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Zhao L, Deng J, Ma LB, Zhang WP, Khalil MM, Karrow NA, Qi DS, Sun LH. Dietary Se deficiency dysregulates metabolic and cell death signaling in aggravating the AFB1 hepatotoxicity of chicks. Food Chem Toxicol 2020; 149:111938. [PMID: 33348051 DOI: 10.1016/j.fct.2020.111938] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 12/09/2020] [Accepted: 12/15/2020] [Indexed: 12/31/2022]
Abstract
The objective of this study was to use isobaric tags for relative and absolute quantitation (iTRAQ) proteomic technology to systematically analyze the hepatotoxic mechanism of aflatoxin B1 (AFB1) and its prevention by Se in broilers. Four groups of day-old broilers were allocated into a 2 × 2 factorial design trial that fed a Se-deficient based diet (BD) or the BD + 1.0 mg AFB1/kg, 0.3 mg Se/kg, or 1.0 mg AFB1/kg plus 0.3 mg Se/kg for 3 wk. Dietary AFB1 increased serum ALT and decreased total protein and albumin concentrations, and induced hepatic histopathological lesions in Se adequate groups. Notably, Se deficiency exacerbated these AFB1-induced changes. Furthermore, Se deficiency reduced hepatic glutathione peroxidase but increased thioredoxin reductase and glutathione S-transferase activities and 8-hydroxydeoxyguanosine concentration in AFB1 administrated groups. Moreover, AFB1 dysregulated 261 co-differentially expressed proteins (DEPs) in both Se adequate and deficiency diets, and Se deficiency dysregulated 64 DEPs in AFB1 administrated diets. These DEPs are mainly related to phase I and II metabolizing enzymes, heat shock proteins, DNA repair, fatty acid metabolism and apoptosis. The in vitro study has verified that aldo-keto reductase family1, member10 plays an important role in AFB1-induced hepatotoxicity and Se-mediated detoxification of AFB1 in a chicken leghorn male hepatoma cells. Conclusively, this study has analyzed the hepatic proteome response to dietary AFB1 and Se, and thus shed new light on the mechanisms of hepatotoxicity of AFB1 and its detoxification by Se in broilers.
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Affiliation(s)
- Ling Zhao
- Department of Animal Nutrition and Feed Science, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Jiang Deng
- Department of Animal Nutrition and Feed Science, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Li-Bao Ma
- Department of Animal Nutrition and Feed Science, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Wan-Po Zhang
- Department of Veterinary Pathology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, China
| | | | | | - De-Sheng Qi
- Department of Animal Nutrition and Feed Science, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China.
| | - Lv-Hui Sun
- Department of Animal Nutrition and Feed Science, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China.
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2
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An Integrated Transcriptome and Proteome Analysis Reveals New Insights into Russeting of Bagging and Non-Bagging "Golden Delicious" Apple. Int J Mol Sci 2019; 20:ijms20184462. [PMID: 31510041 PMCID: PMC6769969 DOI: 10.3390/ijms20184462] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Revised: 09/06/2019] [Accepted: 09/06/2019] [Indexed: 12/12/2022] Open
Abstract
Apple skin russeting naturally occurs in many varieties, particularly in “Golden Delicious” and its pedigree, and is regarded as a non-invasive physiological disorder partly caused by excessive deposition of lignin. However, the understanding of its molecular mechanism is still limited. In this study, we used iTRAQ (isobaric tags for relative and absolute quantitation) and RNA-seq to detect the changes in the expression levels of genes and proteins in three developmental stages of russeting formation, in russeted (non-bagging) and non-russeted (bagging) skin of “Golden Delicious” apple. 2856 differentially expressed genes and 942 differentially expressed proteins in the comparison groups were detected at the transcript level and protein level, respectively. A correlation analysis of the transcriptomics and proteomics data revealed that four genes (MD03G1059200, MD08G1009200, MD17G1092400, and MD17G1225100) involved in lignin biosynthesis are significant changed during apple russeting formation. Additionally, 92 transcription factors, including 4 LIM transcription factors, may be involved in apple russeting formation. Among them, one LIM transcription factor (MD15G1068200) was capable of binding to the PAL-box like (CCACTTGAGTAC) element, which indicated it was potentially involved in lignin biosynthesis. This study will provide further views on the molecular mechanisms controlling apple russeting formation.
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3
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Ramello MC, Benzaïd I, Kuenzi BM, Lienlaf-Moreno M, Kandell WM, Santiago DN, Pabón-Saldaña M, Darville L, Fang B, Rix U, Yoder S, Berglund A, Koomen JM, Haura EB, Abate-Daga D. An immunoproteomic approach to characterize the CAR interactome and signalosome. Sci Signal 2019; 12:12/568/eaap9777. [PMID: 30755478 DOI: 10.1126/scisignal.aap9777] [Citation(s) in RCA: 102] [Impact Index Per Article: 20.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Adoptive transfer of T cells that express a chimeric antigen receptor (CAR) is an approved immunotherapy that may be curative for some hematological cancers. To better understand the therapeutic mechanism of action, we systematically analyzed CAR signaling in human primary T cells by mass spectrometry. When we compared the interactomes and the signaling pathways activated by distinct CAR-T cells that shared the same antigen-binding domain but differed in their intracellular domains and their in vivo antitumor efficacy, we found that only second-generation CARs induced the expression of a constitutively phosphorylated form of CD3ζ that resembled the endogenous species. This phenomenon was independent of the choice of costimulatory domains, or the hinge/transmembrane region. Rather, it was dependent on the size of the intracellular domains. Moreover, the second-generation design was also associated with stronger phosphorylation of downstream secondary messengers, as evidenced by global phosphoproteome analysis. These results suggest that second-generation CARs can activate additional sources of CD3ζ signaling, and this may contribute to more intense signaling and superior antitumor efficacy that they display compared to third-generation CARs. Moreover, our results provide a deeper understanding of how CARs interact physically and/or functionally with endogenous T cell molecules, which will inform the development of novel optimized immune receptors.
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Affiliation(s)
- Maria C Ramello
- Department of Immunology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA
| | - Ismahène Benzaïd
- Department of Immunology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA
| | - Brent M Kuenzi
- Department of Drug Discovery, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA.,Cancer Biology Ph.D. Program, University of South Florida, Tampa, FL 33620, USA
| | - Maritza Lienlaf-Moreno
- Department of Immunology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA
| | - Wendy M Kandell
- Department of Immunology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA.,Cancer Biology Ph.D. Program, University of South Florida, Tampa, FL 33620, USA
| | - Daniel N Santiago
- Department of Immunology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA.,Department of Integrated Mathematical Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA
| | - Mibel Pabón-Saldaña
- Department of Immunology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA.,Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA
| | - Lancia Darville
- Proteomics Core Facility, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA
| | - Bin Fang
- Proteomics Core Facility, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA
| | - Uwe Rix
- Department of Drug Discovery, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA
| | - Sean Yoder
- Molecular Genomics Core Facility, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA
| | - Anders Berglund
- Department of Bioinformatics and Biostatistics, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA
| | - John M Koomen
- Proteomics Core Facility, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA.,Department of Molecular Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA
| | - Eric B Haura
- Department of Thoracic Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA
| | - Daniel Abate-Daga
- Department of Immunology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA. .,Department of Cutaneous Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA.,Department of Oncological Sciences, University of South Florida, Tampa, FL 33612, USA
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4
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Zou Y, Dai W, Lei W, Su S, Huang Q, Zhou Z, Chen C, Li Z. Identification of proteins interacting with pORF5 in the pathogenesis of C. trachomatis. Am J Transl Res 2018; 10:1633-1647. [PMID: 30018706 PMCID: PMC6038076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2016] [Accepted: 03/21/2017] [Indexed: 06/08/2023]
Abstract
OBJECTIVE This study is to identify and investigate the proteins interacting with pORF5 implicated in the pathogenesis of C. trachomatis. METHODS The isobaric tags for relative and absolute quantitation (iTRAQ) approach combined with nano liquid chromatography-tandem mass spectrometry (NanoLC-MS/MS) analysis was applied to identify and quantify the differentially expressed proteins in the pORF5-transfected HeLa (pORF5-HeLa) cells and the control vector-transfected HeLa (vector-HeLa) cells. Quantitative real-time PCR (qRT-PCR) and Western blot analysis were performed to detect the mRNA and protein expression levels. RESULTS Totally 3355 proteins were quantified by employing biological replicates, 314 of which were differentially expressed between the pORF5-HeLa and vector-HeLa cells. Nine differentially expressed proteins (HIST1H1C, HBA1, PARK7, HMGB1, HMGB2, CLIC1, KRT7, SFN, and CDKN2A) were subjected to qRT-PCR, and two over-expressed proteins (HMGB1 and PRAK7) were subjected to the Western blot analysis, to validate the proteomic results. The results from the qRT-PCR and Western blot analysis were consistent with the findings from the proteomic analysis. Moreover, pORF5 could inhibit the TNF-α-induced apoptosis in HeLa cells. Through siRNA-mediated functional screening, the high-mobility group box 1 (HMGB1) was shown to be relevant to the inhibition of the apoptotic response in the host cells. CONCLUSION Identification of key proteins interacting with pORF5 could contribute to the understanding and further exploration of the function of pORF5 in the pathogenic mechanisms of C. trachomatis.
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Affiliation(s)
- Yan Zou
- Pathogenic Biology Institute, School of Medicine, University of South ChinaHengyang 421001, Hunan, China
| | - Wenting Dai
- Pathogenic Biology Institute, School of Medicine, University of South ChinaHengyang 421001, Hunan, China
| | - Wenbo Lei
- Pathogenic Biology Institute, School of Medicine, University of South ChinaHengyang 421001, Hunan, China
| | - Shengmei Su
- Pathogenic Biology Institute, School of Medicine, University of South ChinaHengyang 421001, Hunan, China
| | - Qiulin Huang
- Department of General Surgery, The First Affiliated Hospital of University of South ChinaHengyang 421001, Hunan, China
| | - Zhou Zhou
- Pathogenic Biology Institute, School of Medicine, University of South ChinaHengyang 421001, Hunan, China
| | - Chaoqun Chen
- Pathogenic Biology Institute, School of Medicine, University of South ChinaHengyang 421001, Hunan, China
| | - Zhongyu Li
- Pathogenic Biology Institute, School of Medicine, University of South ChinaHengyang 421001, Hunan, China
- Hunan Province Cooperative Innovation Center for Molecular Target New Drug StudyHengyang 421001, Hunan, China
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5
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Chen J, Liu SS, Kohler A, Yan B, Luo HM, Chen XM, Guo SX. iTRAQ and RNA-Seq Analyses Provide New Insights into Regulation Mechanism of Symbiotic Germination of Dendrobium officinale Seeds (Orchidaceae). J Proteome Res 2017; 16:2174-2187. [DOI: 10.1021/acs.jproteome.6b00999] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- Juan Chen
- Key Laboratory of Bioactive Substances and Resource Utilization of Chinese Herbal Medicine, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, P. R. China
| | - Si Si Liu
- Key Laboratory of Bioactive Substances and Resource Utilization of Chinese Herbal Medicine, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, P. R. China
| | - Annegret Kohler
- UMR
1136 INRA/Université de Lorraine, Interactions Arbres/Micro-organismes,
INRA, Institut National de la Recherche Agronomique, Centre INRA de Nancy, Champenoux 54280, France
| | - Bo Yan
- Key Laboratory of Bioactive Substances and Resource Utilization of Chinese Herbal Medicine, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, P. R. China
| | - Hong Mei Luo
- Key Laboratory of Bioactive Substances and Resource Utilization of Chinese Herbal Medicine, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, P. R. China
| | - Xiao Mei Chen
- Key Laboratory of Bioactive Substances and Resource Utilization of Chinese Herbal Medicine, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, P. R. China
| | - Shun Xing Guo
- Key Laboratory of Bioactive Substances and Resource Utilization of Chinese Herbal Medicine, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, P. R. China
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6
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Sudhir PR, Chen CH. Proteomics-Based Analysis of Protein Complexes in Pluripotent Stem Cells and Cancer Biology. Int J Mol Sci 2016; 17:432. [PMID: 27011181 PMCID: PMC4813282 DOI: 10.3390/ijms17030432] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2015] [Revised: 03/08/2016] [Accepted: 03/16/2016] [Indexed: 12/24/2022] Open
Abstract
A protein complex consists of two or more proteins that are linked together through protein-protein interactions. The proteins show stable/transient and direct/indirect interactions within the protein complex or between the protein complexes. Protein complexes are involved in regulation of most of the cellular processes and molecular functions. The delineation of protein complexes is important to expand our knowledge on proteins functional roles in physiological and pathological conditions. The genetic yeast-2-hybrid method has been extensively used to characterize protein-protein interactions. Alternatively, a biochemical-based affinity purification coupled with mass spectrometry (AP-MS) approach has been widely used to characterize the protein complexes. In the AP-MS method, a protein complex of a target protein of interest is purified using a specific antibody or an affinity tag (e.g., DYKDDDDK peptide (FLAG) and polyhistidine (His)) and is subsequently analyzed by means of MS. Tandem affinity purification, a two-step purification system, coupled with MS has been widely used mainly to reduce the contaminants. We review here a general principle for AP-MS-based characterization of protein complexes and we explore several protein complexes identified in pluripotent stem cell biology and cancer biology as examples.
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Affiliation(s)
| | - Chung-Hsuan Chen
- Genomics Research Center, Academia Sinica, Taipei 11529, Taiwan.
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7
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Identifying novel protein interactions: Proteomic methods, optimisation approaches and data analysis pipelines. Methods 2016; 95:46-54. [DOI: 10.1016/j.ymeth.2015.08.022] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Revised: 08/26/2015] [Accepted: 08/27/2015] [Indexed: 12/21/2022] Open
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8
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Yoshida T, Song L, Bai Y, Kinose F, Li J, Ohaegbulam KC, Muñoz-Antonia T, Qu X, Eschrich S, Uramoto H, Tanaka F, Nasarre P, Gemmill RM, Roche J, Drabkin HA, Haura EB. ZEB1 Mediates Acquired Resistance to the Epidermal Growth Factor Receptor-Tyrosine Kinase Inhibitors in Non-Small Cell Lung Cancer. PLoS One 2016; 11:e0147344. [PMID: 26789630 PMCID: PMC4720447 DOI: 10.1371/journal.pone.0147344] [Citation(s) in RCA: 78] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2015] [Accepted: 01/01/2016] [Indexed: 01/01/2023] Open
Abstract
Epithelial-mesenchymal transition (EMT) is one mechanism of acquired resistance to inhibitors of the epidermal growth factor receptor-tyrosine kinases (EGFR-TKIs) in non-small cell lung cancer (NSCLC). The precise mechanisms of EMT-related acquired resistance to EGFR-TKIs in NSCLC remain unclear. We generated erlotinib-resistant HCC4006 cells (HCC4006ER) by chronic exposure of EGFR-mutant HCC4006 cells to increasing concentrations of erlotinib. HCC4006ER cells acquired an EMT phenotype and activation of the TGF-β/SMAD pathway, while lacking both T790M secondary EGFR mutation and MET gene amplification. We employed gene expression microarrays in HCC4006 and HCC4006ER cells to better understand the mechanism of acquired EGFR-TKI resistance with EMT. At the mRNA level, ZEB1 (TCF8), a known regulator of EMT, was >20-fold higher in HCC4006ER cells than in HCC4006 cells, and increased ZEB1 protein level was also detected. Furthermore, numerous ZEB1 responsive genes, such as CDH1 (E-cadherin), ST14, and vimentin, were coordinately regulated along with increased ZEB1 in HCC4006ER cells. We also identified ZEB1 overexpression and an EMT phenotype in several NSCLC cells and human NSCLC samples with acquired EGFR-TKI resistance. Short-interfering RNA against ZEB1 reversed the EMT phenotype and, importantly, restored erlotinib sensitivity in HCC4006ER cells. The level of micro-RNA-200c, which can negatively regulate ZEB1, was significantly reduced in HCC4006ER cells. Our results suggest that increased ZEB1 can drive EMT-related acquired resistance to EGFR-TKIs in NSCLC. Attempts should be made to explore targeting ZEB1 to resensitize TKI-resistant tumors.
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Affiliation(s)
- Takeshi Yoshida
- Department of Thoracic Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, United States of America
| | - Lanxi Song
- Department of Thoracic Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, United States of America
| | - Yun Bai
- Department of Thoracic Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, United States of America
| | - Fumi Kinose
- Department of Thoracic Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, United States of America
| | - Jiannong Li
- Department of Thoracic Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, United States of America
| | - Kim C. Ohaegbulam
- Department of Molecular Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, United States of America
| | - Teresita Muñoz-Antonia
- Department of Molecular Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, United States of America
| | - Xiaotao Qu
- Department of Biomedical Informatics, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, United States of America
| | - Steven Eschrich
- Department of Biomedical Informatics, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, United States of America
| | - Hidetaka Uramoto
- Second Department of Surgery, School of Medicine, University of Occupational and Environmental Health, Kitakyushu, Fukuoka, Japan
| | - Fumihiro Tanaka
- Second Department of Surgery, School of Medicine, University of Occupational and Environmental Health, Kitakyushu, Fukuoka, Japan
| | - Patrick Nasarre
- Division of Hematology-Oncology, Department of Medicine and the Hollings Cancer Center, Medical University of South Carolina, Charleston, South Carolina, United States of America
| | - Robert M. Gemmill
- Division of Hematology-Oncology, Department of Medicine and the Hollings Cancer Center, Medical University of South Carolina, Charleston, South Carolina, United States of America
| | - Joëlle Roche
- Division of Hematology-Oncology, Department of Medicine and the Hollings Cancer Center, Medical University of South Carolina, Charleston, South Carolina, United States of America
| | - Harry A. Drabkin
- Division of Hematology-Oncology, Department of Medicine and the Hollings Cancer Center, Medical University of South Carolina, Charleston, South Carolina, United States of America
| | - Eric B. Haura
- Department of Thoracic Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, United States of America
- * E-mail:
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9
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Radic-Sarikas B, Rix U, Stukalov A, Gridling M, Müller AC, Colinge J, Superti-Furga G, Bennett KL. Enhancing cognate target elution efficiency in gel-free chemical proteomics. EUPA OPEN PROTEOMICS 2015. [DOI: 10.1016/j.euprot.2015.09.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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10
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Yang TH, Chang HT, Hsiao ES, Sun JL, Wang CC, Wu HY, Liao PC, Wu WS. iPhos: a toolkit to streamline the alkaline phosphatase-assisted comprehensive LC-MS phosphoproteome investigation. BMC Bioinformatics 2014; 15 Suppl 16:S10. [PMID: 25521246 PMCID: PMC4290636 DOI: 10.1186/1471-2105-15-s16-s10] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Background Comprehensive characterization of the phosphoproteome in living cells is critical in signal transduction research. But the low abundance of phosphopeptides among the total proteome in cells remains an obstacle in mass spectrometry-based proteomic analysis. To provide a solution, an alternative analytic strategy to confidently identify phosphorylated peptides by using the alkaline phosphatase (AP) treatment combined with high-resolution mass spectrometry was provided. While the process is applicable, the key integration along the pipeline was mostly done by tedious manual work. Results We developed a software toolkit, iPhos, to facilitate and streamline the work-flow of AP-assisted phosphoproteome characterization. The iPhos tookit includes one assister and three modules. The iPhos Peak Extraction Assister automates the batch mode peak extraction for multiple liquid chromatography mass spectrometry (LC-MS) runs. iPhos Module-1 can process the peak lists extracted from the LC-MS analyses derived from the original and dephosphorylated samples to mine out potential phosphorylated peptide signals based on mass shift caused by the loss of some multiples of phosphate groups. And iPhos Module-2 provides customized inclusion lists with peak retention time windows for subsequent targeted LC-MS/MS experiments. Finally, iPhos Module-3 facilitates to link the peptide identifications from protein search engines to the quantification results from pattern-based label-free quantification tools. We further demonstrated the utility of the iPhos toolkit on the data of human metastatic lung cancer cells (CL1-5). Conclusions In the comparison study of the control group of CL1-5 cell lysates and the treatment group of dasatinib-treated CL1-5 cell lysates, we demonstrated the applicability of the iPhos toolkit and reported the experimental results based on the iPhos-facilitated phosphoproteome investigation. And further, we also compared the strategy with pure DDA-based LC-MS/MS phosphoproteome investigation. The results of iPhos-facilitated targeted LC-MS/MS analysis convey more thorough and confident phosphopeptide identification than the results of pure DDA-based analysis.
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11
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Zhai G, Wu X, Luo Q, Wu K, Zhao Y, Liu J, Xiong S, Feng YQ, Yang L, Wang F. Evaluation of serum phosphopeptides as potential cancer biomarkers by mass spectrometric absolute quantification. Talanta 2014; 125:411-7. [DOI: 10.1016/j.talanta.2014.03.025] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2014] [Revised: 03/10/2014] [Accepted: 03/12/2014] [Indexed: 01/25/2023]
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12
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Huang X, Zeng Y, Xing X, Zeng J, Gao Y, Cai Z, Xu B, Liu X, Huang A, Liu J. Quantitative proteomics analysis of early recurrence/metastasis of huge hepatocellular carcinoma following radical resection. Proteome Sci 2014; 12:22. [PMID: 24839399 PMCID: PMC4023177 DOI: 10.1186/1477-5956-12-22] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2013] [Accepted: 04/17/2014] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Hepatic resection is the preferred treatment for huge hepatocellular carcinoma (>10 cm in diameter; H-HCC). However, the patients with H-HCC suffer from poor prognosis due to the early recurrence/metastasis. The underlying mechanism of H-HCC's early recurrence/metastasis is currently not well understood. RESULTS Here, we describe an Isobaric Tags for relative and absolute quantification (iTRAQ)-based quantitative proteomics approach to analyze the early recurrence/metastasis related proteins of H-HCC after radical resection through multidimensional chromatography coupled with tandem mass spectrometry (2DLC-MS/MS). The different protein expression profiles between the early recurrence/metastasis within 6 months(R/M≤6months) and late recurrence/metastasis within 6-12 months after surgery (R/M6-12months) were confirmed and might reveal different underlying molecular mechanisms. We identified 44 and 49 significantly differentially expressed proteins in the R/M≤6months group and the R/M6-12months group compared to the group who had no recurrence within 2 years post surgery (the NR/M group), respectively. Moreover, among those proteins, S100A12 and AMACR were down regulated in the R/M≤6months group but up-regulated in the R/M6-12months group; and this regulation was further confirmed in mRNA and protein level by Q-PCR, Western-Blot and Immunohistochemistry (IHC). CONCLUSIONS This current study presents the first proteomic profile of the early recurrence/metastasis of H-HCC. The results suggest that S100A12 and AMACR might be potential prognostic markers for predicting the early recurrence/metastasis of H-HCC after hepatectomy.
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Affiliation(s)
- Xinhui Huang
- Mengchao Hepatobiliary Hospital of Fujian Medical University, 350025 Fuzhou, People's Republic of China.,The Liver Center of Fujian Province, Fujian Medical University, 350025 Fuzhou, People's Republic of China
| | - Yongyi Zeng
- Mengchao Hepatobiliary Hospital of Fujian Medical University, 350025 Fuzhou, People's Republic of China.,The Liver Center of Fujian Province, Fujian Medical University, 350025 Fuzhou, People's Republic of China.,Liver Disease Center, The First Affiliated Hospital of Fujian Medical University, 350005 Fuzhou, People's Republic of China
| | - Xiaohua Xing
- Mengchao Hepatobiliary Hospital of Fujian Medical University, 350025 Fuzhou, People's Republic of China.,The Liver Center of Fujian Province, Fujian Medical University, 350025 Fuzhou, People's Republic of China
| | - Jinhua Zeng
- Mengchao Hepatobiliary Hospital of Fujian Medical University, 350025 Fuzhou, People's Republic of China.,The Liver Center of Fujian Province, Fujian Medical University, 350025 Fuzhou, People's Republic of China.,Liver Disease Center, The First Affiliated Hospital of Fujian Medical University, 350005 Fuzhou, People's Republic of China
| | - Yunzhen Gao
- Mengchao Hepatobiliary Hospital of Fujian Medical University, 350025 Fuzhou, People's Republic of China.,The Liver Center of Fujian Province, Fujian Medical University, 350025 Fuzhou, People's Republic of China
| | - Zhixiong Cai
- Mengchao Hepatobiliary Hospital of Fujian Medical University, 350025 Fuzhou, People's Republic of China.,The Liver Center of Fujian Province, Fujian Medical University, 350025 Fuzhou, People's Republic of China
| | - Bo Xu
- Mengchao Hepatobiliary Hospital of Fujian Medical University, 350025 Fuzhou, People's Republic of China.,The Liver Center of Fujian Province, Fujian Medical University, 350025 Fuzhou, People's Republic of China.,Liver Disease Center, The First Affiliated Hospital of Fujian Medical University, 350005 Fuzhou, People's Republic of China
| | - Xiaolong Liu
- Mengchao Hepatobiliary Hospital of Fujian Medical University, 350025 Fuzhou, People's Republic of China.,The Liver Center of Fujian Province, Fujian Medical University, 350025 Fuzhou, People's Republic of China
| | - Aimin Huang
- Mengchao Hepatobiliary Hospital of Fujian Medical University, 350025 Fuzhou, People's Republic of China.,The Liver Center of Fujian Province, Fujian Medical University, 350025 Fuzhou, People's Republic of China.,Department of Pathology, School of Basic Medical Science, Fujian Medical University, 350004 Fuzhou, People's Republic of China
| | - Jingfeng Liu
- Mengchao Hepatobiliary Hospital of Fujian Medical University, 350025 Fuzhou, People's Republic of China.,The Liver Center of Fujian Province, Fujian Medical University, 350025 Fuzhou, People's Republic of China.,Liver Disease Center, The First Affiliated Hospital of Fujian Medical University, 350005 Fuzhou, People's Republic of China
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13
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Viglio S, Stolk J, Iadarola P, Giuliano S, Luisetti M, Salvini R, Fumagalli M, Bardoni A. Respiratory Proteomics Today: Are Technological Advances for the Identification of Biomarker Signatures Catching up with Their Promise? A Critical Review of the Literature in the Decade 2004-2013. Proteomes 2014; 2:18-52. [PMID: 28250368 PMCID: PMC5302730 DOI: 10.3390/proteomes2010018] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2013] [Revised: 01/08/2014] [Accepted: 01/10/2014] [Indexed: 01/14/2023] Open
Abstract
To improve the knowledge on a variety of severe disorders, research has moved from the analysis of individual proteins to the investigation of all proteins expressed by a tissue/organism. This global proteomic approach could prove very useful: (i) for investigating the biochemical pathways involved in disease; (ii) for generating hypotheses; or (iii) as a tool for the identification of proteins differentially expressed in response to the disease state. Proteomics has not been used yet in the field of respiratory research as extensively as in other fields, only a few reproducible and clinically applicable molecular markers, which can assist in diagnosis, having been currently identified. The continuous advances in both instrumentation and methodology, which enable sensitive and quantitative proteomic analyses in much smaller amounts of biological material than before, will hopefully promote the identification of new candidate biomarkers in this area. The aim of this report is to critically review the application over the decade 2004-2013 of very sophisticated technologies to the study of respiratory disorders. The observed changes in protein expression profiles from tissues/fluids of patients affected by pulmonary disorders opens the route for the identification of novel pathological mediators of these disorders.
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Affiliation(s)
- Simona Viglio
- Department of Molecular Medicine, Biochemistry Unit, University of Pavia, Via Taramelli 3/B, Pavia 27100, Italy.
| | - Jan Stolk
- Department of Pulmonology, Leiden University Medical Center, Leiden 2333, The Netherlands.
| | - Paolo Iadarola
- Department of Biology and Biotechnologies, Biochemistry Unit, University of Pavia, Via Taramelli 3/B, Pavia 27100, Italy.
| | - Serena Giuliano
- Department of Molecular Medicine, Biochemistry Unit, University of Pavia, Via Taramelli 3/B, Pavia 27100, Italy.
- Faculty of Science "Parc Valrose", University of Nice "Sophia Antipolis", FRE 3472 CNRS, LP2M Nice, France.
| | - Maurizio Luisetti
- Department of Molecular Medicine, Division of Pneumology, University of Pavia & IRCCS Policlinico San Matteo, Via Taramelli 5, Pavia 27100, Italy.
| | - Roberta Salvini
- Department of Molecular Medicine, Biochemistry Unit, University of Pavia, Via Taramelli 3/B, Pavia 27100, Italy.
| | - Marco Fumagalli
- Department of Biology and Biotechnologies, Biochemistry Unit, University of Pavia, Via Taramelli 3/B, Pavia 27100, Italy.
| | - Anna Bardoni
- Department of Molecular Medicine, Biochemistry Unit, University of Pavia, Via Taramelli 3/B, Pavia 27100, Italy.
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14
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Huber ML, Sacco R, Parapatics K, Skucha A, Khamina K, Müller AC, Rudashevskaya EL, Bennett KL. abFASP-MS: affinity-based filter-aided sample preparation mass spectrometry for quantitative analysis of chemically labeled protein complexes. J Proteome Res 2014; 13:1147-55. [PMID: 24400740 PMCID: PMC3923452 DOI: 10.1021/pr4009892] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
![]()
Affinity
purification coupled to 1-D gel-free liquid chromatography
mass spectrometry (LC–MS) is a well-established and widespread
approach for the analyses of noncovalently interacting protein complexes.
In this study, two proteins conjugated to a streptavidin-binding peptide
and hemagglutinin double tag were expressed in the respective Flp-In
HEK293 cell lines: green fluorescent protein (SH-GFP) and TANK binding
kinase 1 (SH-TBK1_MOUSE). Fluorescent anti-HA immunoblots revealed
that the expression level of SH-GFP was ∼50% lower than that
of SH-TBK1_MOUSE. Subsequently, the input material was normalized
to obtain a similar quantity of purified SH-tagged proteins. Optimization
of the release of protein complexes from the anti-HA-agarose with different eluting agents was then assessed. With
respect to the total number of protein groups identified in the purified
complexes, elution with 2% SDS surpassed both 100 mM glycine and 100
mM formic acid. Relative quantitation of the purified protein complexes
using TMT 6-plex reagents confirmed the higher efficiency of the 2%
SDS elution followed by filter-aided sample preparation (FASP). The
data presented in this study provide a new application of FASP to
quantitative MS analysis of affinity-purified protein complexes. We
have termed the approach abFASP-MS, or affinity-based filter-aided
sample preparation mass spectrometry.
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Affiliation(s)
- Marie L Huber
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences , Lazarettgasse 14, 1090 Vienna, Austria
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15
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Li J, Bennett K, Stukalov A, Fang B, Zhang G, Yoshida T, Okamoto I, Kim JY, Song L, Bai Y, Qian X, Rawal B, Schell M, Grebien F, Winter G, Rix U, Eschrich S, Colinge J, Koomen J, Superti-Furga G, Haura EB. Perturbation of the mutated EGFR interactome identifies vulnerabilities and resistance mechanisms. Mol Syst Biol 2013; 9:705. [PMID: 24189400 PMCID: PMC4039310 DOI: 10.1038/msb.2013.61] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2013] [Accepted: 10/02/2013] [Indexed: 01/06/2023] Open
Abstract
We hypothesized that elucidating the interactome of epidermal growth factor receptor (EGFR) forms that are mutated in lung cancer, via global analysis of protein-protein interactions, phosphorylation, and systematically perturbing the ensuing network nodes, should offer a new, more systems-level perspective of the molecular etiology. Here, we describe an EGFR interactome of 263 proteins and offer a 14-protein core network critical to the viability of multiple EGFR-mutated lung cancer cells. Cells with acquired resistance to EGFR tyrosine kinase inhibitors (TKIs) had differential dependence of the core network proteins based on the underlying molecular mechanisms of resistance. Of the 14 proteins, 9 are shown to be specifically associated with survival of EGFR-mutated lung cancer cell lines. This included EGFR, GRB2, MK12, SHC1, ARAF, CD11B, ARHG5, GLU2B, and CD11A. With the use of a drug network associated with the core network proteins, we identified two compounds, midostaurin and lestaurtinib, that could overcome drug resistance through direct EGFR inhibition when combined with erlotinib. Our results, enabled by interactome mapping, suggest new targets and combination therapies that could circumvent EGFR TKI resistance.
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Affiliation(s)
- Jiannong Li
- Department of Thoracic Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Keiryn Bennett
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Alexey Stukalov
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Bin Fang
- Proteomics and Molecular Oncology Program, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Guolin Zhang
- Department of Thoracic Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Takeshi Yoshida
- Center for Clinical and Translational Research, Kyushu University Hospital, Fukuoka, Japan
| | - Isamu Okamoto
- Center for Clinical and Translational Research, Kyushu University Hospital, Fukuoka, Japan
| | - Jae-Young Kim
- Department of Thoracic Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Lanxi Song
- Department of Thoracic Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Yun Bai
- Department of Thoracic Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Xiaoning Qian
- Department of Computer Science and Engineering, University of South Florida, Tampa, FL, USA
| | - Bhupendra Rawal
- Biostatistics Departments, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Michael Schell
- Biostatistics Departments, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Florian Grebien
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Georg Winter
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Uwe Rix
- Drug Discovery Department, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Steven Eschrich
- Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Jacques Colinge
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - John Koomen
- Proteomics and Molecular Oncology Program, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Giulio Superti-Furga
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Eric B Haura
- Department of Thoracic Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
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16
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Foerster S, Kacprowski T, Dhople VM, Hammer E, Herzog S, Saafan H, Bien-Möller S, Albrecht M, Völker U, Ritter CA. Characterization of the EGFR interactome reveals associated protein complex networks and intracellular receptor dynamics. Proteomics 2013; 13:3131-44. [PMID: 23956138 DOI: 10.1002/pmic.201300154] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2013] [Revised: 07/21/2013] [Accepted: 07/26/2013] [Indexed: 11/05/2022]
Abstract
Growth factor receptor mediated signaling is meanwhile recognized as a complex signaling network, which is initiated by recruiting specific patterns of adaptor proteins to the intracellular domain of epidermal growth factor receptor (EGFR). Approaches to globally identify EGFR-binding proteins are required to elucidate this network. We affinity-purified EGFR with its interacting proteins by coprecipitation from lysates of A431 cells. A total of 183 proteins were repeatedly detected in high-resolution MS measurements. For 15 of these, direct interactions with EGFR were listed in the iRefIndex interaction database, including Grb2, shc-1, SOS1 and 2, STAT 1 and 3, AP2, UBS3B, and ERRFI. The newly developed Cytoscape plugin ModuleGraph allowed retrieving and visualizing 93 well-described protein complexes that contained at least one of the proteins found to interact with EGFR in our experiments. Abundances of 14 proteins were modulated more than twofold upon EGFR activation whereof clathrin-associated adaptor complex AP-2 showed 4.6-fold enrichment. These proteins were further annotated with different cellular compartments. Finally, interactions of AP-2 proteins and the newly discovered interaction of CIP2A could be verified. In conclusion, a powerful technique is presented that allowed identification and quantitative assessment of the EGFR interactome to provide further insight into EGFR signaling.
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Affiliation(s)
- Sarah Foerster
- Department of Clinical Pharmacy, Institute of Pharmacy, Ernst-Moritz-Arndt-University Greifswald, Greifswald, Germany
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17
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Lin HC, Zhang FL, Geng Q, Yu T, Cui YQ, Liu XH, Li J, Yan MX, Liu L, He XH, Li JJ, Yao M. Quantitative proteomic analysis identifies CPNE3 as a novel metastasis-promoting gene in NSCLC. J Proteome Res 2013; 12:3423-33. [PMID: 23713811 DOI: 10.1021/pr400273z] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
To discover metastasis-associated proteins within cancer cells, we used the isobaric tags for relative and absolute quantitation (iTRAQ) approach combined with nano liquid chromatography-tandem mass spectrometry (NanoLC-MS/MS) analysis to identify proteins that were differentially expressed between lung adenocarcinoma cancer cell lines SPC-A-1sci cells with high metastatic potential and parent SPC-A-1 cells with low metastatic potential. By employing biological and technical replicates, we identified 5818 nonredundant proteins and quantified 5443 proteins, 256 of which were differentially expressed in the two cell lines. Through si-RNA-mediated functional screens, Myosin heavy chain 9 (MYH9) and Copine III (CPNE3) were indicated as positively correlating with the migration and invasion properties of SPC-A1sci cells, and the same function of CPNE3 was confirmed in another lung cancer cell line, H1299. Furthermore, overexpressing CPNE3 promoted nonsmall-cell lung cancer (NSCLC) cell line (SPC-A-1 and XL-2) migration and invasion in vitro. Moreover, the targeted knock-down of CPNE3 inhibited the in vivo metastatic abilities of H1299 cells in mouse models. Lastly, immunohistochemistry revealed that the CPNE3 expression level was positively correlated with the clinical stage and TNM classification in NSCLC patients. Taken together, our results indicate that CPNE3 could play a critical role in NSCLC metastasis.
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Affiliation(s)
- He-chun Lin
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200032, China
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18
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Kuzmanov U, Emili A. Protein-protein interaction networks: probing disease mechanisms using model systems. Genome Med 2013; 5:37. [PMID: 23635424 PMCID: PMC3706760 DOI: 10.1186/gm441] [Citation(s) in RCA: 81] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Protein-protein interactions (PPIs) and multi-protein complexes perform central roles in the cellular systems of all living organisms. In humans, disruptions of the normal patterns of PPIs and protein complexes can be causative or indicative of a disease state. Recent developments in the biological applications of mass spectrometry (MS)-based proteomics have expanded the horizon for the application of systematic large-scale mapping of physical interactions to probe disease mechanisms. In this review, we examine the application of MS-based approaches for the experimental analysis of PPI networks and protein complexes, focusing on the different model systems (including human cells) used to study the molecular basis of common diseases such as cancer, cardiomyopathies, diabetes, microbial infections, and genetic and neurodegenerative disorders.
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Affiliation(s)
- Uros Kuzmanov
- Banting and Best Department of Medical Research and Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada
| | - Andrew Emili
- Banting and Best Department of Medical Research and Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada
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19
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A method to resolve the composition of heterogeneous affinity-purified protein complexes assembled around a common protein by chemical cross-linking, gel electrophoresis and mass spectrometry. Nat Protoc 2012; 8:75-97. [PMID: 23237831 DOI: 10.1038/nprot.2012.133] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Protein complexes form, dissociate and re-form in order to perform specific cellular functions. In this two-pronged protocol, noncovalent protein complexes are initially isolated by affinity purification for subsequent identification of the components by liquid chromatography high-resolution mass spectrometry (LC-MS) on a hybrid LTQ Orbitrap Velos. In the second prong of the approach, the affinity-purification strategy includes a chemical cross-linking step to 'freeze' a series of concurrently formed, heterogeneous protein subcomplex species that are visualized by gel electrophoresis. This branch of the methodology amalgamates standard and well-practiced laboratory methods to reveal compositional changes that occur in protein complex architecture. By using mouse N-terminally tagged streptavidin-binding peptide-hemagglutinin-TANK-binding kinase 1 (SH-TBK1), we chemically cross-linked the affinity-purified complex of SH-TBK1 with the homobifunctional lysine-specific reagent bis(sulfosuccinimidyl) suberate (BS(3)), and we separated the resultant protein complexes by denaturation and by silver-stained one- and two-dimensional SDS-PAGE. We observed a range of cross-linked TBK1 complexes of variable pI and M(r) and confirmed them by immunoblotting. LC-MS analysis of in situ-digested cross-linked proteins shows differences in the composition of the TBK1 subcomplexes. The protocol is inherently simple and can be readily extended to the investigation of a range of protein complexes. From cell lysis to data generation by LC-MS, the protocol takes approximately 2.5 to 5.5 d to perform.
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20
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Pichlmair A, Kandasamy K, Alvisi G, Mulhern O, Sacco R, Habjan M, Binder M, Stefanovic A, Eberle CA, Goncalves A, Bürckstümmer T, Müller AC, Fauster A, Holze C, Lindsten K, Goodbourn S, Kochs G, Weber F, Bartenschlager R, Bowie AG, Bennett KL, Colinge J, Superti-Furga G. Viral immune modulators perturb the human molecular network by common and unique strategies. Nature 2012; 487:486-90. [PMID: 22810585 DOI: 10.1038/nature11289] [Citation(s) in RCA: 200] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2011] [Accepted: 06/07/2012] [Indexed: 12/24/2022]
Abstract
Viruses must enter host cells to replicate, assemble and propagate. Because of the restricted size of their genomes, viruses have had to evolve efficient ways of exploiting host cell processes to promote their own life cycles and also to escape host immune defence mechanisms. Many viral open reading frames (viORFs) with immune-modulating functions essential for productive viral growth have been identified across a range of viral classes. However, there has been no comprehensive study to identify the host factors with which these viORFs interact for a global perspective of viral perturbation strategies. Here we show that different viral perturbation patterns of the host molecular defence network can be deduced from a mass-spectrometry-based host-factor survey in a defined human cellular system by using 70 innate immune-modulating viORFs from 30 viral species. The 579 host proteins targeted by the viORFs mapped to an unexpectedly large number of signalling pathways and cellular processes, suggesting yet unknown mechanisms of antiviral immunity. We further experimentally verified the targets heterogeneous nuclear ribonucleoprotein U, phosphatidylinositol-3-OH kinase, the WNK (with-no-lysine) kinase family and USP19 (ubiquitin-specific peptidase 19) as vulnerable nodes in the host cellular defence system. Evaluation of the impact of viral immune modulators on the host molecular network revealed perturbation strategies used by individual viruses and by viral classes. Our data are also valuable for the design of broad and specific antiviral therapies.
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Affiliation(s)
- Andreas Pichlmair
- CeMMResearch Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
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21
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Oak CH, Wilson D, Lee HJ, Lim HJ, Park EK. Potential molecular approaches for the early diagnosis of lung cancer (review). Mol Med Rep 2012; 6:931-6. [PMID: 22923136 DOI: 10.3892/mmr.2012.1042] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2012] [Accepted: 08/13/2012] [Indexed: 11/06/2022] Open
Abstract
Lung cancer is the leading cause of mortality from cancer among men and women worldwide. More individuals die each year of lung cancer than of colon, breast and prostate cancer combined. Despite new diagnostic techniques, the overall 5-year survival rate remains at approximately 15% and the majority of patients still present with advanced disease. Therefore, lung cancer is the most lethal cancer at present. Diagnosing and treating cancer at its early stages, ideally during the precancerous stages, could increase the 5-year survival rate by 3-4‑fold, with the possibility of cure. To date, no screening method has been shown to decrease the disease-specific mortality rate. This review describes issues related to early lung cancer screening and their rationale, the management of primary cancers detected by screening and the different approaches that have been tested for cancer screening; these include imaging techniques, bronchoscopies and molecular screening, such as analysis of epigenomics using different noninvasive or invasive sources, such as blood, sputum, bronchoscopic samples and exhaled breath.
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Affiliation(s)
- Chul Ho Oak
- Department of Internal Medicine, College of Medicine, Kosin University, Busan, Republic of Korea
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22
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Haura EB, Sacco R, Li J, Müller AC, Grebien F, Superti-Furga G, Bennett KL. Optimisation of Downscaled Tandem Affinity Purifications to Identify Core Protein Complexes. ACTA ACUST UNITED AC 2012; 2:55-68. [PMID: 24077984 DOI: 10.5584/jiomics.v2i1.81] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
In this study we show that via stable, retroviral-expression of tagged EGFR del (L747-S752 deletion mutant) in the PC9 lung cancer cell line and stable doxycycline-inducible expression of tagged Grb2 using a Flp-mediated recombination HEK293 cell system, the SH-TAP can be downscaled to 5 to 12.5 mg total protein input (equivalent to 0.5 - 1 × 15 cm culture plate or 4 - 8 × 106 cells). The major constituents of the EGFR del complex (USB3B, GRB2, ERRFI, HSP7C, GRP78, HSP71) and the Grb2 complex (ARHG5, SOS1, ARG35, CBL, CBLB, PTPRA, SOS2, DYN2, WIPF2, IRS4) were identified. Adjustment of the quantity of digested protein injected into the mass spectrometer reveals that optimisation is required as high quantities of material led to a decrease in protein sequence coverage and the loss of some interacting proteins. This investigation should aid other researchers in performing tandem affinity purifications in general, and in particular, from low quantities of input material.
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Affiliation(s)
- Eric B Haura
- Department of Thoracic Oncology Program, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, USA
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23
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Müller AC, Breitwieser FP, Fischer H, Schuster C, Brandt O, Colinge J, Superti-Furga G, Stingl G, Elbe-Bürger A, Bennett KL. A comparative proteomic study of human skin suction blister fluid from healthy individuals using immunodepletion and iTRAQ labeling. J Proteome Res 2012; 11:3715-27. [PMID: 22578099 DOI: 10.1021/pr3002035] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Aberrations in skin morphology and functionality can cause acute and chronic skin-related diseases that are the focus of dermatological research. Mechanically induced skin suction blister fluid may serve as a potential, alternative human body fluid for quantitative mass spectrometry (MS)-based proteomics in order to assist in the understanding of the mechanisms and causes underlying skin-related diseases. The combination of abundant-protein removal with iTRAQ technology and multidimensional fractionation techniques improved the number of identified protein groups. A relative comparison of a cohort of 8 healthy volunteers was thus recruited in order to assess the net variability encountered in a healthy scenario. The technology enabled the identification, to date, of the highest number of reported protein groups (739) with concomitant relative quantitative data for over 90% of all proteins with high reproducibility and accuracy. The use of iTRAQ 8-plex resulted in a 66% decrease in protein identifications but, despite this, provided valuable insight into interindividual differences of the healthy control samples. The geometric mean ratio was close to 1 with 95% of all ratios ranging between 0.45 and 2.05 and a calculated mean coefficient of variation of 15.8%, indicating a lower biological variance than that reported for plasma or urine. By applying a multistep sample processing, the obtained sensitivity and accuracy of quantitative MS analysis demonstrates the prospective value of the approach in future research into skin diseases.
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Affiliation(s)
- André C Müller
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
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24
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Haura EB. From modules to medicine: How modular domains and their associated networks can enable personalized medicine. FEBS Lett 2012; 586:2580-5. [PMID: 22575759 DOI: 10.1016/j.febslet.2012.04.036] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2012] [Revised: 04/18/2012] [Accepted: 04/18/2012] [Indexed: 01/09/2023]
Abstract
Unveiling of cancer genomes is unleashing new therapeutic strategies for cancer. With cancer parts lists in hand, new approaches to personalized medicine can be developed by understanding the assembly of cancer machines using modular domains in proteins and their associated networks. Using the Src-homology-2 (SH2) domain as an example, new profiling approaches can discern global patterns of tyrosine phosphorylation in cancer cells that can enable molecular cancer medicine. Identifying and quantifying protein-protein interactions also has the potential to subtype tumors and guide clinical decision making. These approaches should extend the impact of genomics through viewing the architecture of cancer systems and improve predictions of patient outcome and therapeutic response, as well as guide combination therapy approaches that attack cancer systems.
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Affiliation(s)
- Eric B Haura
- Department of Thoracic Oncology Program and Experimental Therapeutics Program, The H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA.
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25
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Xiao H, Zhang L, Zhou H, Lee JM, Garon EB, Wong DTW. Proteomic analysis of human saliva from lung cancer patients using two-dimensional difference gel electrophoresis and mass spectrometry. Mol Cell Proteomics 2011; 11:M111.012112. [PMID: 22096114 DOI: 10.1074/mcp.m111.012112] [Citation(s) in RCA: 128] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Lung cancer is often asymptomatic or causes only nonspecific symptoms in its early stages. Early detection represents one of the most promising approaches to reduce the growing lung cancer burden. Human saliva is an attractive diagnostic fluid because its collection is less invasive than that of tissue or blood. Profiling of proteins in saliva over the course of disease progression could reveal potential biomarkers indicative of oral or systematic diseases, which may be used extensively in future medical diagnostics. There were 72 subjects enrolled in this study for saliva sample collection according to the approved protocol. Two-dimensional difference gel electrophoresis combined with MS was the platform for salivary proteome separation, quantification, and identification from two pooled samples. Candidate proteomic biomarkers were verified and prevalidated by using immunoassay methods. There were 16 candidate protein biomarkers discovered by two-dimensional difference gel electrophoresis and MS. Three proteins were further verified in the discovery sample set, prevalidation sample set, and lung cancer cell lines. The discriminatory power of these candidate biomarkers in lung cancer patients and healthy control subjects can reach 88.5% sensitivity and 92.3% specificity with AUC = 0.90. This preliminary data report demonstrates that proteomic biomarkers are present in human saliva when people develop lung cancer. The discriminatory power of these candidate biomarkers indicate that a simple saliva test might be established for lung cancer clinical screening and detection.
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Affiliation(s)
- Hua Xiao
- Dental Research Institute, University of California, Los Angeles, Los Angeles, California 90095, USA.
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26
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Savitski MM, Sweetman G, Askenazi M, Marto JA, Lang M, Zinn N, Bantscheff M. Delayed Fragmentation and Optimized Isolation Width Settings for Improvement of Protein Identification and Accuracy of Isobaric Mass Tag Quantification on Orbitrap-Type Mass Spectrometers. Anal Chem 2011; 83:8959-67. [DOI: 10.1021/ac201760x] [Citation(s) in RCA: 84] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
| | | | - Manor Askenazi
- Department of Cancer Biology and Blais Proteomics Center, Dana-Farber Cancer Institute, Boston, Massachusetts 02115-6084, United States
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, United States
- Sudarsky Center for Computational Biology, Department of Biological Chemistry, Hebrew University of Jerusalem, Israel
| | - Jarrod A. Marto
- Department of Cancer Biology and Blais Proteomics Center, Dana-Farber Cancer Institute, Boston, Massachusetts 02115-6084, United States
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Manja Lang
- Cellzome AG, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Nico Zinn
- Cellzome AG, Meyerhofstrasse 1, 69117 Heidelberg, Germany
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Goncalves A, Bürckstümmer T, Dixit E, Scheicher R, Górna MW, Karayel E, Sugar C, Stukalov A, Berg T, Kralovics R, Planyavsky M, Bennett KL, Colinge J, Superti-Furga G. Functional dissection of the TBK1 molecular network. PLoS One 2011; 6:e23971. [PMID: 21931631 PMCID: PMC3169550 DOI: 10.1371/journal.pone.0023971] [Citation(s) in RCA: 100] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2011] [Accepted: 07/28/2011] [Indexed: 01/02/2023] Open
Abstract
TANK-binding kinase 1 (TBK1) and inducible IκB-kinase (IKK-i) are central regulators of type-I interferon induction. They are associated with three adaptor proteins called TANK, Sintbad (or TBKBP1) and NAP1 (or TBKBP2, AZI2) whose functional relationship to TBK1 and IKK-i is poorly understood. We performed a systematic affinity purification–mass spectrometry approach to derive a comprehensive TBK1/IKK-i molecular network. The most salient feature of the network is the mutual exclusive interaction of the adaptors with the kinases, suggesting distinct alternative complexes. Immunofluorescence data indicated that the individual adaptors reside in different subcellular locations. TANK, Sintbad and NAP1 competed for binding of TBK1. The binding site for all three adaptors was mapped to the C-terminal coiled-coil 2 region of TBK1. Point mutants that affect binding of individual adaptors were used to reconstitute TBK1/IKK-i-deficient cells and dissect the functional relevance of the individual kinase-adaptor edges within the network. Using a microarray-derived gene expression signature of TBK1 in response virus infection or poly(I∶C) stimulation, we found that TBK1 activation was strictly dependent on the integrity of the TBK1/TANK interaction.
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Affiliation(s)
- Adriana Goncalves
- CeMM - Research Center for Molecular Medicine, Austrian Academy of Sciences, Vienna, Austria
| | - Tilmann Bürckstümmer
- CeMM - Research Center for Molecular Medicine, Austrian Academy of Sciences, Vienna, Austria
- * E-mail: (TB); (GS-F)
| | - Evelyn Dixit
- CeMM - Research Center for Molecular Medicine, Austrian Academy of Sciences, Vienna, Austria
| | - Ruth Scheicher
- CeMM - Research Center for Molecular Medicine, Austrian Academy of Sciences, Vienna, Austria
| | - Maria W. Górna
- CeMM - Research Center for Molecular Medicine, Austrian Academy of Sciences, Vienna, Austria
| | - Evren Karayel
- CeMM - Research Center for Molecular Medicine, Austrian Academy of Sciences, Vienna, Austria
| | - Cristina Sugar
- CeMM - Research Center for Molecular Medicine, Austrian Academy of Sciences, Vienna, Austria
| | - Alexey Stukalov
- CeMM - Research Center for Molecular Medicine, Austrian Academy of Sciences, Vienna, Austria
| | - Tiina Berg
- CeMM - Research Center for Molecular Medicine, Austrian Academy of Sciences, Vienna, Austria
| | - Robert Kralovics
- CeMM - Research Center for Molecular Medicine, Austrian Academy of Sciences, Vienna, Austria
| | - Melanie Planyavsky
- CeMM - Research Center for Molecular Medicine, Austrian Academy of Sciences, Vienna, Austria
| | - Keiryn L. Bennett
- CeMM - Research Center for Molecular Medicine, Austrian Academy of Sciences, Vienna, Austria
| | - Jacques Colinge
- CeMM - Research Center for Molecular Medicine, Austrian Academy of Sciences, Vienna, Austria
| | - Giulio Superti-Furga
- CeMM - Research Center for Molecular Medicine, Austrian Academy of Sciences, Vienna, Austria
- * E-mail: (TB); (GS-F)
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28
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Song L, Rawal B, Nemeth JA, Haura EB. JAK1 activates STAT3 activity in non-small-cell lung cancer cells and IL-6 neutralizing antibodies can suppress JAK1-STAT3 signaling. Mol Cancer Ther 2011; 10:481-94. [PMID: 21216930 DOI: 10.1158/1535-7163.mct-10-0502] [Citation(s) in RCA: 136] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Members of the signal transducer and activator of transcription (STAT) family of transcription factors are potential targets for the treatment and prevention of cancers including non-small-cell lung cancer. STAT proteins can be phosphorylated and activated by diverse upstream kinases including cytokine receptors and tyrosine kinases. We examined STAT protein activation in lung cancer cell lines including those with activating mutations in the EGFR and examined upstream kinases responsible for STAT3 phosphorylation and activation using small molecules, antibodies, and RNA interference. We found more pronounced STAT3 activation in cells with activating EGFR mutations, yet inhibition of EGFR activity had no effect on STAT3 activation. Inhibition of JAK1 with small molecules or RNA interference resulted in loss of STAT3 tyrosine phosphorylation and inhibition of cell growth. An interleukin-6 neutralizing antibody, siltuximab (CNTO 328) could inhibit STAT3 tyrosine phosphorylation in a cell-dependent manner. Siltuximab could completely inhibit STAT3 tyrosine phosphorylation in H1650 cells, and this resulted in inhibition of lung cancer cell growth in vivo. Combined EGFR inhibition with erlotinib and siltuximab resulted in dual inhibition of both tyrosine and serine STAT3 phosphorylation, more pronounced inhibition of STAT3 transcriptional activity, and translated into combined effects on lung cancer growth in a mouse model. Our results suggest that JAK1 is responsible for STAT3 activation in lung cancer cells and that indirect attacks on JAK1-STAT3 using an IL-6 neutralizing antibody with or without EGFR inhibition can inhibit lung cancer growth in lung cancer subsets.
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Affiliation(s)
- Lanxi Song
- Thoracic Oncology and Experimental Therapeutics Programs H. Lee Moffitt Cancer Center and Research Institute MRC3 East, Room 3056F, 12902 Magnolia Drive Tampa, Florida 33612-9497, USA
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