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Integrative Bioinformatic Analysis of Transcriptomic Data Identifies Conserved Molecular Pathways Underlying Ionizing Radiation-Induced Bystander Effects (RIBE)

Ionizing radiation-induced bystander effects (RIBE) encompass a number of effects with potential for a plethora of damages in adjacent non-irradiated tissue. The cascade of molecular events is initiated in response to the exposure to ionizing radiation (IR), something that may occur during diagnosti...

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Autores principales: Yeles, Constantinos, Vlachavas, Efstathios-Iason, Papadodima, Olga, Pilalis, Eleftherios, Vorgias, Constantinos E., Georgakilas, Alexandros G., Chatziioannou, Aristotelis
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2017
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5742808/
https://www.ncbi.nlm.nih.gov/pubmed/29186820
http://dx.doi.org/10.3390/cancers9120160
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author Yeles, Constantinos
Vlachavas, Efstathios-Iason
Papadodima, Olga
Pilalis, Eleftherios
Vorgias, Constantinos E.
Georgakilas, Alexandros G.
Chatziioannou, Aristotelis
author_facet Yeles, Constantinos
Vlachavas, Efstathios-Iason
Papadodima, Olga
Pilalis, Eleftherios
Vorgias, Constantinos E.
Georgakilas, Alexandros G.
Chatziioannou, Aristotelis
author_sort Yeles, Constantinos
collection PubMed
description Ionizing radiation-induced bystander effects (RIBE) encompass a number of effects with potential for a plethora of damages in adjacent non-irradiated tissue. The cascade of molecular events is initiated in response to the exposure to ionizing radiation (IR), something that may occur during diagnostic or therapeutic medical applications. In order to better investigate these complex response mechanisms, we employed a unified framework integrating statistical microarray analysis, signal normalization, and translational bioinformatics functional analysis techniques. This approach was applied to several microarray datasets from Gene Expression Omnibus (GEO) related to RIBE. The analysis produced lists of differentially expressed genes, contrasting bystander and irradiated samples versus sham-irradiated controls. Furthermore, comparative molecular analysis through BioInfoMiner, which integrates advanced statistical enrichment and prioritization methodologies, revealed discrete biological processes, at the cellular level. For example, the negative regulation of growth, cellular response to Zn(2+)-Cd(2+), and Wnt and NIK/NF-kappaB signaling, thus refining the description of the phenotypic landscape of RIBE. Our results provide a more solid understanding of RIBE cell-specific response patterns, especially in the case of high-LET radiations, like α-particles and carbon-ions.
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spelling pubmed-57428082017-12-29 Integrative Bioinformatic Analysis of Transcriptomic Data Identifies Conserved Molecular Pathways Underlying Ionizing Radiation-Induced Bystander Effects (RIBE) Yeles, Constantinos Vlachavas, Efstathios-Iason Papadodima, Olga Pilalis, Eleftherios Vorgias, Constantinos E. Georgakilas, Alexandros G. Chatziioannou, Aristotelis Cancers (Basel) Article Ionizing radiation-induced bystander effects (RIBE) encompass a number of effects with potential for a plethora of damages in adjacent non-irradiated tissue. The cascade of molecular events is initiated in response to the exposure to ionizing radiation (IR), something that may occur during diagnostic or therapeutic medical applications. In order to better investigate these complex response mechanisms, we employed a unified framework integrating statistical microarray analysis, signal normalization, and translational bioinformatics functional analysis techniques. This approach was applied to several microarray datasets from Gene Expression Omnibus (GEO) related to RIBE. The analysis produced lists of differentially expressed genes, contrasting bystander and irradiated samples versus sham-irradiated controls. Furthermore, comparative molecular analysis through BioInfoMiner, which integrates advanced statistical enrichment and prioritization methodologies, revealed discrete biological processes, at the cellular level. For example, the negative regulation of growth, cellular response to Zn(2+)-Cd(2+), and Wnt and NIK/NF-kappaB signaling, thus refining the description of the phenotypic landscape of RIBE. Our results provide a more solid understanding of RIBE cell-specific response patterns, especially in the case of high-LET radiations, like α-particles and carbon-ions. MDPI 2017-11-25 /pmc/articles/PMC5742808/ /pubmed/29186820 http://dx.doi.org/10.3390/cancers9120160 Text en © 2017 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Yeles, Constantinos
Vlachavas, Efstathios-Iason
Papadodima, Olga
Pilalis, Eleftherios
Vorgias, Constantinos E.
Georgakilas, Alexandros G.
Chatziioannou, Aristotelis
Integrative Bioinformatic Analysis of Transcriptomic Data Identifies Conserved Molecular Pathways Underlying Ionizing Radiation-Induced Bystander Effects (RIBE)
title Integrative Bioinformatic Analysis of Transcriptomic Data Identifies Conserved Molecular Pathways Underlying Ionizing Radiation-Induced Bystander Effects (RIBE)
title_full Integrative Bioinformatic Analysis of Transcriptomic Data Identifies Conserved Molecular Pathways Underlying Ionizing Radiation-Induced Bystander Effects (RIBE)
title_fullStr Integrative Bioinformatic Analysis of Transcriptomic Data Identifies Conserved Molecular Pathways Underlying Ionizing Radiation-Induced Bystander Effects (RIBE)
title_full_unstemmed Integrative Bioinformatic Analysis of Transcriptomic Data Identifies Conserved Molecular Pathways Underlying Ionizing Radiation-Induced Bystander Effects (RIBE)
title_short Integrative Bioinformatic Analysis of Transcriptomic Data Identifies Conserved Molecular Pathways Underlying Ionizing Radiation-Induced Bystander Effects (RIBE)
title_sort integrative bioinformatic analysis of transcriptomic data identifies conserved molecular pathways underlying ionizing radiation-induced bystander effects (ribe)
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5742808/
https://www.ncbi.nlm.nih.gov/pubmed/29186820
http://dx.doi.org/10.3390/cancers9120160
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