | - Christian Neri
- Sorbonne Universités, Université Pierre et Marie Curie (UPMC) Paris 06, CNRS UMR 8256, Institut de Biologie Paris-Seine (IBPS), Place Jussieu, F-75005, Paris, France
| | - Robert Nisticò
- Department of Biology, University of Rome “Tor Vergata” & Pharmacology of Synaptic Disease Lab, European Brain Research Institute (E.B.R.I.), Rome, Italy
| | - Francis Nyasse-Messene
- Sorbonne Université, Inserm, CNRS, Institut du Cerveau et de la Moelle Épinière (ICM), Département de Neurologie, Institut de la Mémoire et de la Maladie d’Alzheimer (IM2A), Hôpital Pitié-Salpêtrière, Boulevard de l’hôpital, F-75013, Paris, France
| | - Craig Ritchie
- Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, UK
| | - Simone Rossi
- Department of Medicine, Surgery and Neurosciences, Unit of Neurology and Clinical Neurophysiology, Brain Investigation & Neuromodulation Lab. (Si-BIN Lab.), University of Siena, Siena, Italy
- Department of Medicine, Surgery and Neurosciences, Section of Human Physiology University of Siena, Siena, Italy
| | - Emiliano Santarnecchi
- Department of Medicine, Surgery and Neurosciences, Unit of Neurology and Clinical Neurophysiology, Brain Investigation & Neuromodulation Lab. (Si-BIN Lab.), University of Siena, Siena, Italy
- Berenson-Allen Center for Noninvasive Brain Stimulation, Department of Neurology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Olaf Sporns
- Department of Psychological and Brain Sciences, Indiana University, Bloomington, IN, USA
- IU Network Science Institute, Indiana University, Bloomington, IN, USA
| | | | - Andrea Vergallo
- AXA Research Fund & Sorbonne Université Chair, Paris, France
- Sorbonne Université, AP-HP, GRC n° 21, Alzheimer Precision Medicine (APM), Hôpital de la Pitié-Salpêtrière, Boulevard de l’hôpital, F-75013, Paris, France
- Institut du Cerveau et de la Moelle Épinière (ICM), INSERM U 1127, CNRS UMR 7225, Boulevard de l’hôpital, F-75013, Paris, France
- Institut de la Mémoire et de la Maladie d’Alzheimer (IM2A), Département de Neurologie, Hôpital de la Pitié-Salpêtrière, AP-HP, Boulevard de l’hôpital, F-75013, Paris, France
| | - Nicolas Villain
- Sorbonne Université, AP-HP, GRC n° 21, Alzheimer Precision Medicine (APM), Hôpital de la Pitié-Salpêtrière, Boulevard de l’hôpital, F-75013, Paris, France
- Institut du Cerveau et de la Moelle Épinière (ICM), INSERM U 1127, CNRS UMR 7225, Boulevard de l’hôpital, F-75013, Paris, France
- Institut de la Mémoire et de la Maladie d’Alzheimer (IM2A), Département de Neurologie, Hôpital de la Pitié-Salpêtrière, AP-HP, Boulevard de l’hôpital, F-75013, Paris, France
| | | | - Francesco Garaci
- Department of Biomedicine and Prevention, University of Rome “Tor Vergata”, Rome, Italy
- Casa di Cura “San Raffaele Cassino”, Cassino, Italy
| | - Simone Lista
- AXA Research Fund & Sorbonne Université Chair, Paris, France
- Sorbonne Université, AP-HP, GRC n° 21, Alzheimer Precision Medicine (APM), Hôpital de la Pitié-Salpêtrière, Boulevard de l’hôpital, F-75013, Paris, France
- Institut du Cerveau et de la Moelle Épinière (ICM), INSERM U 1127, CNRS UMR 7225, Boulevard de l’hôpital, F-75013, Paris, France
- Institut de la Mémoire et de la Maladie d’Alzheimer (IM2A), Département de Neurologie, Hôpital de la Pitié-Salpêtrière, AP-HP, Boulevard de l’hôpital, F-75013, Paris, France
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19
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Baldacci F, Lista S, O'Bryant SE, Ceravolo R, Toschi N, Hampel H. Blood-Based Biomarker Screening with Agnostic Biological Definitions for an Accurate Diagnosis Within the Dimensional Spectrum of Neurodegenerative Diseases. Methods Mol Biol 2018; 1750:139-155. [PMID: 29512070 DOI: 10.1007/978-1-4939-7704-8_9] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The discovery, development, and validation of novel candidate biomarkers in Alzheimer's disease (AD) and other neurodegenerative diseases (NDs) are increasingly gaining momentum. As a result, evolving diagnostic research criteria of NDs are beginning to integrate biofluid and neuroimaging indicators of pathophysiological mechanisms. More than 10% of people aged over 65 suffer from NDs. There is an urgent need for a refined two-stage diagnostic model to first initiate an early, sensitive, and noninvasive process in primary care settings. Individuals that meet detection criteria will then be channeled to more specific, costly (positron-emission tomography), and invasive (cerebrospinal fluid) assessment methods for confirmatory biological characterization and diagnosis.A reliable and sensitive blood test for AD and other NDs is not yet established; however, it would provide the golden screening gate for an efficient primary care management. A limitation to the development of a large-scale blood-screening biomarker-based test is the traditional application of clinically descriptive criteria for the categorization of single late-stage ND constructs. These are genetically and biologically heterogeneous, reflected in multiple pathophysiological mechanisms and subsequent pathologies throughout a dimensional continuum. Evidence suggests that a shared, "open-source" integrated multilevel categorization of NDs that clusters individuals based on descriptive clinical phenotypes and pathophysiological biomarker signatures will provide the next incremental step toward an improved diagnostic process of NDs. This intermediate objective toward unbiased biomarker-guided early detection of individuals at risk for NDs is currently carried out by the international pilot Alzheimer Precision Medicine Initiative Cohort Program (APMI-CP).
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Affiliation(s)
- Filippo Baldacci
- AXA Research Fund & UPMC Chair, F-75013, Paris, France.,Sorbonne Université, AP-HP, GRC n° 21, Alzheimer Precision Medicine (APM), Hôpital de la Pitié-Salpêtrière, Boulevard de l'hôpital, F-75013, Paris, France.,Institut du Cerveau et de la Moelle Épinière (ICM), INSERM U 1127, CNRS UMR 7225, Boulevard de l'hôpital, F-75013, Paris, France.,Institut de la Mémoire et de la Maladie d'Alzheimer (IM2A), Département de Neurologie, Hôpital de la Pitié-Salpêtrière, AP-HP, Boulevard de l'hôpital, F-75013, Paris, France.,Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| | - Simone Lista
- AXA Research Fund & UPMC Chair, F-75013, Paris, France. .,Sorbonne Université, AP-HP, GRC n° 21, Alzheimer Precision Medicine (APM), Hôpital de la Pitié-Salpêtrière, Boulevard de l'hôpital, F-75013, Paris, France. .,Institut du Cerveau et de la Moelle Épinière (ICM), INSERM U 1127, CNRS UMR 7225, Boulevard de l'hôpital, F-75013, Paris, France. .,Institut de la Mémoire et de la Maladie d'Alzheimer (IM2A), Département de Neurologie, Hôpital de la Pitié-Salpêtrière, AP-HP, Boulevard de l'hôpital, F-75013, Paris, France.
| | - Sid E O'Bryant
- Institute for Healthy Aging, University of North Texas Health Science Center, Fort Worth, TX, USA
| | - Roberto Ceravolo
- Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| | - Nicola Toschi
- Department of Biomedicine and Prevention, University of Rome "Tor Vergata", Rome, Italy.,Department of Radiology"Athinoula A. Martinos", Center for Biomedical Imaging, Boston, MA, USA.,Harvard Medical School, Boston, MA, USA
| | - Harald Hampel
- AXA Research Fund & UPMC Chair, F-75013, Paris, France.,Sorbonne Université, AP-HP, GRC n° 21, Alzheimer Precision Medicine (APM), Hôpital de la Pitié-Salpêtrière, Boulevard de l'hôpital, F-75013, Paris, France.,Institut du Cerveau et de la Moelle Épinière (ICM), INSERM U 1127, CNRS UMR 7225, Boulevard de l'hôpital, F-75013, Paris, France.,Institut de la Mémoire et de la Maladie d'Alzheimer (IM2A), Département de Neurologie, Hôpital de la Pitié-Salpêtrière, AP-HP, Boulevard de l'hôpital, F-75013, Paris, France
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20
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Tripathi S, Lloyd-Price J, Ribeiro A, Yli-Harja O, Dehmer M, Emmert-Streib F. sgnesR: An R package for simulating gene expression data from an underlying real gene network structure considering delay parameters. BMC Bioinformatics 2017; 18:325. [PMID: 28676075 PMCID: PMC5496254 DOI: 10.1186/s12859-017-1731-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Accepted: 06/15/2017] [Indexed: 01/04/2023] Open
Abstract
Background sgnesR (Stochastic Gene Network Expression Simulator in R) is an R package that provides an interface to simulate gene expression data from a given gene network using the stochastic simulation algorithm (SSA). The package allows various options for delay parameters and can easily included in reactions for promoter delay, RNA delay and Protein delay. A user can tune these parameters to model various types of reactions within a cell. As examples, we present two network models to generate expression profiles. We also demonstrated the inference of networks and the evaluation of association measure of edge and non-edge components from the generated expression profiles. Results The purpose of sgnesR is to enable an easy to use and a quick implementation for generating realistic gene expression data from biologically relevant networks that can be user selected. Conclusions sgnesR is freely available for academic use. The R package has been tested for R 3.2.0 under Linux, Windows and Mac OS X. Electronic supplementary material The online version of this article (doi:10.1186/s12859-017-1731-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Shailesh Tripathi
- Predictive Medicine and Data Analytics Lab, Department of Signal Processing, Tampere University of Technology, Tampere, Finland
| | - Jason Lloyd-Price
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Harvard University, Boston, USA.,Laboratory of Biosystem Dynamics, Department of Signal Processing, Tampere University of Technology, Tampere, Finland
| | - Andre Ribeiro
- Laboratory of Biosystem Dynamics, Department of Signal Processing, Tampere University of Technology, Tampere, Finland.,Institute of Biosciences and Medical Technology, Tampere, Finland
| | - Olli Yli-Harja
- Institute of Biosciences and Medical Technology, Tampere, Finland.,Computational Systems Biology, Department of Signal Processing, Tampere University of Technology, Tampere, Finland
| | - Matthias Dehmer
- Institute for Theoretical Informatics, Mathematics and Operations Research, Department of Computer Science, Universität der Bundeswehr München, Munich, Germany
| | - Frank Emmert-Streib
- Predictive Medicine and Data Analytics Lab, Department of Signal Processing, Tampere University of Technology, Tampere, Finland. .,Institute of Biosciences and Medical Technology, Tampere, Finland.
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Abstract
Metabolism is highly complex and involves thousands of different connected reactions; it is therefore necessary to use mathematical models for holistic studies. The use of mathematical models in biology is referred to as systems biology. In this review, the principles of systems biology are described, and two different types of mathematical models used for studying metabolism are discussed: kinetic models and genome-scale metabolic models. The use of different omics technologies, including transcriptomics, proteomics, metabolomics, and fluxomics, for studying metabolism is presented. Finally, the application of systems biology for analyzing global regulatory structures, engineering the metabolism of cell factories, and analyzing human diseases is discussed.
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Affiliation(s)
- Jens Nielsen
- Department of Biology and Biological Engineering, Chalmers University of Technology, SE41128 Gothenburg, Sweden; .,Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK2800 Lyngby, Denmark.,Science for Life Laboratory, Royal Institute of Technology, SE17121 Stockholm, Sweden
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22
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23
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Kang UB, Marto JA. Leucine-rich repeat kinase 2 and Parkinson's disease. Proteomics 2016; 17. [PMID: 27723254 DOI: 10.1002/pmic.201600092] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Revised: 09/13/2016] [Accepted: 10/06/2016] [Indexed: 12/21/2022]
Abstract
Leucine-rich repeat kinase 2 (LRRK2) is a large multidomain protein that is expressed in many tissues and participates in numerous biological pathways. Mutations in LRRK2 are recognized as genetic risk factors for familial Parkinson's disease (PD) and may also represent causal factors in the more common sporadic form of PD. The structure of LRRK2 comprises a combination of GTPase, kinase, and scaffolding domains. This functional diversity, combined with a potentially central role in genetic and idiopathic PD motivates significant effort to further credential LRRK2 as a therapeutic target. Here, we review the current understanding for LRRK2 function in normal physiology and PD, with emphasis on insight gained from proteomic approaches.
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Affiliation(s)
- Un-Beom Kang
- Department of Cancer Biology and Blais Proteomics Center, Dana-Farber Cancer Institute, Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Jarrod A Marto
- Department of Cancer Biology and Blais Proteomics Center, Dana-Farber Cancer Institute, Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
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24
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A Conversation on Data Mining Strategies in LC-MS Untargeted Metabolomics: Pre-Processing and Pre-Treatment Steps. Metabolites 2016; 6:metabo6040040. [PMID: 27827887 PMCID: PMC5192446 DOI: 10.3390/metabo6040040] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Revised: 10/27/2016] [Accepted: 10/27/2016] [Indexed: 12/24/2022] Open
Abstract
Untargeted metabolomic studies generate information-rich, high-dimensional, and complex datasets that remain challenging to handle and fully exploit. Despite the remarkable progress in the development of tools and algorithms, the "exhaustive" extraction of information from these metabolomic datasets is still a non-trivial undertaking. A conversation on data mining strategies for a maximal information extraction from metabolomic data is needed. Using a liquid chromatography-mass spectrometry (LC-MS)-based untargeted metabolomic dataset, this study explored the influence of collection parameters in the data pre-processing step, scaling and data transformation on the statistical models generated, and feature selection, thereafter. Data obtained in positive mode generated from a LC-MS-based untargeted metabolomic study (sorghum plants responding dynamically to infection by a fungal pathogen) were used. Raw data were pre-processed with MarkerLynxTM software (Waters Corporation, Manchester, UK). Here, two parameters were varied: the intensity threshold (50-100 counts) and the mass tolerance (0.005-0.01 Da). After the pre-processing, the datasets were imported into SIMCA (Umetrics, Umea, Sweden) for more data cleaning and statistical modeling. In addition, different scaling (unit variance, Pareto, etc.) and data transformation (log and power) methods were explored. The results showed that the pre-processing parameters (or algorithms) influence the output dataset with regard to the number of defined features. Furthermore, the study demonstrates that the pre-treatment of data prior to statistical modeling affects the subspace approximation outcome: e.g., the amount of variation in X-data that the model can explain and predict. The pre-processing and pre-treatment steps subsequently influence the number of statistically significant extracted/selected features (variables). Thus, as informed by the results, to maximize the value of untargeted metabolomic data, understanding of the data structures and exploration of different algorithms and methods (at different steps of the data analysis pipeline) might be the best trade-off, currently, and possibly an epistemological imperative.
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25
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Gao M, Cheng K, Yin H. Targeting protein-protein interfaces using macrocyclic peptides. Biopolymers 2016; 104:310-6. [PMID: 25664609 DOI: 10.1002/bip.22625] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Revised: 01/29/2015] [Accepted: 02/01/2015] [Indexed: 01/10/2023]
Abstract
Protein-protein interactions (PPIs) are critical in numerous biological processes including signaling transduction, function regulations, and disease development. To regulate PPIs has been thought to be challenging due to their highly dynamic and expansive interfacial areas. Nonetheless, successful examples have been reported of targeting PPIs using small molecules, peptides, and proteins. Peptides, especially macrocyclic peptides have proven to be a particularly useful tool to inhibit PPIs for their exquisite potency, stability and selectivity. Herein we review the recent developments of this area of research, focusing on the macrocyclic peptides isolated from natural products, identified from library screening, and rationally designed based on structures, as PPI regulators.
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Affiliation(s)
- Meng Gao
- Department of Chemistry, Center of Basic Molecular Science, Tsinghua University, Beijing, China , 100082
| | - Kui Cheng
- Department of Chemistry, Center of Basic Molecular Science, Tsinghua University, Beijing, China , 100082
| | - Hang Yin
- Department of Chemistry, Center of Basic Molecular Science, Tsinghua University, Beijing, China , 100082.,Department of Chemistry and Biochemistry, the BioFrontiers Institute, University of Colorado Boulder, Boulder, CO, 80309-0596
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26
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Vasilopoulou CG, Margarity M, Klapa MI. Metabolomic Analysis in Brain Research: Opportunities and Challenges. Front Physiol 2016; 7:183. [PMID: 27252656 PMCID: PMC4878281 DOI: 10.3389/fphys.2016.00183] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Accepted: 05/09/2016] [Indexed: 12/11/2022] Open
Abstract
Metabolism being a fundamental part of molecular physiology, elucidating the structure and regulation of metabolic pathways is crucial for obtaining a comprehensive perspective of cellular function and understanding the underlying mechanisms of its dysfunction(s). Therefore, quantifying an accurate metabolic network activity map under various physiological conditions is among the major objectives of systems biology in the context of many biological applications. Especially for CNS, metabolic network activity analysis can substantially enhance our knowledge about the complex structure of the mammalian brain and the mechanisms of neurological disorders, leading to the design of effective therapeutic treatments. Metabolomics has emerged as the high-throughput quantitative analysis of the concentration profile of small molecular weight metabolites, which act as reactants and products in metabolic reactions and as regulatory molecules of proteins participating in many biological processes. Thus, the metabolic profile provides a metabolic activity fingerprint, through the simultaneous analysis of tens to hundreds of molecules of pathophysiological and pharmacological interest. The application of metabolomics is at its standardization phase in general, and the challenges for paving a standardized procedure are even more pronounced in brain studies. In this review, we support the value of metabolomics in brain research. Moreover, we demonstrate the challenges of designing and setting up a reliable brain metabolomic study, which, among other parameters, has to take into consideration the sex differentiation and the complexity of brain physiology manifested in its regional variation. We finally propose ways to overcome these challenges and design a study that produces reproducible and consistent results.
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Affiliation(s)
- Catherine G Vasilopoulou
- Metabolic Engineering and Systems Biology Laboratory, Institute of Chemical Engineering Sciences, Foundation for Research and Technology-Hellas (FORTH/ICE-HT)Patras, Greece; Human and Animal Physiology Laboratory, Department of Biology, University of PatrasPatras, Greece
| | - Marigoula Margarity
- Human and Animal Physiology Laboratory, Department of Biology, University of Patras Patras, Greece
| | - Maria I Klapa
- Metabolic Engineering and Systems Biology Laboratory, Institute of Chemical Engineering Sciences, Foundation for Research and Technology-Hellas (FORTH/ICE-HT)Patras, Greece; Departments of Chemical and Biomolecular Engineering and Bioengineering, University of MarylandCollege Park, MD, USA
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27
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Zheng A, Luo J, Meng K, Li J, Bryden WL, Chang W, Zhang S, Wang LXN, Liu G, Yao B. Probiotic (Enterococcus faecium) induced responses of the hepatic proteome improves metabolic efficiency of broiler chickens (Gallus gallus). BMC Genomics 2016; 17:89. [PMID: 26830196 PMCID: PMC4736614 DOI: 10.1186/s12864-016-2371-5] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Accepted: 01/06/2016] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND The liver plays important roles in nutrient metabolism, detoxification and immunity. Enterococcus faecium (E. faecium) is a probiotic that has been shown to have positive effects on broiler production. However, its molecular effects on liver metabolism have not been characterized. This study aims to further identify the biological roles of E. faecium by characterizing the hepatic proteomic changes of broilers (Gallus gallus) fed E. faecium using two-dimensional fluorescence difference gel electrophoresis (2-D DIGE) and mass spectrometry (MS). RESULTS Thirty-three proteins (50 protein spots) involved in nutrient metabolism, immunity and the antioxidant system were shown to be differentially expressed in the liver of broilers fed E. faecium than from birds not fed the probiotic. The biological processes of sulphur amino acids, vitamin and cellular hormone metabolism, sulphur compound biosynthesis and protein tetramerization were enhanced in the liver of broilers fed E. faecium. However, proteins involved in calcium ion flux, cell redox homeostasis and platelet activation related to hepatic immune responses were down-regulated in broilers fed E. faecium. These results indicate that the supplementation of poultry feed with E. faecium may alter the partitioning of nutrients and promote optimal nutrient utilization. CONCLUSIONS This study assists in unraveling the molecular effects of the dietary probiotic, E. faecium, in the liver of broiler chickens. It shows that the probiotic improves the metabolism of nutrients and decreases inflammatory responses. Our findings extend previous knowledge of the mechanism of dietary probiotic action and provide new findings for research and future probiotic development.
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Affiliation(s)
- Aijuan Zheng
- Key Laboratory of Feed Biotechnology of Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, People's Republic of China.
| | - Jianjie Luo
- Key Laboratory of Feed Biotechnology of Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, People's Republic of China.
| | - Kun Meng
- Key Laboratory of Feed Biotechnology of Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, People's Republic of China.
| | - Jianke Li
- Key Laboratory of Pollinating Insect Biology of Ministry of Agriculture, Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing, 100093, People's Republic of China.
| | - Wayne L Bryden
- School of Agriculture and Food Sciences, University of Queensland, Gatton, QLD, 4343, Australia.
| | - Wenhuan Chang
- Key Laboratory of Feed Biotechnology of Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, People's Republic of China.
| | - Shu Zhang
- Key Laboratory of Feed Biotechnology of Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, People's Republic of China.
| | - L X N Wang
- School of Agriculture and Food Sciences, University of Queensland, Gatton, QLD, 4343, Australia.
| | - Guohua Liu
- Key Laboratory of Feed Biotechnology of Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, People's Republic of China.
| | - Bin Yao
- Key Laboratory of Feed Biotechnology of Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, People's Republic of China.
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28
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Castrillo JI, Oliver SG. Alzheimer's as a Systems-Level Disease Involving the Interplay of Multiple Cellular Networks. Methods Mol Biol 2016; 1303:3-48. [PMID: 26235058 DOI: 10.1007/978-1-4939-2627-5_1] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Alzheimer's disease (AD), and many neurodegenerative disorders, are multifactorial in nature. They involve a combination of genomic, epigenomic, interactomic and environmental factors. Progress is being made, and these complex diseases are beginning to be understood as having their origin in altered states of biological networks at the cellular level. In the case of AD, genomic susceptibility and mechanisms leading to (or accompanying) the impairment of the central Amyloid Precursor Protein (APP) processing and tau networks are widely accepted as major contributors to the diseased state. The derangement of these networks may result in both the gain and loss of functions, increased generation of toxic species (e.g., toxic soluble oligomers and aggregates) and imbalances, whose effects can propagate to supra-cellular levels. Although well sustained by empirical data and widely accepted, this global perspective often overlooks the essential roles played by the main counteracting homeostatic networks (e.g., protein quality control/proteostasis, unfolded protein response, protein folding chaperone networks, disaggregases, ER-associated degradation/ubiquitin proteasome system, endolysosomal network, autophagy, and other stress-protective and clearance networks), whose relevance to AD is just beginning to be fully realized. In this chapter, an integrative perspective is presented. Alzheimer's disease is characterized to be a result of: (a) intrinsic genomic/epigenomic susceptibility and, (b) a continued dynamic interplay between the deranged networks and the central homeostatic networks of nerve cells. This interplay of networks will underlie both the onset and rate of progression of the disease in each individual. Integrative Systems Biology approaches are required to effect its elucidation. Comprehensive Systems Biology experiments at different 'omics levels in simple model organisms, engineered to recapitulate the basic features of AD may illuminate the onset and sequence of events underlying AD. Indeed, studies of models of AD in simple organisms, differentiated cells in culture and rodents are beginning to offer hope that the onset and progression of AD, if detected at an early stage, may be stopped, delayed, or even reversed, by activating or modulating networks involved in proteostasis and the clearance of toxic species. In practice, the incorporation of next-generation neuroimaging, high-throughput and computational approaches are opening the way towards early diagnosis well before irreversible cell death. Thus, the presence or co-occurrence of: (a) accumulation of toxic Aβ oligomers and tau species; (b) altered splicing and transcriptome patterns; (c) impaired redox, proteostatic, and metabolic networks together with, (d) compromised homeostatic capacities may constitute relevant 'AD hallmarks at the cellular level' towards reliable and early diagnosis. From here, preventive lifestyle changes and tailored therapies may be investigated, such as combined strategies aimed at both lowering the production of toxic species and potentiating homeostatic responses, in order to prevent or delay the onset, and arrest, alleviate, or even reverse the progression of the disease.
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Affiliation(s)
- Juan I Castrillo
- Department of Biochemistry & Cambridge Systems Biology Centre, University of Cambridge, Sanger Building, 80 Tennis Court Road, Cambridge, CB2 1GA, UK,
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29
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30
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Palacios-Moreno J, Foltz L, Guo A, Stokes MP, Kuehn ED, George L, Comb M, Grimes ML. Neuroblastoma tyrosine kinase signaling networks involve FYN and LYN in endosomes and lipid rafts. PLoS Comput Biol 2015; 11:e1004130. [PMID: 25884760 PMCID: PMC4401789 DOI: 10.1371/journal.pcbi.1004130] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2014] [Accepted: 01/14/2015] [Indexed: 12/16/2022] Open
Abstract
Protein phosphorylation plays a central role in creating a highly dynamic network of interacting proteins that reads and responds to signals from growth factors in the cellular microenvironment. Cells of the neural crest employ multiple signaling mechanisms to control migration and differentiation during development. It is known that defects in these mechanisms cause neuroblastoma, but how multiple signaling pathways interact to govern cell behavior is unknown. In a phosphoproteomic study of neuroblastoma cell lines and cell fractions, including endosomes and detergent-resistant membranes, 1622 phosphorylated proteins were detected, including more than half of the receptor tyrosine kinases in the human genome. Data were analyzed using a combination of graph theory and pattern recognition techniques that resolve data structure into networks that incorporate statistical relationships and protein-protein interaction data. Clusters of proteins in these networks are indicative of functional signaling pathways. The analysis indicates that receptor tyrosine kinases are functionally compartmentalized into distinct collaborative groups distinguished by activation and intracellular localization of SRC-family kinases, especially FYN and LYN. Changes in intracellular localization of activated FYN and LYN were observed in response to stimulation of the receptor tyrosine kinases, ALK and KIT. The results suggest a mechanism to distinguish signaling responses to activation of different receptors, or combinations of receptors, that govern the behavior of the neural crest, which gives rise to neuroblastoma. Neuroblastoma is a childhood cancer for which therapeutic progress has been slow. We analyzed a large number phosphorylated proteins in neuroblastoma cells to discern patterns that indicate functional signal transduction pathways. To analyze the data, we developed novel techniques that resolve data structure and visualize that structure as networks that represent both protein interactions and statistical relationships. We also fractionated neuroblastoma cells to examine the location of signaling proteins in different membrane fractions and organelles. The analysis revealed that signaling pathways are functionally and physically compartmentalized into distinct collaborative groups distinguished by phosphorylation patterns and intracellular localization. We found that two related proteins (FYN and LYN) act like central hubs in the tyrosine kinase signaling network that change intracellular localization and activity in response to activation of different receptors.
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Affiliation(s)
- Juan Palacios-Moreno
- Division of Biological Sciences, Center for Structural and Functional Neuroscience, University of Montana, Missoula, Montana, United States of America
| | - Lauren Foltz
- Division of Biological Sciences, Center for Structural and Functional Neuroscience, University of Montana, Missoula, Montana, United States of America
| | - Ailan Guo
- Cell Signaling Technology, Inc., Danvers, Massachusetts, United States of America
| | - Matthew P. Stokes
- Cell Signaling Technology, Inc., Danvers, Massachusetts, United States of America
| | - Emily D. Kuehn
- Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Lynn George
- Department of Cell Biology and Neuroscience, Montana State University, Bozeman, Montana, United States of America
| | - Michael Comb
- Cell Signaling Technology, Inc., Danvers, Massachusetts, United States of America
| | - Mark L. Grimes
- Division of Biological Sciences, Center for Structural and Functional Neuroscience, University of Montana, Missoula, Montana, United States of America
- * E-mail:
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31
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Bridging topological and functional information in protein interaction networks by short loops profiling. Sci Rep 2015; 5:8540. [PMID: 25703051 PMCID: PMC5224520 DOI: 10.1038/srep08540] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2014] [Accepted: 01/23/2015] [Indexed: 11/09/2022] Open
Abstract
Protein-protein interaction networks (PPINs) have been employed to identify potential novel interconnections between proteins as well as crucial cellular functions. In this study we identify fundamental principles of PPIN topologies by analysing network motifs of short loops, which are small cyclic interactions of between 3 and 6 proteins. We compared 30 PPINs with corresponding randomised null models and examined the occurrence of common biological functions in loops extracted from a cross-validated high-confidence dataset of 622 human protein complexes. We demonstrate that loops are an intrinsic feature of PPINs and that specific cell functions are predominantly performed by loops of different lengths. Topologically, we find that loops are strongly related to the accuracy of PPINs and define a core of interactions with high resilience. The identification of this core and the analysis of loop composition are promising tools to assess PPIN quality and to uncover possible biases from experimental detection methods. More than 96% of loops share at least one biological function, with enrichment of cellular functions related to mRNA metabolic processing and the cell cycle. Our analyses suggest that these motifs can be used in the design of targeted experiments for functional phenotype detection.
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Bhat A, Dakna M, Mischak H. Integrating proteomics profiling data sets: a network perspective. Methods Mol Biol 2015; 1243:237-53. [PMID: 25384750 DOI: 10.1007/978-1-4939-1872-0_14] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Understanding disease mechanisms often requires complex and accurate integration of cellular pathways and molecular networks. Systems biology offers the possibility to provide a comprehensive map of the cell's intricate wiring network, which can ultimately lead to decipher the disease phenotype. Here, we describe what biological pathways are, how they function in normal and abnormal cellular systems, limitations faced by databases for integrating data, and highlight how network models are emerging as a powerful integrative framework to understand and interpret the roles of proteins and peptides in diseases.
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Affiliation(s)
- Akshay Bhat
- Mosaiques-Diagnostics GmbH, Mellendorfer Straße 7-9, D-30625, Hannover, Germany,
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33
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Abstract
The rising cost of healthcare, the rising cost for drug development, the patent cliff for Big pharma, shorter patent protection, decrease reimbursement, and the recession have made it more difficult for the pharmaceutical and biotechnology industry to develop drugs. Due to the unsustainable amount of time and money in developing a drug that will have a significant return on investment (ROI) it has become hard to sustain a robust pipeline. The industry is transforming its business model to meet these challenges. In essence a paradigm shift is occurring; the old “closed” model is giving way to a new “open” business model. Drug development—then and now How systems biology is accelerating drug development and approval. The new business model: pharma/biotech is going “open” FDA is going “open”—what does this mean for drug approval?
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Emmert-Streib F, Tripathi S, Simoes RDM, Hawwa AF, Dehmer M. The human disease network. ACTA ACUST UNITED AC 2014. [DOI: 10.4161/sysb.22816] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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35
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Gkourogianni A, Kosteria I, Telonis AG, Margeli A, Mantzou E, Konsta M, Loutradis D, Mastorakos G, Papassotiriou I, Klapa MI, Kanaka-Gantenbein C, Chrousos GP. Plasma metabolomic profiling suggests early indications for predisposition to latent insulin resistance in children conceived by ICSI. PLoS One 2014; 9:e94001. [PMID: 24728198 PMCID: PMC3984097 DOI: 10.1371/journal.pone.0094001] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2013] [Accepted: 03/11/2014] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND There have been increasing indications about an epigenetically-based elevated predisposition of assisted reproductive technology (ART) offspring to insulin resistance, which can lead to an unfavorable cardio-metabolic profile in adult life. However, the relevant long-term systematic molecular studies are limited, especially for the IntraCytoplasmic Sperm Injection (ICSI) method, introduced in 1992. In this study, we carefully defined a group of 42 prepubertal ICSI and 42 naturally conceived (NC) children. We assessed differences in their metabolic profile based on biochemical measurements, while, for a subgroup, plasma metabolomic analysis was also performed, investigating any relevant insulin resistance indices. METHODS & RESULTS Auxological and biochemical parameters of 42 6.8±2.1 yrs old ICSI-conceived and 42 age-matched controls were measured. Significant differences between the groups were determined using univariate and multivariate statistics, indicating low urea and low-grade inflammation markers (YKL-40, hsCRP) and high triiodothyronine (T3) in ICSI-children compared to controls. Moreover, plasma metabolomic analysis carried out for a subgroup of 10 ICSI- and 10 NC girls using Gas Chromatography-Mass Spectrometry (GC-MS) indicated clear differences between the two groups, characterized by 36 metabolites linked to obesity, insulin resistance and metabolic syndrome. Notably, the distinction between the two girl subgroups was accentuated when both their biochemical and metabolomic measurements were employed. CONCLUSIONS The present study contributes a large auxological and biochemical dataset of a well-defined group of pre-pubertal ICSI-conceived subjects to the research of the ART effect to the offspring's health. Moreover, it is the first time that the relevant usefulness of metabolomics was investigated. The acquired results are consistent with early insulin resistance in ICSI-offspring, paving the way for further systematic investigations. These data support that metabolomics may unravel metabolic differences before they become clinically or biochemically evident, underlining its utility in the ART research.
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Affiliation(s)
- Alexandra Gkourogianni
- Division of Endocrinology, Diabetes and Metabolism, First Department of Pediatrics, University of Athens Medical School, Athens, Greece
| | - Ioanna Kosteria
- Division of Endocrinology, Diabetes and Metabolism, First Department of Pediatrics, University of Athens Medical School, Athens, Greece
| | - Aristeidis G. Telonis
- Metabolic Engineering and Systems Biology Laboratory, Institute of Chemical Engineering Sciences, Foundation for Research and Technology-Hellas (FORTH/ICE-HT), Patras, Greece
- Graduate Program “Biological Technology”, Department of Biology, University of Patras, Greece
| | - Alexandra Margeli
- Department of Clinical Biochemistry, “Aghia Sophia” Children's Hospital, Athens, Greece
| | - Emilia Mantzou
- Endocrine Unit, Department of Endocrinology and Metabolism, Evgenidion Hospital, Athens, Greece
| | - Maria Konsta
- Division of Endocrinology, Diabetes and Metabolism, First Department of Pediatrics, University of Athens Medical School, Athens, Greece
| | - Dimitrios Loutradis
- Division of In Vitro Fertilization, First Department of Obstetrics and Gynecology, University of Athens Medical School, Athens, Greece
| | - George Mastorakos
- Division of Endocrinology, Second Department of Obstetrics and Gynecology, University of Athens Medical School, Athens, Greece
| | - Ioannis Papassotiriou
- Department of Clinical Biochemistry, “Aghia Sophia” Children's Hospital, Athens, Greece
| | - Maria I. Klapa
- Metabolic Engineering and Systems Biology Laboratory, Institute of Chemical Engineering Sciences, Foundation for Research and Technology-Hellas (FORTH/ICE-HT), Patras, Greece
| | - Christina Kanaka-Gantenbein
- Division of Endocrinology, Diabetes and Metabolism, First Department of Pediatrics, University of Athens Medical School, Athens, Greece
| | - George P. Chrousos
- Division of Endocrinology, Diabetes and Metabolism, First Department of Pediatrics, University of Athens Medical School, Athens, Greece
- * E-mail:
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Abstract
Natural selection defined by differential survival and reproduction of individuals in populations is influenced by genetic, developmental, and environmental factors operating at every age and stage in human life history: generation of gametes, conception, birth, maturation, reproduction, senescence, and death. Biological systems are built upon a hierarchical organization nesting subcellular organelles, cells, tissues, and organs within individuals, individuals within families, and families within populations, and the latter among other populations. Natural selection often acts simultaneously at more than one level of biological organization and on specific traits, which we define as multilevel selection. Under this model, the individual is a fundamental unit of biological organization and also of selection, imbedded in a larger evolutionary context, just as it is a unit of medical intervention imbedded in larger biological, cultural, and environmental contexts. Here, we view human health and life span as necessary consequences of natural selection, operating at all levels and phases of biological hierarchy in human life history as well as in sociological and environmental milieu. An understanding of the spectrum of opportunities for natural selection will help us develop novel approaches to improving healthy life span through specific and global interventions that simultaneously focus on multiple levels of biological organization. Indeed, many opportunities exist to apply multilevel selection models employed in evolutionary biology and biodemography to improving human health at all hierarchical levels. Multilevel selection perspective provides a rational theoretical foundation for a synthesis of medicine and evolution that could lead to discovering effective predictive, preventive, palliative, potentially curative, and individualized approaches in medicine and in global health programs.
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Seo H, Kim W, Lee J, Youn B. Network-based approaches for anticancer therapy (Review). Int J Oncol 2013; 43:1737-44. [PMID: 24085339 DOI: 10.3892/ijo.2013.2114] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2013] [Accepted: 08/23/2013] [Indexed: 12/16/2022] Open
Abstract
Cancer is a complex disease resulting from alterations of multiple signaling networks. Cancer networks have been identified as scale-free networks and may contain a functionally important key player called a hub that is linked to a large number of interactors. Since a hub can serve as a biological marker in a given network, targeting the hub could be an effective strategy for enhancing the efficacy of cancer treatment. Chemotherapies and radiotherapies are generally used to treat tumors not amenable to resection, and target single or multiple molecules associated with hubs. However, these therapies may unexpectedly induce the resistance of cancer cells to drugs and radiation. Cancer cells can overcome therapy-induced damage via the activation of back-up signaling pathways and flexible modulation of affected networks. These activities are considered to be the main reasons for chemoresistance and radioresistance, and subsequent failure of cancer therapies. Much effort is required to identify the key molecules that control the modulation of signaling networks in response to drugs and radiation. Network-based therapy that affects network flexibility, including rewired network structures and hub molecules in these networks, could minimize the occurrence of side-effects and be a promising strategy for enhancing the therapeutic efficacy of cancer treatments. This review is intended to offer an overview of current research efforts including ones focused on cancer-associated complex networks, their modulation in response to cancer therapy, and further strategies targeting networks that may improve cancer treatment efficacy.
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Affiliation(s)
- Hyunjeong Seo
- Department of Biological Sciences, College of Natural Sciences, Pusan National University, Busan 609-735, Republic of Korea
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38
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Network-based approaches in drug discovery and early development. Clin Pharmacol Ther 2013; 94:651-8. [PMID: 24025802 DOI: 10.1038/clpt.2013.176] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2013] [Accepted: 09/03/2013] [Indexed: 12/20/2022]
Abstract
Identification of novel targets is a critical first step in the drug discovery and development process. Most diseases such as cancer, metabolic disorders, and neurological disorders are complex, and their pathogenesis involves multiple genetic and environmental factors. Finding a viable drug target-drug combination with high potential for yielding clinical success within the efficacy-toxicity spectrum is extremely challenging. Many examples are now available in which network-based approaches show potential for the identification of novel targets and for the repositioning of established targets. The objective of this article is to highlight network approaches for identifying novel targets with greater chances of gaining approved drugs with maximal efficacy and minimal side effects. Further enhancement of these approaches may emerge from effectively integrating computational systems biology with pharmacodynamic systems analysis. Coupling genomics, proteomics, and metabolomics databases with systems pharmacology modeling may aid in the development of disease-specific networks that can be further used to build confidence in target identification.
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Luo J, Zheng A, Meng K, Chang W, Bai Y, Li K, Cai H, Liu G, Yao B. Proteome changes in the intestinal mucosa of broiler (Gallus gallus) activated by probiotic Enterococcus faecium. J Proteomics 2013; 91:226-41. [PMID: 23899589 DOI: 10.1016/j.jprot.2013.07.017] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2013] [Revised: 07/06/2013] [Accepted: 07/15/2013] [Indexed: 12/27/2022]
Abstract
UNLABELLED Probiotics are supplemented to animal diet to support a well-balanced gut microbiota, finally contributing to improved health. The molecular mechanism of probiotics in animal intestine improvement is yet unclear. We investigated the production parameters, gut morphology and microbiota, and mucosal proteome of Arbor Acres broilers (Gallus gallus) supplemented with Enterococcus faecium by performing denaturing gradient gel electrophoresis, quantitative real-time PCR, two-dimensional fluorescence difference gel electrophoresis, and mass spectrometry. E. faecium supplementation promoted the development of immune organs and gut microvilli and enlarged the gut microbial diversity and population. However, it had no effects on daily weight gain and feed intake, and slightly enhanced feed conversion ratio. A total of 42 intestinal mucosal proteins were found to be differentially abundant. Four of them are related to intestinal structure and may extend the absorptive surface area. Of 17 differential proteins related to immune and antioxidant systems, only six are abundant in the broilers fed E. faecium, indicating that these chickens employ less nutrients and energy to deal with immune and antioxidant stresses. These findings have important implications for understanding the probiotic mechanisms of E. faecium on broiler intestine. BIOLOGICAL SIGNIFICANCE Probiotic supplementation to animal diet is closely related with improved health. The objective of this study is to determine the molecular mechanisms of probiotic E. faecium achieving its biological mission in the gut of Arbor Acres broilers (G. gallus). E. faecium supplementation did not improve daily weight gain and feed intake; however, it had effects on immune organ and gut microvillus development, and gut microbial diversity and population. Quantitative proteomic analysis of the intestinal mucosa of broilers treated with E. faecium identified 42 intestinal mucosal proteins related to substance metabolism, immune and antioxidant systems, and cell structure. This study identified the E. faecium derived probiotic mechanism on the proteome level.
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Affiliation(s)
- Jianjie Luo
- Key Laboratory of Feed Biotechnology of Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, People's Republic of China
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Ragunath P, Abhinand P. Systems biological approach to investigate the lack of familial link between Down's Syndrome & Neural Tube Disorders. Bioinformation 2013; 9:610-6. [PMID: 23904737 PMCID: PMC3725001 DOI: 10.6026/97320630009610] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2013] [Accepted: 06/06/2013] [Indexed: 11/23/2022] Open
Abstract
UNLABELLED Systems Biology involves the study of the interactions of biological systems and ultimately their functions. Down's syndrome (DS) is one of the most common genetic disorders which are caused by complete, or occasionally partial, triplication of chromosome 21, characterized by cognitive and language dysfunction coupled with sensory and neuromotor deficits. Neural Tube Disorders (NTDs) are a group of congenital malformations of the central nervous system and neighboring structures related to defective neural tube closure during the first trimester of pregnancy usually occurring between days 18-29 of gestation. Several studies in the past have provided considerable evidence that abnormal folate and methyl metabolism are associated with onset of DS & NTDs. There is a possible common etiological pathway for both NTDs and Down's syndrome. But, various research studies over the years have indicated very little evidence for familial link between the two disorders. Our research aimed at the gene expression profiling of microarray datasets pertaining to the two disorders to identify genes whose expression levels are significantly altered in these conditions. The genes which were 1.5 fold unregulated and having a p-value <0.05 were filtered out and gene interaction network were constructed for both NTDs and DS. The top ranked dense clique for both the disorders were recognized and over representation analysis was carried out for each of the constituent genes. The comprehensive manual analysis of these genes yields a hypothetical understanding of the lack of familial link between DS and NTDs. There were no genes involved with folic acid present in the dense cliques. Only - CBL, EGFR genes were commonly present, which makes the allelic variants of these genes - good candidates for future studies regarding the familial link between DS and NTDs. ABBREVIATIONS NTD - Neural Tube Disorders, DS - Down's Syndrome, MTHFR - Methylenetetrahydrofolate reductase, MTRR- 5 - methyltetrahydrofolate-homocysteine methyltransferase reductase.
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Affiliation(s)
- Pk Ragunath
- Department of Bioinformatics, Sri Ramachandra University, Porur, Chennai - 600 116, India
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de Matos Simoes R, Dehmer M, Emmert-Streib F. Interfacing cellular networks of S. cerevisiae and E. coli: connecting dynamic and genetic information. BMC Genomics 2013; 14:324. [PMID: 23663484 PMCID: PMC3698017 DOI: 10.1186/1471-2164-14-324] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2012] [Accepted: 04/25/2013] [Indexed: 12/11/2022] Open
Abstract
Background In recent years, various types of cellular networks have penetrated biology and are nowadays used omnipresently for studying eukaryote and prokaryote organisms. Still, the relation and the biological overlap among phenomenological and inferential gene networks, e.g., between the protein interaction network and the gene regulatory network inferred from large-scale transcriptomic data, is largely unexplored. Results We provide in this study an in-depth analysis of the structural, functional and chromosomal relationship between a protein-protein network, a transcriptional regulatory network and an inferred gene regulatory network, for S. cerevisiae and E. coli. Further, we study global and local aspects of these networks and their biological information overlap by comparing, e.g., the functional co-occurrence of Gene Ontology terms by exploiting the available interaction structure among the genes. Conclusions Although the individual networks represent different levels of cellular interactions with global structural and functional dissimilarities, we observe crucial functions of their network interfaces for the assembly of protein complexes, proteolysis, transcription, translation, metabolic and regulatory interactions. Overall, our results shed light on the integrability of these networks and their interfacing biological processes.
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Affiliation(s)
- Ricardo de Matos Simoes
- Computational Biology and Machine Learning Laboratory Center for Cancer Research and Cell Biology, School of Medicine, Dentistry and Biomedical Sciences Faculty of Medicine, Health and Life Sciences, Queen's University, 97 Lisburn Road, Belfast, UK
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Towards systems biology of mycotoxin regulation. Toxins (Basel) 2013; 5:675-82. [PMID: 23598563 PMCID: PMC3705286 DOI: 10.3390/toxins5040675] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2013] [Revised: 03/22/2013] [Accepted: 04/10/2013] [Indexed: 11/16/2022] Open
Abstract
Systems biology is a scientific approach that integrates many scientific disciplines to develop a comprehensive understanding of biological phenomena, thus allowing the prediction and accurate simulation of complex biological behaviors. It may be presumptuous to write about toxin regulation at the level of systems biology, but the last decade of research is leading us closer than ever to this approach. Past research has delineated multiple levels of regulation in the pathways leading to the biosynthesis of secondary metabolites, including mycotoxins. At the top of this hierarchy, the global or master transcriptional regulators perceive various environmental cues such as climatic conditions, the availability of nutrients, and the developmental stages of the organism. Information accumulated from various inputs is integrated through a complex web of signalling networks to generate the eventual outcome. This review will focus on adapting techniques such as chemical and other genetic tools available in the model system Saccharomyces cerevisiae, to disentangle the various biological networks involved in the biosynthesis of mycotoxins in the Fusarium spp.
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43
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Robinson CM, Zhou X, Rajaiya J, Yousuf MA, Singh G, DeSerres JJ, Walsh MP, Wong S, Seto D, Dyer DW, Chodosh J, Jones MS. Predicting the next eye pathogen: analysis of a novel adenovirus. mBio 2013; 4:e00595-12. [PMID: 23572555 PMCID: PMC3622935 DOI: 10.1128/mbio.00595-12] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2012] [Accepted: 03/12/2013] [Indexed: 01/07/2023] Open
Abstract
UNLABELLED For DNA viruses, genetic recombination, addition, and deletion represent important evolutionary mechanisms. Since these genetic alterations can lead to new, possibly severe pathogens, we applied a systems biology approach to study the pathogenicity of a novel human adenovirus with a naturally occurring deletion of the canonical penton base Arg-Gly-Asp (RGD) loop, thought to be critical to cellular entry by adenoviruses. Bioinformatic analysis revealed a new highly recombinant species D human adenovirus (HAdV-D60). A synthesis of in silico and laboratory approaches revealed a potential ocular tropism for the new virus. In vivo, inflammation induced by the virus was dramatically greater than that by adenovirus type 37, a major eye pathogen, possibly due to a novel alternate ligand, Tyr-Gly-Asp (YGD), on the penton base protein. The combination of bioinformatics and laboratory simulation may have important applications in the prediction of tissue tropism for newly discovered and emerging viruses. IMPORTANCE The ongoing dance between a virus and its host distinctly shapes how the virus evolves. While human adenoviruses typically cause mild infections, recent reports have described newly characterized adenoviruses that cause severe, sometimes fatal human infections. Here, we report a systems biology approach to show how evolution has affected the disease potential of a recently identified novel human adenovirus. A comprehensive understanding of viral evolution and pathogenicity is essential to our capacity to foretell the potential impact on human disease for new and emerging viruses.
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MESH Headings
- Adenoviridae Infections/virology
- Adenoviruses, Human/genetics
- Adenoviruses, Human/isolation & purification
- Adenoviruses, Human/pathogenicity
- Amino Acid Sequence
- Animals
- Cell Line
- DNA, Viral/chemistry
- DNA, Viral/genetics
- Disease Models, Animal
- Eye Diseases/virology
- Female
- Humans
- Infant, Newborn
- Male
- Mice
- Mice, Inbred C57BL
- Models, Molecular
- Molecular Sequence Data
- Protein Conformation
- Sequence Alignment
- Sequence Analysis, DNA
- Sequence Deletion
- Systems Biology
- Viral Proteins/chemistry
- Viral Proteins/genetics
- Viral Tropism
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Affiliation(s)
- Christopher M. Robinson
- Department of Ophthalmology, Howe Laboratory, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, Massachusetts, USA
| | - Xiaohong Zhou
- Department of Ophthalmology, Howe Laboratory, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, Massachusetts, USA
| | - Jaya Rajaiya
- Department of Ophthalmology, Howe Laboratory, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, Massachusetts, USA
| | - Mohammad A. Yousuf
- Department of Ophthalmology, Howe Laboratory, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, Massachusetts, USA
| | - Gurdeep Singh
- Department of Ophthalmology, Howe Laboratory, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, Massachusetts, USA
| | | | - Michael P. Walsh
- School of Systems Biology, George Mason University, Manassas, Virginia, USA
| | - Sallene Wong
- Provincial Laboratory for Public Health, Calgary, Alberta, Canada
| | - Donald Seto
- School of Systems Biology, George Mason University, Manassas, Virginia, USA
| | - David W. Dyer
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, USA
| | - James Chodosh
- Department of Ophthalmology, Howe Laboratory, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, Massachusetts, USA
| | - Morris S. Jones
- School of Systems Biology, George Mason University, Manassas, Virginia, USA
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Bizzarri M, Palombo A, Cucina A. Theoretical aspects of Systems Biology. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2013; 112:33-43. [PMID: 23562476 DOI: 10.1016/j.pbiomolbio.2013.03.019] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2013] [Revised: 03/20/2013] [Accepted: 03/25/2013] [Indexed: 12/20/2022]
Abstract
The natural world consists of hierarchical levels of complexity that range from subatomic particles and molecules to ecosystems and beyond. This implies that, in order to explain the features and behavior of a whole system, a theory might be required that would operate at the corresponding hierarchical level, i.e. where self-organization processes take place. In the past, biological research has focused on questions that could be answered by a reductionist program of genetics. The organism (and its development) was considered an epiphenomenona of its genes. However, a profound rethinking of the biological paradigm is now underway and it is likely that such a process will lead to a conceptual revolution emerging from the ashes of reductionism. This revolution implies the search for general principles on which a cogent theory of biology might rely. Because much of the logic of living systems is located at higher levels, it is imperative to focus on them. Indeed, both evolution and physiology work on these levels. Thus, by no means Systems Biology could be considered a 'simple' 'gradual' extension of Molecular Biology.
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Affiliation(s)
- Mariano Bizzarri
- Department of Experimental Medicine, Systems Biology Group Lab, Sapienza University of Rome, via Scarpa 14-16, 00161 Rome, Italy.
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45
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Tripathi S, Glazko GV, Emmert-Streib F. Ensuring the statistical soundness of competitive gene set approaches: gene filtering and genome-scale coverage are essential. Nucleic Acids Res 2013; 41:e82. [PMID: 23389952 PMCID: PMC3627569 DOI: 10.1093/nar/gkt054] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
In this article, we focus on the analysis of competitive gene set methods for detecting the statistical significance of pathways from gene expression data. Our main result is to demonstrate that some of the most frequently used gene set methods, GSEA, GSEArot and GAGE, are severely influenced by the filtering of the data in a way that such an analysis is no longer reconcilable with the principles of statistical inference, rendering the obtained results in the worst case inexpressive. A possible consequence of this is that these methods can increase their power by the addition of unrelated data and noise. Our results are obtained within a bootstrapping framework that allows a rigorous assessment of the robustness of results and enables power estimates. Our results indicate that when using competitive gene set methods, it is imperative to apply a stringent gene filtering criterion. However, even when genes are filtered appropriately, for gene expression data from chips that do not provide a genome-scale coverage of the expression values of all mRNAs, this is not enough for GSEA, GSEArot and GAGE to ensure the statistical soundness of the applied procedure. For this reason, for biomedical and clinical studies, we strongly advice not to use GSEA, GSEArot and GAGE for such data sets.
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Affiliation(s)
- Shailesh Tripathi
- Computational Biology and Machine Learning Laboratory, Center for Cancer Research and Cell Biology, School of Medicine, Dentistry and Biomedical Sciences, Queen's University Belfast, Belfast, 97 Lisburn Road, Belfast BT9 7BL, UK
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46
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Emmert-Streib F, Abogunrin F, de Matos Simoes R, Duggan B, Ruddock MW, Reid CN, Roddy O, White L, O'Kane HF, O'Rourke D, Anderson NH, Nambirajan T, Williamson KE. Collectives of diagnostic biomarkers identify high-risk subpopulations of hematuria patients: exploiting heterogeneity in large-scale biomarker data. BMC Med 2013; 11:12. [PMID: 23327460 PMCID: PMC3570289 DOI: 10.1186/1741-7015-11-12] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/17/2012] [Accepted: 01/17/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Ineffective risk stratification can delay diagnosis of serious disease in patients with hematuria. We applied a systems biology approach to analyze clinical, demographic and biomarker measurements (n = 29) collected from 157 hematuric patients: 80 urothelial cancer (UC) and 77 controls with confounding pathologies. METHODS On the basis of biomarkers, we conducted agglomerative hierarchical clustering to identify patient and biomarker clusters. We then explored the relationship between the patient clusters and clinical characteristics using Chi-square analyses. We determined classification errors and areas under the receiver operating curve of Random Forest Classifiers (RFC) for patient subpopulations using the biomarker clusters to reduce the dimensionality of the data. RESULTS Agglomerative clustering identified five patient clusters and seven biomarker clusters. Final diagnoses categories were non-randomly distributed across the five patient clusters. In addition, two of the patient clusters were enriched with patients with 'low cancer-risk' characteristics. The biomarkers which contributed to the diagnostic classifiers for these two patient clusters were similar. In contrast, three of the patient clusters were significantly enriched with patients harboring 'high cancer-risk" characteristics including proteinuria, aggressive pathological stage and grade, and malignant cytology. Patients in these three clusters included controls, that is, patients with other serious disease and patients with cancers other than UC. Biomarkers which contributed to the diagnostic classifiers for the largest 'high cancer- risk' cluster were different than those contributing to the classifiers for the 'low cancer-risk' clusters. Biomarkers which contributed to subpopulations that were split according to smoking status, gender and medication were different. CONCLUSIONS The systems biology approach applied in this study allowed the hematuric patients to cluster naturally on the basis of the heterogeneity within their biomarker data, into five distinct risk subpopulations. Our findings highlight an approach with the promise to unlock the potential of biomarkers. This will be especially valuable in the field of diagnostic bladder cancer where biomarkers are urgently required. Clinicians could interpret risk classification scores in the context of clinical parameters at the time of triage. This could reduce cystoscopies and enable priority diagnosis of aggressive diseases, leading to improved patient outcomes at reduced costs.
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Affiliation(s)
- Frank Emmert-Streib
- Centre for Cancer Research & Cell Biology, Queens University Belfast, Belfast, Northern Ireland
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Treagust DF, Tsui CY. Conclusion: Contributions of Multiple Representations to Biological Education. MODELS AND MODELING IN SCIENCE EDUCATION 2013. [PMCID: PMC7120393 DOI: 10.1007/978-94-007-4192-8_19] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Affiliation(s)
- David F. Treagust
- Science and Mathematics Education Centre, Curtin University, Kent Street, Bentley, Perth, 6102 West Australia Australia
| | - Chi-Yan Tsui
- Science and Mathematics Education Centre, Curtin University, Glenveagh Dr, Mt Roskill 30, Auckland, 1041 New Zealand
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Robinson A, Causer RJ, Dixon NE. Architecture and conservation of the bacterial DNA replication machinery, an underexploited drug target. Curr Drug Targets 2012; 13:352-72. [PMID: 22206257 PMCID: PMC3290774 DOI: 10.2174/138945012799424598] [Citation(s) in RCA: 87] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2011] [Revised: 11/03/2011] [Accepted: 11/05/2011] [Indexed: 11/22/2022]
Abstract
New antibiotics with novel modes of action are required to combat the growing threat posed by multi-drug resistant bacteria. Over the last decade, genome sequencing and other high-throughput techniques have provided tremendous insight into the molecular processes underlying cellular functions in a wide range of bacterial species. We can now use these data to assess the degree of conservation of certain aspects of bacterial physiology, to help choose the best cellular targets for development of new broad-spectrum antibacterials. DNA replication is a conserved and essential process, and the large number of proteins that interact to replicate DNA in bacteria are distinct from those in eukaryotes and archaea; yet none of the antibiotics in current clinical use acts directly on the replication machinery. Bacterial DNA synthesis thus appears to be an underexploited drug target. However, before this system can be targeted for drug design, it is important to understand which parts are conserved and which are not, as this will have implications for the spectrum of activity of any new inhibitors against bacterial species, as well as the potential for development of drug resistance. In this review we assess similarities and differences in replication components and mechanisms across the bacteria, highlight current progress towards the discovery of novel replication inhibitors, and suggest those aspects of the replication machinery that have the greatest potential as drug targets.
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Affiliation(s)
- Andrew Robinson
- School of Chemistry, University of Wollongong, NSW 2522, Australia
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49
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Boyle JJ. Heme and haemoglobin direct macrophage Mhem phenotype and counter foam cell formation in areas of intraplaque haemorrhage. Curr Opin Lipidol 2012; 23:453-61. [PMID: 22777293 DOI: 10.1097/mol.0b013e328356b145] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
PURPOSE OF REVIEW Several studies have recently shown that haemoglobin drives a novel macrophage subset that is protected from foam cell formation. RECENT FINDINGS In a previously overlooked area, two centres have independently shown that heme and haemoglobin drive an atheroprotective macrophage subset. We compare and contrast the approaches and findings of the laboratories and discuss some of the underlying biology and implications, concentrating on the aspects of lipidological relevance. SUMMARY Treatments based on direct heme-mimetics or other agonists of this pathway have enormous potential for linked antioxidant protection via heme oxygenase 1 and reduced foam cell formation via liver X receptor, a potent combination for treating atherosclerosis.
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50
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Abstract
BACKGROUND The concept of conserved processes presents unique opportunities for using nonhuman animal models in biomedical research. However, the concept must be examined in the context that humans and nonhuman animals are evolved, complex, adaptive systems. Given that nonhuman animals are examples of living systems that are differently complex from humans, what does the existence of a conserved gene or process imply for inter-species extrapolation? METHODS We surveyed the literature including philosophy of science, biological complexity, conserved processes, evolutionary biology, comparative medicine, anti-neoplastic agents, inhalational anesthetics, and drug development journals in order to determine the value of nonhuman animal models when studying conserved processes. RESULTS Evolution through natural selection has employed components and processes both to produce the same outcomes among species but also to generate different functions and traits. Many genes and processes are conserved, but new combinations of these processes or different regulation of the genes involved in these processes have resulted in unique organisms. Further, there is a hierarchy of organization in complex living systems. At some levels, the components are simple systems that can be analyzed by mathematics or the physical sciences, while at other levels the system cannot be fully analyzed by reducing it to a physical system. The study of complex living systems must alternate between focusing on the parts and examining the intact whole organism while taking into account the connections between the two. Systems biology aims for this holism. We examined the actions of inhalational anesthetic agents and anti-neoplastic agents in order to address what the characteristics of complex living systems imply for inter-species extrapolation of traits and responses related to conserved processes. CONCLUSION We conclude that even the presence of conserved processes is insufficient for inter-species extrapolation when the trait or response being studied is located at higher levels of organization, is in a different module, or is influenced by other modules. However, when the examination of the conserved process occurs at the same level of organization or in the same module, and hence is subject to study solely by reductionism, then extrapolation is possible.
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Affiliation(s)
- Ray Greek
- Americans For Medical Advancement (www.AFMA-curedisease.org), 2251 Refugio Rd, Goleta, CA, 93117, USA
| | - Mark J Rice
- Department of Anesthesiology, University of Florida College of Medicine, PO Box 100254, Gainesville, FL, 32610-0254, USA
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