1
|
Rani N, Singla RK, Narwal S, Tanushree, Kumar N, Rahman MM. Medicinal Plants Used as an Alternative to Treat Gingivitis and Periodontitis. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE : ECAM 2022; 2022:2327641. [PMID: 37941972 PMCID: PMC10630018 DOI: 10.1155/2022/2327641] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 08/14/2022] [Accepted: 08/20/2022] [Indexed: 11/10/2023]
Abstract
For various ailments, natural remedies have been traditionally used. To defend against common disorders, medicinal plants are progressively used as nutritional supplements. Gingivitis and periodontitis are widespread and can affect most of the world's population. Gingivitis is a very common, nondestructive inflammatory disease of gums that causes redness and irritation of the gingiva (gums), but periodontitis causes permanent damage to teeth' subsidiary structures. Herbal medicines are getting popular for the treatment of such types of disorders due to being economical with their medicinal effectiveness, compatibility, and nontoxicity. Traditional chemical therapies can cause cell toxicity along with their disease-curing effects. In this article, we discussed the medicinal plants that can be used as an alternative for the treatment of gingivitis (early-stage gum disease) and periodontitis (chronic-stage gum disease).
Collapse
Affiliation(s)
- Neeraj Rani
- Department of Pharmaceutical Sciences, Chaudhary Bansi Lal University, Bhiwani, HR, India
| | - Rajeev K. Singla
- Institutes for Systems Genetics, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu 610041, Sichuan, China
- iGlobal Research and Publishing Foundation, New Delhi, India
| | - Sonia Narwal
- Panipat Institute of Engineering and Technology, Pattikaliyana, Panipat, HR, India
| | - Tanushree
- Department of Pharmaceutical Sciences, Chaudhary Bansi Lal University, Bhiwani, HR, India
| | - Nitish Kumar
- Department of Pharmaceutical Sciences, Chaudhary Bansi Lal University, Bhiwani, HR, India
| | - Md. Mominur Rahman
- Department of Pharmacy, Faculty of Allied Health Sciences, Daffodil International University, Dhaka 1207, Bangladesh
| |
Collapse
|
2
|
|
3
|
Kurgan S, Kantarci A. Molecular basis for immunohistochemical and inflammatory changes during progression of gingivitis to periodontitis. Periodontol 2000 2017; 76:51-67. [DOI: 10.1111/prd.12146] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/14/2016] [Indexed: 12/22/2022]
|
4
|
Ghafari M, Mashaghi A. On the role of topology in regulating transcriptional cascades. Phys Chem Chem Phys 2017; 19:25168-25179. [DOI: 10.1039/c7cp02671d] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Topology of interactions in a transcriptional cascade determines the behavior of its signal-response profile and the activation states of genes.
Collapse
Affiliation(s)
- Mahan Ghafari
- Leiden Academic Centre for Drug Research
- Faculty of Mathematics and Natural Sciences
- Leiden University
- Leiden
- The Netherlands
| | - Alireza Mashaghi
- Leiden Academic Centre for Drug Research
- Faculty of Mathematics and Natural Sciences
- Leiden University
- Leiden
- The Netherlands
| |
Collapse
|
5
|
Satyavathi VV, Narra D, Nagaraju J. Noduler an immune protein augments infection-induced cell proliferation through cross-talking with p38 MAPK. Immunobiology 2016; 221:387-97. [DOI: 10.1016/j.imbio.2015.09.018] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2014] [Revised: 08/02/2015] [Accepted: 09/10/2015] [Indexed: 12/01/2022]
|
6
|
van Wijk R, Tans SJ, Wolde PRT, Mashaghi A. Non-monotonic dynamics and crosstalk in signaling pathways and their implications for pharmacology. Sci Rep 2015; 5:11376. [PMID: 26087464 PMCID: PMC5155565 DOI: 10.1038/srep11376] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2015] [Accepted: 05/22/2015] [Indexed: 12/19/2022] Open
Abstract
Currently, drug discovery approaches commonly assume a monotonic dose-response relationship. However, the assumption of monotonicity is increasingly being challenged. Here we show that for two simple interacting linear signaling pathways that carry two different signals with different physiological responses, a non-monotonic input-output relation can arise with simple network topologies including coherent and incoherent feed-forward loops. We show that non-monotonicity of the response functions has severe implications for pharmacological treatment. Fundamental constraints are imposed on the effectiveness and toxicity of any drug independent of its chemical nature and selectivity due to the specific network structure.
Collapse
Affiliation(s)
- Roeland van Wijk
- FOM Institute AMOLF, Science Park 104, 1098 XG Amsterdam, The Netherlands
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Lorentzweg 1, 2628 CJ Delft, the Netherlands
| | - Sander J. Tans
- FOM Institute AMOLF, Science Park 104, 1098 XG Amsterdam, The Netherlands
| | | | | |
Collapse
|
7
|
Cappuccio A, Tieri P, Castiglione F. Multiscale modelling in immunology: a review. Brief Bioinform 2015; 17:408-18. [PMID: 25810307 DOI: 10.1093/bib/bbv012] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2014] [Accepted: 01/30/2015] [Indexed: 01/26/2023] Open
Abstract
One of the greatest challenges in biomedicine is to get a unified view of observations made from the molecular up to the organism scale. Towards this goal, multiscale models have been highly instrumental in contexts such as the cardiovascular field, angiogenesis, neurosciences and tumour biology. More recently, such models are becoming an increasingly important resource to address immunological questions as well. Systematic mining of the literature in multiscale modelling led us to identify three main fields of immunological applications: host-virus interactions, inflammatory diseases and their treatment and development of multiscale simulation platforms for immunological research and for educational purposes. Here, we review the current developments in these directions, which illustrate that multiscale models can consistently integrate immunological data generated at several scales, and can be used to describe and optimize therapeutic treatments of complex immune diseases.
Collapse
Affiliation(s)
- Antonio Cappuccio
- Laboratory of Integrative biology of human dendritic cells and T cells, U932 Immunity and cancer, Institut Curie, 26 Rue d`Ulm, 75005 Paris, France
| | - Paolo Tieri
- Institute for Applied Mathematics (IAC), National Research Council of Italy (CNR), Via dei Taurini 19, 00185 Rome, Italy
| | - Filippo Castiglione
- Institute for Applied Mathematics (IAC), National Research Council of Italy (CNR), Via dei Taurini 19, 00185 Rome, Italy
| |
Collapse
|
8
|
Subramanian N, Torabi-Parizi P, Gottschalk RA, Germain RN, Dutta B. Network representations of immune system complexity. WILEY INTERDISCIPLINARY REVIEWS-SYSTEMS BIOLOGY AND MEDICINE 2015; 7:13-38. [PMID: 25625853 PMCID: PMC4339634 DOI: 10.1002/wsbm.1288] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/25/2014] [Revised: 12/09/2014] [Accepted: 12/11/2014] [Indexed: 12/25/2022]
Abstract
The mammalian immune system is a dynamic multiscale system composed of a hierarchically organized set of molecular, cellular, and organismal networks that act in concert to promote effective host defense. These networks range from those involving gene regulatory and protein–protein interactions underlying intracellular signaling pathways and single‐cell responses to increasingly complex networks of in vivo cellular interaction, positioning, and migration that determine the overall immune response of an organism. Immunity is thus not the product of simple signaling events but rather nonlinear behaviors arising from dynamic, feedback‐regulated interactions among many components. One of the major goals of systems immunology is to quantitatively measure these complex multiscale spatial and temporal interactions, permitting development of computational models that can be used to predict responses to perturbation. Recent technological advances permit collection of comprehensive datasets at multiple molecular and cellular levels, while advances in network biology support representation of the relationships of components at each level as physical or functional interaction networks. The latter facilitate effective visualization of patterns and recognition of emergent properties arising from the many interactions of genes, molecules, and cells of the immune system. We illustrate the power of integrating ‘omics’ and network modeling approaches for unbiased reconstruction of signaling and transcriptional networks with a focus on applications involving the innate immune system. We further discuss future possibilities for reconstruction of increasingly complex cellular‐ and organism‐level networks and development of sophisticated computational tools for prediction of emergent immune behavior arising from the concerted action of these networks. WIREs Syst Biol Med 2015, 7:13–38. doi: 10.1002/wsbm.1288 This article is categorized under:
Analytical and Computational Methods > Computational Methods Laboratory Methods and Technologies > Macromolecular Interactions, Methods
Collapse
Affiliation(s)
- Naeha Subramanian
- Institute for Systems Biology, Seattle, WA, USA; Laboratory of Systems Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | | | | | | | | |
Collapse
|
9
|
Evolutionary Developmental Biology and the Limits of Philosophical Accounts of Mechanistic Explanation. HISTORY, PHILOSOPHY AND THEORY OF THE LIFE SCIENCES 2015. [DOI: 10.1007/978-94-017-9822-8_7] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
|
10
|
Clancy T, Hovig E. From proteomes to complexomes in the era of systems biology. Proteomics 2014; 14:24-41. [PMID: 24243660 DOI: 10.1002/pmic.201300230] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2013] [Revised: 10/22/2013] [Accepted: 11/06/2013] [Indexed: 01/16/2023]
Abstract
Protein complexes carry out almost the entire signaling and functional processes in the cell. The protein complex complement of a cell, and its network of complex-complex interactions, is referred to here as the complexome. Computational methods to predict protein complexes from proteomics data, resulting in network representations of complexomes, have recently being developed. In addition, key advances have been made toward understanding the network and structural organization of complexomes. We review these bioinformatics advances, and their discovery-potential, as well as the merits of integrating proteomics data with emerging methods in systems biology to study protein complex signaling. It is envisioned that improved integration of proteomics and systems biology, incorporating the dynamics of protein complexes in space and time, may lead to more predictive models of cell signaling networks for effective modulation.
Collapse
Affiliation(s)
- Trevor Clancy
- Department of Tumor Biology, Institute for Cancer Research, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway
| | | |
Collapse
|
11
|
Sjoelund V, Smelkinson M, Nita-Lazar A. Phosphoproteome profiling of the macrophage response to different toll-like receptor ligands identifies differences in global phosphorylation dynamics. J Proteome Res 2014; 13:5185-97. [PMID: 24941444 PMCID: PMC4227906 DOI: 10.1021/pr5002466] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
![]()
Toll-like
receptors (TLRs) are among the first sensors that detect
infection and drive immune response. Macrophages encountering a pathogen
are usually stimulated not by one TLR, but by a combination of TLRs
engaged by distinct microbe ligands. To understand the integrated
signaling under complex conditions, we investigated the differences
in the phosphoprotein signaling cascades triggered by TLR2, TLR4,
and TLR7 ligands using a single responding cell population. We performed
a global, quantitative, early poststimulation kinetic analysis of
the mouse macrophage phosphoproteome using stable isotope labeling
with amino acids coupled to phosphopeptide enrichment and high-resolution
mass spectrometry. For each TLR ligand, we found marked elevation
of phosphorylation of cytoskeleton components, GTPases of the Rho
family, and phospholipase C signaling pathway proteins. Phosphorylation
of proteins involved in phagocytosis was only seen in response to
TLR2 and TLR4 but not to TLR7 activation. Changes in the phosphorylation
of proteins involved in endocytosis were delayed in response to TLR2
as compared to TLR4 ligands. These findings reveal that the phosphoproteomic
response to stimulation of distinct TLRs varies both in the major
modification targets and the phosphorylation dynamics. These results
advance the understanding of how macrophages sense and respond to
a diverse set of TLR stimuli.
Collapse
Affiliation(s)
- Virginie Sjoelund
- Laboratory of Systems Biology, and §Research Technology Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health , Bethesda, Maryland 20892, United States
| | | | | |
Collapse
|
12
|
de Groot PG, Urbanus RT. Cellular signaling by antiphospholipid antibodies. J Thromb Haemost 2014; 12:773-5. [PMID: 24612457 DOI: 10.1111/jth.12540] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2014] [Accepted: 02/07/2014] [Indexed: 11/28/2022]
Affiliation(s)
- P G de Groot
- Department of Clinical Chemistry and Haematology, University of Utrecht, University Medical Center Utrecht, Utrecht, the Netherlands
| | | |
Collapse
|
13
|
Chylek LA, Holowka DA, Baird BA, Hlavacek WS. An Interaction Library for the FcεRI Signaling Network. Front Immunol 2014; 5:172. [PMID: 24782869 PMCID: PMC3995055 DOI: 10.3389/fimmu.2014.00172] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2013] [Accepted: 03/31/2014] [Indexed: 12/20/2022] Open
Abstract
Antigen receptors play a central role in adaptive immune responses. Although the molecular networks associated with these receptors have been extensively studied, we currently lack a systems-level understanding of how combinations of non-covalent interactions and post-translational modifications are regulated during signaling to impact cellular decision-making. To fill this knowledge gap, it will be necessary to formalize and piece together information about individual molecular mechanisms to form large-scale computational models of signaling networks. To this end, we have developed an interaction library for signaling by the high-affinity IgE receptor, FcεRI. The library consists of executable rules for protein–protein and protein–lipid interactions. This library extends earlier models for FcεRI signaling and introduces new interactions that have not previously been considered in a model. Thus, this interaction library is a toolkit with which existing models can be expanded and from which new models can be built. As an example, we present models of branching pathways from the adaptor protein Lat, which influence production of the phospholipid PIP3 at the plasma membrane and the soluble second messenger IP3. We find that inclusion of a positive feedback loop gives rise to a bistable switch, which may ensure robust responses to stimulation above a threshold level. In addition, the library is visualized to facilitate understanding of network circuitry and identification of network motifs.
Collapse
Affiliation(s)
- Lily A Chylek
- Department of Chemistry and Chemical Biology, Cornell University , Ithaca, NY , USA ; Los Alamos National Laboratory, Theoretical Division, Center for Non-linear Studies , Los Alamos, NM , USA
| | - David A Holowka
- Department of Chemistry and Chemical Biology, Cornell University , Ithaca, NY , USA
| | - Barbara A Baird
- Department of Chemistry and Chemical Biology, Cornell University , Ithaca, NY , USA
| | - William S Hlavacek
- Los Alamos National Laboratory, Theoretical Division, Center for Non-linear Studies , Los Alamos, NM , USA
| |
Collapse
|
14
|
Tieri P, Nardini C. Signalling pathway database usability: lessons learned. MOLECULAR BIOSYSTEMS 2014; 9:2401-7. [PMID: 23942525 DOI: 10.1039/c3mb70242a] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
BACKGROUND issues and limitations related to accessibility, understandability and ease of use of signalling pathway databases may hamper or divert research workflow, leading, in the worst case, to the generation of confusing reference frameworks and misinterpretation of experimental results. In an attempt to retrieve signalling pathway data related to a specific set of test genes, we queried and analysed the results from six of the major curated signalling pathway databases: Reactome, PathwayCommons, KEGG, InnateDB, PID, and Wikipathways. FINDINGS although we expected differences - often a desirable feature for the integration of each individual query, we observed variations of exceptional magnitude, with disproportionate quality and quantity of the results. Some of the more remarkable differences can be explained by the diverse conceptual designs and purposes of the databases, the types of data stored and the structure of the query, as well as by missing or erroneous descriptions of the search procedure. To go beyond the mere enumeration of these problems, we identified a number of operational features, in particular inner and cross coherence, which, once quantified, offer objective criteria to choose the best source of information. CONCLUSIONS in silico biology heavily relies on the information stored in databases. To ensure that computational biology mirrors biological reality and offers focused hypotheses to be experimentally validated, coherence of data codification is crucial and yet highly underestimated. We make practical recommendations for the end-user to cope with the current state of the databases as well as for the maintainers of those databases to contribute to the goal of the full enactment of the open data paradigm.
Collapse
Affiliation(s)
- Paolo Tieri
- Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Yue Yang Road 320, Shanghai, P. R. China
| | | |
Collapse
|
15
|
T cell activation induces CuZn superoxide dismutase (SOD)-1 intracellular re-localization, production and secretion. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2014; 1843:265-74. [DOI: 10.1016/j.bbamcr.2013.10.020] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2013] [Revised: 10/21/2013] [Accepted: 10/24/2013] [Indexed: 01/22/2023]
|
16
|
Mobashir M, Madhusudhan T, Isermann B, Beyer T, Schraven B. Negative interactions and feedback regulations are required for transient cellular response. Sci Rep 2014; 4:3718. [PMID: 24430195 PMCID: PMC3893651 DOI: 10.1038/srep03718] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2013] [Accepted: 12/19/2013] [Indexed: 12/21/2022] Open
Abstract
Signal transduction is a process required to conduct information from a receptor to the nucleus. This process is vital for the control of cellular function and fate. The dynamics of signaling activation and inhibition determine processes such as apoptosis, proliferation, and differentiation. Thus, it is important to understand the factors modulating transient and sustained response. To address this question, by applying mathematical approach we have studied the factors which can alter the activation nature of downstream signaling molecules. The factors which we have investigated are loops (feed forward and feedback loops), cross-talk of signal transduction pathways, and the change in the concentration of the signaling molecules. Based on our results we conclude that among these factors feedback loop and the cross-talks which directly inhibit the target protein dominantly controls the transient cellular response.
Collapse
Affiliation(s)
- Mohammad Mobashir
- Institute of Molecular and Clinical Immunology, Otto-von-Guericke University, 39120, Magdeburg, Germany
| | - Thati Madhusudhan
- Institute of Clinical Chemistry and Pathobiochemistry, Otto-von-Guericke University, 39120, Magdeburg, Germany
| | - Berend Isermann
- Institute of Clinical Chemistry and Pathobiochemistry, Otto-von-Guericke University, 39120, Magdeburg, Germany
| | - Tilo Beyer
- Institute of Molecular and Clinical Immunology, Otto-von-Guericke University, 39120, Magdeburg, Germany
| | - Burkhart Schraven
- 1] Institute of Molecular and Clinical Immunology, Otto-von-Guericke University, 39120, Magdeburg, Germany [2] Department of Immune Control, Helmholtz Centre for Infectious Disease (HZI), Inhoffenstrasse 7, 38124 Braunschweig, Germany
| |
Collapse
|
17
|
Molecular signatures of antibody responses derived from a systems biology study of five human vaccines. Nat Immunol 2013; 15:195-204. [PMID: 24336226 PMCID: PMC3946932 DOI: 10.1038/ni.2789] [Citation(s) in RCA: 515] [Impact Index Per Article: 46.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2013] [Accepted: 11/14/2013] [Indexed: 12/18/2022]
Abstract
Many vaccines induce protective immunity via antibodies. Recent studies have used systems biological approaches to determine signatures that predict vaccine immunity in humans, but whether there is a ‘universal signature’ that can predict antibody responses to any vaccine, is unknown. Here we performed systems analyses of immune responses to the meningococcal polysaccharide and conjugate vaccines in healthy adults, in the broader context of our previous studies with the yellow fever and two influenza vaccines. To achieve this, we performed a large-scale network integration of public human blood transcriptomes, and systems-scale databases in specific biological contexts, and deduced a set of blood transcription modules. These modules revealed distinct transcriptional signatures of antibody responses to different classes of vaccines providing key insights into primary viral, protein recall and anti-polysaccharide responses. These results illuminate the early transcriptional programs orchestrating vaccine immunity in humans, and demonstrate the power of integrative network modeling.
Collapse
|
18
|
Brigandt I. Systems biology and the integration of mechanistic explanation and mathematical explanation. STUDIES IN HISTORY AND PHILOSOPHY OF BIOLOGICAL AND BIOMEDICAL SCIENCES 2013; 44:477-492. [PMID: 23863399 DOI: 10.1016/j.shpsc.2013.06.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2012] [Revised: 06/12/2013] [Accepted: 06/14/2013] [Indexed: 06/02/2023]
Abstract
The paper discusses how systems biology is working toward complex accounts that integrate explanation in terms of mechanisms and explanation by mathematical models-which some philosophers have viewed as rival models of explanation. Systems biology is an integrative approach, and it strongly relies on mathematical modeling. Philosophical accounts of mechanisms capture integrative in the sense of multilevel and multifield explanations, yet accounts of mechanistic explanation (as the analysis of a whole in terms of its structural parts and their qualitative interactions) have failed to address how a mathematical model could contribute to such explanations. I discuss how mathematical equations can be explanatorily relevant. Several cases from systems biology are discussed to illustrate the interplay between mechanistic research and mathematical modeling, and I point to questions about qualitative phenomena (rather than the explanation of quantitative details), where quantitative models are still indispensable to the explanation. Systems biology shows that a broader philosophical conception of mechanisms is needed, which takes into account functional-dynamical aspects, interaction in complex networks with feedback loops, system-wide functional properties such as distributed functionality and robustness, and a mechanism's ability to respond to perturbations (beyond its actual operation). I offer general conclusions for philosophical accounts of explanation.
Collapse
Affiliation(s)
- Ingo Brigandt
- Department of Philosophy, University of Alberta, 2-40 Assiniboia Hall, Edmonton, AB T6G2E7, Canada.
| |
Collapse
|
19
|
Csermely P, Korcsmáros T, Kiss HJM, London G, Nussinov R. Structure and dynamics of molecular networks: a novel paradigm of drug discovery: a comprehensive review. Pharmacol Ther 2013; 138:333-408. [PMID: 23384594 PMCID: PMC3647006 DOI: 10.1016/j.pharmthera.2013.01.016] [Citation(s) in RCA: 511] [Impact Index Per Article: 46.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2013] [Accepted: 01/22/2013] [Indexed: 02/02/2023]
Abstract
Despite considerable progress in genome- and proteome-based high-throughput screening methods and in rational drug design, the increase in approved drugs in the past decade did not match the increase of drug development costs. Network description and analysis not only give a systems-level understanding of drug action and disease complexity, but can also help to improve the efficiency of drug design. We give a comprehensive assessment of the analytical tools of network topology and dynamics. The state-of-the-art use of chemical similarity, protein structure, protein-protein interaction, signaling, genetic interaction and metabolic networks in the discovery of drug targets is summarized. We propose that network targeting follows two basic strategies. The "central hit strategy" selectively targets central nodes/edges of the flexible networks of infectious agents or cancer cells to kill them. The "network influence strategy" works against other diseases, where an efficient reconfiguration of rigid networks needs to be achieved by targeting the neighbors of central nodes/edges. It is shown how network techniques can help in the identification of single-target, edgetic, multi-target and allo-network drug target candidates. We review the recent boom in network methods helping hit identification, lead selection optimizing drug efficacy, as well as minimizing side-effects and drug toxicity. Successful network-based drug development strategies are shown through the examples of infections, cancer, metabolic diseases, neurodegenerative diseases and aging. Summarizing >1200 references we suggest an optimized protocol of network-aided drug development, and provide a list of systems-level hallmarks of drug quality. Finally, we highlight network-related drug development trends helping to achieve these hallmarks by a cohesive, global approach.
Collapse
Affiliation(s)
- Peter Csermely
- Department of Medical Chemistry, Semmelweis University, P.O. Box 260, H-1444 Budapest 8, Hungary.
| | | | | | | | | |
Collapse
|
20
|
Sadler T, Scarpa M, Rieder F, West G, Stylianou E. Cytokine-induced chromatin modifications of the type I collagen alpha 2 gene during intestinal endothelial-to-mesenchymal transition. Inflamm Bowel Dis 2013; 19:1354-64. [PMID: 23635716 PMCID: PMC3684204 DOI: 10.1097/mib.0b013e318281f37a] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
BACKGROUND Fibrosis of the intestine is currently an irreversible complication of inflammatory bowel disease; yet, little is understood of the underlying pathogenesis and antifibrotic strategies remain elusive. To develop effective therapies, knowledge of the mechanism of transcription and excessive deposition of type I collagen, a hallmark of fibrosis, is needed. We have shown previously that endothelial-to-mesenchymal transition (EndoMT) contributes to the pool of intestinal fibrotic cells and that a cytokine cocktail (interleukin 1-β, tumor necrosis factor α, and transforming growth factor β) induces collagen I alpha 2 (COL1A2) mRNA and protein. METHODS Chromatin immunoprecipitation assays on pure cultures of human intestinal mucosal endothelial cells undergoing EndoMT were performed with antibodies to specific histone modifications and RNA polymerase II. Reverse transcriptase-PCR was used to quantify the levels of Col1A2 and endothelial-specific von Willebrand factor (vWF) mRNA. RESULTS We showed that cytokines induce selective chromatin modifications (histone 4 hyperacetylation, and hypermethylation of histone 3) and phosphorylated RNA polymerase II at the COL1A2 promoter. Hypoacetylated and hypomethylated histone 3 was detected on the repressed vWF gene. Prolonged exposure to cytokines (16 days) retained hyperacetylation of select lysines in H4 on the COL1A2 promoter. Removal of cytokines after 16 days and continued culture for 10 days showed persistent hyperacetylation at lysine 16 in histone H4. CONCLUSIONS This is the first study to show that COL1A2 gene expression is associated with cytokine-induced, temporally ordered, and persistent chromatin modifications and suggests that these are important determinants of gene expression in EndoMT and intestinal fibrosis.
Collapse
Affiliation(s)
- Tammy Sadler
- Department of Pathobiology, Lerner Research Institute, 9500 Euclid Avenue, Cleveland, OH 44195, USA
| | - Melania Scarpa
- Department of Pathobiology, Lerner Research Institute, 9500 Euclid Avenue, Cleveland, OH 44195, USA,Melania Scarpa, current address: Istituto Oncologico Veneto, I.R.C.C.S., Padua, Italy
| | - Florian Rieder
- Department of Pathobiology, Lerner Research Institute, 9500 Euclid Avenue, Cleveland, OH 44195, USA,Department of Gastroenterology & Hepatology, Digestive Disease Institute, Cleveland Clinic Foundation, 9500 Euclid Avenue, Cleveland, 44195, USA
| | - Gail West
- Department of Pathobiology, Lerner Research Institute, 9500 Euclid Avenue, Cleveland, OH 44195, USA
| | - Eleni Stylianou
- Department of Pathobiology, Lerner Research Institute, 9500 Euclid Avenue, Cleveland, OH 44195, USA,Department of Gastroenterology & Hepatology, Digestive Disease Institute, Cleveland Clinic Foundation, 9500 Euclid Avenue, Cleveland, 44195, USA,To who correspondence should be addressed: Dr. Eleni Stylianou, B.Sc. Ph.D., Department of Pathobiology, Lerner Research Institute, Cleveland Clinic, 9500 Euclid Avenue/NC-22, Cleveland, OH 44195. Tel: 216-445-7156; Fax: 216-636-0104,
| |
Collapse
|
21
|
Fazekas D, Koltai M, Türei D, Módos D, Pálfy M, Dúl Z, Zsákai L, Szalay-Bekő M, Lenti K, Farkas IJ, Vellai T, Csermely P, Korcsmáros T. SignaLink 2 - a signaling pathway resource with multi-layered regulatory networks. BMC SYSTEMS BIOLOGY 2013; 7:7. [PMID: 23331499 PMCID: PMC3599410 DOI: 10.1186/1752-0509-7-7] [Citation(s) in RCA: 134] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/13/2012] [Accepted: 01/16/2013] [Indexed: 12/18/2022]
Abstract
BACKGROUND Signaling networks in eukaryotes are made up of upstream and downstream subnetworks. The upstream subnetwork contains the intertwined network of signaling pathways, while the downstream regulatory part contains transcription factors and their binding sites on the DNA as well as microRNAs and their mRNA targets. Currently, most signaling and regulatory databases contain only a subsection of this network, making comprehensive analyses highly time-consuming and dependent on specific data handling expertise. The need for detailed mapping of signaling systems is also supported by the fact that several drug development failures were caused by undiscovered cross-talk or regulatory effects of drug targets. We previously created a uniformly curated signaling pathway resource, SignaLink, to facilitate the analysis of pathway cross-talks. Here, we present SignaLink 2, which significantly extends the coverage and applications of its predecessor. DESCRIPTION We developed a novel concept to integrate and utilize different subsections (i.e., layers) of the signaling network. The multi-layered (onion-like) database structure is made up of signaling pathways, their pathway regulators (e.g., scaffold and endocytotic proteins) and modifier enzymes (e.g., phosphatases, ubiquitin ligases), as well as transcriptional and post-transcriptional regulators of all of these components. The user-friendly website allows the interactive exploration of how each signaling protein is regulated. The customizable download page enables the analysis of any user-specified part of the signaling network. Compared to other signaling resources, distinctive features of SignaLink 2 are the following: 1) it involves experimental data not only from humans but from two invertebrate model organisms, C. elegans and D. melanogaster; 2) combines manual curation with large-scale datasets; 3) provides confidence scores for each interaction; 4) operates a customizable download page with multiple file formats (e.g., BioPAX, Cytoscape, SBML). Non-profit users can access SignaLink 2 free of charge at http://SignaLink.org. CONCLUSIONS With SignaLink 2 as a single resource, users can effectively analyze signaling pathways, scaffold proteins, modifier enzymes, transcription factors and miRNAs that are important in the regulation of signaling processes. This integrated resource allows the systems-level examination of how cross-talks and signaling flow are regulated, as well as provide data for cross-species comparisons and drug discovery analyses.
Collapse
Affiliation(s)
- Dávid Fazekas
- Department of Genetics, Eötvös Loránd University, Pázmány P. s. 1C, H-1117, Budapest, Hungary
| | - Mihály Koltai
- Statistical and Biological Physics Group of the Hungarian Acad. of Sciences, Pázmány P. s. 1A, H-1117, Budapest, Hungary
- Department of Biological Physics, Eötvös Loránd University, Pázmány P. s. 1A, H-1117, Budapest, Hungary
| | - Dénes Türei
- Department of Genetics, Eötvös Loránd University, Pázmány P. s. 1C, H-1117, Budapest, Hungary
- Department of Medical Chemistry, Semmelweis University, PO Box 260, H-1444, Budapest, Hungary
| | - Dezső Módos
- Department of Genetics, Eötvös Loránd University, Pázmány P. s. 1C, H-1117, Budapest, Hungary
- Department of Medical Chemistry, Semmelweis University, PO Box 260, H-1444, Budapest, Hungary
- Department of Morphology and Physiology, Semmelweis University, Vas u. 17, H-1088, Budapest, Hungary
| | - Máté Pálfy
- Department of Genetics, Eötvös Loránd University, Pázmány P. s. 1C, H-1117, Budapest, Hungary
| | - Zoltán Dúl
- Department of Genetics, Eötvös Loránd University, Pázmány P. s. 1C, H-1117, Budapest, Hungary
- Department of Medical Chemistry, Semmelweis University, PO Box 260, H-1444, Budapest, Hungary
| | - Lilian Zsákai
- Department of Genetics, Eötvös Loránd University, Pázmány P. s. 1C, H-1117, Budapest, Hungary
- Department of Medical Chemistry, Semmelweis University, PO Box 260, H-1444, Budapest, Hungary
| | - Máté Szalay-Bekő
- Department of Medical Chemistry, Semmelweis University, PO Box 260, H-1444, Budapest, Hungary
| | - Katalin Lenti
- Department of Genetics, Eötvös Loránd University, Pázmány P. s. 1C, H-1117, Budapest, Hungary
- Department of Morphology and Physiology, Semmelweis University, Vas u. 17, H-1088, Budapest, Hungary
| | - Illés J Farkas
- Statistical and Biological Physics Group of the Hungarian Acad. of Sciences, Pázmány P. s. 1A, H-1117, Budapest, Hungary
| | - Tibor Vellai
- Department of Genetics, Eötvös Loránd University, Pázmány P. s. 1C, H-1117, Budapest, Hungary
| | - Péter Csermely
- Department of Medical Chemistry, Semmelweis University, PO Box 260, H-1444, Budapest, Hungary
| | - Tamás Korcsmáros
- Department of Genetics, Eötvös Loránd University, Pázmány P. s. 1C, H-1117, Budapest, Hungary
- Department of Medical Chemistry, Semmelweis University, PO Box 260, H-1444, Budapest, Hungary
| |
Collapse
|
22
|
Abstract
Because of the potent effector mechanisms of the immune system, the potential for self-destructive immune responses is especially high and many negative regulatory modalities exist to prevent excessive tissue damage. This Commentary places such regulatory mechanisms in the larger context of system organization on many scales. The sometimes counterintuitive nature of feedback control is discussed and a case is made for greater attention to quantitative spatiotemporal aspects of regulation, rather than limiting the discussion to the qualitative descriptions of pathways that dominate at present.
Collapse
Affiliation(s)
- Ronald N Germain
- Lymphocyte Biology Section, Laboratory of Systems Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA.
| |
Collapse
|
23
|
Pálfy M, Reményi A, Korcsmáros T. Endosomal crosstalk: meeting points for signaling pathways. Trends Cell Biol 2012; 22:447-56. [PMID: 22796207 PMCID: PMC3430897 DOI: 10.1016/j.tcb.2012.06.004] [Citation(s) in RCA: 89] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2012] [Revised: 06/18/2012] [Accepted: 06/19/2012] [Indexed: 12/30/2022]
Abstract
Endocytosis participates in downregulating incoming signals, but 'signaling endosomes' may also serve as physical platforms for crosstalk between signaling pathways. Here, we briefly review the role of endosomes in signaling crosstalk and suggest that endosome-associated scaffold proteins mediate this crosstalk. In addition, using a proteome-wide in silico approach - in which we analyze endosome-binding properties and the capacity of candidates to recruit signaling proteins from more than one distinct pathway - we extend the list of putative crosstalk-mediating endosomal scaffolds. Because endosomal crosstalk may be an important systems-level regulator of pathway communication, scaffold proteins that mediate this crosstalk could be potential targets for pharmacological intervention and synthetic engineering.
Collapse
Affiliation(s)
- Máté Pálfy
- Department of Genetics, Eötvös Loránd University, Pázmány P. s. 1/C, Budapest, H-1117, Hungary
| | - Attila Reményi
- Department of Biochemistry, Eötvös Loránd University, Pázmány P. s. 1/C, Budapest, H-1117, Hungary
| | - Tamás Korcsmáros
- Department of Genetics, Eötvös Loránd University, Pázmány P. s. 1/C, Budapest, H-1117, Hungary
- Department of Medical Chemistry, Semmelweis University, Tűzoltó u. 37-47, Budapest, H-1094, Hungary
| |
Collapse
|
24
|
Ku CJ, Wang Y, Weiner OD, Altschuler SJ, Wu LF. Network crosstalk dynamically changes during neutrophil polarization. Cell 2012; 149:1073-83. [PMID: 22632971 DOI: 10.1016/j.cell.2012.03.044] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2011] [Revised: 11/29/2011] [Accepted: 03/21/2012] [Indexed: 01/09/2023]
Abstract
How complex signaling networks shape highly coordinated, multistep cellular responses is poorly understood. Here, we made use of a network-perturbation approach to investigate causal influences, or "crosstalk," among signaling modules involved in the cytoskeletal response of neutrophils to chemoattractant. We quantified the intensity and polarity of cytoskeletal marker proteins over time to characterize stereotyped cellular responses. Analyzing the effects of network disruptions revealed that, not only does crosstalk evolve rapidly during polarization, but also that intensity and polarity responses are influenced by different patterns of crosstalk. Interestingly, persistent crosstalk is arranged in a surprisingly simple circuit: a linear cascade from front to back to microtubules influences intensities, and a feed-forward network in the reverse direction influences polarity. Our approach provided a rational strategy for decomposing a complex, dynamically evolving signaling system and revealed evolving paths of causal influence that shape the neutrophil polarization response.
Collapse
Affiliation(s)
- Chin-Jen Ku
- Department of Pharmacology, Green Center for Systems Biology, Simmons Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | | | | | | | | |
Collapse
|
25
|
Crites TJ, Chen L, Varma R. A TIRF microscopy technique for real-time, simultaneous imaging of the TCR and its associated signaling proteins. J Vis Exp 2012:3892. [PMID: 22472646 PMCID: PMC3460565 DOI: 10.3791/3892] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Signaling is initiated through the T Cell Receptor (TCR) when it is engaged by antigenic peptide fragments bound by Major Histocompatibility Complex (pMHC) proteins expressed on the surface of antigen presenting cells (APCs). The TCR complex is composed of the ligand binding TCRαβ heterodimer that associates non-covalently with CD3 dimers (the εδ and εγ heterodimers and the ζζ homodimer)1. Upon engagement of the receptor, the CD3 ζ chains are phosphorylated by the Src family kinase, Lck. This leads to the recruitment of the Syk family kinase, Zap70, which is then phosphorylated and activated by Lck. After that, Zap70 phosphorylates the adapter proteins LAT and SLP76, initiating the formation of the proximal signaling complex containing a large number of different signaling molecules2. The formation of this complex eventually results in calcium and Ras-dependent transcription factor activation and the consequent initiation of a complex series of gene expression programs that give rise to T cell differentiation2. TCR signals (and the resulting state of differentiation) are modulated by many other factors, including antigen potency and crosstalk with co-stimulatory/co-inhibitory, chemokine, and cytokine receptors 3-4. Studying the spatial and temporal organization of the proximal signaling complex under various stimulation conditions is, therefore, key to understanding the TCR signaling pathway as well as its regulation by other signaling pathways. One very useful model system to study signaling initiated by the TCR at the plasma membrane in T cells is glass-supported lipid bilayers, as described previously5-6. They can be utilized to present antigenic pMHC complexes, adhesion, and co-stimulatory molecules to T cells-serving as artificial APCs. By imaging the T cells interacting with the lipid bilayer using total internal reflection fluorescence microscopy (TIRFM), we can restrict the excitation to within 100 nm of the space between the glass and the cell surface 7-8. This allows us to image primarily the signaling events occurring at the plasma membrane. As we are interested in imaging the recruitment of signaling proteins to the TCR complex, we describe a two-camera TIRF imaging system wherein the TCR, labeled with fluorescent Fab (fragment antigen binding) fragments of the H57 antibody (purified from hybridoma H57-597, ATCC, ATCC Number:HB-218) which is specific for TCRβ, and signaling proteins, tagged with GFP, may be imaged simultaneously and in real time. This strategy is necessary due to the highly dynamic nature of both the T cells and of the signaling events that are occurring at the TCR. This imaging modality has allowed researchers to image single ligands 9-11 as well as recruitment of signaling molecules to activated receptors and is an excellent system to study biochemistry in-situ12-16.
Collapse
Affiliation(s)
- Travis J Crites
- Laboratory of Cellular and Molecular Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health
| | | | | |
Collapse
|
26
|
Tieri P, Termanini A, Bellavista E, Salvioli S, Capri M, Franceschi C. Charting the NF-κB pathway interactome map. PLoS One 2012; 7:e32678. [PMID: 22403694 PMCID: PMC3293857 DOI: 10.1371/journal.pone.0032678] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2011] [Accepted: 01/28/2012] [Indexed: 01/05/2023] Open
Abstract
Inflammation is part of a complex physiological response to harmful stimuli and pathogenic stress. The five components of the Nuclear Factor κB (NF-κB) family are prominent mediators of inflammation, acting as key transcriptional regulators of hundreds of genes. Several signaling pathways activated by diverse stimuli converge on NF-κB activation, resulting in a regulatory system characterized by high complexity. It is increasingly recognized that the number of components that impinges upon phenotypic outcomes of signal transduction pathways may be higher than those taken into consideration from canonical pathway representations. Scope of the present analysis is to provide a wider, systemic picture of the NF-κB signaling system. Data from different sources such as literature, functional enrichment web resources, protein-protein interaction and pathway databases have been gathered, curated, integrated and analyzed in order to reconstruct a single, comprehensive picture of the proteins that interact with, and participate to the NF-κB activation system. Such a reconstruction shows that the NF-κB interactome is substantially different in quantity and quality of components with respect to canonical representations. The analysis highlights that several neglected but topologically central proteins may play a role in the activation of NF-κB mediated responses. Moreover the interactome structure fits with the characteristics of a bow tie architecture. This interactome is intended as an open network resource available for further development, refinement and analysis.
Collapse
Affiliation(s)
- Paolo Tieri
- CIG Luigi Galvani Interdept Center, University of Bologna, Bologna, Italy.
| | | | | | | | | | | |
Collapse
|
27
|
How the TCR balances sensitivity and specificity for the recognition of self and pathogens. Nat Immunol 2012; 13:121-8. [PMID: 22261968 DOI: 10.1038/ni.2190] [Citation(s) in RCA: 142] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The T cell repertoire is generated during thymic development in preparation for the response to antigens from pathogens. The T cell repertoire is shaped by positive selection, which requires recognition by the T cell antigen receptor (TCR) of complexes of self peptide and major histocompatibility complex proteins (self-pMHC) with low affinity, and negative selection, which eliminates T cells with TCRs that recognize self-pMHC with high affinity. This generates a repertoire with low affinity for self-pMHC but high affinity for foreign antigens. The TCR must successfully engage both of these ligands for development, homeostasis and immune responses. This review discusses mechanisms underlying the interaction of the TCR with peptide-major histocompatibility complex ligands of varying affinity and highlights signaling mechanisms that enable the TCR to generate different responses to very distinct ligands.
Collapse
|
28
|
Chevrier N, Mertins P, Artyomov MN, Shalek AK, Iannacone M, Ciaccio MF, Gat-Viks I, Tonti E, DeGrace MM, Clauser KR, Garber M, Eisenhaure TM, Yosef N, Robinson J, Sutton A, Andersen MS, Root DE, von Andrian U, Jones RB, Park H, Carr SA, Regev A, Amit I, Hacohen N. Systematic discovery of TLR signaling components delineates viral-sensing circuits. Cell 2012; 147:853-67. [PMID: 22078882 DOI: 10.1016/j.cell.2011.10.022] [Citation(s) in RCA: 151] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2011] [Revised: 04/27/2011] [Accepted: 10/17/2011] [Indexed: 12/30/2022]
Abstract
Deciphering the signaling networks that underlie normal and disease processes remains a major challenge. Here, we report the discovery of signaling components involved in the Toll-like receptor (TLR) response of immune dendritic cells (DCs), including a previously unkown pathway shared across mammalian antiviral responses. By combining transcriptional profiling, genetic and small-molecule perturbations, and phosphoproteomics, we uncover 35 signaling regulators, including 16 known regulators, involved in TLR signaling. In particular, we find that Polo-like kinases (Plk) 2 and 4 are essential components of antiviral pathways in vitro and in vivo and activate a signaling branch involving a dozen proteins, among which is Tnfaip2, a gene associated with autoimmune diseases but whose role was unknown. Our study illustrates the power of combining systematic measurements and perturbations to elucidate complex signaling circuits and discover potential therapeutic targets.
Collapse
Affiliation(s)
- Nicolas Chevrier
- Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02142, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
29
|
Meliopoulos VA, Andersen LE, Birrer KF, Simpson KJ, Lowenthal JW, Bean AGD, Stambas J, Stewart CR, Tompkins SM, van Beusechem VW, Fraser I, Mhlanga M, Barichievy S, Smith Q, Leake D, Karpilow J, Buck A, Jona G, Tripp RA. Host gene targets for novel influenza therapies elucidated by high-throughput RNA interference screens. FASEB J 2012; 26:1372-86. [PMID: 22247330 PMCID: PMC3316894 DOI: 10.1096/fj.11-193466] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Influenza virus encodes only 11 viral proteins but replicates in a broad range of avian and mammalian species by exploiting host cell functions. Genome-wide RNA interference (RNAi) has proven to be a powerful tool for identifying the host molecules that participate in each step of virus replication. Meta-analysis of findings from genome-wide RNAi screens has shown influenza virus to be dependent on functional nodes in host cell pathways, requiring a wide variety of molecules and cellular proteins for replication. Because rapid evolution of the influenza A viruses persistently complicates the effectiveness of vaccines and therapeutics, a further understanding of the complex host cell pathways coopted by influenza virus for replication may provide new targets and strategies for antiviral therapy. RNAi genome screening technologies together with bioinformatics can provide the ability to rapidly identify specific host factors involved in resistance and susceptibility to influenza virus, allowing for novel disease intervention strategies.
Collapse
Affiliation(s)
- Victoria A Meliopoulos
- Department of Infectious Diseases, University of Georgia, 111 Carlton St., Athens, GA 30602, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
30
|
Raju R, Nanjappa V, Balakrishnan L, Radhakrishnan A, Thomas JK, Sharma J, Tian M, Palapetta SM, Subbannayya T, Sekhar NR, Muthusamy B, Goel R, Subbannayya Y, Telikicherla D, Bhattacharjee M, Pinto SM, Syed N, Srikanth MS, Sathe GJ, Ahmad S, Chavan SN, Kumar GSS, Marimuthu A, Prasad TSK, Harsha HC, Rahiman BA, Ohara O, Bader GD, Sujatha Mohan S, Schiemann WP, Pandey A. NetSlim: high-confidence curated signaling maps. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2011; 2011:bar032. [PMID: 21959865 PMCID: PMC3263596 DOI: 10.1093/database/bar032] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
We previously developed NetPath as a resource for comprehensive manually curated signal transduction pathways. The pathways in NetPath contain a large number of molecules and reactions which can sometimes be difficult to visualize or interpret given their complexity. To overcome this potential limitation, we have developed a set of more stringent curation and inclusion criteria for pathway reactions to generate high-confidence signaling maps. NetSlim is a new resource that contains this ‘core’ subset of reactions for each pathway for easy visualization and manipulation. The pathways in NetSlim are freely available at http://www.netpath.org/netslim. Database URL:www.netpath.org/netslim
Collapse
Affiliation(s)
- Rajesh Raju
- Institute of Bioinformatics, International Tech Park, Bangalore, India
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
31
|
Wojcechowskyj JA, Lee JY, Seeholzer SH, Doms RW. Quantitative phosphoproteomics of CXCL12 (SDF-1) signaling. PLoS One 2011; 6:e24918. [PMID: 21949786 PMCID: PMC3176801 DOI: 10.1371/journal.pone.0024918] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2011] [Accepted: 08/19/2011] [Indexed: 11/18/2022] Open
Abstract
CXCL12 (SDF-1) is a chemokine that binds to and signals through the seven transmembrane receptor CXCR4. The CXCL12/CXCR4 signaling axis has been implicated in both cancer metastases and human immunodeficiency virus type 1 (HIV-1) infection and a more complete understanding of CXCL12/CXCR4 signaling pathways may support efforts to develop therapeutics for these diseases. Mass spectrometry-based phosphoproteomics has emerged as an important tool in studying signaling networks in an unbiased fashion. We employed stable isotope labeling with amino acids in cell culture (SILAC) quantitative phosphoproteomics to examine the CXCL12/CXCR4 signaling axis in the human lymphoblastic CEM cell line. We quantified 4,074 unique SILAC pairs from 1,673 proteins and 89 phosphopeptides were deemed CXCL12-responsive in biological replicates. Several well established CXCL12-responsive phosphosites such as AKT (pS473) and ERK2 (pY204) were confirmed in our study. We also validated two novel CXCL12-responsive phosphosites, stathmin (pS16) and AKT1S1 (pT246) by Western blot. Pathway analysis and comparisons with other phosphoproteomic datasets revealed that genes from CXCL12-responsive phosphosites are enriched for cellular pathways such as T cell activation, epidermal growth factor and mammalian target of rapamycin (mTOR) signaling, pathways which have previously been linked to CXCL12/CXCR4 signaling. Several of the novel CXCL12-responsive phosphoproteins from our study have also been implicated with cellular migration and HIV-1 infection, thus providing an attractive list of potential targets for the development of cancer metastasis and HIV-1 therapeutics and for furthering our understanding of chemokine signaling regulation by reversible phosphorylation.
Collapse
Affiliation(s)
- Jason A. Wojcechowskyj
- Department of Microbiology, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Jessica Y. Lee
- Protein and Proteomics Core, Children's Hospital of Philadelphia Research Institute, Philadelphia, Pennsylvania, United States of America
| | - Steven H. Seeholzer
- Protein and Proteomics Core, Children's Hospital of Philadelphia Research Institute, Philadelphia, Pennsylvania, United States of America
| | - Robert W. Doms
- Department of Microbiology, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, United States of America
- * E-mail:
| |
Collapse
|
32
|
Li S, Zhang B, Zhang N. Network target for screening synergistic drug combinations with application to traditional Chinese medicine. BMC SYSTEMS BIOLOGY 2011; 5 Suppl 1:S10. [PMID: 21689469 PMCID: PMC3121110 DOI: 10.1186/1752-0509-5-s1-s10] [Citation(s) in RCA: 246] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
BACKGROUND Multicomponent therapeutics offer bright prospects for the control of complex diseases in a synergistic manner. However, finding ways to screen the synergistic combinations from numerous pharmacological agents is still an ongoing challenge. RESULTS In this work, we proposed for the first time a "network target"-based paradigm instead of the traditional "single target"-based paradigm for virtual screening and established an algorithm termed NIMS (Network target-based Identification of Multicomponent Synergy) to prioritize synergistic agent combinations in a high throughput way. NIMS treats a disease-specific biological network as a therapeutic target and assumes that the relationship among agents can be transferred to network interactions among the molecular level entities (targets or responsive gene products) of agents. Then, two parameters in NIMS, Topology Score and Agent Score, are created to evaluate the synergistic relationship between each given agent combinations. Taking the empirical multicomponent system traditional Chinese medicine (TCM) as an illustrative case, we applied NIMS to prioritize synergistic agent pairs from 63 agents on a pathological process instanced by angiogenesis. The NIMS outputs can not only recover five known synergistic agent pairs, but also obtain experimental verification for synergistic candidates combined with, for example, a herbal ingredient Sinomenine, which outperforms the meet/min method. The robustness of NIMS was also showed regarding the background networks, agent genes and topological parameters, respectively. Finally, we characterized the potential mechanisms of multicomponent synergy from a network target perspective. CONCLUSIONS NIMS is a first-step computational approach towards identification of synergistic drug combinations at the molecular level. The network target-based approaches may adjust current virtual screen mode and provide a systematic paradigm for facilitating the development of multicomponent therapeutics as well as the modernization of TCM.
Collapse
Affiliation(s)
- Shao Li
- MOE Key Laboratory of Bioinformatics and Bioinformatics Division, TNLIST / Department of Automation, Tsinghua University, Beijing 100084, China
| | - Bo Zhang
- MOE Key Laboratory of Bioinformatics and Bioinformatics Division, TNLIST / Department of Automation, Tsinghua University, Beijing 100084, China
| | - Ningbo Zhang
- MOE Key Laboratory of Bioinformatics and Bioinformatics Division, TNLIST / Department of Automation, Tsinghua University, Beijing 100084, China
| |
Collapse
|
33
|
Germain RN, Meier-Schellersheim M, Nita-Lazar A, Fraser IDC. Systems biology in immunology: a computational modeling perspective. Annu Rev Immunol 2011; 29:527-85. [PMID: 21219182 DOI: 10.1146/annurev-immunol-030409-101317] [Citation(s) in RCA: 139] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Systems biology is an emerging discipline that combines high-content, multiplexed measurements with informatic and computational modeling methods to better understand biological function at various scales. Here we present a detailed review of the methods used to create computational models and to conduct simulations of immune function. We provide descriptions of the key data-gathering techniques employed to generate the quantitative and qualitative data required for such modeling and simulation and summarize the progress to date in applying these tools and techniques to questions of immunological interest, including infectious disease. We include comments on what insights modeling can provide that complement information obtained from the more familiar experimental discovery methods used by most investigators and the reasons why quantitative methods are needed to eventually produce a better understanding of immune system operation in health and disease.
Collapse
Affiliation(s)
- Ronald N Germain
- Program in Systems Immunology and Infectious Disease Modeling, National Institute of Allergy and Infectious Disease, Laboratory of Immunology, National Institutes of Health, Bethesda, Maryland 20892, USA.
| | | | | | | |
Collapse
|
34
|
Bendall SC, Simonds EF, Qiu P, Amir EAD, Krutzik PO, Finck R, Bruggner RV, Melamed R, Trejo A, Ornatsky OI, Balderas RS, Plevritis SK, Sachs K, Pe'er D, Tanner SD, Nolan GP. Single-cell mass cytometry of differential immune and drug responses across a human hematopoietic continuum. Science 2011; 332:687-96. [PMID: 21551058 DOI: 10.1126/science.1198704] [Citation(s) in RCA: 1697] [Impact Index Per Article: 130.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Flow cytometry is an essential tool for dissecting the functional complexity of hematopoiesis. We used single-cell "mass cytometry" to examine healthy human bone marrow, measuring 34 parameters simultaneously in single cells (binding of 31 antibodies, viability, DNA content, and relative cell size). The signaling behavior of cell subsets spanning a defined hematopoietic hierarchy was monitored with 18 simultaneous markers of functional signaling states perturbed by a set of ex vivo stimuli and inhibitors. The data set allowed for an algorithmically driven assembly of related cell types defined by surface antigen expression, providing a superimposable map of cell signaling responses in combination with drug inhibition. Visualized in this manner, the analysis revealed previously unappreciated instances of both precise signaling responses that were bounded within conventionally defined cell subsets and more continuous phosphorylation responses that crossed cell population boundaries in unexpected manners yet tracked closely with cellular phenotype. Collectively, such single-cell analyses provide system-wide views of immune signaling in healthy human hematopoiesis, against which drug action and disease can be compared for mechanistic studies and pharmacologic intervention.
Collapse
Affiliation(s)
- Sean C Bendall
- Baxter Laboratory in Stem Cell Biology, Department of Microbiology and Immunology, Stanford University, Stanford, CA 94305, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
35
|
Clancy T, Pedicini M, Castiglione F, Santoni D, Nygaard V, Lavelle TJ, Benson M, Hovig E. Immunological network signatures of cancer progression and survival. BMC Med Genomics 2011; 4:28. [PMID: 21453479 PMCID: PMC3094196 DOI: 10.1186/1755-8794-4-28] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2010] [Accepted: 03/31/2011] [Indexed: 12/13/2022] Open
Abstract
Background The immune contribution to cancer progression is complex and difficult to characterize. For example in tumors, immune gene expression is detected from the combination of normal, tumor and immune cells in the tumor microenvironment. Profiling the immune component of tumors may facilitate the characterization of the poorly understood roles immunity plays in cancer progression. However, the current approaches to analyze the immune component of a tumor rely on incomplete identification of immune factors. Methods To facilitate a more comprehensive approach, we created a ranked immunological relevance score for all human genes, developed using a novel strategy that combines text mining and information theory. We used this score to assign an immunological grade to gene expression profiles, and thereby quantify the immunological component of tumors. This immunological relevance score was benchmarked against existing manually curated immune resources as well as high-throughput studies. To further characterize immunological relevance for genes, the relevance score was charted against both the human interactome and cancer information, forming an expanded interactome landscape of tumor immunity. We applied this approach to expression profiles in melanomas, thus identifying and grading their immunological components, followed by identification of their associated protein interactions. Results The power of this strategy was demonstrated by the observation of early activation of the adaptive immune response and the diversity of the immune component during melanoma progression. Furthermore, the genome-wide immunological relevance score classified melanoma patient groups, whose immunological grade correlated with clinical features, such as immune phenotypes and survival. Conclusions The assignment of a ranked immunological relevance score to all human genes extends the content of existing immune gene resources and enriches our understanding of immune involvement in complex biological networks. The application of this approach to tumor immunity represents an automated systems strategy that quantifies the immunological component in complex disease. In so doing, it stratifies patients according to their immune profiles, which may lead to effective computational prognostic and clinical guides.
Collapse
Affiliation(s)
- Trevor Clancy
- Department of Tumor Biology, Institute for Cancer Research, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway.
| | | | | | | | | | | | | | | |
Collapse
|
36
|
Drosophila Ras/MAPK signalling regulates innate immune responses in immune and intestinal stem cells. EMBO J 2011; 30:1123-36. [PMID: 21297578 DOI: 10.1038/emboj.2011.4] [Citation(s) in RCA: 94] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2010] [Accepted: 12/22/2010] [Indexed: 11/08/2022] Open
Abstract
Immune signalling pathways need to be tightly regulated as overactivation of these pathways can result in chronic inflammatory diseases and cancer. NF-κB signalling and associated innate immune pathways are crucial in the first line of defense against infection in all animals. In a genome-wide RNAi screen for modulators of Drosophila immune deficiency (IMD)/NF-κB signalling, we identified components of the Ras/MAPK pathway as essential for suppression of IMD pathway activity, even in the absence of an immune challenge. Downregulation of Ras/MAPK activity mimics the induction of innate immune responses by microbial patterns. Conversely, ectopic Ras/MAPK pathway activation results in the suppression of Drosophila IMD/NF-κB signalling. Mechanistically, we show that the Ras/MAPK pathway acts by inducing transcription of the IMD pathway inhibitor Pirk/Rudra/PIMS. Finally, in vivo experiments demonstrate a requirement for Ras/MAPK signalling in restricting innate immune responses in haemocytes, fat body and adult intestinal stem cells. Our observations provide an example of a pathway that promotes cell proliferation and has simultaneously been utilized to limit the immune response.
Collapse
|
37
|
Activation or tolerance of natural killer cells is modulated by ligand quality in a nonmonotonic manner. Biophys J 2011; 99:2028-37. [PMID: 20923636 DOI: 10.1016/j.bpj.2010.07.061] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2009] [Revised: 07/19/2010] [Accepted: 07/22/2010] [Indexed: 11/21/2022] Open
Abstract
Natural killer (NK) cells extend important immune resistance in vertebrates by lysing infected and tumor cells. A fine balance between opposing signals generated by a diverse set of stimulatory and inhibitory NK-cell receptors determines the fate of target cells interacting with the NK cells. We have developed a mathematical model involving membrane proximal initial signaling events that provides novel mechanistic insights into how activation of NK cells is modulated by the half-life of receptor-ligand interaction and ligand concentrations. We show that strong stimulatory ligands produce digital activation, whereas weaker stimulatory ligands can mediate inhibition by strengthening the signals generated by inhibitory ligands, as indicated in experiments in knockout mice. We find under certain conditions, counterintuitively, inhibitory receptors can help mediate activation instead of inhibition. Mechanistic insights gained from NK-cell signaling can facilitate understanding of complex signaling responses that occur due to cross talk between dueling signaling pathways in other cell types.
Collapse
|
38
|
|
39
|
Navratil V, de Chassey B, Meyniel L, Pradezynski F, André P, Rabourdin-Combe C, Lotteau V. System-level comparison of protein-protein interactions between viruses and the human type I interferon system network. J Proteome Res 2010; 9:3527-36. [PMID: 20459142 DOI: 10.1021/pr100326j] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Innate immunity has evolved complex molecular pathways to protect organisms from viral infections. One pivotal line of cellular defense is the induction of the antiviral effect of interferon. To circumvent this primary response and achieve their own replication, viruses have developed complex molecular strategies. Here, we provide a systems-level study of the human type I interferon system subversion by the viral proteome, by reconstructing the underlying protein-protein interaction network. At this network level, viruses establish a massive and a gradual attack, from receptors to transcription factors, by interacting preferentially with highly connected and central proteins as well as interferon-induced proteins. We also demonstrate that viruses significantly target 22% of the proteins directly interacting with the type I interferon system network, suggesting the relevance of our network-based method to identify new candidates involved in the regulation of the antiviral response. Finally, based on the comparative analysis of interactome profiles across four viral families, we provide evidence of common and differential targeting strategies.
Collapse
Affiliation(s)
- V Navratil
- Université de Lyon, France, INSERM, U851, 21 Avenue Tony Garnier, Lyon, F-69007, France.
| | | | | | | | | | | | | |
Collapse
|
40
|
Schirbel A, Fiocchi C. Inflammatory bowel disease: Established and evolving considerations on its etiopathogenesis and therapy. J Dig Dis 2010; 11:266-76. [PMID: 20883422 DOI: 10.1111/j.1751-2980.2010.00449.x] [Citation(s) in RCA: 84] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Modern studies of inflammatory bowel disease (IBD) pathogenesis have been pursued for about four decades, a period of time where the pace of progress has been steadily increasing. This progress has occurred in parallel with and is largely due to developments in multiple basic scientific disciplines that range from population and social studies, genetics, microbiology, immunology, biochemistry, cellular and molecular biology, and DNA engineering. From this cumulative and constantly expanding knowledge base the fundamental pillars of IBD pathogenesis appear to have been identified and consolidated during the last couple of decades. Presently there is a general consensus among basic IBD investigators that both Crohn's disease (CD) and ulcerative colitis (UC) are the result of the combined effects of four basic components: global changes in the environment, the input of multiple genetic variations, alterations in the intestinal microbiota, and aberrations of innate and adaptive immune responses. There is also agreement on the conclusion that none of these four components can by itself trigger or maintain intestinal inflammation. A combination of various factors, and most likely of all four factors, is probably needed to bring about CD or UC in individual patients, but each patient or set of patients seems to have a different combination of alterations leading to the disease. This would imply that different causes and diverse mechanisms underlie IBD, and this could also explain why every patient displays his or her own clinical manifestations and a personalized response to therapy, and requires tailored approaches with different medications. While we are becoming increasingly aware of the importance of this individual variability, we have only a superficial notion of the reasons why this occurs, as hinted by the uniqueness of the genetic background and of the gut flora in each person. So, we are apparently facing the paradox of having to deal with the tremendous complexity of the mechanisms responsible for chronic intestinal inflammation in the setting of each patient's individuality in the response to this biological complexity. This obviously poses considerable challenges to reaching a full understanding of IBD pathogenesis, but being aware of the difficulties is the first step in finding answers to them.
Collapse
Affiliation(s)
- Anja Schirbel
- Department of Hepatology and Gastroenterology, Charité- Universitätsmedizin, Berlin, Germany
| | | |
Collapse
|
41
|
Benhamou M, Blank U. Stimulus-secretion coupling by high-affinity IgE receptor: new developments. FEBS Lett 2010; 584:4941-8. [PMID: 20851120 DOI: 10.1016/j.febslet.2010.09.023] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2010] [Revised: 08/20/2010] [Accepted: 09/13/2010] [Indexed: 12/20/2022]
Abstract
Stimulation of mast cells through their high affinity IgE receptor (FcεRI) leads to the secretion of pre- and neoformed soluble mediators through vesicular carriers. This process is highly regulated in order to adapt the secretion of these potentially dangerous factors to the physiological needs. This regulation requires numerous essential effectors that are necessary to transmit the initial signal of FcεRI aggregation and couple it to the sophisticated secretory machinery of membrane fusion. Studies in recent years have led to the discovery of a series of new effector molecules that link FcεRI to secretion. We describe here some of the new developments that have allowed to obtain a clearer picture of stimulus/secretion coupling in mast cells.
Collapse
|
42
|
Rosen DB, Putta S, Covey T, Huang YW, Nolan GP, Cesano A, Minden MD, Fantl WJ. Distinct patterns of DNA damage response and apoptosis correlate with Jak/Stat and PI3kinase response profiles in human acute myelogenous leukemia. PLoS One 2010; 5:e12405. [PMID: 20811632 PMCID: PMC2928279 DOI: 10.1371/journal.pone.0012405] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2010] [Accepted: 07/26/2010] [Indexed: 12/27/2022] Open
Abstract
Background Single cell network profiling (SCNP) utilizing flow cytometry measures alterations in intracellular signaling responses. Here SCNP was used to characterize Acute Myeloid Leukemia (AML) disease subtypes based on survival, DNA damage response and apoptosis pathways. Methodology and Principal Findings Thirty four diagnostic non-M3 AML samples from patients with known clinical outcome were treated with a panel of myeloid growth factors and cytokines, as well as with apoptosis-inducing agents. Analysis of induced Jak/Stat and PI3K pathway responses in blasts from individual patient samples identified subgroups with distinct signaling profiles that were not seen in the absence of a modulator. In vitro exposure of patient samples to etoposide, a DNA damaging agent, revealed three distinct “DNA damage response (DDR)/apoptosis” profiles: 1) AML blasts with a defective DDR and failure to undergo apoptosis; 2) AML blasts with proficient DDR and failure to undergo apoptosis; 3) AML blasts with proficiency in both DDR and apoptosis pathways. Notably, AML samples from clinical responders fell within the “DDR/apoptosis” proficient profile and, as well, had low PI3K and Jak/Stat signaling responses. In contrast, samples from clinical non responders had variable signaling profiles often with in vitro apoptotic failure and elevated PI3K pathway activity. Individual patient samples often harbored multiple, distinct, leukemia-associated cell populations identifiable by their surface marker expression, functional performance of signaling pathway in the face of cytokine or growth factor stimulation, as well as their response to apoptosis-inducing agents. Conclusions and Significance Characterizing and tracking changes in intracellular pathway profiles in cell subpopulations both at baseline and under therapeutic pressure will likely have important clinical applications, potentially informing the selection of beneficial targeted agents, used either alone or in combination with chemotherapy.
Collapse
Affiliation(s)
- David B. Rosen
- Nodality, Inc., South San Francisco, California, United States of America
| | - Santosh Putta
- Nodality, Inc., South San Francisco, California, United States of America
| | - Todd Covey
- Nodality, Inc., South San Francisco, California, United States of America
| | - Ying-Wen Huang
- Nodality, Inc., South San Francisco, California, United States of America
| | - Garry P. Nolan
- Baxter Laboratory for Stem Cell Biology, Department of Microbiology and Immunology, Stanford University, Stanford, California, United States of America
| | - Alessandra Cesano
- Nodality, Inc., South San Francisco, California, United States of America
| | | | - Wendy J. Fantl
- Baxter Laboratory for Stem Cell Biology, Department of Microbiology and Immunology, Stanford University, Stanford, California, United States of America
- Nodality, Inc., South San Francisco, California, United States of America
- * E-mail:
| |
Collapse
|
43
|
Pascual V, Chaussabel D, Banchereau J. A genomic approach to human autoimmune diseases. Annu Rev Immunol 2010; 28:535-71. [PMID: 20192809 DOI: 10.1146/annurev-immunol-030409-101221] [Citation(s) in RCA: 116] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The past decade has seen an explosion in the use of DNA-based microarrays. These techniques permit assessment of RNA abundance on a genome-wide scale. Medical applications emerged in the field of cancer, with studies of both solid tumors and hematological malignancies leading to the development of tests that are now used to personalize therapeutic options. Microarrays have also been used to analyze the blood transcriptome in a wide range of diseases. In human autoimmune diseases, these studies are showing potential for identifying therapeutic targets as well as biomarkers for diagnosis, assessment of disease activity, and response to treatment. More quantitative and sensitive high-throughput RNA profiling methods are starting to be available and will be necessary for transcriptome analyses to become routine tests in the clinical setting. We expect this to crystallize within the coming decade, as these methods become part of the personalized medicine armamentarium.
Collapse
Affiliation(s)
- Virginia Pascual
- Baylor Institute for Immunology Research, INSERM U, Dallas, Texas 75204, USA.
| | | | | |
Collapse
|
44
|
White RJ, Sharrocks AD. Coordinated control of the gene expression machinery. Trends Genet 2010; 26:214-20. [PMID: 20381190 DOI: 10.1016/j.tig.2010.02.004] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2010] [Revised: 02/19/2010] [Accepted: 02/19/2010] [Indexed: 01/06/2023]
Abstract
Gene expression is a multi-step process starting from transcribing DNA through to the eventual production of proteins or RNA products. It is important that this process is controlled coordinately to ensure that all steps function in a concerted manner. Signal transduction pathways orchestrate such control and bring about wholesale changes in the gene expression profiles of cells that ultimately determine their phenotype. Recent studies on the MAP kinase and mTOR signaling pathways in mammalian cells have illustrated how integrated responses to signaling pathways are achieved. This occurs at both the transcriptional level, through the coordinate regulation of RNA polymerases I-III and downstream in the coordinate regulation of transcription with RNA processing and translation.
Collapse
Affiliation(s)
- Robert J White
- Beatson Institute for Cancer Research, Garscube Estate, Switchback Road, Bearsden, Glasgow, G61 1BD, UK
| | | |
Collapse
|
45
|
Huang Y, Li S. Detection of characteristic sub pathway network for angiogenesis based on the comprehensive pathway network. BMC Bioinformatics 2010; 11 Suppl 1:S32. [PMID: 20122205 PMCID: PMC3009504 DOI: 10.1186/1471-2105-11-s1-s32] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Background Pathways in biological system often cooperate with each other to function. Changes of interactions among pathways tightly associate with alterations in the properties and functions of the cell and hence alterations in the phenotype. So, the pathway interactions and especially their changes over time corresponding to specific phenotype are critical to understanding cell functions and phenotypic plasticity. Methods With prior-defined pathways and incorporated protein-protein interaction (PPI) data, we counted PPIs between corresponding gene sets of each pair of distinct pathways to construct a comprehensive pathway network. Then we proposed a novel concept, characteristic sub pathway network (CSPN), to realize the phenotype-specific pathway interactions. By adding gene expression data regarding a given phenotype, angiogenesis, active PPIs corresponding to stimulation of interleukin-1 (IL-1) and tumor necrosis factor α (TNF-α) on human umbilical vein endothelial cells (HUVECs) respectively were derived. Two kinds of CSPN, namely the static or the dynamic CSPN, were detected by counting active PPIs. Results A comprehensive pathway network containing 37 signalling pathways as nodes and 263 pathway interactions were obtained. Two phenotype-specific CSPNs for angiogenesis, corresponding to stimulation of IL-1 and TNF-α on HUVEC respectively, were addressed. From phenotype-specific CSPNs, a static CSPN involving interactions among B cell receptor, T cell receptor, Toll-like receptor, MAPK, VEGF, and ErbB signalling pathways, and a dynamic CSPN involving interactions among TGF-β, Wnt, p53 signalling pathways and cell cycle pathway, were detected for angiogenesis on HUVEC after stimulation of IL-1 and TNF-α respectively. We inferred that, in certain case, the static CSPN maintains related basic functions of the cells, whereas the dynamic CSPN manifests the cells' plastic responses to stimulus and therefore reflects the cells' phenotypic plasticity. Conclusion The comprehensive pathway network helps us realize the cooperative behaviours among pathways. Moreover, two kinds of potential CSPNs found in this work, the static CSPN and the dynamic CSPN, are helpful to deeply understand the specific function of HUVEC and its phenotypic plasticity in regard to angiogenesis.
Collapse
Affiliation(s)
- Yezhou Huang
- MOE Key Laboratory of Bioinformatics and Bioinformatics Div, TNLIST/Department of Automation, Tsinghua University, Beijing 100084, PR China.
| | | |
Collapse
|
46
|
Davis DM. Mechanisms and functions for the duration of intercellular contacts made by lymphocytes. Nat Rev Immunol 2009; 9:543-55. [PMID: 19609264 DOI: 10.1038/nri2602] [Citation(s) in RCA: 78] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Communication across intercellular contacts is central to establishing appropriate innate and adaptive immune responses. Recent imaging of lymphocyte interactions suggests that a complex orchestration of cell-cell contact times is a key correlate to establishing appropriate immune responses. Here I review the molecular and cellular processes that influence the duration of intercellular contacts, including integrin activation and dynamic changes in membrane morphology. I discuss how these processes can be regulated, for example, by the balance of activating and inhibitory receptor signals, and how they can establish the appropriate outcome for individual cell-cell interactions.
Collapse
Affiliation(s)
- Daniel M Davis
- Division of Cell and Molecular Biology, Sir Alexander Fleming Building, Imperial College London, South Kensington, London, SW7 2AZ, UK.
| |
Collapse
|