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Yu J, Murthy V, Liu SL. Relating GPI-Anchored Ly6 Proteins uPAR and CD59 to Viral Infection. Viruses 2019; 11:E1060. [PMID: 31739586 PMCID: PMC6893729 DOI: 10.3390/v11111060] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Revised: 11/10/2019] [Accepted: 11/12/2019] [Indexed: 12/30/2022] Open
Abstract
The Ly6 (lymphocyte antigen-6)/uPAR (urokinase-type plasminogen activator receptor) superfamily protein is a group of molecules that share limited sequence homology but conserved three-fingered structures. Despite diverse cellular functions, such as in regulating host immunity, cell adhesion, and migration, the physiological roles of these factors in vivo remain poorly characterized. Notably, increasing research has focused on the interplays between Ly6/uPAR proteins and viral pathogens, the results of which have provided new insight into viral entry and virus-host interactions. While LY6E (lymphocyte antigen 6 family member E), one key member of the Ly6E/uPAR-family proteins, has been extensively studied, other members have not been well characterized. Here, we summarize current knowledge of Ly6/uPAR proteins related to viral infection, with a focus on uPAR and CD59. Our goal is to provide an up-to-date view of the Ly6/uPAR-family proteins and associated virus-host interaction and viral pathogenesis.
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Affiliation(s)
- Jingyou Yu
- Center for Retrovirus Research, The Ohio State University, Columbus, OH 43210, USA; (J.Y.); (V.M.)
- Department of Veterinary Biosciences, The Ohio State University, Columbus, OH 43210, USA
| | - Vaibhav Murthy
- Center for Retrovirus Research, The Ohio State University, Columbus, OH 43210, USA; (J.Y.); (V.M.)
- Department of Veterinary Biosciences, The Ohio State University, Columbus, OH 43210, USA
| | - Shan-Lu Liu
- Center for Retrovirus Research, The Ohio State University, Columbus, OH 43210, USA; (J.Y.); (V.M.)
- Department of Veterinary Biosciences, The Ohio State University, Columbus, OH 43210, USA
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH 43210, USA
- Viruses and Emerging Pathogens Program, Infectious Diseases Institute, The Ohio State University, Columbus, OH 43210, USA
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Schüler E, Rudqvist N, Parris TZ, Langen B, Spetz J, Helou K, Forssell-Aronsson E. Time- and dose rate-related effects of internal (177)Lu exposure on gene expression in mouse kidney tissue. Nucl Med Biol 2014; 41:825-32. [PMID: 25156037 DOI: 10.1016/j.nucmedbio.2014.07.010] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2014] [Revised: 07/10/2014] [Accepted: 07/15/2014] [Indexed: 10/25/2022]
Abstract
INTRODUCTION The kidneys are the dose-limiting organs in some radionuclide therapy regimens. However, the biological impact of internal exposure from radionuclides is still not fully understood. The aim of this study was to examine the effects of dose rate and time after i.v. injection of (177)LuCl3 on changes in transcriptional patterns in mouse kidney tissue. METHODS To investigate the effect of dose rate, female Balb/c nude mice were i.v. injected with 11, 5.6, 1.6, 0.8, 0.30, and 0 MBq of (177)LuCl3, and killed at 3, 6, 24, 48, 168, and 24 hours after injection, respectively. Furthermore, the effect of time after onset of exposure was analysed using mice injected with 0.26, 2.4, and 8.2 MBq of (177)LuCl3, and killed at 45, 90, and 140 days after injection. Global transcription patterns of irradiated kidney cortex and medulla were assessed and enriched biological processes were determined from the regulated gene sets using Gene Ontology terms. RESULTS The average dose rates investigated were 1.6, 0.84, 0.23, 0.11 and 0.028 mGy/min, with an absorbed dose of 0.3 Gy. At 45, 90 and 140 days, the absorbed doses were estimated to 0.3, 3, and 10 Gy. In general, the number of differentially regulated transcripts increased with time after injection, and decreased with absorbed dose for both kidney cortex and medulla. Differentially regulated transcripts were predominantly involved in metabolic and stress response-related processes dependent on dose rate, as well as transcripts associated with metabolic and cellular integrity at later time points. CONCLUSION The observed transcriptional response in kidney tissue was diverse due to difference in absorbed dose, dose rate and time after exposure. Nevertheless, several transcripts were significantly regulated in all groups despite differences in exposure parameters, which may indicate potential biomarkers for exposure of kidney tissue.
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Affiliation(s)
- Emil Schüler
- Department of Radiation Physics, Institute of Clinical Sciences, Sahlgrenska Cancer Center, Sahlgrenska Academy at the University of Gothenburg, Sahlgrenska University Hospital, Gothenburg, Sweden.
| | - Nils Rudqvist
- Department of Radiation Physics, Institute of Clinical Sciences, Sahlgrenska Cancer Center, Sahlgrenska Academy at the University of Gothenburg, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Toshima Z Parris
- Department of Oncology, Institute of Clinical Sciences, Sahlgrenska Cancer Center, Sahlgrenska Academy at the University of Gothenburg, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Britta Langen
- Department of Radiation Physics, Institute of Clinical Sciences, Sahlgrenska Cancer Center, Sahlgrenska Academy at the University of Gothenburg, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Johan Spetz
- Department of Radiation Physics, Institute of Clinical Sciences, Sahlgrenska Cancer Center, Sahlgrenska Academy at the University of Gothenburg, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Khalil Helou
- Department of Oncology, Institute of Clinical Sciences, Sahlgrenska Cancer Center, Sahlgrenska Academy at the University of Gothenburg, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Eva Forssell-Aronsson
- Department of Radiation Physics, Institute of Clinical Sciences, Sahlgrenska Cancer Center, Sahlgrenska Academy at the University of Gothenburg, Sahlgrenska University Hospital, Gothenburg, Sweden; Department of Medical Physics and Biomedical Engineering, Sahlgrenska University Hospital, Gothenburg, Sweden
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Reisz JA, Bansal N, Qian J, Zhao W, Furdui CM. Effects of ionizing radiation on biological molecules--mechanisms of damage and emerging methods of detection. Antioxid Redox Signal 2014; 21:260-92. [PMID: 24382094 PMCID: PMC4060780 DOI: 10.1089/ars.2013.5489] [Citation(s) in RCA: 486] [Impact Index Per Article: 44.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/19/2013] [Revised: 12/07/2013] [Accepted: 01/01/2014] [Indexed: 12/13/2022]
Abstract
SIGNIFICANCE The detrimental effects of ionizing radiation (IR) involve a highly orchestrated series of events that are amplified by endogenous signaling and culminating in oxidative damage to DNA, lipids, proteins, and many metabolites. Despite the global impact of IR, the molecular mechanisms underlying tissue damage reveal that many biomolecules are chemoselectively modified by IR. RECENT ADVANCES The development of high-throughput "omics" technologies for mapping DNA and protein modifications have revolutionized the study of IR effects on biological systems. Studies in cells, tissues, and biological fluids are used to identify molecular features or biomarkers of IR exposure and response and the molecular mechanisms that regulate their expression or synthesis. CRITICAL ISSUES In this review, chemical mechanisms are described for IR-induced modifications of biomolecules along with methods for their detection. Included with the detection methods are crucial experimental considerations and caveats for their use. Additional factors critical to the cellular response to radiation, including alterations in protein expression, metabolomics, and epigenetic factors, are also discussed. FUTURE DIRECTIONS Throughout the review, the synergy of combined "omics" technologies such as genomics and epigenomics, proteomics, and metabolomics is highlighted. These are anticipated to lead to new hypotheses to understand IR effects on biological systems and improve IR-based therapies.
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Affiliation(s)
- Julie A Reisz
- Section on Molecular Medicine, Department of Internal Medicine, Wake Forest School of Medicine , Winston-Salem, North Carolina
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Huumonen K, Korkalainen M, Boman E, Heikkilä J, Höytö A, Lahtinen T, Luukkonen J, Viluksela M, Naarala J, Juutilainen J. Dose- and time-dependent changes of micronucleus frequency and gene expression in the progeny of irradiated cells: two components in radiation-induced genomic instability? Mutat Res 2014; 765:32-39. [PMID: 24797401 DOI: 10.1016/j.mrfmmm.2014.04.010] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2013] [Revised: 04/11/2014] [Accepted: 04/12/2014] [Indexed: 06/03/2023]
Abstract
Murine embryonic C3H/10T½ fibroblasts were exposed to X-rays at doses of 0.2, 0.5, 1, 2 or 5 Gy. To follow the development of radiation-induced genomic instability (RIGI), the frequency of micronuclei was measured with flow cytometry at 2 days after exposure and in the progeny of the irradiated cells at 8 and 15 days after exposure. Gene expression was measured at the same points in time by PCR arrays profiling the expression of 84 cancer-relevant genes. The micronucleus results showed a gradual decrease in the slope of the dose-response curve between days 2 and 15. The data were consistent with a model assuming two components in RIGI. The first component is characterized by dose-dependent increase in micronuclei. It may persist more than ten cell generations depending on dose, but eventually disappears. The second component is more persistent and independent of dose above a threshold higher than 0.2 Gy. Gene expression analysis 2 days after irradiation at 5 Gy showed consistent changes in genes that typically respond to DNA damage. However, the consistency of changes decreased with time, suggesting that non-specificity and increased heterogeneity of gene expression are characteristic to the second, more persistent component of RIGI.
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Affiliation(s)
- Katriina Huumonen
- University of Eastern Finland, Department of Environmental Science, P.O. Box 1627, 70211 Kuopio, Finland
| | - Merja Korkalainen
- National Institute for Health and Welfare, Department of Environmental Health, P.O. Box 95, 70701 Kuopio, Finland
| | - Eeva Boman
- Kuopio University Hospital, Cancer Center, P.O. Box 1777, 70211 Kuopio, Finland
| | - Janne Heikkilä
- Kuopio University Hospital, Cancer Center, P.O. Box 1777, 70211 Kuopio, Finland
| | - Anne Höytö
- University of Eastern Finland, Department of Environmental Science, P.O. Box 1627, 70211 Kuopio, Finland
| | - Tapani Lahtinen
- Kuopio University Hospital, Cancer Center, P.O. Box 1777, 70211 Kuopio, Finland
| | - Jukka Luukkonen
- University of Eastern Finland, Department of Environmental Science, P.O. Box 1627, 70211 Kuopio, Finland
| | - Matti Viluksela
- National Institute for Health and Welfare, Department of Environmental Health, P.O. Box 95, 70701 Kuopio, Finland
| | - Jonne Naarala
- University of Eastern Finland, Department of Environmental Science, P.O. Box 1627, 70211 Kuopio, Finland
| | - Jukka Juutilainen
- University of Eastern Finland, Department of Environmental Science, P.O. Box 1627, 70211 Kuopio, Finland.
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Ewis AA, Zhelev Z, Bakalova R, Fukuoka S, Shinohara Y, Ishikawa M, Baba Y. A history of microarrays in biomedicine. Expert Rev Mol Diagn 2014; 5:315-28. [PMID: 15934810 DOI: 10.1586/14737159.5.3.315] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The fundamental strategy of the current postgenomic era or the era of functional genomics is to expand the scale of biologic research from studying single genes or proteins to studying all genes or proteins simultaneously using a systematic approach. As recently developed methods for obtaining genome-wide mRNA expression data, oligonucleotide and DNA microarrays are particularly powerful in the context of knowing the entire genome sequence and can provide a global view of changes in gene expression patterns in response to physiologic alterations or manipulation of transcriptional regulators. In biomedical research, such an approach will ultimately determine biologic behavior of both normal and diseased tissues, which may provide insights into disease mechanisms and identify novel markers and candidates for diagnostic, prognostic and therapeutic intervention. However, microarray technology is still in a continuous state of evolution and development, and it may take time to implement microarrays as a routine medical device. Many limitations exist and many challenges remain to be achieved to help inclusion of microarrays in clinical medicine. In this review, a brief history of microarrays in biomedical research is provided, including experimental overview, limitations, challenges and future developments.
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Affiliation(s)
- Ashraf A Ewis
- Single-Molecule Bioanalysis Laboratory, National Institute of Advanced Industrial Science & Technology (AIST), Hayashi-cho 2217-14, Takamatsu City, Kagawa Prefecture, 761-0395 Japan.
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Schüler E, Rudqvist N, Parris TZ, Langen B, Helou K, Forssell-Aronsson E. Transcriptional response of kidney tissue after 177Lu-octreotate administration in mice. Nucl Med Biol 2013; 41:238-47. [PMID: 24434014 DOI: 10.1016/j.nucmedbio.2013.12.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2013] [Revised: 10/29/2013] [Accepted: 12/03/2013] [Indexed: 10/25/2022]
Abstract
INTRODUCTION The kidneys are one of the main dose limiting organs in (177)Lu-octreotate therapy of neuroendocrine tumors. Therefore, biomarkers for radiation damage would be of great importance in this type of therapy. The purpose of this study was to investigate the absorbed dose dependency on early transcriptional changes in the kidneys from (177)Lu-octreotate exposure. METHODS Female Balb/c nude mice were i.v. injected with 1.3, 3.6, 14, 45 or 140 MBq (177)Lu-octreotate. The animals were killed 24 h after injection followed by excision of the kidneys. The absorbed dose to the kidneys ranged between 0.13 and 13 Gy. Total RNA was extracted from separated renal tissue samples, and applied to Illumina MouseRef-8 Whole-Genome Expression Beadchips to identify regulated transcripts after irradiation. Nexus Expression 2.0 and Gene Ontology terms were used for data processing and to determine affected biological processes. RESULTS Distinct transcriptional responses were observed following (177)Lu-octreotate administration. A higher number of differentially expressed transcripts were observed in the kidney medulla (480) compared to cortex (281). In addition, 39 transcripts were regulated at all absorbed dose levels in the medulla, compared to 32 in the cortex. Three biological processes in the cortex and five in the medulla were also shared by all absorbed dose levels. Strong association to metabolism was found among the affected processes in both tissues. Furthermore, an association with cellular and developmental processes was prominent in kidney medulla, while transport and immune response were prominent in kidney cortex. CONCLUSION Specific biological and dose-dependent responses were observed in both tissues. The number of affected transcripts and biological processes revealed distinct response differences between the absorbed doses delivered to the tissues.
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Affiliation(s)
- Emil Schüler
- Department of Radiation Physics, Institute of Clinical Sciences, Sahlgrenska Cancer Center, Sahlgrenska Academy at the University of Gothenburg, Sahlgrenska University Hospital, Gothenburg, Sweden.
| | - Nils Rudqvist
- Department of Radiation Physics, Institute of Clinical Sciences, Sahlgrenska Cancer Center, Sahlgrenska Academy at the University of Gothenburg, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Toshima Z Parris
- Department of Oncology, Institute of Clinical Sciences, Sahlgrenska Cancer Center, Sahlgrenska Academy at the University of Gothenburg, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Britta Langen
- Department of Radiation Physics, Institute of Clinical Sciences, Sahlgrenska Cancer Center, Sahlgrenska Academy at the University of Gothenburg, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Khalil Helou
- Department of Oncology, Institute of Clinical Sciences, Sahlgrenska Cancer Center, Sahlgrenska Academy at the University of Gothenburg, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Eva Forssell-Aronsson
- Department of Radiation Physics, Institute of Clinical Sciences, Sahlgrenska Cancer Center, Sahlgrenska Academy at the University of Gothenburg, Sahlgrenska University Hospital, Gothenburg, Sweden
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Jaafar L, Podolsky RH, Dynan WS. Long-term effects of ionizing radiation on gene expression in a zebrafish model. PLoS One 2013; 8:e69445. [PMID: 23936019 PMCID: PMC3728329 DOI: 10.1371/journal.pone.0069445] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2013] [Accepted: 06/07/2013] [Indexed: 01/31/2023] Open
Abstract
Understanding how initial radiation injury translates into long-term effects is an important problem in radiation biology. Here, we define a set of changes in the transcription profile that are associated with the long-term response to radiation exposure. The study was performed in vivo using zebrafish, an established radiobiological model organism. To study the long-term response, 24 hour post-fertilization embryos were exposed to 0.1 Gy (low dose) or 1.0 Gy (moderate dose) of whole-body gamma radiation and allowed to develop for 16 weeks. Liver mRNA profiles were then analyzed using the Affymetrix microarray platform, with validation by quantitative PCR. As a basis for comparison, 16-week old adults were exposed at the same doses and analyzed after 4 hours. Statistical analysis was performed in a way to minimize the effects of multiple comparisons. The responses to these two treatment regimes differed greatly: 360 probe sets were associated primarily with the long-term response, whereas a different 2062 probe sets were associated primarily with the response when adults of the same age were irradiated 4 hours before exposure. Surprisingly, a ten-fold difference in radiation dose (0.1 versus 1.0 Gy) had little effect. Analysis at the gene and pathway level indicated that the long-term response includes the induction of cytokine and inflammatory regulators and transcription and growth factors. The acute response includes the induction of p53 target genes and modulation of the hypoxia-induced transcription factor-C/EBP axis. Results help define genes and pathways affected in the long-term, low and moderate dose radiation response and differentiate them from those affected in an acute response in the same tissue.
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Affiliation(s)
- Lahcen Jaafar
- Institute of Molecular Medicine and Genetics, Georgia Regents University, Augusta, Georgia, United States of America
- Departments of Radiation Oncology and Winship Cancer Institute, Emory University School of Medicine, Atlanta, Georgia, United States of America
| | - Robert H. Podolsky
- Center for Biotechnology and Genomic Medicine, Georgia Regents University, Augusta, Georgia, United States of America
| | - William S. Dynan
- Institute of Molecular Medicine and Genetics, Georgia Regents University, Augusta, Georgia, United States of America
- Departments of Radiation Oncology and Winship Cancer Institute, Emory University School of Medicine, Atlanta, Georgia, United States of America
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia, United States of America
- * E-mail:
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Langen B, Rudqvist N, Parris TZ, Schüler E, Helou K, Forssell-Aronsson E. Comparative analysis of transcriptional gene regulation indicates similar physiologic response in mouse tissues at low absorbed doses from intravenously administered 211At. J Nucl Med 2013; 54:990-8. [PMID: 23658216 DOI: 10.2967/jnumed.112.114462] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
UNLABELLED (211)At is a promising therapeutic radionuclide because of the nearly optimal biological effectiveness of emitted α-particles. Unbound (211)At accumulates in the thyroid gland and in other vital normal tissues. However, few studies have been performed that assess the (211)At-induced normal-tissue damage in vivo. Knowledge about the extent and quality of resulting responses in various organs offers a new venue for reducing risks and side effects and increasing the overall well-being of the patient during and after therapy. METHODS Female BALB/c nude mice were injected intravenously with 0.064-42 kBq of (211)At or mock-treated, and the kidneys, liver, lungs, and spleen were excised 24 h after injection. A transcriptional gene expression analysis was performed in triplicate using RNA microarray technology. Biological processes associated with regulated transcripts were grouped into 8 main categories with 31 subcategories according to gene ontology terms for comparison of regulatory profiles. RESULTS A substantial decrease in the total number of regulated transcripts was observed between 0.64 and 1.8 kBq of (211)At for all investigated tissues. Few genes were differentially regulated in each tissue at all absorbed doses. In all tissues, most of these genes showed a nonmonotonous dependence on absorbed dose. However, the direction of regulation generally remained uniform for a given gene. Few known radiation-associated genes were regulated on the transcriptional level, and their expression profile generally appeared to be dose-independent and tissue-specific. The regulatory profiles of categorized biological processes were tissue-specific and reflected the shift in regulatory intensity between 0.64 and 1.8 kBq of (211)At. The profiles revealed strongly regulated and nonregulated subcategories. CONCLUSION The strong regulatory change observed between 0.64 and 1.8 kBq is hypothesized to result not only from low-dose effects in each tissue but also from physiologic responses to ionizing radiation-induced damage to, for example, the (211)At-accumulating thyroid gland. The presented results demonstrate the complexity of responses to radionuclides in vivo and highlight the need for further research to also consider physiology in ionizing radiation-induced responses.
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Affiliation(s)
- Britta Langen
- Department of Radiation Physics, Institute of Clinical Sciences, Sahlgrenska Cancer Center, Sahlgrenska Academy, University of Gothenburg, Sahlgrenska University Hospital, Gothenburg, Sweden.
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Ranjan A, Kaur N, Tiwari V, Singh Y, Chaturvedi MM, Tandon V. 3,4-Dimethoxyphenyl Bis-benzimidazole Derivative, Mitigates Radiation-Induced DNA Damage. Radiat Res 2013; 179:647-62. [DOI: 10.1667/rr3246.1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Atul Ranjan
- Department of Chemistry, University of Delhi, Delhi, India
| | - Navrinder Kaur
- Department of Chemistry, University of Delhi, Delhi, India
| | - Vinod Tiwari
- Department of Chemistry, University of Delhi, Delhi, India
| | - Yogendra Singh
- Institute of Genomics and Integrative Biology, Delhi, India
| | | | - Vibha Tandon
- Department of Chemistry, University of Delhi, Delhi, India
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Yang HJ, Kim N, Seong KM, Youn H, Youn B. Investigation of radiation-induced transcriptome profile of radioresistant non-small cell lung cancer A549 cells using RNA-seq. PLoS One 2013; 8:e59319. [PMID: 23533613 PMCID: PMC3606344 DOI: 10.1371/journal.pone.0059319] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2012] [Accepted: 02/13/2013] [Indexed: 11/19/2022] Open
Abstract
Radioresistance is a main impediment to effective radiotherapy for non-small cell lung cancer (NSCLC). Despite several experimental and clinical studies of resistance to radiation, the precise mechanism of radioresistance in NSCLC cells and tissues still remains unclear. This result could be explained by limitation of previous researches such as a partial understanding of the cellular radioresistance mechanism at a single molecule level. In this study, we aimed to investigate extensive radiation responses in radioresistant NSCLC cells and to identify radioresistance-associating factors. For the first time, using RNA-seq, a massive sequencing-based approach, we examined whole-transcriptome alteration in radioresistant NSCLC A549 cells under irradiation, and verified significant radiation-altered genes and their chromosome distribution patterns. Also, bioinformatic approaches (GO analysis and IPA) were performed to characterize the radiation responses in radioresistant A549 cells. We found that epithelial–mesenchymal transition (EMT), migration and inflammatory processes could be meaningfully related to regulation of radiation responses in radioresistant A549 cells. Based on the results of bioinformatic analysis for the radiation-induced transcriptome alteration, we selected seven significant radiation-altered genes (SESN2, FN1, TRAF4, CDKN1A, COX-2, DDB2 and FDXR) and then compared radiation effects in two types of NSCLC cells with different radiosensitivity (radioresistant A549 cells and radiosensitive NCI-H460 cells). Interestingly, under irradiation, COX-2 showed the most significant difference in mRNA and protein expression between A549 and NCI-H460 cells. IR-induced increase of COX-2 expression was appeared only in radioresistant A549 cells. Collectively, we suggest that COX-2 (also known as prostaglandin-endoperoxide synthase 2 (PTGS2)) could have possibility as a putative biomarker for radioresistance in NSCLC cells.
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Affiliation(s)
- Hee Jung Yang
- Department of Biological Sciences, Pusan National University, Busan, Republic of Korea
| | - Namshin Kim
- Korean Bioinformation Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
| | - Ki Moon Seong
- Division of Radiation Effect Research, Radiation Health Research Institute, Korea Hydro & Nuclear Power Co., Ltd., Seoul, Republic of Korea
| | - HyeSook Youn
- Department of Bioscience & Biotechnology, Institute of Bioscience, Sejong University, Seoul, Republic of Korea
| | - BuHyun Youn
- Department of Biological Sciences, Pusan National University, Busan, Republic of Korea
- * E-mail:
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Cohen EP, Lenarczyk M, Fish BL, Jia S, Hessner MJ, Moulder JE. Evaluation of Genomic Evidence for Oxidative Stress in Experimental Radiation Nephropathy. ACTA ACUST UNITED AC 2013; 2. [PMID: 24818171 DOI: 10.4172/2327-5790.1000101] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
BACKGROUND Chronic persistent oxidative stress has been proposed as a mechanism for late radiation injury to normal tissue. Using biochemical, histological, and pharmacological techniques, we have not been able to confirm this hypothesis for late renal radiation injury. Gene expression may be more revealing, especially since the initial effects of radiation are to damage DNA. METHODS Gene array studies were done using kidney tissue from irradiated rats, with particular attention to genes pertinent to oxidative stress. The time points were from 1 to 49 days after irradiation. Cellular RNA and mitochondrial DNA were isolated, for gene expression analysis and common deletion testing, respectively. RESULTS For the gene expression studies, and from over 30,000 transcripts, only nine related to oxidative stress had 1.4 fold or greater changes in expression. Mitochondrial DNA showed no changes in the common deletion. CONCLUSION These studies do not support the hypothesis of chronic oxidative stress as a mechanism for radiation nephropathy.
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Affiliation(s)
- Eric P Cohen
- Department of Medicine, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Marek Lenarczyk
- Department of Radiation Oncology, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Brian L Fish
- Department of Radiation Oncology, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Shuang Jia
- Department of Pediatrics, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Martin J Hessner
- Department of Pediatrics, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - John E Moulder
- Department of Radiation Oncology, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
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12
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Radiation-induced genomic instability in Caenorhabditis elegans. Mutat Res 2012; 748:36-41. [PMID: 22796420 DOI: 10.1016/j.mrgentox.2012.06.010] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2011] [Revised: 05/27/2012] [Accepted: 06/24/2012] [Indexed: 11/23/2022]
Abstract
Radiation-induced genomic instability has been well documented, particularly in vitro. However, the understanding of its mechanisms and their consequences in vivo is still limited. In this study, Caenorhabditis elegans (C. elegans; strain CB665) nematodes were exposed to X-rays at doses of 0.1, 1, 3 or 10Gy. The endpoints were measured several generations after exposure and included mutations in the movement-related gene unc-58, alterations in gene expression analysed with oligoarrays containing the entire C. elegans genome, and micro-satellite mutations measured by capillary electrophoresis. The progeny of the irradiated nematodes showed an increased mutation frequency in the unc-58 gene, with a maximum response observed at 1Gy. Significant differences were also found in gene expression between the irradiated (1Gy) and non-irradiated nematode lines. Differences in gene expression did not show clear clustering into certain gene categories, suggesting that the instability might be a chaotic process rather than a result of changes in the function of few specific genes such as, e.g., those responsible for DNA repair. Increased heterogeneity in gene expression, which has previously been described in irradiated cultured human lymphocytes, was also observed in the present study in C. elegans, the coefficient of variation of gene expression being higher in the progeny of irradiated nematodes than in control nematodes. To the best of our knowledge, this is the first publication reporting radiation-induced genomic instability in C. elegans.
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Schüler E, Parris TZ, Rudqvist N, Helou K, Forssell-Aronsson E. Effects of internal low-dose irradiation from 131I on gene expression in normal tissues in Balb/c mice. EJNMMI Res 2011; 1:29. [PMID: 22214497 PMCID: PMC3251037 DOI: 10.1186/2191-219x-1-29] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2011] [Accepted: 11/28/2011] [Indexed: 11/10/2022] Open
Abstract
Background The aim of this study was to investigate the global gene expression response of normal tissues following internal low absorbed dose irradiation of 131I. Methods Balb/c mice were intravenously injected with 13 to 260 kBq of 131I and euthanized 24 h after injection. Kidneys, liver, lungs, and spleen were surgically removed. The absorbed dose to the tissues was 0.1 to 9.7 mGy. Total RNA was extracted, and Illumina MouseRef-8 Whole-Genome Expression BeadChips (Illumina, Inc., San Diego, California, USA) were used to compare the gene expression of the irradiated tissues to that of non-irradiated controls. The Benjamini-Hochberg method was used to determine differentially expressed transcripts and control for false discovery rate. Only transcripts with a modulation of 1.5-fold or higher, either positively or negatively regulated, were included in the analysis. Results The number of transcripts affected ranged from 260 in the kidney cortex to 857 in the lungs. The majority of the affected transcripts were specific for the different absorbed doses delivered, and few transcripts were shared between the different tissues investigated. The response of the transcripts affected at all dose levels was generally found to be independent of dose, and only a few transcripts showed increasing or decreasing regulation with increasing absorbed dose. Few biological processes were affected at all absorbed dose levels studied or in all tissues studied. The types of biological processes affected were clearly tissue-dependent. Immune response was the only biological process affected in all tissues, and processes affected in more than three tissues were primarily associated with the response to stimuli and metabolism. Conclusion Despite the low absorbed doses delivered to the tissues investigated, a surprisingly strong response was observed. Affected biological processes were primarily associated with the normal function of the tissues, and only small deviations from the normal metabolic activity in the tissues were induced.
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Affiliation(s)
- Emil Schüler
- Department of Radiation Physics, Institute of Clinical Sciences, Sahlgrenska Cancer Center, Sahlgrenska Academy at the University of Gothenburg, Sahlgrenska University hospital, Gothenburg, 413 45, Sweden.
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Zhang J, Yang Y, Wang Y, Zhang J, Wang Z, Yin M, Shen X. Identification of hub genes related to the recovery phase of irradiation injury by microarray and integrated gene network analysis. PLoS One 2011; 6:e24680. [PMID: 21931809 PMCID: PMC3172286 DOI: 10.1371/journal.pone.0024680] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2011] [Accepted: 08/18/2011] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND Irradiation commonly causes long-term bone marrow injury charactertized by defective HSC self-renewal and a decrease in HSC reserve. However, the effect of high-dose IR on global gene expression during bone marrow recovery remains unknown. METHODOLOGY Microarray analysis was used to identify differentially expressed genes that are likely to be critical for bone marrow recovery. Multiple bioinformatics analyses were conducted to identify key hub genes, pathways and biological processes. PRINCIPAL FINDINGS 1) We identified 1302 differentially expressed genes in murine bone marrow at 3, 7, 11 and 21 days after irradiation. Eleven of these genes are known to be HSC self-renewal associated genes, including Adipoq, Ccl3, Ccnd1, Ccnd2, Cdkn1a, Cxcl12, Junb, Pten, Tal1, Thy1 and Tnf; 2) These 1302 differentially expressed genes function in multiple biological processes of immunity, including hematopoiesis and response to stimuli, and cellular processes including cell proliferation, differentiation, adhesion and signaling; 3) Dynamic Gene Network analysis identified a subgroup of 25 core genes that participate in immune response, regulation of transcription and nucleosome assembly; 4) A comparison of our data with known irradiation-related genes extracted from literature showed 42 genes that matched the results of our microarray analysis, thus demonstrated consistency between studies; 5) Protein-protein interaction network and pathway analyses indicated several essential protein-protein interactions and signaling pathways, including focal adhesion and several immune-related signaling pathways. CONCLUSIONS Comparisons to other gene array datasets indicate that global gene expression profiles of irradiation damaged bone marrow show significant differences between injury and recovery phases. Our data suggest that immune response (including hematopoiesis) can be considered as a critical biological process in bone marrow recovery. Several critical hub genes that are key members of significant pathways or gene networks were identified by our comprehensive analysis.
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Affiliation(s)
- Jing Zhang
- School of Pharmacy, Shanghai Jiao Tong University, Shanghai, China
- Department of Internal Medicine, No. 455 Hospital, Shanghai, China
| | - Yue Yang
- School of Pharmacy, Shanghai Jiao Tong University, Shanghai, China
| | - Yin Wang
- Department of Internal Medicine, No. 455 Hospital, Shanghai, China
| | - Jinyuan Zhang
- Department of Internal Medicine, No. 455 Hospital, Shanghai, China
| | - Zejian Wang
- School of Pharmacy, Shanghai Jiao Tong University, Shanghai, China
| | - Ming Yin
- School of Pharmacy, Shanghai Jiao Tong University, Shanghai, China
| | - Xudong Shen
- Department of Internal Medicine, No. 455 Hospital, Shanghai, China
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Cohen EP, Bruder ED, Cullinan WE, Ziegler D, Raff H. Effect of high-dose total body irradiation on ACTH, corticosterone, and catecholamines in the rat. Transl Res 2011; 157:38-47. [PMID: 21146149 PMCID: PMC3053012 DOI: 10.1016/j.trsl.2010.09.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/30/2010] [Revised: 09/27/2010] [Accepted: 09/29/2010] [Indexed: 10/18/2022]
Abstract
Total body irradiation (TBI) or partial body irradiation is a distinct risk of accidental, wartime, or terrorist events. Total body irradiation is also used as conditioning therapy before hematopoietic stem cell transplantation. This therapy can result in injury to multiple tissues and might result in death as a result of multiorgan failure. The hypothalamic-pituitary-adrenal (HPA) axis could play a causative role in those injuries, in addition to being activated under conditions of stress. In a rat model of TBI, we have established that radiation nephropathy is a significant lethal complication, which is caused by hypertension and uremia. The current study assessed HPA axis function in rats undergoing TBI. Using a head-shielded model of TBI, we found an enhanced response to corticotropin-releasing hormone (CRH) in vitro in pituitaries from irradiated compared with nonirradiated rats at both 8 and 70 days after 10-Gy single fraction TBI. At 70, but not 8 days, plasma adrenocorticotrophic hormone (ACTH) and corticosterone levels were increased significantly in irradiated compared with nonirradiated rats. Plasma aldosterone was not affected by TBI at either time point, whereas plasma renin activity was decreased in irradiated rats at 8 days. Basal and stimulated adrenal steroid synthesis in vitro was not affected by TBI. In addition, plasma epinephrine was decreased at 70 days after TBI. The hypothalamic expression of CRH messenger RNA (mRNA) and hippocampal expression of glucocorticoid receptor mRNA were unchanged by irradiation. We conclude that the hypertension of radiation nephropathy is not aldosterone or catecholamine-dependent but that there is an abscopal activation of the HPA axis after 10 Gy TBI. This activation was attributable at least partially to enhanced pituitary ACTH production.
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16
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Westbury CB, Reis-Filho JS, Dexter T, Mahler-Araujo B, Fenwick K, Iravani M, Grigoriadis A, Parry S, Robertson D, Mackay A, Ashworth A, Yarnold JR, Isacke CM. Genome-wide transcriptomic profiling of microdissected human breast tissue reveals differential expression of KIT (c-Kit, CD117) and oestrogen receptor-alpha (ERalpha) in response to therapeutic radiation. J Pathol 2009; 219:131-40. [PMID: 19562735 DOI: 10.1002/path.2581] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The pathogenesis of late normal tissue fibrosis after high-dose ionizing radiation involves multiple cell types and signalling pathways but is not well understood. To identify the molecular changes occurring after radiotherapy, paired normal tissue samples were collected from the non-irradiated breast and from the treated breast of women who had undergone curative radiotherapy for early breast cancer months or years previously. As radiation may induce distinct transcriptional changes in the different components of the breast, laser capture microdissection and gene expression microarray profiling were performed separately for epithelial and stromal components and selected genes were validated using immunohistochemistry. In the epithelial compartment, a reduction of KIT (c-Kit; CD117) and a reciprocal increase in ESR1 (oestrogen receptor-alpha, ERalpha) mRNA and protein levels were seen in irradiated compared to non-irradiated samples. In the stromal compartment, extracellular matrix genes including FN1 (fibronectin 1) and CTGF (connective tissue growth factor; CCN2) were increased. Further investigation revealed that c-Kit and ERalpha were expressed in distinct subpopulations of luminal epithelial cells. Interlobular c-Kit-positive mast cells were also increased in irradiated cases not showing features of post-radiation atrophy. Pathway analysis revealed 'cancer, reproductive system disease and tumour morphology' as the most significantly enriched network in the epithelial compartment, whereas in the stromal component, a significant enrichment for 'connective tissue disorders, dermatological diseases and conditions, genetic disorder' and 'cancer, tumour morphology, infection mechanism' networks was observed. These data identify previously unreported changes in the epithelial compartment and show altered expression of genes implicated in late normal tissue injury in the stromal compartment of normal breast tissue. The findings are relevant to both fibrosis and atrophy occurring after radiotherapy for early breast cancer.
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Affiliation(s)
- Charlotte B Westbury
- Breakthrough Breast Cancer Research Centre, Institute of Cancer Research, London, UK
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Taki K, Wang B, Nakajima T, Wu J, Ono T, Uehara Y, Matsumoto T, Oghiso Y, Tanaka K, Ichinohe K, Nakamura S, Tanaka S, Magae J, Kakimoto A, Nenoi M. Microarray analysis of differentially expressed genes in the kidneys and testes of mice after long-term irradiation with low-dose-rate gamma-rays. JOURNAL OF RADIATION RESEARCH 2009; 50:241-252. [PMID: 19398854 DOI: 10.1269/jrr.09011] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Measuring global gene expression using cDNA or oligonucleotide microarrays is an effective approach to understanding the complex mechanisms of the effects of radiation. However, few studies have been carried out that investigate gene expression in vivo after prolonged exposure to low-dose-rate radiation. In this study, C57BL/6J mice were continuously irradiated with gamma-rays for 485 days at dose-rates of 0.032-13 microGy/min. Gene expression profiles in the kidney and testis from irradiated and unirradiated mice were analyzed, and differentially expressed genes were identified. A combination of pathway analysis and hierarchical clustering of differentially expressed genes revealed that expression of genes involved in mitochondrial oxidative phosphorylation was elevated in the kidney after irradiation at the dose-rates of 0.65 microGy/min and 13 microGy/min. Expression of cell cycle-associated genes was not profoundly modulated in the kidney, in contrast to the response to acute irradiation, suggesting a threshold in the dose-rate for modulation of the expression of cell cycle-related genes in vivo following exposure to radiation. We demonstrated that changes to the gene expression profile in the testis were largely different from those in the kidney. The Gene Ontology categories "DNA metabolism", "response to DNA damage" and "DNA replication" overlapped significantly with the clusters of genes whose expression decreased with an increase in the dose-rate to the testis. These observations provide a fundamental insight into the organ-specific responses to low-dose-rate radiation.
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Affiliation(s)
- Keiko Taki
- Radiation Effect Mechanisms Research Group, National Institute of Radiological Sciences, 9-1 Anagawa-4-chome, Inage-ku, Chiba, Japan
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18
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Kruse JJCM, Floot BGJ, te Poele JAM, Russell NS, Stewart FA. Radiation-induced activation of TGF-beta signaling pathways in relation to vascular damage in mouse kidneys. Radiat Res 2009; 171:188-97. [PMID: 19267544 DOI: 10.1667/rr1526.1] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
The purpose of this study was to investigate the long-term effects of radiation-induced alterations in TGF-beta signaling pathways with respect to the development of vascular damage in the irradiated kidney. Total RNA was isolated from mouse kidneys at 1-30 weeks after irradiation, and quantitative real-time PCR analyses were performed for TGF-beta receptors (ALK1, ALK5, endoglin), downstream mediators (Smad7, CTGF), and downstream targets (PAI-1 and Id-1). Expression of endoglin and Smad7 protein as well as nucleo-cytoplasmic distribution of phospho Smad 2/3 and phospho Smad 1/5 was analyzed by immunohistochemistry. Radiation caused a rapid and persistent increase in expression of TGF-beta receptors and mediators from 1-30 weeks after treatment. Expression of Id-1, a downstream target of endothelial cell specific receptor ALK1, was transiently increased (1-10 weeks after irradiation) but returned to control levels at later times. Expression of PAI-1, a downstream target of ALK5, increased progressively from 10-30 weeks after irradiation. These results show that radiation activated TGF-beta signaling pathways in the kidney and shifted the balance in favor of ALK5 signaling, which generally inhibits endothelial cell proliferation and migration. We hypothesize that prolonged activation of ALK5 signaling and relative suppression of ALK1 signaling may provide an explanation for the telangiectatic phenotype observed in irradiated kidneys.
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Affiliation(s)
- Jacqueline J C M Kruse
- Division of Experimental Therapy, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands
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19
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Katayama K, Kawano M, Naito I, Ishikawa H, Sado Y, Asakawa N, Murata T, Oosugi K, Kiyohara M, Ishikawa E, Ito M, Nomura S. Irradiation prolongs survival of Alport mice. J Am Soc Nephrol 2008; 19:1692-700. [PMID: 18480315 DOI: 10.1681/asn.2007070829] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Alport syndrome is a hereditary nephropathy that results in irreversible, progressive renal failure. Recent reports suggested that bone marrow transplantation (BMT) has a beneficial, short-term effect on renal injury in Alport (Col4a3(-/-)) mice, but its long-term effects, especially with regard to survival, are unknown. In this study, Alport mice received a transplant of either wild-type or Col4a3(-/-) bone marrow cells. Surprising, laboratory evaluations and renal histology demonstrated similar findings in both transplanted groups. Transplanted cells accounted for >10% of glomerular cells at 8 wk, but type IV collagen alpha3 chains were not detected in glomerular basement membranes of either group by immunofluorescence or Western blot analysis, although Col4a3 mRNA in the kidney could be amplified by reverse transcription-PCR in knockout mice that received a transplant of wild-type bone marrow. Both transplanted groups, however, survived approximately 1.5 times longer than untreated knockout mice (log rank P < 0.05). These data suggested that irradiation, which preceded BMT, may have conferred a survival benefit; therefore, the survival time of knockout mice was assessed after sublethal irradiation (3, 6, and 7 Gy) without subsequent BMT. A strong positive correlation between irradiation dosage and survival time was identified (P < 0.0001). In conclusion, the improved survival observed in Alport mice that received a transplant of wild-type bone marrow might be primarily attributed to as-yet-unidentified effects of irradiation.
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Affiliation(s)
- Kan Katayama
- Department of Cardiology and Nephrology, Mie University Graduate School of Medicine, Mie, 21-153 Noda, Tsu, Mie, 514-0826, Japan.
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20
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Lin R, Sun Y, Li C, Xie C, Wang S. Identification of differentially expressed genes in human lymphoblastoid cells exposed to irradiation and suppression of radiation-induced apoptosis with antisense oligonucleotides against caspase-4. Oligonucleotides 2007; 17:314-26. [PMID: 17854271 DOI: 10.1089/oli.2007.0064] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
To identify candidate genes in response to ionizing radiation (IR) and discover new targets for basic research and radiation protection, whole human genome bioarrays were used to examine gene expression profiles in human lymphoblastoid AHH-1 cells exposed to IR. The results were confirmed by semiquantitative reverse transcription-polymerase chain reaction (RT-PCR). In addition, the effects of ionizing radiation on cell growth, cell cycles and apoptosis were also examined. The microarray analysis revealed a set of IR responsive genes, including 906 genes at 4 hours and 789 genes at 24 hours after exposure to 5 Gy IR. The processes of cell cycles, apoptosis, signal transduction, and DNA repair involved a high percentage of IR responsive genes, among which, caspase-4 was most strongly induced by irradiation. Consistent with this, downregulation of caspase-4 expression by antisense oligonucleotides significantly increased cell viability and protected cells from undergoing apoptosis induced by IR. Taken together, the results suggested that caspase-4 plays an important role in radiation-induced apoptosis.
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Affiliation(s)
- Ruxian Lin
- Beijing Institute of Radiation Medicine, Beijing 100850, P.R. China
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21
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Kruse JJCM, Stewart FA. Gene expression arrays as a tool to unravel mechanisms of normal tissue radiation injury and prediction of response. World J Gastroenterol 2007; 13:2669-74. [PMID: 17569134 PMCID: PMC4147114 DOI: 10.3748/wjg.v13.i19.2669] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Over the past 5 years there has been a rapid increase in the use of microarray technology in the field of cancer research. The majority of studies use microarray analysis of tumor biopsies for profiling of molecular characteristics in an attempt to produce robust classifiers for prognosis. There are now several published gene sets that have been shown to predict for aggressive forms of breast cancer, where patients are most likely to benefit from adjuvant chemotherapy and tumors most likely to develop distant metastases, or be resistant to treatment. The number of publications relating to the use of microarrays for analysis of normal tissue damage, after cancer treatment or genotoxic exposure, is much more limited. A PubMed literature search was conducted using the following keywords and combination of terms: radiation, normal tissue, microarray, gene expression profiling, prediction. With respect to normal tissue radiation injury, microarrays have been used in three ways: (1) to generate gene signatures to identify sensitive and resistant populations (prognosis); (2) to identify sets of biomarker genes for estimating radiation exposure, either accidental or as a result of terrorist attack (diagnosis); (3) to identify genes and pathways involved in tissue response to injury (mechanistic). In this article we will review all (relevant) papers that covered our literature search criteria on microarray technology as it has been applied to normal tissue radiation biology and discuss how successful this has been in defining predisposition markers for radiation sensitivity or how it has helped us to unravel molecular mechanisms leading to acute and late tissue toxicity. We also discuss some of the problems and limitations in application and interpretation of such data.
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Affiliation(s)
- Jacqueline J C M Kruse
- The Netherlands Cancer Institute, Department of Experimental Therapy (H6), Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
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22
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West CML, Elliott RM, Burnet NG. The genomics revolution and radiotherapy. Clin Oncol (R Coll Radiol) 2007; 19:470-80. [PMID: 17419040 DOI: 10.1016/j.clon.2007.02.016] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2007] [Accepted: 02/28/2007] [Indexed: 10/23/2022]
Abstract
The expansion of our knowledge through the Human Genome Project has been accompanied by the development of new high-throughput techniques, which provide extensive capabilities for the analysis of a large number of genes or the whole genome. These assays can be carried out in various clinical samples at the DNA (genome), RNA (transcriptome) or protein (proteome) level. There is a belief that this genomic revolution, i.e. sequencing of the human genome and developments in high-throughput technology, heralds a future of personalised medicine. For clinical oncology, this progress should increase the possibility of predicting individual patient responses to radiotherapy. This review highlights some of the work involving sparsely ionising radiation and the new technologies.
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Affiliation(s)
- C M L West
- Academic Radiation Oncology, University of Manchester, Christie Hospital NHS Trust, Manchester M20 4BX, UK.
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23
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Malone J, Ullrich R. Novel Radiation Response Genes Identified in Gene-Trapped MCF10A Mammary Epithelial Cells. Radiat Res 2007; 167:176-84. [PMID: 17390725 DOI: 10.1667/rr0656.1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
We have used a gene-trapping strategy to screen human mammary epithelial cells for radiation response genes. Relative mRNA expression levels of five candidate genes in MCF10A cells were analyzed, both with and without exposure to radiation. In all five cases, the trapped genes were significantly down-regulated after radiation treatment. Sequence analysis of the fusion transcripts identified the trapped genes: (1) the human androgen receptor, (2) the uncharacterized DREV1 gene, which has known homology to DNA methyltransferases, (3) the human creatine kinase gene, (4) the human eukaryotic translation elongation factor 1 beta 2, and (5) the human ribosomal protein L27. All five genes were down-regulated significantly after treatment with varying doses of ionizing radiation (0.10 to 4.0 Gy) and at varying times (2-30 h after treatment). The genes were also analyzed in human fibroblast and lymphoblastoid cell lines to determine whether the radiation response being observed was cell-type specific. The results verified that the observed radiation response was not a cell-type-specific phenomenon, suggesting that the genes play essential roles in the radiation damage control pathways. This study demonstrates the potential of the gene-trap approach for the identification and functional analysis of novel radiation response genes.
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Affiliation(s)
- Jennifer Malone
- Department of Pathology, University of Colorado Health Sciences Center, Aurora, Colorado 80045-0508, USA.
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Yamamoto N, Ikeda C, Yakushiji T, Nomura T, Katakura A, Shibahara T, Mizoe JE. Genetic Effects of X-Ray and Carbon Ion Irradiation in Head and Neck Carcinoma Cell Lines. THE BULLETIN OF TOKYO DENTAL COLLEGE 2007; 48:177-85. [DOI: 10.2209/tdcpublication.48.177] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Sathish P, Withana N, Biswas M, Bryant C, Templeton K, Al-Wahb M, Smith-Espinoza C, Roche JR, Elborough KM, Phillips JR. Transcriptome analysis reveals season-specific rbcS gene expression profiles in diploid perennial ryegrass (Lolium perenne L.). PLANT BIOTECHNOLOGY JOURNAL 2007; 5:146-61. [PMID: 17207264 DOI: 10.1111/j.1467-7652.2006.00228.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Perennial ryegrass (Lolium perenne L.) is a major grass species used for forage and turf throughout the world, and gains by conventional breeding have reached a plateau. Perennial ryegrass is an outcrossing, self-incompatible diploid (2n = 2x = 14) with a relatively large genome (4067 Mbp/diploid genome; Evans, G.M., Rees, H., Snell, C.L. and Sun, S. (1972) The relation between nuclear DNA amount and the duration of the mitotic cycle. Chrom. Today, 3, 24-31). Using tissues sourced from active pastures during the peak of the autumn, winter, spring and summer seasons, we analysed the ryegrass transcriptome employing a Serial Analysis of Gene Expression (SAGE) protocol, with the dual goals of understanding the seasonal changes in perennial ryegrass gene expression and enhancing our ability to select genes for genetic manipulation. A total of 159,002 14-mer SAGE tags was sequenced and mapped to the perennial ryegrass DNA database, comprising methyl-filtered (GeneThresher) and expressed sequence tag (EST) sequences. The analysis of 14,559 unique SAGE tags, which were present more than once in our SAGE library, revealed 964, 1331, 346 and 131 exclusive transcripts to autumn, winter, spring and summer, respectively. Intriguingly, our analysis of the SAGE tags revealed season-specific expression profiles for the small subunit of ribulose-1,5-bisphosphate carboxylase (Rubisco), LprbcS. The transcript level for LprbcS was highest in spring, and then decreased gradually between summer and winter. Five different copies of LprbcS were revealed in ryegrass, with one possibly producing splice variant transcripts. Two highly expressed LprbcS genes were reported, one of which was not active in autumn. Another LprbcS gene showed an inverse expression profile to the autumn inactive LprbcS in a manner to compensate the expression level.
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Affiliation(s)
- Puthigae Sathish
- Pastoral Genomics, c/o ViaLactia Biosciences (NZ) Ltd, PO Box 109185, Newmarket, Auckland 1149, New Zealand.
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26
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Birkenkamp KU, Essafi A, van der Vos KE, da Costa M, Hui RCY, Holstege F, Koenderman L, Lam EWF, Coffer PJ. FOXO3a induces differentiation of Bcr-Abl-transformed cells through transcriptional down-regulation of Id1. J Biol Chem 2006; 282:2211-20. [PMID: 17132628 DOI: 10.1074/jbc.m606669200] [Citation(s) in RCA: 69] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Leukemic transformation often requires activation of protein kinase B (PKB/c-Akt) and is characterized by increased proliferation, decreased apoptosis, and a differentiation block. PKB phosphorylates and inactivates members of the FOXO subfamily of Forkhead transcription factors. It has been suggested that hyperactivation of PKB maintains the leukemic phenotype through actively repressing FOXO-mediated regulation of specific genes. We have found expression of the transcriptional repressor Id1 (inhibitor of DNA binding 1) to be abrogated by FOXO3a activation. Inhibition of PKB activation or growth factor deprivation also resulted in strong down-regulation of Id1 promoter activity, Id1 mRNA, and protein expression. Id1 is highly expressed in Bcr-Abl-transformed K562 cells, correlating with high PKB activation and FOXO3a phosphorylation. Inhibition of Bcr-Abl by the chemical inhibitor STI571 resulted in activation of FOXO3a and down-regulation of Id1 expression. By performing chromatin immunoprecipitation assays and promoter-mutation analysis, we demonstrate that FOXO3a acts as a transcriptional repressor by directly binding to the Id1 promoter. STI571 treatment, or expression of constitutively active FOXO3a, resulted in erythroid differentiation of K562 cells, which was inhibited by ectopic expression of Id1. Taken together our data strongly suggest that high expression of Id1, through PKB-mediated inhibition of FOXO3a, is critical for maintenance of the leukemic phenotype.
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Affiliation(s)
- Kim U Birkenkamp
- Molecular Immunology Laboratory, Department of Immunology, University Medical Center, KC.02.085.2, Lundiaan 6, 3584-CX Utrecht, The Netherlands
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27
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Zhao W, Chuang EY, Mishra M, Awwad R, Bisht K, Sun L, Nguyen P, Pennington JD, Wang TJC, Bradbury CM, Huang L, Chen Z, Bar-Sela G, Robbins MEC, Gius D. Distinct effects of ionizing radiation on in vivo murine kidney and brain normal tissue gene expression. Clin Cancer Res 2006; 12:3823-30. [PMID: 16778110 DOI: 10.1158/1078-0432.ccr-05-2418] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
PURPOSE There is a growing awareness that radiation-induced normal tissue injury in late-responding organs, such as the brain, kidney, and lung, involves complex and dynamic responses between multiple cell types that not only lead to targeted cell death but also acute and chronic alterations in cell function. The specific genes involved in the acute and chronic responses of these late-responding normal tissues remain ill defined; understanding these changes is critical to understanding the mechanism of organ damage. As such, the aim of the present study was to identify candidate genes involved in the development of radiation injury in the murine kidney and brain using microarray analysis. EXPERIMENTAL DESIGN A multimodality experimental approach combined with a comprehensive expression analysis was done to determine changes in normal murine tissue gene expression at 8 and 24 hours after irradiation. RESULTS A comparison of the gene expression patterns in normal mouse kidney and brain was strikingly different. This observation was surprising because it has been long assumed that the changes in irradiation-induced gene expression in normal tissues are preprogrammed genetic changes that are not affected by tissue-specific origin. CONCLUSIONS This study shows the potential of microarray analysis to identify gene expression changes in irradiated normal tissue cells and suggests how normal cells respond to the damaging effects of ionizing radiation is complex and markedly different in cells of differing origin.
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Affiliation(s)
- Weiling Zhao
- Department of Radiation Oncology, Brain Tumor Center of Wake Forest University, Wake Forest University School of Medicine, Winston-Salem, North Carolina, USA
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Higo M, Uzawa K, Kawata T, Kato Y, Kouzu Y, Yamamoto N, Shibahara T, Mizoe JE, Ito H, Tsujii H, Tanzawa H. Enhancement of SPHK1 in vitro by carbon ion irradiation in oral squamous cell carcinoma. Int J Radiat Oncol Biol Phys 2006; 65:867-75. [PMID: 16751068 DOI: 10.1016/j.ijrobp.2006.02.048] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2005] [Revised: 02/07/2006] [Accepted: 02/13/2006] [Indexed: 01/28/2023]
Abstract
PURPOSE The purpose of this study was to assess the gene expression changes in oral squamous cell carcinoma (OSCC) cells after carbon ion irradiation. METHODS AND MATERIALS Three OSCC cell lines (HSC2, Ca9-22, and HSC3) were irradiated with accelerated carbon ion beams or X-rays using three different doses. The cellular sensitivities were determined by clonogenic survival assay. To identify genes the expression of which is influenced by carbon ion irradiation in a dose-dependent manner, we performed Affymetrix GeneChip analysis with HG-U133 plus 2.0 arrays containing 54,675 probe sets. The identified genes were analyzed using the Ingenuity Pathway Analysis Tool to investigate the functional network and gene ontology. Changes in mRNA expression in the genes were assessed by real-time reverse transcriptase-polymerase chain reaction. RESULTS We identified 98 genes with expression levels that were altered significantly at least twofold in each of the three carbon-irradiated OSCC cell lines at all dose points compared with nonirradiated control cells. Among these, SPHK1, the expression of which was significantly upregulated by carbon ion irradiation, was modulated little by X-rays. The function of SPHK1 related to cellular growth and proliferation had the highest p value (p = 9.25e-7 to 2.19e-2). Real-time reverse transcriptase-polymerase chain reaction analysis showed significantly elevated SPHK1 expression levels after carbon ion irradiation (p < 0.05), consistent with microarray data. Clonogenic survival assay indicated that carbon ion irradiation could induce cell death in Ca9-22 cells more effectively than X-rays. CONCLUSIONS Our findings suggest that SPHK1 helps to elucidate the molecular mechanisms and processes underlying the biologic response to carbon ion beams in OSCC.
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Affiliation(s)
- Morihiro Higo
- Department of Clinical Molecular Biology, Graduate School of Medicine, Chiba University, Chiba, Japan
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Reits EA, Hodge JW, Herberts CA, Groothuis TA, Chakraborty M, Wansley EK, Camphausen K, Luiten RM, de Ru AH, Neijssen J, Griekspoor A, Mesman E, Verreck FA, Spits H, Schlom J, van Veelen P, Neefjes JJ. Radiation modulates the peptide repertoire, enhances MHC class I expression, and induces successful antitumor immunotherapy. ACTA ACUST UNITED AC 2006; 203:1259-71. [PMID: 16636135 PMCID: PMC3212727 DOI: 10.1084/jem.20052494] [Citation(s) in RCA: 1338] [Impact Index Per Article: 70.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Radiotherapy is one of the most successful cancer therapies. Here the effect of irradiation on antigen presentation by MHC class I molecules was studied. Cell surface expression of MHC class I molecules was increased for many days in a radiation dose-dependent manner as a consequence of three responses. Initially, enhanced degradation of existing proteins occurred which resulted in an increased intracellular peptide pool. Subsequently, enhanced translation due to activation of the mammalian target of rapamycin pathway resulted in increased peptide production, antigen presentation, as well as cytotoxic T lymphocyte recognition of irradiated cells. In addition, novel proteins were made in response to gamma-irradiation, resulting in new peptides presented by MHC class I molecules, which were recognized by cytotoxic T cells. We show that immunotherapy is successful in eradicating a murine colon adenocarcinoma only when preceded by radiotherapy of the tumor tissue. Our findings indicate that directed radiotherapy can improve the efficacy of tumor immunotherapy.
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Affiliation(s)
- Eric A Reits
- Division of Tumor Biology, The Netherlands Cancer Institute, 1066 CX, Amsterdam, The Netherlands
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30
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Andratschke N, Schnaiter A, Schnaitera A, Weber WA, Cai L, Caia L, Schill S, Wiedenmann N, Schwaiger M, Molls M, Nieder C. Preclinical evaluation of erythropoietin administration in a model of radiation-induced kidney dysfunction. Int J Radiat Oncol Biol Phys 2006; 64:1513-8. [PMID: 16580501 DOI: 10.1016/j.ijrobp.2005.11.042] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2005] [Revised: 11/24/2005] [Accepted: 11/30/2005] [Indexed: 10/24/2022]
Abstract
PURPOSE To test whether the clinically available growth factor erythropoietin (EPO) influences radiation-induced normal-tissue damage in a model of kidney dysfunction. METHODS Animal experiments were conducted to test the role of EPO administration in a C3H mouse model of unilateral kidney irradiation with 6, 8, and 10 Gy and to assess the effects of 2 different dose levels of EPO. The kidney function was assessed before radiotherapy, as well as 19, 25, 31, and 37 weeks thereafter by means of (99m)Tc-dimercaptosuccinat scans (static scintigraphy). RESULTS Concomitant EPO administration significantly increased the degree of radiation-induced kidney dysfunction. A dose of 2,000 IU/kg body weight per injection tended to cause more damage than the lower dose of 500 IU/kg. CONCLUSION Administration of growth factors concomitant to radiotherapy might modify the development of kidney dysfunction. Although insulin-like growth factor-1 has previously been shown to protect the kidney, such an effect could not be demonstrated for EPO. The latter agent even increased the development of nephropathy.
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Affiliation(s)
- Nicolaus Andratschke
- Department of Radiation Oncology, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany
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Rødningen OK, Overgaard J, Alsner J, Hastie T, Børresen-Dale AL. Microarray analysis of the transcriptional response to single or multiple doses of ionizing radiation in human subcutaneous fibroblasts. Radiother Oncol 2005; 77:231-40. [PMID: 16297999 DOI: 10.1016/j.radonc.2005.09.020] [Citation(s) in RCA: 73] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2005] [Revised: 09/27/2005] [Accepted: 09/29/2005] [Indexed: 11/19/2022]
Abstract
BACKGROUND AND PURPOSE Transcriptional profiling of fibroblasts derived from breast cancer patients might improve our understanding of subcutaneous radiation-induced fibrosis. The aim of this study was to get a comprehensive overview of the changes in gene expression in subcutaneous fibroblast cell lines after various ionizing radiation (IR) schemes in order to provide information on potential targets for prevention and to suggest candidate genes for SNP association studies aimed at predicting individual risk of radiation-induced morbidity. PATIENTS AND METHODS Thirty different human fibroblast cell lines were included in the study, and two different radiation schemes; single dose experiments with 3.5 Gy or fractionated with 3 x 3.5 Gy. Expression analyses were performed on unexposed and exposed cells after different time points. The IR response was analyzed using the statistical method Significance Analysis of Microarrays (SAM). RESULTS While many of the identified genes were involved in known IR response pathways like cell cycle arrest, proliferation and detoxification, a substantial fraction of the genes were involved in processes not previously associated with IR response. Of particular interest is genes involved in ECM remodelling, Wnt signalling and IGF signalling. Many of the genes were identified after a single dose, but transcriptional changes in genes related to ROS scavenging and ECM remodelling were most profound after a fractionated scheme. CONCLUSIONS We have identified a number of IR response pathways in fibroblasts derived from breast cancer patients. Besides previously identified pathways, we have identified new pathways and genes that could be relevant for prevention and intervention studies of subcutaneous radiation-induced fibrosis as well as being candidates for SNP association studies.
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Affiliation(s)
- Olaug Kristin Rødningen
- Department of Genetics, Institute of Cancer Research, Faculty Division, The Norwegian Radium Hospital, University of Oslo, Norway.
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Augustine AD, Gondré-Lewis T, McBride W, Miller L, Pellmar TC, Rockwell S. Animal models for radiation injury, protection and therapy. Radiat Res 2005; 164:100-9. [PMID: 15966769 DOI: 10.1667/rr3388] [Citation(s) in RCA: 58] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Current events throughout the world underscore the growing threat of different forms of terrorism, including radiological or nuclear attack. Pharmaceutical products and other approaches are needed to protect the civilian population from radiation and to treat those with radiation-induced injuries. In the event of an attack, radiation exposures will be heterogeneous in terms of both dose and quality, depending on the type of device used and each victim's location relative to the radiation source. Therefore, methods are needed to protect against and treat a wide range of early and slowly developing radiation-induced injuries. Equally important is the development of rapid and accurate biodosimetry methods for estimating radiation doses to individuals and guiding clinical treatment decisions. Acute effects of high-dose radiation include hematopoietic cell loss, immune suppression, mucosal damage (gastrointestinal and oral), and potential injury to other sites such as the lung, kidney and central nervous system (CNS). Long-term effects, as a result of both high- and low-dose radiation, include dysfunction or fibrosis in a wide range of organs and tissues and cancer. The availability of appropriate types of animal models, as well as adequate numbers of animals, is likely to be a major bottleneck in the development of new or improved radioprotectors, mitigators and therapeutic agents to prevent or treat radiation injuries and of biodosimetry methods to measure radiation doses to individuals.
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Affiliation(s)
- Alison Deckhut Augustine
- Division of Allergy, Immunology and Transplantation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892-6601, USA.
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Snyder AR, Morgan WF. Lack of consensus gene expression changes associated with radiation-induced chromosomal instability. DNA Repair (Amst) 2005; 4:958-70. [PMID: 15996903 DOI: 10.1016/j.dnarep.2005.04.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2004] [Revised: 03/30/2005] [Accepted: 04/09/2005] [Indexed: 10/25/2022]
Abstract
The relatively high frequency with which ionizing radiation induces genomic instability suggests that a gene mutation occurring after irradiation is an unlikely cause of the phenotype. To search for mechanism(s) of initiation and perpetuation of this instability phenotype, gene expression profiles of clones exhibiting delayed chromosomal instability were analyzed. Microarray analysis using two pools of isogenic radiation-induced chromosomally unstable clones compared to an irradiated but chromosomally stable clone uncovered a set of 68 differentially expressed genes using two methods of analysis. Unexpectedly, all 68 genes were under-expressed relative to the chromosomally stable reference clone. Further analysis of the candidates placed the differentially expressed genes into pathways implicating differential MAP kinase signaling, ubiquitin/proteasome function, DNA repair, cell cycle control, lipid signaling, nucleotide metabolism, and other potentially disrupted pathways. Validation studies using northern and western blotting, and functional assays concluded that although differences in some of these pathways exist, no single gene or molecular pathway was found to be differentially regulated in all of the chromosomally unstable clones tested. Inferred from these data is that there are multiple potential molecular pathways and/or events that maintain the unstable phenotype, and no single expression pattern is linked to instability in the unstable clones analyzed.
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Affiliation(s)
- Andrew R Snyder
- Molecular and Cell Biology Graduate Program, Bressler Research Building, University of Maryland, 655 West Baltimore Street, Baltimore, MD 21201, USA
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Snyder AR, Morgan WF. Radiation-induced chromosomal instability and gene expression profiling: searching for clues to initiation and perpetuation. Mutat Res 2005; 568:89-96. [PMID: 15530542 DOI: 10.1016/j.mrfmmm.2004.06.048] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2004] [Revised: 05/21/2004] [Accepted: 06/02/2004] [Indexed: 01/30/2023]
Abstract
Radiation-induced genomic instability (RIGI) manifests in the progeny of cells surviving ionizing radiation (IR), and can be measured using such endpoints as delayed mutation, micronuclei formation, and chromosomal instability. The frequency of RIGI is relatively high, exceeding the gene mutation rate of IR by orders of magnitude, leading to conjecture that a gene mutation is not the cause of the phenotype. We have started to explore whether differential gene expression patterns are associated with the instability phenotype, in order to shed light on its initiation and perpetuation. Using GM10115 human-hamster hybrid-derived chromosomally stable and radiation-induced unstable clones, gene expression patterns were analyzed using microarray analysis. Two methods were used to find differentially expressed genes, and all candidate genes identified by these methods were under-expressed relative to the chromosomally stable reference sample. Among this set differentially expressed genes identified were two candidates with a relationship to the ubiquitin/proteasome pathway. While follow-up gene expression analyses have confirmed the under-expression of these two genes in some of our chromosomally unstable clones, preliminary functional studies have been unable to demonstrate a link to instability. It is anticipated that as we apply this technology to the study of radiation-induced genomic instability, clues to its onset will be revealed, ultimately contributing to a greater understanding of the mechanisms of radiation carcinogenesis.
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Affiliation(s)
- Andrew R Snyder
- Molecular and Cell Biology Graduate Program, University of Maryland, Bressler Research Building, Room 7-010, 655 West Baltimore Street, Baltimore, MD 21201-1559, USA.
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Wakui M, Morel L, Butfiloski EJ, Kim C, Sobel ES. Genetic Dissection of Systemic Lupus Erythematosus Pathogenesis: Partial Functional Complementation betweenSle1andSle3/5Demonstrates Requirement for Intracellular Coexpression for Full Phenotypic Expression of Lupus. THE JOURNAL OF IMMUNOLOGY 2005; 175:1337-45. [PMID: 16002739 DOI: 10.4049/jimmunol.175.2.1337] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Sle1 on chromosome 1 and Sle3/5 on chromosome 7 are two of the most critical lupus susceptibility loci of the New Zealand Black/White-derived NZM2410 mouse strain. In contrast to C57BL/6 mice congenic for either Sle1 (B6.Sle1) or Sle3/5 (B6.Sle3/5), strains that express only a modest lupus-related phenotype, the bicongenic B6.Sle1.Sle3/5 strain has a robust phenotype, suggesting a critical role for epistatic interactions in lupus pathogenesis. Mixed chimera experiments indicated that the two loci are functionally expressed by different cell populations and predicted that phenotypic expression of the phenotypic features of the B6.Sle1.Sle3/5 strain could be fully reproduced with a combination of B6.Sle1 and B6.Sle3/5 bone marrow. Contrary to our expectations, there was only a partial functional complementation in these mixed chimeras. Spleen enlargement, CD4:CD8 ratio elevation, and epitope spreading of autoantibodies were fully developed in B6+B6.Sle1.Sle3/5 but not in B6.Sle1+B6.Sle3/5 mixed chimeras. This study is the first to present evidence that the pathways mediated by two critical lupus susceptibility loci derived from the New Zealand White strain must be integrated intracellularly for epistatic interactions to occur. Our mixed chimera approach continues to provide novel insights into the functional genetic pathways underlying this important murine model of systemic autoimmunity.
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Affiliation(s)
- Masatoshi Wakui
- Department of Medicine and Division of Rheumatology and Clinical Immunology, College of Medicine, University of Florida, Gainesville, FL 32610, USA
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Liang M, Cowley AW, Hessner MJ, Lazar J, Basile DP, Pietrusz JL. Transcriptome analysis and kidney research: Toward systems biology. Kidney Int 2005; 67:2114-22. [PMID: 15882254 DOI: 10.1111/j.1523-1755.2005.00315.x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
An enormous amount of data has been generated in kidney research using transcriptome analysis techniques. In this review article, we first describe briefly the principles and major characteristics of several of these techniques. We then summarize the progress in kidney research that has been made by using transcriptome analysis, emphasizing the experience gained and the lessons learned. Several technical issues regarding DNA microarray are highlighted because of the rapidly increased use of this technology. It appears clear from this brief survey that transcriptome analysis is an effective and important tool for question-driven exploratory science. To further enhance the power of this and other high throughput, as well as conventional approaches, in future studies of the kidney, we propose a multidimensional systems biology paradigm that integrates investigation at multiple levels of biologic regulation toward the goal of achieving a global understanding of physiology and pathophysiology.
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Affiliation(s)
- Mingyu Liang
- Department of Physiology, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, USA.
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37
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Stone HB, Moulder JE, Coleman CN, Ang KK, Anscher MS, Barcellos-Hoff MH, Dynan WS, Fike JR, Grdina DJ, Greenberger JS, Hauer-Jensen M, Hill RP, Kolesnick RN, Macvittie TJ, Marks C, McBride WH, Metting N, Pellmar T, Purucker M, Robbins ME, Schiestl RH, Seed TM, Tomaszewski JE, Travis EL, Wallner PE, Wolpert M, Zaharevitz D. Models for Evaluating Agents Intended for the Prophylaxis, Mitigation and Treatment of Radiation Injuries Report of an NCI Workshop, December 3–4, 2003. Radiat Res 2004; 162:711-28. [PMID: 15548121 DOI: 10.1667/rr3276] [Citation(s) in RCA: 184] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
To develop approaches to prophylaxis/protection, mitigation and treatment of radiation injuries, appropriate models are needed that integrate the complex events that occur in the radiation-exposed organism. While the spectrum of agents in clinical use or preclinical development is limited, new research findings promise improvements in survival after whole-body irradiation and reductions in the risk of adverse effects of radiotherapy. Approaches include agents that act on the initial radiochemical events, agents that prevent or reduce progression of radiation damage, and agents that facilitate recovery from radiation injuries. While the mechanisms of action for most of the agents with known efficacy are yet to be fully determined, many seem to be operating at the tissue, organ or whole animal level as well as the cellular level. Thus research on prophylaxis/protection, mitigation and treatment of radiation injuries will require studies in whole animal models. Discovery, development and delivery of effective radiation modulators will also require collaboration among researchers in diverse fields such as radiation biology, inflammation, physiology, toxicology, immunology, tissue injury, drug development and radiation oncology. Additional investment in training more scientists in radiation biology and in the research portfolio addressing radiological and nuclear terrorism would benefit the general population in case of a radiological terrorism event or a large-scale accidental event as well as benefit patients treated with radiation.
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Affiliation(s)
- Helen B Stone
- National Cancer Institute, Bethesda, Maryland 20892, USA.
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