Proteomic Analysis Implicates Dominant Alterations of RNA Metabolism and the Proteasome Pathway in the Cellular Response to Carbon-Ion Irradiation

PLOS ONE, Dec 2019

Radiotherapy with heavy ions is considered advantageous compared to irradiation with photons due to the characteristics of the Braggs peak and the high linear energy transfer (LET) value. To understand the mechanisms of cellular responses to different LET values and dosages of heavy ion radiation, we analyzed the proteomic profiles of mouse embryo fibroblast MEF cells exposed to two doses from different LET values of heavy ion 12C. Total proteins were extracted from these cells and examined by Q Exactive with Liquid Chromatography (LC)—Electrospray Ionization (ESI) Tandem MS (MS/MS). Using bioinformatics approaches, differentially expressed proteins with 1.5 or 2.0-fold changes between different dosages of exposure were compared. With the higher the dosage and/or LET of ion irradiation, the worse response the cells were in terms of protein expression. For instance, compared to the control (0 Gy), 771 (20.2%) proteins in cells irradiated at 0.2 Gy of carbon-ion radiation with 12.6 keV/μm, 313 proteins (8.2%) in cells irradiated at 2 Gy of carbon-ion radiation with 12.6 keV/μm, and 243 proteins (6.4%) in cells irradiated at 2 Gy of carbon-ion radiation with 31.5 keV/μm exhibited changes of 1.5-fold or greater. Gene ontology (GO) analysis, Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis, Munich Information Center for Protein Sequences (MIPS) analysis, and BioCarta analysis all indicated that RNA metabolic processes (RNA splicing, destabilization and deadenylation) and proteasome pathways may play key roles in the cellular response to heavy-ion irradiation. Proteasome pathways ranked highest among all biological processes associated with heavy carbon-ion irradiation. In addition, network analysis revealed that cellular pathways involving proteins such as Col1a1 and Fn1 continued to respond to high dosages of heavy-ion irradiation, suggesting that these pathways still protect cells against damage. However, pathways such as those involving Ikbkg1 responded better at lower dosages than at higher dosages, implying that cell damage would occur when the networks involving these proteins stop responding. Our investigation provides valuable proteomic information for elucidating the mechanism of biological effects induced by carbon ions in general.

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Proteomic Analysis Implicates Dominant Alterations of RNA Metabolism and the Proteasome Pathway in the Cellular Response to Carbon-Ion Irradiation

October Proteomic Analysis Implicates Dominant Alterations of RNA Metabolism and the Proteasome Pathway in the Cellular Response to Carbon-Ion Irradiation Yu Wang 0 1 Hua Guan 0 1 Da-Fei Xie 0 1 Yi Xie 1 Xiao-Dan Liu 0 1 Qi Wang 0 1 Li Sui 1 Man Song 0 1 Hong Zhang 1 Jianhua Zhou 1 Ping-Kun Zhou 0 1 0 Department of Radiation Toxicology and Oncology, Beijing Key Laboratory for Radiation Biology, Beijing Institute of Radiation Medicine , Beijing , China , 2 Department of Heavy Ion Radiation Medicine, Institute of Modern Physics, Chinese Academy of Sciences , Lanzhou 730000, China, 3 iBioinfo Groups, Lexington , Massachusetts 02421, United States of America, 4 Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions, School of Radiation Medicine and Protection, Soochow University , Suzhou , China , 5 China Institute of Atomic Energy , Beijing 102413, China , 6 Department of Neuroregeneration, Nantong University , Nantong , China 1 Editor: Eric Y. Chuang, National Taiwan University , TAIWAN Radiotherapy with heavy ions is considered advantageous compared to irradiation with photons due to the characteristics of the Braggs peak and the high linear energy transfer (LET) value. To understand the mechanisms of cellular responses to different LET values and dosages of heavy ion radiation, we analyzed the proteomic profiles of mouse embryo fibroblast MEF cells exposed to two doses from different LET values of heavy ion 12C. Total proteins were extracted from these cells and examined by Q Exactive with Liquid Chromatography (LC)ÐElectrospray Ionization (ESI) Tandem MS (MS/MS). Using bioinformatics approaches, differentially expressed proteins with 1.5 or 2.0-fold changes between different dosages of exposure were compared. With the higher the dosage and/or LET of ion irradiation, the worse response the cells were in terms of protein expression. For instance, compared to the control (0 Gy), 771 (20.2%) proteins in cells irradiated at 0.2 Gy of carbon-ion radiation with 12.6 keV/μm, 313 proteins (8.2%) in cells irradiated at 2 Gy of carbon-ion radiation with 12.6 keV/μm, and 243 proteins (6.4%) in cells irradiated at 2 Gy of carbon-ion radiation with 31.5 keV/μm exhibited changes of 1.5-fold or greater. Gene ontology (GO) analysis, Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis, Munich Information Center for Protein Sequences (MIPS) analysis, and BioCarta analysis all indicated that RNA metabolic processes (RNA splicing, destabilization and deadenylation) and proteasome pathways may play key roles in the cellular response to heavy-ion irradiation. Proteasome pathways ranked highest among all biological processes associated with heavy carbon-ion irradiation. In addition, network analysis revealed that cellular pathways involving proteins such as Col1a1 and Fn1 continued to respond to high dosages of heavy-ion irradiation, suggesting that these pathways still protect cells against damage. However, - OPEN ACCESS Data Availability Statement: All relevant data are within the paper and its Supporting Information files. Funding: This work was supported by the National Natural Science Foundation of China (# U1432248). The author JZ is a professor at Nantong University, Nantong, China. He is also affiliated with iBioinfo Groups. The author played a role in data collection, analysis and discussion, and preparation of the manuscript as a professor at Nantong University. iBioinfo Groups only provided financial support in the form of salary for JZ, but did not have any additional role in the study design, data collection and analysis, decision to publish, or preparation of the manuscript. pathways such as those involving Ikbkg1 responded better at lower dosages than at higher dosages, implying that cell damage would occur when the networks involving these proteins stop responding. Our investigation provides valuable proteomic information for elucidating the mechanism of biological effects induced by carbon ions in general. Introduction Radiotherapy using heavy ions beams or protons is becoming an important component of malignant tumor therapy [ 1, 2 ]. Heavy-ion radiation has a number of advantages for cancer radiotherapy over photon therapy. The major advantage is the inverted dose profile, which features a sharp longitudinal dose drop, referred to as the Bragg peak, at the end of the particle range [3]. The increased therapeutic ratio permits dose escalation within the tumor, consequently resulting in improved tumor control. Another advantage is the high linear energy transfer (LET) characteristics of heavy-ion beams [ 4 ]. The biological consequences of radiation exposure depend not only on the radiation dose and dose rate but also on the radiation quality. High-LET radiation, such as carbon-ion beam, deposits higher energy in tissues and causes greater damage than low-LET γ- or X-ray irradiation [ 4, 5 ]. The radiation energy deposition increases as the LET value incre (...truncated)


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Yu Wang, Hua Guan, Da-Fei Xie, Yi Xie, Xiao-Dan Liu, Qi Wang, Li Sui, Man Song, Hong Zhang, Jianhua Zhou, Ping-Kun Zhou. Proteomic Analysis Implicates Dominant Alterations of RNA Metabolism and the Proteasome Pathway in the Cellular Response to Carbon-Ion Irradiation, PLOS ONE, 2016, Volume 11, Issue 10, DOI: 10.1371/journal.pone.0163896