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Vashishta M, Kumar V, Guha C, Wu X, Dwarakanath BS. Enhanced Glycolysis Confers Resistance Against Photon but Not Carbon Ion Irradiation in Human Glioma Cell Lines. Cancer Manag Res 2023; 15:1-16. [PMID: 36628255 PMCID: PMC9826608 DOI: 10.2147/cmar.s385968] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Accepted: 12/17/2022] [Indexed: 01/05/2023] Open
Abstract
Purpose Metabolic reprogramming is a key hallmark in various malignancies and poses a challenge in achieving success with various therapies. Enhanced glycolysis is known to confer resistance against photon irradiation while the tumor response to carbon ion irradiation (CII) has not been investigated. This study aimed to investigate the effects of enhanced glycolysis on the response of human glioma cell lines to CII compared to the response to X-rays. Material and Methods Glycolysis was stimulated using Dinitrophenol (DNP), a mild OXPHOS inhibitor, in three human glioma cell lines (U251, U87, and LN229) and assessed by monitoring glucose uptake and utilization as well as expression of regulators of glycolysis (glucose transporter protein type 1(Glut1), hexokinase-II (HKII), and Pyruvate Kinase-2 (PKM2). Radiation (X-rays and CII) induced loss of clonogenic survival growth inhibition and perturbations in cell cycle progression (G2+M block), cytogenetic damage (micronuclei formation), apoptosis, necrosis (reflecting interphase death), and cell migration (Scratch assay) were investigated as parameters of radiation response. Results DNP (1 mM) enhanced the expression levels of GLUT1, HKII, and PKM2 by 30-60% and glucose uptake as well as usage by nearly 3 folds in U251 cells suggesting the stimulation of glycolysis. Enhanced glycolysis attenuated the loss of clonogenic survival with D10 doses increasing by 20% to 65% in these cell lines, while no significant changes were noted following CII. Concomitantly, dose-dependent growth inhibition, and cytogenetic damage as well as apoptosis and necrosis induced by X-rays were also reduced by elevated glycolysis in U251 and LN229 cells by 20-50%. However, stimulation of glycolysis enhanced the X-ray-induced cell migration, while it had negligible effect on migration following CII. Conclusion Our results suggest that enhanced glycolysis confers resistance against X-ray-induced cell death and migration, while it may not significantly alter the cellular responses to carbon ion irradiation.
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Affiliation(s)
- Mohit Vashishta
- R&D Department, Shanghai Proton and Heavy Ion Center (SPHIC), Shanghai, People’s Republic of China,Shanghai Key Laboratory of Radiation Oncology (20dz2261000), Shanghai, People’s Republic of China,Shanghai Engineering Research Center of Proton and Heavy Ion Radiation Therapy, Shanghai, People’s Republic of China,Rangel College of Pharmacy, Texas A&M University, College Station, TX, USA
| | - Vivek Kumar
- R&D Department, Shanghai Proton and Heavy Ion Center (SPHIC), Shanghai, People’s Republic of China,Shanghai Key Laboratory of Radiation Oncology (20dz2261000), Shanghai, People’s Republic of China,Shanghai Engineering Research Center of Proton and Heavy Ion Radiation Therapy, Shanghai, People’s Republic of China
| | - Chandan Guha
- Albert Einstein College of Medicine, The Bronx, NY, USA
| | - Xiaodong Wu
- R&D Department, Shanghai Proton and Heavy Ion Center (SPHIC), Shanghai, People’s Republic of China,Shanghai Key Laboratory of Radiation Oncology (20dz2261000), Shanghai, People’s Republic of China,Shanghai Engineering Research Center of Proton and Heavy Ion Radiation Therapy, Shanghai, People’s Republic of China
| | - Bilikere S Dwarakanath
- R&D Department, Shanghai Proton and Heavy Ion Center (SPHIC), Shanghai, People’s Republic of China,Shanghai Key Laboratory of Radiation Oncology (20dz2261000), Shanghai, People’s Republic of China,Shanghai Engineering Research Center of Proton and Heavy Ion Radiation Therapy, Shanghai, People’s Republic of China,Central Research Facility, Sri Ramachandra Institute of Higher Education and Research, Porur, ChennaiIndia,Indian Academy Degree College Autonomous (IADC-A), Bengaluru, Karnataka, India,Correspondence: Bilikere S Dwarakanath, Indian Academy Degree College Autonomous (IADC-A), 230, Hennur Main Rd, Meganahalli, Kalyan Nagar, Bengaluru, Karnataka, 560043, India, Tel +91 9952081077, Email
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2
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Identification of the key genes and pathways involved in the tumorigenesis and prognosis of kidney renal clear cell carcinoma. Sci Rep 2020; 10:4271. [PMID: 32144299 PMCID: PMC7060270 DOI: 10.1038/s41598-020-61162-4] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2019] [Accepted: 02/17/2020] [Indexed: 11/09/2022] Open
Abstract
Kidney renal clear cell carcinoma (KIRC) is the most common renal cell carcinoma (RCC). However, patients with KIRC usually have poor prognosis due to limited biomarkers for early detection and prognosis prediction. In this study, we analysed key genes and pathways involved in KIRC from an array dataset including 26 tumour and 26 adjacent normal tissue samples. Weighted gene co-expression network analysis (WGCNA) was performed with the WGCNA package, and 20 modules were characterized as having the highest correlation with KIRC. The upregulated genes in the tumour samples are involved in the innate immune response, whereas the downregulated genes contribute to the cellular catabolism of glucose, amino acids and fatty acids. Furthermore, the key genes were evaluated through a protein-protein interaction (PPI) network combined with a co-expression network. The comparatively lower expression of AGXT, PTGER3 and SLC12A3 in tumours correlates with worse prognosis in KIRC patients, while higher expression of ALOX5 predicts reduced survival. Our integrated analysis illustrated the hub genes involved in KIRC tumorigenesis, shedding light on the development of prognostic markers. Further understanding of the function of the identified KIRC hub genes could provide deep insights into the molecular mechanisms of KIRC.
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Fan PC, Zhang Y, Wang Y, Wei W, Zhou YX, Xie Y, Wang X, Qi YZ, Chang L, Jia ZP, Zhou Z, Guan H, Zhang H, Xu P, Zhou PK. Quantitative proteomics reveals mitochondrial respiratory chain as a dominant target for carbon ion radiation: Delayed reactive oxygen species generation caused DNA damage. Free Radic Biol Med 2019; 130:436-445. [PMID: 30395972 DOI: 10.1016/j.freeradbiomed.2018.10.449] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/18/2018] [Revised: 10/27/2018] [Accepted: 10/29/2018] [Indexed: 01/09/2023]
Abstract
Heavy ion radiotherapy has shown great promise for cancer therapy. Understanding the cellular response mechanism to heavy ion radiation is required to explore measures of overcoming devastating side effects. Here, we performed a quantitative proteomic analysis to investigate the mechanism of carbon ion irradiation on human AHH-1 lymphoblastoid cells. We identified 4602 proteins and quantified 4569 proteins showing high coverage in the mitochondria. Data are available via ProteomeXchange with identifier PXD008351. After stringent filtering, 290 proteins were found to be significantly up-regulated and 16 proteins were down-regulated. Functional analysis revealed that these up-regulated proteins were enriched in the process of DNA damage repair, mitochondrial ribosome, and particularly mitochondrial respiratory chain, accounting for approximately 50% of the accumulated proteins. Bioinformatics and functional analysis demonstrated that these up-regulated mitochondrial respiratory chain proteins enhanced ATP production and simultaneously reactive oxygen species release. More importantly, increased reactive oxygen species led to secondary organelle injury and lagged DNA double-strand breaks. Consistently, the expression of antioxidant enzymes was up-regulated for free radical scavenging. The mechanism of lagged secondary injury originated from disturbances in the mitochondrial respiratory chain. Our results provided a novel target for cell self-repair against heavy ion radiation-induced cellular damage.
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Affiliation(s)
- Peng-Cheng Fan
- State Key Laboratory of Proteomics, National Center for Protein Sciences Beijing, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing102206, China; Beijing Key Laboratory for Radiobiology, Department of Radiation Toxicology and Oncology, Beijing Institute of Radiation Medicine, Beijing 100850, China; Key Laboratory of the Plateau of Environmental Damage Control, General Hospital of Lanzhou, Lanzhou 730050, China
| | - Yao Zhang
- State Key Laboratory of Proteomics, National Center for Protein Sciences Beijing, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing102206, China; State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, College of Ecology and Evolution, Sun Yat-Sen University, Guangzhou 510275, China
| | - Yu Wang
- Beijing Key Laboratory for Radiobiology, Department of Radiation Toxicology and Oncology, Beijing Institute of Radiation Medicine, Beijing 100850, China
| | - Wei Wei
- State Key Laboratory of Proteomics, National Center for Protein Sciences Beijing, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing102206, China
| | - Yan-Xia Zhou
- State Key Laboratory of Proteomics, National Center for Protein Sciences Beijing, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing102206, China
| | - Yi Xie
- Department of Heavy Ion Radiation Medicine, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou 730000, China
| | - Xin Wang
- Key Laboratory of the Plateau of Environmental Damage Control, General Hospital of Lanzhou, Lanzhou 730050, China
| | - Ying-Zi Qi
- State Key Laboratory of Proteomics, National Center for Protein Sciences Beijing, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing102206, China
| | - Lei Chang
- State Key Laboratory of Proteomics, National Center for Protein Sciences Beijing, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing102206, China
| | - Zheng-Ping Jia
- Key Laboratory of the Plateau of Environmental Damage Control, General Hospital of Lanzhou, Lanzhou 730050, China
| | - Zhe Zhou
- Beijing Key Laboratory for Radiobiology, Department of Radiation Toxicology and Oncology, Beijing Institute of Radiation Medicine, Beijing 100850, China
| | - Hua Guan
- Beijing Key Laboratory for Radiobiology, Department of Radiation Toxicology and Oncology, Beijing Institute of Radiation Medicine, Beijing 100850, China
| | - Hong Zhang
- Department of Heavy Ion Radiation Medicine, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou 730000, China
| | - Ping Xu
- State Key Laboratory of Proteomics, National Center for Protein Sciences Beijing, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing102206, China; Key Laboratory of Combinatorial Biosynthesis and Drug Discovery of Ministry of Education, School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China.
| | - Ping-Kun Zhou
- Beijing Key Laboratory for Radiobiology, Department of Radiation Toxicology and Oncology, Beijing Institute of Radiation Medicine, Beijing 100850, China.
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Chaiswing L, Weiss HL, Jayswal RD, St. Clair DK, Kyprianou N. Profiles of Radioresistance Mechanisms in Prostate Cancer. Crit Rev Oncog 2018; 23:39-67. [PMID: 29953367 PMCID: PMC6231577 DOI: 10.1615/critrevoncog.2018025946] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Radiation therapy (RT) is commonly used for the treatment of localized prostate cancer (PCa). However, cancer cells often develop resistance to radiation through unknown mechanisms and pose an intractable challenge. Radiation resistance is highly unpredictable, rendering the treatment less effective in many patients and frequently causing metastasis and cancer recurrence. Understanding the molecular events that cause radioresistance in PCa will enable us to develop adjuvant treatments for enhancing the efficacy of RT. Radioresistant PCa depends on the elevated DNA repair system and the intracellular levels of reactive oxygen species (ROS) to proliferate, self-renew, and scavenge anti-cancer regimens, whereas the elevated heat shock protein 90 (HSP90) and the epithelial-mesenchymal transition (EMT) enable radioresistant PCa cells to metastasize after exposure to radiation. The up-regulation of the DNA repairing system, ROS, HSP90, and EMT effectors has been studied extensively, but not targeted by adjuvant therapy of radioresistant PCa. Here, we emphasize the effects of ionizing radiation and the mechanisms driving the emergence of radioresistant PCa. We also address the markers of radioresistance, the gene signatures for the predictive response to radiotherapy, and novel therapeutic platforms for targeting radioresistant PCa. This review provides significant insights into enhancing the current knowledge and the understanding toward optimization of these markers for the treatment of radioresistant PCa.
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Affiliation(s)
| | - Heidi L. Weiss
- The Markey Biostatistics and Bioinformatics Shared Resource Facility
| | - Rani D. Jayswal
- The Markey Biostatistics and Bioinformatics Shared Resource Facility
| | | | - Natasha Kyprianou
- Department of Toxicology and Cancer Biology
- Department of Urology
- Department of Biochemistry, University of Kentucky, Lexington, Kentucky
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5
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Chang L, Graham P, Hao J, Ni J, Deng J, Bucci J, Malouf D, Gillatt D, Li Y. Cancer stem cells and signaling pathways in radioresistance. Oncotarget 2017; 7:11002-17. [PMID: 26716904 PMCID: PMC4905454 DOI: 10.18632/oncotarget.6760] [Citation(s) in RCA: 88] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Accepted: 12/22/2015] [Indexed: 12/17/2022] Open
Abstract
Radiation therapy (RT) is one of the most important strategies in cancer treatment. Radioresistance (the failure to RT) results in locoregional recurrence and metastasis. Therefore, it is critically important to investigate the mechanisms leading to cancer radioresistance to overcome this problem and increase patients' survival. Currently, the majority of the radioresistance-associated researches have focused on preclinical studies. Although the exact mechanisms of cancer radioresistance have not been fully uncovered, accumulating evidence supports that cancer stem cells (CSCs) and different signaling pathways play important roles in regulating radiation response and radioresistance. Therefore, targeting CSCs or signaling pathway proteins may hold promise for developing novel combination modalities and overcoming radioresistance. The present review focuses on the key evidence of CSC markers and several important signaling pathways in cancer radioresistance and explores innovative approaches for future radiation treatment.
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Affiliation(s)
- Lei Chang
- Cancer Care Centre, St George Hospital, Kogarah, NSW, Australia.,St George and Sutherland Clinical School, Faculty of Medicine, University of New South Wales, Kensington, NSW, Australia
| | - Peter Graham
- Cancer Care Centre, St George Hospital, Kogarah, NSW, Australia.,St George and Sutherland Clinical School, Faculty of Medicine, University of New South Wales, Kensington, NSW, Australia
| | - Jingli Hao
- Cancer Care Centre, St George Hospital, Kogarah, NSW, Australia.,St George and Sutherland Clinical School, Faculty of Medicine, University of New South Wales, Kensington, NSW, Australia
| | - Jie Ni
- Cancer Care Centre, St George Hospital, Kogarah, NSW, Australia.,St George and Sutherland Clinical School, Faculty of Medicine, University of New South Wales, Kensington, NSW, Australia
| | - Junli Deng
- Cancer Care Centre, St George Hospital, Kogarah, NSW, Australia.,St George and Sutherland Clinical School, Faculty of Medicine, University of New South Wales, Kensington, NSW, Australia
| | - Joseph Bucci
- Cancer Care Centre, St George Hospital, Kogarah, NSW, Australia.,St George and Sutherland Clinical School, Faculty of Medicine, University of New South Wales, Kensington, NSW, Australia
| | - David Malouf
- Department of Urology, St George Hospital, Kogarah, NSW, Australia
| | - David Gillatt
- Department of Urology, St George Hospital, Kogarah, NSW, Australia.,Australian School of Advanced Medicine, Macquarie University, Sydney, NSW, Australia
| | - Yong Li
- Cancer Care Centre, St George Hospital, Kogarah, NSW, Australia.,St George and Sutherland Clinical School, Faculty of Medicine, University of New South Wales, Kensington, NSW, Australia
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6
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Identification of protein biomarkers and signaling pathways associated with prostate cancer radioresistance using label-free LC-MS/MS proteomic approach. Sci Rep 2017; 7:41834. [PMID: 28225015 PMCID: PMC5320484 DOI: 10.1038/srep41834] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Accepted: 12/28/2016] [Indexed: 12/20/2022] Open
Abstract
Identifying biomarkers and signaling pathways are important for the management of prostate cancer (CaP) radioresistance. In this study, we identified differential proteins and signaling pathways from parental CaP cell lines and CaP radioresistant (RR) sublines using a label-free LC-MS/MS proteomics approach. A total of 309 signaling pathway proteins were identified to be significantly altered between CaP and CaP-RR cells (p ≤ 0.05, fold differences >1.5, ≥80% power). Among these proteins, nineteen are common among three paired CaP cell lines and associated with metastasis, progression and radioresistance. The PI3K/Akt, VEGF and glucose metabolism pathways were identified as the main pathways associated with CaP radioresistance. In addition, the identified potential protein markers were further validated in CaP-RR cell lines and subcutaneous (s.c) animal xenografts by western blotting and immunohistochemistry, respectively and protein aldolase A (ALDOA) was selected for a radiosensitivity study. We found the depletion of ALDOA combined with radiotherapy effectively reduced colony formation, induced more apoptosis and increased radiosensitivity in CaP-RR cells. Our findings indicate that CaP radioresistance is caused by multifactorial traits and downregulation of ALDOA increases radiosensitivity in CaP-RR cells, suggesting that controlling these identified proteins or signaling pathways in combination with radiotherapy may hold promise to overcome CaP radioresistance.
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7
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Tian F, Zhao J, Fan X, Kang Z. Weighted gene co-expression network analysis in identification of metastasis-related genes of lung squamous cell carcinoma based on the Cancer Genome Atlas database. J Thorac Dis 2017; 9:42-53. [PMID: 28203405 PMCID: PMC5303106 DOI: 10.21037/jtd.2017.01.04] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Accepted: 10/20/2016] [Indexed: 11/06/2022]
Abstract
BACKGROUND Lung squamous cell carcinoma (lung SCC) is a common type of malignancy. Its pathogenesis mechanism of tumor development is unclear. The aim of this study was to identify key genes for diagnosis biomarkers in lung SCC metastasis. METHODS We searched and downloaded mRNA expression data and clinical data from The Cancer Genome Atlas (TCGA) database to identify differences in mRNA expression of primary tumor tissues from lung SCC with and without metastasis. Gene co-expression network analysis, protein-protein interaction (PPI) network, Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis and quantitative real-time polymerase chain reactions (qRT-PCR) were used to explore the biological functions of the identified dysregulated genes. RESULTS Four hundred and eighty-two differentially expressed genes (DEGs) were identified between lung SCC with and without metastasis. Nineteen modules were identified in lung SCC through weighted gene co-expression network analysis (WGCNA). Twenty-three DEGs and 26 DEGs were significantly enriched in the respective pink and black module. KEGG pathway analysis displayed that 26 DEGs in the black module were significantly enriched in bile secretion pathway. Forty-nine DEGs in the two gene co-expression module were used to construct PPI network. CFTR in the black module was the hub protein, had the connectivity with 182 genes. The results of qRT-PCR displayed that FIGF, SFTPD, DYNLRB2 were significantly down-regulated in the tumor samples of lung SCC with metastasis and CFTR, SCGB3A2, SSTR1, SCTR, ROPN1L had the down-regulation tendency in lung SCC with metastasis compared to lung SCC without metastasis. CONCLUSIONS The dysregulated genes including CFTR, SCTR and FIGF might be involved in the pathology of lung SCC metastasis and could be used as potential diagnosis biomarkers or therapeutic targets for lung SCC.
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Affiliation(s)
- Feng Tian
- Department of Respiratory Medicine, Linyi People’s Hospital, Linyi 276000, China
| | - Jinlong Zhao
- Department of Thoracic Surgery, Linyi People’s Hospital, Linyi 276000, China
| | - Xinlei Fan
- Department of Internal Medicine, Shandong Medical College, Linyi 276000, China
| | - Zhenxing Kang
- Department of Respiratory Medicine, The Third People’s Hospital of Linyi, Linyi 276000, China
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Wang Y, Guan H, Xie DF, Xie Y, Liu XD, Wang Q, Sui L, Song M, Zhang H, Zhou J, Zhou PK. Proteomic Analysis Implicates Dominant Alterations of RNA Metabolism and the Proteasome Pathway in the Cellular Response to Carbon-Ion Irradiation. PLoS One 2016; 11:e0163896. [PMID: 27711237 PMCID: PMC5053480 DOI: 10.1371/journal.pone.0163896] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2015] [Accepted: 09/18/2016] [Indexed: 12/25/2022] Open
Abstract
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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Affiliation(s)
- Yu Wang
- Department of Radiation Toxicology and Oncology, Beijing Key Laboratory for Radiation Biology, Beijing Institute of Radiation Medicine, Beijing, China
| | - Hua Guan
- Department of Radiation Toxicology and Oncology, Beijing Key Laboratory for Radiation Biology, Beijing Institute of Radiation Medicine, Beijing, China
| | - Da-Fei Xie
- Department of Radiation Toxicology and Oncology, Beijing Key Laboratory for Radiation Biology, Beijing Institute of Radiation Medicine, Beijing, China
| | - Yi Xie
- Department of Heavy Ion Radiation Medicine, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou 730000, China
| | - Xiao-Dan Liu
- Department of Radiation Toxicology and Oncology, Beijing Key Laboratory for Radiation Biology, Beijing Institute of Radiation Medicine, Beijing, China
| | - Qi Wang
- Department of Radiation Toxicology and Oncology, Beijing Key Laboratory for Radiation Biology, Beijing Institute of Radiation Medicine, Beijing, China
| | - Li Sui
- China Institute of Atomic Energy, Beijing 102413, China
| | - Man Song
- Department of Radiation Toxicology and Oncology, Beijing Key Laboratory for Radiation Biology, Beijing Institute of Radiation Medicine, Beijing, China
- Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions, School of Radiation Medicine and Protection, Soochow University, Suzhou, China
| | - Hong Zhang
- Department of Heavy Ion Radiation Medicine, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou 730000, China
| | - Jianhua Zhou
- iBioinfo Groups, Lexington, Massachusetts 02421, United States of America
- Department of Neuroregeneration, Nantong University, Nantong, China
- * E-mail: (PKZ); (JZ)
| | - Ping-Kun Zhou
- Department of Radiation Toxicology and Oncology, Beijing Key Laboratory for Radiation Biology, Beijing Institute of Radiation Medicine, Beijing, China
- Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions, School of Radiation Medicine and Protection, Soochow University, Suzhou, China
- * E-mail: (PKZ); (JZ)
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Inzhevatkin EV, Savchenko AA. The nonspecific metabolic reaction of cells to extreme exposures. BIOL BULL+ 2016. [DOI: 10.1134/s1062359016010064] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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10
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Shi K, Bing ZT, Cao GQ, Guo L, Cao YN, Jiang HO, Zhang MX. Identify the signature genes for diagnose of uveal melanoma by weight gene co-expression network analysis. Int J Ophthalmol 2015; 8:269-74. [PMID: 25938039 DOI: 10.3980/j.issn.2222-3959.2015.02.10] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2014] [Accepted: 12/08/2014] [Indexed: 02/05/2023] Open
Abstract
AIM To identify and understand the relationship between co-expression pattern and clinic traits in uveal melanoma, weighted gene co-expression network analysis (WGCNA) is applied to investigate the gene expression levels and patient clinic features. Uveal melanoma is the most common primary eye tumor in adults. Although many studies have identified some important genes and pathways that were relevant to progress of uveal melanoma, the relationship between co-expression and clinic traits in systems level of uveal melanoma is unclear yet. We employ WGCNA to investigate the relationship underlying molecular and phenotype in this study. METHODS Gene expression profile of uveal melanoma and patient clinic traits were collected from the Gene Expression Omnibus (GEO) database. The gene co-expression is calculated by WGCNA that is the R package software. The package is used to analyze the correlation between pairs of expression levels of genes. The function of the genes were annotated by gene ontology (GO). RESULTS In this study, we identified four co-expression modules significantly correlated with clinic traits. Module blue positively correlated with radiotherapy treatment. Module purple positively correlates with tumor location (sclera) and negatively correlates with patient age. Module red positively correlates with sclera and negatively correlates with thickness of tumor. Module black positively correlates with the largest tumor diameter (LTD). Additionally, we identified the hug gene (top connectivity with other genes) in each module. The hub gene RPS15A, PTGDS, CD53 and MSI2 might play a vital role in progress of uveal melanoma. CONCLUSION From WGCNA analysis and hub gene calculation, we identified RPS15A, PTGDS, CD53 and MSI2 might be target or diagnosis for uveal melanoma.
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Affiliation(s)
- Kai Shi
- Department of Ophthalmology, West China Hospital, Sichuan University, Chendu 610041, Sichuan Province, China ; Molecular Medicine Research Center, West China Hospital, Sichuan University, Chendu 610041, Sichuan Province, China
| | - Zhi-Tong Bing
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou 730000, Gansu Province, China
| | - Gui-Qun Cao
- Molecular Medicine Research Center, West China Hospital, Sichuan University, Chendu 610041, Sichuan Province, China
| | - Ling Guo
- College of Electrical Engineering, Northwest University for Nationalities, Lanzhou 730030, Gansu Province, China
| | - Ya-Na Cao
- Department of Ophthalmology, West China Hospital, Sichuan University, Chendu 610041, Sichuan Province, China ; Molecular Medicine Research Center, West China Hospital, Sichuan University, Chendu 610041, Sichuan Province, China
| | - Hai-Ou Jiang
- Molecular Medicine Research Center, West China Hospital, Sichuan University, Chendu 610041, Sichuan Province, China
| | - Mei-Xia Zhang
- Department of Ophthalmology, West China Hospital, Sichuan University, Chendu 610041, Sichuan Province, China ; Molecular Medicine Research Center, West China Hospital, Sichuan University, Chendu 610041, Sichuan Province, China
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11
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Zhang H, Xu Y, Papanastasopoulos P, Stebbing J, Giamas G. Broader implications of SILAC-based proteomics for dissecting signaling dynamics in cancer. Expert Rev Proteomics 2014; 11:713-31. [PMID: 25345469 DOI: 10.1586/14789450.2014.971115] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Large-scale transcriptome and epigenome analyses have been widely utilized to discover gene alterations implicated in cancer development at the genetic level. However, mapping of signaling dynamics at the protein level is likely to be more insightful and needed to complement massive genomic data. Stable isotope labeling with amino acids in cell culture (SILAC)-based proteomic analysis represents one of the most promising comparative quantitative methods that has been extensively employed in proteomic research. This technology allows for global, robust and confident identification and quantification of signal perturbations important for the progress of human diseases, particularly malignancies. The present review summarizes the latest applications of in vitro and in vivo SILAC-based proteomics in identifying global proteome/phosphoproteome and genome-wide protein-protein interactions that contribute to oncogenesis, highlighting the recent advances in dissecting signaling dynamics in cancer.
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Affiliation(s)
- Hua Zhang
- Department of Surgery and Cancer, Division of Cancer, Imperial College London, Hammersmith Hospital Campus, ICTEM Building, Du Cane Road, London, W12 ONN, UK
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