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Akuwudike P, López-Riego M, Marczyk M, Kocibalova Z, Brückner F, Polańska J, Wojcik A, Lundholm L. Short- and long-term effects of radiation exposure at low dose and low dose rate in normal human VH10 fibroblasts. Front Public Health 2023; 11:1297942. [PMID: 38162630 PMCID: PMC10755029 DOI: 10.3389/fpubh.2023.1297942] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Accepted: 11/20/2023] [Indexed: 01/03/2024] Open
Abstract
Introduction Experimental studies complement epidemiological data on the biological effects of low doses and dose rates of ionizing radiation and help in determining the dose and dose rate effectiveness factor. Methods Human VH10 skin fibroblasts exposed to 25, 50, and 100 mGy of 137Cs gamma radiation at 1.6, 8, 12 mGy/h, and at a high dose rate of 23.4 Gy/h, were analyzed for radiation-induced short- and long-term effects. Two sample cohorts, i.e., discovery (n = 30) and validation (n = 12), were subjected to RNA sequencing. The pool of the results from those six experiments with shared conditions (1.6 mGy/h; 24 h), together with an earlier time point (0 h), constituted a third cohort (n = 12). Results The 100 mGy-exposed cells at all abovementioned dose rates, harvested at 0/24 h and 21 days after exposure, showed no strong gene expression changes. DMXL2, involved in the regulation of the NOTCH signaling pathway, presented a consistent upregulation among both the discovery and validation cohorts, and was validated by qPCR. Gene set enrichment analysis revealed that the NOTCH pathway was upregulated in the pooled cohort (p = 0.76, normalized enrichment score (NES) = 0.86). Apart from upregulated apical junction and downregulated DNA repair, few pathways were consistently changed across exposed cohorts. Concurringly, cell viability assays, performed 1, 3, and 6 days post irradiation, and colony forming assay, seeded just after exposure, did not reveal any statistically significant early effects on cell growth or survival patterns. Tendencies of increased viability (day 6) and reduced colony size (day 21) were observed at 12 mGy/h and 23.4 Gy/min. Furthermore, no long-term changes were observed in cell growth curves generated up to 70 days after exposure. Discussion In conclusion, low doses of gamma radiation given at low dose rates had no strong cytotoxic effects on radioresistant VH10 cells.
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Affiliation(s)
- Pamela Akuwudike
- Centre for Radiation Protection Research, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Milagrosa López-Riego
- Centre for Radiation Protection Research, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Michal Marczyk
- Department of Data Science and Engineering, Silesian University of Technology, Gliwice, Poland
- Yale Cancer Center, Yale School of Medicine, New Haven, CT, United States
| | - Zuzana Kocibalova
- Centre for Radiation Protection Research, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Fabian Brückner
- Centre for Radiation Protection Research, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Joanna Polańska
- Department of Data Science and Engineering, Silesian University of Technology, Gliwice, Poland
| | - Andrzej Wojcik
- Centre for Radiation Protection Research, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
- Institute of Biology, Jan Kochanowski University, Kielce, Poland
| | - Lovisa Lundholm
- Centre for Radiation Protection Research, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
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Putt KS, Du Y, Fu H, Zhang ZY. High-throughput screening strategies for space-based radiation countermeasure discovery. LIFE SCIENCES IN SPACE RESEARCH 2022; 35:88-104. [PMID: 36336374 DOI: 10.1016/j.lssr.2022.07.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 06/13/2022] [Accepted: 07/19/2022] [Indexed: 06/16/2023]
Abstract
As humanity begins to venture further into space, approaches to better protect astronauts from the hazards found in space need to be developed. One particular hazard of concern is the complex radiation that is ever present in deep space. Currently, it is unlikely enough spacecraft shielding could be launched that would provide adequate protection to astronauts during long-duration missions such as a journey to Mars and back. In an effort to identify other means of protection, prophylactic radioprotective drugs have been proposed as a potential means to reduce the biological damage caused by this radiation. Unfortunately, few radioprotectors have been approved by the FDA for usage and for those that have been developed, they protect normal cells/tissues from acute, high levels of radiation exposure such as that from oncology radiation treatments. To date, essentially no radioprotectors have been developed that specifically counteract the effects of chronic low-dose rate space radiation. This review highlights how high-throughput screening (HTS) methodologies could be implemented to identify such a radioprotective agent. Several potential target, pathway, and phenotypic assays are discussed along with potential challenges towards screening for radioprotectors. Utilizing HTS strategies such as the ones proposed here have the potential to identify new chemical scaffolds that can be developed into efficacious radioprotectors that are specifically designed to protect astronauts during deep space journeys. The overarching goal of this review is to elicit broader interest in applying drug discovery techniques, specifically HTS towards the identification of radiation countermeasures designed to be efficacious towards the biological insults likely to be encountered by astronauts on long duration voyages.
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Affiliation(s)
- Karson S Putt
- Institute for Drug Discovery, Purdue University, West Lafayette IN 47907 USA
| | - Yuhong Du
- Department of Pharmacology and Chemical Biology and Emory Chemical Biology Discovery Center, Emory University School of Medicine, Atlanta, GA 30322 USA
| | - Haian Fu
- Department of Pharmacology and Chemical Biology and Emory Chemical Biology Discovery Center, Emory University School of Medicine, Atlanta, GA 30322 USA
| | - Zhong-Yin Zhang
- Institute for Drug Discovery, Purdue University, West Lafayette IN 47907 USA; Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette IN 47907 USA.
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Grandt CL, Brackmann LK, Poplawski A, Schwarz H, Hummel-Bartenschlager W, Hankeln T, Kraemer C, Marini F, Zahnreich S, Schmitt I, Drees P, Mirsch J, Grabow D, Schmidberger H, Binder H, Hess M, Galetzka D, Marron M. Radiation-response in primary fibroblasts of long-term survivors of childhood cancer with and without second primary neoplasms: the KiKme study. Mol Med 2022; 28:105. [PMID: 36068491 PMCID: PMC9450413 DOI: 10.1186/s10020-022-00520-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 07/28/2022] [Indexed: 02/07/2023] Open
Abstract
Background The etiology and most risk factors for a sporadic first primary neoplasm in childhood or subsequent second primary neoplasms are still unknown. One established causal factor for therapy-associated second primary neoplasms is the exposure to ionizing radiation during radiation therapy as a mainstay of cancer treatment. Second primary neoplasms occur in 8% of all cancer survivors within 30 years after the first diagnosis in Germany, but the underlying factors for intrinsic susceptibilities have not yet been clarified. Thus, the purpose of this nested case–control study was the investigation and comparison of gene expression and affected pathways in primary fibroblasts of childhood cancer survivors with a first primary neoplasm only or with at least one subsequent second primary neoplasm, and controls without neoplasms after exposure to a low and a high dose of ionizing radiation. Methods Primary fibroblasts were obtained from skin biopsies from 52 adult donors with a first primary neoplasm in childhood (N1), 52 with at least one additional primary neoplasm (N2+), as well as 52 without cancer (N0) from the KiKme study. Cultured fibroblasts were exposed to a high [2 Gray (Gy)] and a low dose (0.05 Gy) of X-rays. Messenger ribonucleic acid was extracted 4 h after exposure and Illumina-sequenced. Differentially expressed genes (DEGs) were computed using limma for R, selected at a false discovery rate level of 0.05, and further analyzed for pathway enrichment (right-tailed Fisher’s Exact Test) and (in-) activation (z ≥|2|) using Ingenuity Pathway Analysis. Results After 0.05 Gy, least DEGs were found in N0 (n = 236), compared to N1 (n = 653) and N2+ (n = 694). The top DEGs with regard to the adjusted p-value were upregulated in fibroblasts across all donor groups (SESN1, MDM2, CDKN1A, TIGAR, BTG2, BLOC1S2, PPM1D, PHLDB3, FBXO22, AEN, TRIAP1, and POLH). Here, we observed activation of p53 Signaling in N0 and to a lesser extent in N1, but not in N2+. Only in N0, DNA (excision-) repair (involved genes: CDKN1A, PPM1D, and DDB2) was predicted to be a downstream function, while molecular networks in N2+ were associated with cancer, as well as injury and abnormalities (among others, downregulation of MSH6, CCNE2, and CHUK). After 2 Gy, the number of DEGs was similar in fibroblasts of all donor groups and genes with the highest absolute log2 fold-change were upregulated throughout (CDKN1A, TIGAR, HSPA4L, MDM2, BLOC1SD2, PPM1D, SESN1, BTG2, FBXO22, PCNA, and TRIAP1). Here, the p53 Signaling-Pathway was activated in fibroblasts of all donor groups. The Mitotic Roles of Polo Like Kinase-Pathway was inactivated in N1 and N2+. Molecular Mechanisms of Cancer were affected in fibroblasts of all donor groups. P53 was predicted to be an upstream regulator in fibroblasts of all donor groups and E2F1 in N1 and N2+. Results of the downstream analysis were senescence in N0 and N2+, transformation of cells in N0, and no significant effects in N1. Seven genes were differentially expressed in reaction to 2 Gy dependent on the donor group (LINC00601, COBLL1, SESN2, BIN3, TNFRSF10A, EEF1AKNMT, and BTG2). Conclusion Our results show dose-dependent differences in the radiation response between N1/N2+ and N0. While mechanisms against genotoxic stress were activated to the same extent after a high dose in all groups, the radiation response was impaired after a low dose in N1/N2+, suggesting an increased risk for adverse effects including carcinogenesis, particularly in N2+. Supplementary Information The online version contains supplementary material available at 10.1186/s10020-022-00520-6.
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Affiliation(s)
- Caine Lucas Grandt
- Leibniz Institute for Prevention Research and Epidemiology, BIPS, Achterstraße 30, 28359, Bremen, Germany.,Faculty of Human and Health Sciences, University of Bremen, Bremen, Germany
| | - Lara Kim Brackmann
- Leibniz Institute for Prevention Research and Epidemiology, BIPS, Achterstraße 30, 28359, Bremen, Germany
| | - Alicia Poplawski
- Institute of Medical Biostatistics, Epidemiology and Informatics (IMBEI), University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - Heike Schwarz
- Leibniz Institute for Prevention Research and Epidemiology, BIPS, Achterstraße 30, 28359, Bremen, Germany
| | | | - Thomas Hankeln
- Institute of Organismic and Molecular Evolution, Molecular Genetics and Genome Analysis, Johannes Gutenberg University Mainz, Mainz, Germany
| | - Christiane Kraemer
- Institute of Organismic and Molecular Evolution, Molecular Genetics and Genome Analysis, Johannes Gutenberg University Mainz, Mainz, Germany
| | - Federico Marini
- Institute of Medical Biostatistics, Epidemiology and Informatics (IMBEI), University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - Sebastian Zahnreich
- Department of Radiation Oncology and Radiation Therapy, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - Iris Schmitt
- Department of Radiation Oncology and Radiation Therapy, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - Philipp Drees
- Department of Orthopaedics and Traumatology, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - Johanna Mirsch
- Radiation Biology and DNA Repair, Technical University of Darmstadt, Darmstadt, Germany
| | - Desiree Grabow
- Division of Childhood Cancer Epidemiology, German Childhood Cancer Registry, Institute of Medical Biostatistics, Epidemiology and Informatics (IMBEI), University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - Heinz Schmidberger
- Department of Radiation Oncology and Radiation Therapy, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - Harald Binder
- Institute of Medical Biometry and Statistics, Faculty of Medicine and Medical Center, University of Freiburg, Freiburg, Germany
| | - Moritz Hess
- Institute of Medical Biometry and Statistics, Faculty of Medicine and Medical Center, University of Freiburg, Freiburg, Germany
| | - Danuta Galetzka
- Department of Radiation Oncology and Radiation Therapy, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - Manuela Marron
- Leibniz Institute for Prevention Research and Epidemiology, BIPS, Achterstraße 30, 28359, Bremen, Germany.
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Cioffi DL, Fontana L, Leso V, Dolce P, Vitale R, Vetrani I, Galdi A, Iavicoli I. Low dose ionizing radiation exposure and risk of thyroid functional alterations in healthcare workers. Eur J Radiol 2020; 132:109279. [DOI: 10.1016/j.ejrad.2020.109279] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Revised: 09/01/2020] [Accepted: 09/05/2020] [Indexed: 02/07/2023]
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Comparison of time and dose dependent gene expression and affected pathways in primary human fibroblasts after exposure to ionizing radiation. Mol Med 2020; 26:85. [PMID: 32907548 PMCID: PMC7488023 DOI: 10.1186/s10020-020-00203-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2020] [Accepted: 07/23/2020] [Indexed: 02/08/2023] Open
Abstract
Background Exposure to ionizing radiation induces complex stress responses in cells, which can lead to adverse health effects such as cancer. Although a variety of studies investigated gene expression and affected pathways in human fibroblasts after exposure to ionizing radiation, the understanding of underlying mechanisms and biological effects is still incomplete due to different experimental settings and small sample sizes. Therefore, this study aims to identify the time point with the highest number of differentially expressed genes and corresponding pathways in primary human fibroblasts after irradiation at two preselected time points. Methods Fibroblasts from skin biopsies of 15 cell donors were exposed to a high (2Gy) and a low (0.05Gy) dose of X-rays. RNA was extracted and sequenced 2 h and 4 h after exposure. Differentially expressed genes with an adjusted p-value < 0.05 were flagged and used for pathway analyses including prediction of upstream and downstream effects. Principal component analyses were used to examine the effect of two different sequencing runs on quality metrics and variation in expression and alignment and for explorative analysis of the radiation dose and time point of analysis. Results More genes were differentially expressed 4 h after exposure to low and high doses of radiation than after 2 h. In experiments with high dose irradiation and RNA sequencing after 4 h, inactivation of the FAT10 cancer signaling pathway and activation of gluconeogenesis I, glycolysis I, and prostanoid biosynthesis was observed taking p-value (< 0.05) and (in) activating z-score (≥2.00 or ≤ − 2.00) into account. Two hours after high dose irradiation, inactivation of small cell lung cancer signaling was observed. For low dose irradiation experiments, we did not detect any significant (p < 0.05 and z-score ≥ 2.00 or ≤ − 2.00) activated or inactivated pathways for both time points. Conclusions Compared to 2 h after irradiation, a higher number of differentially expressed genes were found 4 h after exposure to low and high dose ionizing radiation. Differences in gene expression were related to signal transduction pathways of the DNA damage response after 2 h and to metabolic pathways, that might implicate cellular senescence, after 4 h. The time point 4 h will be used to conduct further irradiation experiments in a larger sample.
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Kanakoglou DS, Michalettou TD, Vasileiou C, Gioukakis E, Maneta D, Kyriakidis KV, Georgakilas AG, Michalopoulos I. Effects of High-Dose Ionizing Radiation in Human Gene Expression: A Meta-Analysis. Int J Mol Sci 2020; 21:E1938. [PMID: 32178397 PMCID: PMC7139561 DOI: 10.3390/ijms21061938] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Revised: 03/06/2020] [Accepted: 03/09/2020] [Indexed: 12/16/2022] Open
Abstract
The use of high-dose Ionizing Radiation (IR) is currently one of the most common modalities in treatment of many types of cancer. The objective of this work was to investigate the effects of high-dose ionizing radiation on healthy human tissue, utilizing quantitative analysis of gene expression. To this end, publicly available transcriptomics datasets from human samples irradiated with a high dose of radiation and non-irradiated (control) ones were selected, and gene expression was determined using RNA-Seq data analysis. Raw data from these studies were subjected to quality control and trimming. Mapping of RNA-Seq reads was performed by the partial selective alignment method, and differential gene expression analysis was conducted. Subsequently, a meta-analysis was performed to select differentially expressed genes across datasets. Based on the differentially expressed genes discovered by meta-analysis, we constructed a protein-to-protein interaction network, and we identified biological pathways and processes related to high-dose IR effects. Our findings suggest that cell cycle arrest is activated, supported by our top down-regulated genes associated with cell cycle activation. DNA repair genes are down-regulated in their majority. However, several genes implicated in the nucleotide excision repair pathway are upregulated. Nevertheless, apoptotic mechanisms seem to be activated probably due to severe high-dose-induced complex DNA damage. The significant upregulation of CDKN1A, as a downstream gene of TP53, further validates programmed cell death. Finally, down-regulation of TIMELESS, signifies a correlation between IR response and circadian rhythm. Nonetheless, high-dose IR exposure effects regarding normal tissue (radiation toxicity) and its possible long-term outcomes should be studied to a greater extend.
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Affiliation(s)
- Dimitrios S. Kanakoglou
- Centre of Systems Biology, Biomedical Research Foundation, Academy of Athens, 115 27 Athens, Greece; (D.S.K.); (T.-D.M.); (C.V.); (E.G.); (D.M.); (K.V.K.)
- Section of Cell Biology and Biophysics, Department of Biology, School of Sciences, National and Kapodistrian University of Athens, 157 01 Athens, Greece
| | - Theodora-Dafni Michalettou
- Centre of Systems Biology, Biomedical Research Foundation, Academy of Athens, 115 27 Athens, Greece; (D.S.K.); (T.-D.M.); (C.V.); (E.G.); (D.M.); (K.V.K.)
- Section of Cell Biology and Biophysics, Department of Biology, School of Sciences, National and Kapodistrian University of Athens, 157 01 Athens, Greece
- DNA Damage Laboratory, Physics Department, School of Applied Mathematical and Physical Sciences, National Technical University of Athens, 157 80 Athens, Greece;
| | - Christina Vasileiou
- Centre of Systems Biology, Biomedical Research Foundation, Academy of Athens, 115 27 Athens, Greece; (D.S.K.); (T.-D.M.); (C.V.); (E.G.); (D.M.); (K.V.K.)
- DNA Damage Laboratory, Physics Department, School of Applied Mathematical and Physical Sciences, National Technical University of Athens, 157 80 Athens, Greece;
| | - Evangelos Gioukakis
- Centre of Systems Biology, Biomedical Research Foundation, Academy of Athens, 115 27 Athens, Greece; (D.S.K.); (T.-D.M.); (C.V.); (E.G.); (D.M.); (K.V.K.)
- DNA Damage Laboratory, Physics Department, School of Applied Mathematical and Physical Sciences, National Technical University of Athens, 157 80 Athens, Greece;
| | - Dorothea Maneta
- Centre of Systems Biology, Biomedical Research Foundation, Academy of Athens, 115 27 Athens, Greece; (D.S.K.); (T.-D.M.); (C.V.); (E.G.); (D.M.); (K.V.K.)
- DNA Damage Laboratory, Physics Department, School of Applied Mathematical and Physical Sciences, National Technical University of Athens, 157 80 Athens, Greece;
| | - Konstantinos V. Kyriakidis
- Centre of Systems Biology, Biomedical Research Foundation, Academy of Athens, 115 27 Athens, Greece; (D.S.K.); (T.-D.M.); (C.V.); (E.G.); (D.M.); (K.V.K.)
- Laboratory of Pharmacology, School of Pharmacy, Aristotle University of Thessaloniki, 541 24 Thessaloniki, Greece
| | - Alexandros G. Georgakilas
- DNA Damage Laboratory, Physics Department, School of Applied Mathematical and Physical Sciences, National Technical University of Athens, 157 80 Athens, Greece;
| | - Ioannis Michalopoulos
- Centre of Systems Biology, Biomedical Research Foundation, Academy of Athens, 115 27 Athens, Greece; (D.S.K.); (T.-D.M.); (C.V.); (E.G.); (D.M.); (K.V.K.)
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The Role of the Nuclear Factor κB Pathway in the Cellular Response to Low and High Linear Energy Transfer Radiation. Int J Mol Sci 2018; 19:ijms19082220. [PMID: 30061500 PMCID: PMC6121395 DOI: 10.3390/ijms19082220] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2018] [Revised: 07/24/2018] [Accepted: 07/24/2018] [Indexed: 12/19/2022] Open
Abstract
Astronauts are exposed to considerable doses of space radiation during long-term space missions. As complete shielding of the highly energetic particles is impracticable, the cellular response to space-relevant radiation qualities has to be understood in order to develop countermeasures and to reduce radiation risk uncertainties. The transcription factor Nuclear Factor κB (NF-κB) plays a fundamental role in the immune response and in the pathogenesis of many diseases. We have previously shown that heavy ions with a linear energy transfer (LET) of 100–300 keV/µm have a nine times higher potential to activate NF-κB compared to low-LET X-rays. Here, chemical inhibitor studies using human embryonic kidney cells (HEK) showed that the DNA damage sensor Ataxia telangiectasia mutated (ATM) and the proteasome were essential for NF-κB activation in response to X-rays and heavy ions. NF-κB’s role in cellular radiation response was determined by stable knock-down of the NF-κB subunit RelA. Transfection of a RelA short-hairpin RNA plasmid resulted in higher sensitivity towards X-rays, but not towards heavy ions. Reverse Transcriptase real-time quantitative PCR (RT-qPCR) showed that after exposure to X-rays and heavy ions, NF-κB predominantly upregulates genes involved in intercellular communication processes. This process is strictly NF-κB dependent as the response is completely absent in RelA knock-down cells. NF-κB’s role in the cellular radiation response depends on the radiation quality.
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Grison S, Elmhiri G, Gloaguen C, Elie C, Kereselidze D, Tack K, Lestaevel P, Legendre A, Manens L, Benadjaoud MA, Lobaccaro JM, Souidi M. Low dose of uranium induces multigenerational epigenetic effects in rat kidney. Int J Radiat Biol 2018; 94:975-984. [PMID: 29962262 DOI: 10.1080/09553002.2018.1493242] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
PURPOSE A protocol of chronic exposure to low dose of uranium was established in order to distinguish the sexual differences and the developmental process that are critical windows for epigenetic effects over generations. METHODS Both male and female rats were contaminated through their drinking water with a non-toxic solution of uranyl nitrate for 9 months. The exposed generation (F0) and the following two generations (F1 and F2) were examined. Clinical monitoring, global DNA methylation profile and DNA methyltransferases (DNMTs) gene expression were analyzed in kidneys. RESULTS While the body weight of F1 males increased, a small decrease in kidney and body weight was observed in F2 males. In addition, global DNA hypermethylation profile in kidney cells was observed in F1 and F2 males. qPCR results reveal a significant increase of methyltransferase genes expression (DNMT1 and DNMT3a) for F2 females. CONCLUSIONS In the field of public health policy and to raise attention to generational effects for the risk assessment of the environmental exposures, low doses of uranium do not imply clinical effects on adult exposed rats. However, our results confirm the importance of the developmental windows' sensitivity in addition to the sexual dimorphisms of the offspring.
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Affiliation(s)
- Stéphane Grison
- a PSE-SANTE, SESANE, LRTOX , Institut de Radioprotection et de Sûreté Nucléaire , Fontenay-aux-Roses , France
| | - Ghada Elmhiri
- a PSE-SANTE, SESANE, LRTOX , Institut de Radioprotection et de Sûreté Nucléaire , Fontenay-aux-Roses , France
| | - Céline Gloaguen
- a PSE-SANTE, SESANE, LRTOX , Institut de Radioprotection et de Sûreté Nucléaire , Fontenay-aux-Roses , France
| | - Christelle Elie
- a PSE-SANTE, SESANE, LRTOX , Institut de Radioprotection et de Sûreté Nucléaire , Fontenay-aux-Roses , France
| | - Dimitri Kereselidze
- a PSE-SANTE, SESANE, LRTOX , Institut de Radioprotection et de Sûreté Nucléaire , Fontenay-aux-Roses , France
| | - Karine Tack
- a PSE-SANTE, SESANE, LRTOX , Institut de Radioprotection et de Sûreté Nucléaire , Fontenay-aux-Roses , France
| | - Philippe Lestaevel
- a PSE-SANTE, SESANE, LRTOX , Institut de Radioprotection et de Sûreté Nucléaire , Fontenay-aux-Roses , France
| | - Audrey Legendre
- a PSE-SANTE, SESANE, LRTOX , Institut de Radioprotection et de Sûreté Nucléaire , Fontenay-aux-Roses , France
| | - Line Manens
- a PSE-SANTE, SESANE, LRTOX , Institut de Radioprotection et de Sûreté Nucléaire , Fontenay-aux-Roses , France
| | - Mohamed Amine Benadjaoud
- b PSE-SANTE, SERAMED , Institut de Radioprotection et de Sûreté Nucléaire , Fontenay-aux-Roses , France
| | - Jean-Marc Lobaccaro
- c GReD, UMR CNRS 6293-INSERM U1103 , Université Clermont Auvergne , Aubière , France
| | - Maâmar Souidi
- a PSE-SANTE, SESANE, LRTOX , Institut de Radioprotection et de Sûreté Nucléaire , Fontenay-aux-Roses , France
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Yim JH, Yun JM, Kim JY, Lee IK, Nam SY, Kim CS. Phosphoprotein profiles of candidate markers for early cellular responses to low-dose γ-radiation in normal human fibroblast cells. JOURNAL OF RADIATION RESEARCH 2017; 58:329-340. [PMID: 28122968 PMCID: PMC5440887 DOI: 10.1093/jrr/rrw126] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Revised: 08/24/2016] [Accepted: 12/09/2016] [Indexed: 05/24/2023]
Abstract
Ionizing radiation causes biological damage that leads to severe health effects. However, the effects and subsequent health implications caused by exposure to low-dose radiation are unclear. The objective of this study was to determine phosphoprotein profiles in normal human fibroblast cell lines in response to low-dose and high-dose γ-radiation. We examined the cellular response in MRC-5 cells 0.5 h after exposure to 0.05 or 2 Gy. Using 1318 antibodies by antibody array, we observed ≥1.3-fold increases in a number of identified phosphoproteins in cells subjected to low-dose (0.05 Gy) and high-dose (2 Gy) radiation, suggesting that both radiation levels stimulate distinct signaling pathways. Low-dose radiation induced nucleic acid-binding transcription factor activity, developmental processes, and multicellular organismal processes. By contrast, high-dose radiation stimulated apoptotic processes, cell adhesion and regulation, and cellular organization and biogenesis. We found that phospho-BTK (Tyr550) and phospho-Gab2 (Tyr643) protein levels at 0.5 h after treatment were higher in cells subjected to low-dose radiation than in cells treated with high-dose radiation. We also determined that the phosphorylation of BTK and Gab2 in response to ionizing radiation was regulated in a dose-dependent manner in MRC-5 and NHDF cells. Our study provides new insights into the biological responses to low-dose γ-radiation and identifies potential candidate markers for monitoring exposure to low-dose ionizing radiation.
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Affiliation(s)
- Ji-Hye Yim
- Radiation Health Institute, Korea Hydro & Nuclear Power Co. Ltd, Seongnam-si, Gyeonggi-do, 13605, Korea
| | - Jung Mi Yun
- Radiation Health Institute, Korea Hydro & Nuclear Power Co. Ltd, Seongnam-si, Gyeonggi-do, 13605, Korea
| | - Ji Young Kim
- Radiation Health Institute, Korea Hydro & Nuclear Power Co. Ltd, Seongnam-si, Gyeonggi-do, 13605, Korea
| | - In Kyung Lee
- Radiation Health Institute, Korea Hydro & Nuclear Power Co. Ltd, Seongnam-si, Gyeonggi-do, 13605, Korea
| | - Seon Young Nam
- Radiation Health Institute, Korea Hydro & Nuclear Power Co. Ltd, Seongnam-si, Gyeonggi-do, 13605, Korea
| | - Cha Soon Kim
- Radiation Health Institute, Korea Hydro & Nuclear Power Co. Ltd, Seongnam-si, Gyeonggi-do, 13605, Korea
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Lee J, Kim HJ, Yi JY. A secretome analysis reveals that PPARα is upregulated by fractionated-dose γ-irradiation in three-dimensional keratinocyte cultures. Biochem Biophys Res Commun 2017; 482:270-276. [PMID: 27845041 DOI: 10.1016/j.bbrc.2016.11.053] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Accepted: 11/10/2016] [Indexed: 10/20/2022]
Abstract
Studies have shown that γ-irradiation induces various biological responses, including oxidative stress and apoptosis, as well as cellular repair and immune system responses. However, most such studies have been performed using traditional two-dimensional cell culture systems, which are limited in their ability to faithfully represent in vivo conditions. A three-dimensional (3D) environment composed of properly interconnected and differentiated cells that allow communication and cooperation among cells via secreted molecules would be expected to more accurately reflect cellular responses. Here, we investigated γ-irradiation-induced changes in the secretome of 3D-cultured keratinocytes. An analysis of keratinocyte secretome profiles following fractionated-dose γ-irradiation revealed changes in genes involved in cell adhesion, angiogenesis, and the immune system. Notably, peroxisome proliferator-activated receptor-α (PPARα) was upregulated in response to fractionated-dose γ-irradiation. This upregulation was associated with an increase in the transcription of known PPARα target genes in secretome, including angiopoietin-like protein 4, dermokine and kallikrein-related peptide 12, which were differentially regulated by fractionated-dose γ-irradiation. Collectively, our data imply a mechanism linking γ-irradiation and secretome changes, and suggest that these changes could play a significant role in the coordinated cellular responses to harmful ionizing radiation, such as those associated with radiation therapy. This extension of our understanding of γ-irradiation-induced secretome changes has the potential to improve radiation therapy strategies.
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Affiliation(s)
- Jeeyong Lee
- Division of Basic Radiation Bioscience, Korea Institute of Radiological and Medical Sciences, Seoul, Republic of Korea
| | - Hyun-Ji Kim
- Division of Basic Radiation Bioscience, Korea Institute of Radiological and Medical Sciences, Seoul, Republic of Korea
| | - Jae Youn Yi
- Division of Basic Radiation Bioscience, Korea Institute of Radiological and Medical Sciences, Seoul, Republic of Korea.
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11
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Menon SS, Uppal M, Randhawa S, Cheema MS, Aghdam N, Usala RL, Ghosh SP, Cheema AK, Dritschilo A. Radiation Metabolomics: Current Status and Future Directions. Front Oncol 2016; 6:20. [PMID: 26870697 PMCID: PMC4736121 DOI: 10.3389/fonc.2016.00020] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2015] [Accepted: 01/18/2016] [Indexed: 12/25/2022] Open
Abstract
Human exposure to ionizing radiation (IR) disrupts normal metabolic processes in cells and organs by inducing complex biological responses that interfere with gene and protein expression. Conventional dosimetry, monitoring of prodromal symptoms, and peripheral lymphocyte counts are of limited value as organ- and tissue-specific biomarkers for personnel exposed to radiation, particularly, weeks or months after exposure. Analysis of metabolites generated in known stress-responsive pathways by molecular profiling helps to predict the physiological status of an individual in response to environmental or genetic perturbations. Thus, a multi-metabolite profile obtained from a high-resolution mass spectrometry-based metabolomics platform offers potential for identification of robust biomarkers to predict radiation toxicity of organs and tissues resulting from exposures to therapeutic or non-therapeutic IR. Here, we review the status of radiation metabolomics and explore applications as a standalone technology, as well as its integration in systems biology, to facilitate a better understanding of the molecular basis of radiation response. Finally, we draw attention to the identification of specific pathways that can be targeted for the development of therapeutics to alleviate or mitigate harmful effects of radiation exposure.
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Affiliation(s)
- Smrithi S Menon
- Department of Oncology, Georgetown University Medical Center , Washington, DC , USA
| | - Medha Uppal
- Department of Oncology, Georgetown University Medical Center , Washington, DC , USA
| | - Subeena Randhawa
- Department of Oncology, Georgetown University Medical Center , Washington, DC , USA
| | - Mehar S Cheema
- Department of Radiation Medicine, Georgetown University Medical Center , Washington, DC , USA
| | - Nima Aghdam
- Lombardi Comprehensive Cancer Center, Georgetown University Medical Center , Washington, DC , USA
| | - Rachel L Usala
- School of Medicine, Georgetown University Medical Center , Washington, DC , USA
| | - Sanchita P Ghosh
- Armed Forces Radiobiology Research Institute , Bethesda, MD , USA
| | - Amrita K Cheema
- Department of Oncology, Georgetown University Medical Center , Washington, DC , USA
| | - Anatoly Dritschilo
- Department of Radiation Medicine, Georgetown University Medical Center , Washington, DC , USA
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12
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Global Gene Expression Alterations as a Crucial Constituent of Human Cell Response to Low Doses of Ionizing Radiation Exposure. Int J Mol Sci 2015; 17:ijms17010055. [PMID: 26729107 PMCID: PMC4730300 DOI: 10.3390/ijms17010055] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2015] [Revised: 12/21/2015] [Accepted: 12/28/2015] [Indexed: 12/19/2022] Open
Abstract
Exposure to ionizing radiation (IR) is inevitable to humans in real-life scenarios; the hazards of IR primarily stem from its mutagenic, carcinogenic, and cell killing ability. For many decades, extensive research has been conducted on the human cell responses to IR delivered at a low dose/low dose (LD) rate. These studies have shown that the molecular-, cellular-, and tissue-level responses are different after low doses of IR (LDIR) compared to those observed after a short-term high-dose IR exposure (HDIR). With the advent of high-throughput technologies in the late 1990s, such as DNA microarrays, changes in gene expression have also been found to be ubiquitous after LDIR. Very limited subset of genes has been shown to be consistently up-regulated by LDIR, including CDKN1A. Further research on the biological effects and mechanisms induced by IR in human cells demonstrated that the molecular and cellular processes, including transcriptional alterations, activated by LDIR are often related to protective responses and, sometimes, hormesis. Following LDIR, some distinct responses were observed, these included bystander effects, and adaptive responses. Changes in gene expression, not only at the level of mRNA, but also miRNA, have been found to crucially underlie these effects having implications for radiation protection purposes.
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13
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Kim CS, Seong KM, Lee BS, Lee IK, Yang KH, Kim JY, Nam SY. Chronic low-dose γ-irradiation of Drosophila melanogaster larvae induces gene expression changes and enhances locomotive behavior. JOURNAL OF RADIATION RESEARCH 2015; 56:475-484. [PMID: 25792464 PMCID: PMC4426922 DOI: 10.1093/jrr/rru128] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/11/2014] [Revised: 12/15/2014] [Accepted: 12/27/2014] [Indexed: 06/04/2023]
Abstract
Although radiation effects have been extensively studied, the biological effects of low-dose radiation (LDR) are controversial. This study investigates LDR-induced alterations in locomotive behavior and gene expression profiles of Drosophila melanogaster. We measured locomotive behavior using larval pupation height and the rapid iterative negative geotaxis (RING) assay after exposure to 0.1 Gy γ-radiation (dose rate of 16.7 mGy/h). We also observed chronic LDR effects on development (pupation and eclosion rates) and longevity (life span). To identify chronic LDR effects on gene expression, we performed whole-genome expression analysis using gene-expression microarrays, and confirmed the results using quantitative real-time PCR. The pupation height of the LDR-treated group at the first larval instar was significantly higher (∼2-fold increase in PHI value, P < 0.05). The locomotive behavior of LDR-treated male flies (∼3 - 5 weeks of age) was significantly increased by 7.7%, 29% and 138%, respectively (P < 0.01), but pupation and eclosion rates and life spans were not significantly altered. Genome-wide expression analysis identified 344 genes that were differentially expressed in irradiated larvae compared with in control larvae. We identified several genes belonging to larval behavior functional groups such as locomotion (1.1%), oxidation reduction (8.0%), and genes involved in conventional functional groups modulated by irradiation such as defense response (4.9%), and sensory and perception (2.5%). Four candidate genes were confirmed as differentially expressed genes in irradiated larvae using qRT-PCR (>2-fold change). These data suggest that LDR stimulates locomotion-related genes, and these genes can be used as potential markers for LDR.
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Affiliation(s)
- Cha Soon Kim
- Low-dose Radiation Research Team, Radiation Health Institute, Korea Hydro and Nuclear Power Co. Ltd, Seoul 132-703, Korea
| | - Ki Moon Seong
- National Radiation Emergency Medical Center, Korea Institute of Radiological and Medical Sciences, Seoul 139-736, Korea
| | - Byung Sub Lee
- Low-dose Radiation Research Team, Radiation Health Institute, Korea Hydro and Nuclear Power Co. Ltd, Seoul 132-703, Korea
| | - In Kyung Lee
- Low-dose Radiation Research Team, Radiation Health Institute, Korea Hydro and Nuclear Power Co. Ltd, Seoul 132-703, Korea
| | - Kwang Hee Yang
- Low-dose Radiation Research Team, Radiation Health Institute, Korea Hydro and Nuclear Power Co. Ltd, Seoul 132-703, Korea
| | - Ji-Young Kim
- Low-dose Radiation Research Team, Radiation Health Institute, Korea Hydro and Nuclear Power Co. Ltd, Seoul 132-703, Korea
| | - Seon Young Nam
- Low-dose Radiation Research Team, Radiation Health Institute, Korea Hydro and Nuclear Power Co. Ltd, Seoul 132-703, Korea
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14
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Il'yasova D, Kinev A, Melton CD, Davis FG. Donor-specific cell-based assays in studying sensitivity to low-dose radiation: a population-based perspective. Front Public Health 2014; 2:244. [PMID: 25478557 PMCID: PMC4235273 DOI: 10.3389/fpubh.2014.00244] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2014] [Accepted: 11/05/2014] [Indexed: 01/19/2023] Open
Abstract
Currently, a linear no-threshold model is used to estimate health risks associated with exposure to low-dose radiation, a prevalent exposure in the general population, because the direct estimation from epidemiological studies suffers from uncertainty. This model has been criticized based on unique biology of low-dose radiation. Whether the departure from linearity is toward increased or decreased risk is intensely debated. We present an approach based on individual radiosensitivity testing and discuss how individual radiosensitivity can be assessed with the goal to develop a quantifiable measure of cellular response that can be conducted via high-throughput population testing.
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Affiliation(s)
- Dora Il'yasova
- Division of Epidemiology and Biostatistics, School of Public Health, Georgia State University , Atlanta, GA , USA
| | | | - C David Melton
- Division of Epidemiology and Biostatistics, School of Public Health, Georgia State University , Atlanta, GA , USA
| | - Faith G Davis
- School of Public Health, University of Alberta , Edmonton, AB , Canada
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15
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Differential network analyses of Alzheimer's disease identify early events in Alzheimer's disease pathology. Int J Alzheimers Dis 2014; 2014:721453. [PMID: 25147748 PMCID: PMC4132486 DOI: 10.1155/2014/721453] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2014] [Revised: 06/13/2014] [Accepted: 06/18/2014] [Indexed: 01/07/2023] Open
Abstract
In late-onset Alzheimer's disease (AD), multiple brain regions are not affected simultaneously. Comparing the gene expression of the affected regions to identify the differences in the biological processes perturbed can lead to greater insight into AD pathogenesis and early characteristics. We identified differentially expressed (DE) genes from single cell microarray data of four AD affected brain regions: entorhinal cortex (EC), hippocampus (HIP), posterior cingulate cortex (PCC), and middle temporal gyrus (MTG). We organized the DE genes in the four brain regions into region-specific gene coexpression networks. Differential neighborhood analyses in the coexpression networks were performed to identify genes with low topological overlap (TO) of their direct neighbors. The low TO genes were used to characterize the biological differences between two regions. Our analyses show that increased oxidative stress, along with alterations in lipid metabolism in neurons, may be some of the very early events occurring in AD pathology. Cellular defense mechanisms try to intervene but fail, finally resulting in AD pathology as the disease progresses. Furthermore, disease annotation of the low TO genes in two independent protein interaction networks has resulted in association between cancer, diabetes, renal diseases, and cardiovascular diseases.
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16
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El-Saghire H, Vandevoorde C, Ost P, Monsieurs P, Michaux A, De Meerleer G, Baatout S, Thierens H. Intensity modulated radiotherapy induces pro-inflammatory and pro-survival responses in prostate cancer patients. Int J Oncol 2014; 44:1073-83. [PMID: 24435511 PMCID: PMC3977809 DOI: 10.3892/ijo.2014.2260] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2013] [Accepted: 11/11/2013] [Indexed: 12/21/2022] Open
Abstract
Intensity modulated radiotherapy (IMRT) is one of the modern conformal radiotherapies that is widely used within the context of cancer patient treatment. It uses multiple radiation beams targeted to the tumor, however, large volumes of the body receive low doses of irradiation. Using γ-H2AX and global genome expression analysis, we studied the biological responses induced by low doses of ionizing radiation in prostate cancer patients following IMRT. By means of different bioinformatics analyses, we report that IMRT induced an inflammatory response via the induction of viral, adaptive, and innate immune signaling. In response to growth factors and immune-stimulatory signaling, positive regulation in the progression of cell cycle and DNA replication were induced. This denotes pro-inflammatory and pro-survival responses. Furthermore, double strand DNA breaks were induced in every patient 30 min after the treatment and remaining DNA repair and damage signaling continued after 18-24 h. Nine genes belonging to inflammatory responses (TLR3, SH2D1A and IL18), cell cycle progression (ORC4, SMC2 and CCDC99) and DNA damage and repair (RAD17, SMC6 and MRE11A) were confirmed by quantitative RT-PCR. This study emphasizes that the risk assessment of health effects from the out-of-field low doses during IMRT should be of concern, as these may increase the risk of secondary cancers and/or systemic inflammation.
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Affiliation(s)
- Houssein El-Saghire
- Radiobiology Unit, Molecular and Cellular Biology, Belgian Nuclear Research Centre (SCK·CEN), Mol, Belgium
| | | | - Piet Ost
- Department of Radiation Oncology, Ghent University Hospital, Gent, Belgium
| | - Pieter Monsieurs
- Radiobiology Unit, Molecular and Cellular Biology, Belgian Nuclear Research Centre (SCK·CEN), Mol, Belgium
| | - Arlette Michaux
- Radiobiology Unit, Molecular and Cellular Biology, Belgian Nuclear Research Centre (SCK·CEN), Mol, Belgium
| | - Gert De Meerleer
- Department of Radiation Oncology, Ghent University Hospital, Gent, Belgium
| | - Sarah Baatout
- Radiobiology Unit, Molecular and Cellular Biology, Belgian Nuclear Research Centre (SCK·CEN), Mol, Belgium
| | - Hubert Thierens
- Department of Basic Medical Sciences, Ghent University, Gent, Belgium
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17
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Prilutsky D, Palmer NP, Smedemark-Margulies N, Schlaeger TM, Margulies DM, Kohane IS. iPSC-derived neurons as a higher-throughput readout for autism: promises and pitfalls. Trends Mol Med 2013; 20:91-104. [PMID: 24374161 DOI: 10.1016/j.molmed.2013.11.004] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2013] [Revised: 11/20/2013] [Accepted: 11/21/2013] [Indexed: 12/13/2022]
Abstract
The elucidation of disease etiologies and establishment of robust, scalable, high-throughput screening assays for autism spectrum disorders (ASDs) have been impeded by both inaccessibility of disease-relevant neuronal tissue and the genetic heterogeneity of the disorder. Neuronal cells derived from induced pluripotent stem cells (iPSCs) from autism patients may circumvent these obstacles and serve as relevant cell models. To date, derived cells are characterized and screened by assessing their neuronal phenotypes. These characterizations are often etiology-specific or lack reproducibility and stability. In this review, we present an overview of efforts to study iPSC-derived neurons as a model for autism, and we explore the plausibility of gene expression profiling as a reproducible and stable disease marker.
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Affiliation(s)
- Daria Prilutsky
- Center for Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA
| | - Nathan P Palmer
- Center for Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA
| | | | | | - David M Margulies
- Center for Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA; Divisions of Genetics and Developmental Medicine, Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Isaac S Kohane
- Center for Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA.
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18
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Co-expression network analysis and genetic algorithms for gene prioritization in preeclampsia. BMC Med Genomics 2013; 6:51. [PMID: 24219996 PMCID: PMC3829810 DOI: 10.1186/1755-8794-6-51] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2013] [Accepted: 11/08/2013] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND In this study, we explored the gene prioritization in preeclampsia, combining co-expression network analysis and genetic algorithms optimization approaches. We analysed five public projects obtaining 1,146 significant genes after cross-platform and processing of 81 and 149 microarrays in preeclamptic and normal conditions, respectively. METHODS After co-expression network construction, modular and node analysis were performed using several approaches. Moreover, genetic algorithms were also applied in combination with the nearest neighbour and discriminant analysis classification methods. RESULTS Significant differences were found in the genes connectivity distribution, both in normal and preeclampsia conditions pointing to the need and importance of examining connectivity alongside expression for prioritization. We discuss the global as well as intra-modular connectivity for hubs detection and also the utility of genetic algorithms in combination with the network information. FLT1, LEP, INHA and ENG genes were identified according to the literature, however, we also found other genes as FLNB, INHBA, NDRG1 and LYN highly significant but underexplored during normal pregnancy or preeclampsia. CONCLUSIONS Weighted genes co-expression network analysis reveals a similar distribution along the modules detected both in normal and preeclampsia conditions. However, major differences were obtained by analysing the nodes connectivity. All models obtained by genetic algorithm procedures were consistent with a correct classification, higher than 90%, restricting to 30 variables in both classification methods applied.Combining the two methods we identified well known genes related to preeclampsia, but also lead us to propose new candidates poorly explored or completely unknown in the pathogenesis of preeclampsia, which may have to be validated experimentally.
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