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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| Format: | Article |
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MDPI AG
2017-11-01
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| Series: | Cancers |
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| Online Access: | https://www.mdpi.com/2072-6694/9/12/160 |
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| author | Constantinos Yeles Efstathios-Iason Vlachavas Olga Papadodima Eleftherios Pilalis Constantinos E. Vorgias Alexandros G. Georgakilas Aristotelis Chatziioannou |
| author_facet | Constantinos Yeles Efstathios-Iason Vlachavas Olga Papadodima Eleftherios Pilalis Constantinos E. Vorgias Alexandros G. Georgakilas Aristotelis Chatziioannou |
| author_sort | Constantinos Yeles |
| collection | DOAJ |
| 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 Zn2+-Cd2+, 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. |
| first_indexed | 2024-03-12T08:30:15Z |
| format | Article |
| id | doaj.art-df83f6da1f324adbbd476164138f4fd4 |
| institution | Directory Open Access Journal |
| issn | 2072-6694 |
| language | English |
| last_indexed | 2024-03-12T08:30:15Z |
| publishDate | 2017-11-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Cancers |
| spelling | doaj.art-df83f6da1f324adbbd476164138f4fd42023-09-02T17:48:33ZengMDPI AGCancers2072-66942017-11-0191216010.3390/cancers9120160cancers9120160Integrative Bioinformatic Analysis of Transcriptomic Data Identifies Conserved Molecular Pathways Underlying Ionizing Radiation-Induced Bystander Effects (RIBE)Constantinos Yeles0Efstathios-Iason Vlachavas1Olga Papadodima2Eleftherios Pilalis3Constantinos E. Vorgias4Alexandros G. Georgakilas5Aristotelis Chatziioannou6Department of Biochemistry and Molecular Biology, Faculty of Biology, National and Kapodistrian University of Athens, Zografou Campus, 15701 Athens, GreeceMetabolic Engineering and Bioinformatics Research Team, Institute of Biology Medicinal Chemistry & Biotechnology, National Hellenic Research Foundation, 11635 Athens, GreeceMetabolic Engineering and Bioinformatics Research Team, Institute of Biology Medicinal Chemistry & Biotechnology, National Hellenic Research Foundation, 11635 Athens, GreeceEnios Applications Private Limited Company, A17671 Athens, GreeceDepartment of Biochemistry and Molecular Biology, Faculty of Biology, National and Kapodistrian University of Athens, Zografou Campus, 15701 Athens, GreecePhysics Department, School of Applied Mathematical and Physical Sciences, National Technical University of Athens (NTUA), Zografou, 15780 Athens, GreeceMetabolic Engineering and Bioinformatics Research Team, Institute of Biology Medicinal Chemistry & Biotechnology, National Hellenic Research Foundation, 11635 Athens, GreeceIonizing 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 Zn2+-Cd2+, 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.https://www.mdpi.com/2072-6694/9/12/160bioinformaticsionizing radiationmicroarraysradiation-induced bystander effectstranscriptomics |
| spellingShingle | Constantinos Yeles Efstathios-Iason Vlachavas Olga Papadodima Eleftherios Pilalis Constantinos E. Vorgias Alexandros G. Georgakilas Aristotelis Chatziioannou Integrative Bioinformatic Analysis of Transcriptomic Data Identifies Conserved Molecular Pathways Underlying Ionizing Radiation-Induced Bystander Effects (RIBE) Cancers bioinformatics ionizing radiation microarrays radiation-induced bystander effects transcriptomics |
| 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 | bioinformatics ionizing radiation microarrays radiation-induced bystander effects transcriptomics |
| url | https://www.mdpi.com/2072-6694/9/12/160 |
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