SWATH-based proteomics identified carbonic anhydrase 2 as a potential diagnosis biomarker for nasopharyngeal carcinoma

Scientific Reports

Volumn 7, Issue , 2017, Pages

  Luo, Yanzhang ^a   Mok, Tin Seak ^a,b   Lin, Xiuxian ^a   Zhang, Wanling ^a   Cui, Yizhi ^a   Guo, Jiahui ^a   Chen, Xing ^a   Zhang, Tao ^a   Wang, Tong ^a  

^a JINAN UNIVERSITY   (China)

^b Department of Obstetric amp Gynecology of Centro Hospitalar Conde S Januário of Macao Special Administrative Region of People Republic of China   (Macao)

Author keywords

[No Author keywords available]

Indexed keywords

CARBONATE DEHYDRATASE II; TUMOR MARKER;

CARCINOMA; HUMAN; MASS SPECTROMETRY; METABOLISM; NASOPHARYNX TUMOR; PROCEDURES; PROTEOMICS; SENSITIVITY AND SPECIFICITY; TUMOR CELL LINE;

BIOMARKERS, TUMOR; CARBONIC ANHYDRASE II; CARCINOMA; CELL LINE, TUMOR; HUMANS; MASS SPECTROMETRY; NASOPHARYNGEAL NEOPLASMS; PROTEOMICS; SENSITIVITY AND SPECIFICITY;

EID: 85010886954     PISSN: None     EISSN: 20452322     Source Type: Journal    
DOI: 10.1038/srep41191     Document Type: Article

References (51)

1. Xu, C., Chen, Y. P. & Ma, J. Clinical trials in nasopharyngeal carcinoma-past, present and future. Chin Clin Oncol 5, 20, doi: 10.21037/cco.2016.03.12 (2016).
2. Zhang, L. F., et al. Incidence trend of nasopharyngeal carcinoma from 1987 to 2011 in Sihui County, Guangdong Province, South China: an age-period-cohort analysis. Chin J Cancer 34, 350-357, doi: 10.1186/s40880-015-0018-6 (2015).
3. Lee, A. W., et al. Treatment results for nasopharyngeal carcinoma in the modern era: the Hong Kong experience. Int J Radiat Oncol Biol Phys 61, 1107-1116, doi: 10.1016/j.ijrobp.2004.07.702 (2005).
4. Sun, Y., et al. Induction chemotherapy plus concurrent chemoradiotherapy versus concurrent chemoradiotherapy alone in locoregionally advanced nasopharyngeal carcinoma: a phase 3, multicentre, randomised controlled trial. Lancet Oncol 17, 1509-1520, doi: 10.1016/S1470-2045(16)30410-7 (2016).
5. Ye, S. B., et al. Exosomal miR-24-3p impedes T-cell function by targeting FGF11 and serves as a potential prognostic biomarker for nasopharyngeal carcinoma. J Pathol 240, 329-340, doi: 10.1002/path.4781 (2016).
6. Spence, T., Bruce, J., Yip, K. W. & Liu, F. F. MicroRNAs in nasopharyngeal carcinoma. Chin Clin Oncol 5, 17, doi: 10.21037/cco.2016.03.09 (2016).
7. Zou, Z. W., et al. LncRNA ANRIL is up-regulated in nasopharyngeal carcinoma and promotes the cancer progression via increasing proliferation, reprograming cell glucose metabolism and inducing side-population stem-like cancer cells. Oncotarget, doi: 10.18632/oncotarget.11437 (2016).
8. Chan, K. H., et al. EBV specific antibody-based and DNA-based assays in serologic diagnosis of nasopharyngeal carcinoma. Int J Cancer 105, 706-709, doi: 10.1002/ijc.11130 (2003).
9. Chen, Y., et al. Diagnostic Value of Serum Epstein-Barr Virus Capsid Antigen-IgA for Nasopharyngeal Carcinoma: a Meta-Analysis Based on 21 Studies. Clin Lab 62, 1155-1166 (2016).
10. Fung, S. Y., Lam, J. W. & Chan, K. C. Clinical utility of circulating Epstein-Barr virus DNA analysis for the management of nasopharyngeal carcinoma. Chin Clin Oncol 5, 18, doi: 10.21037/cco.2016.03.07 (2016).
11. Leung, S. F., et al. Plasma Epstein-Barr viral deoxyribonucleic acid quantitation complements tumor-node-metastasis staging prognostication in nasopharyngeal carcinoma. J Clin Oncol 24, 5414-5418, doi: 10.1200/JCO.2006.07.7982 (2006).
12. Song, L. B., et al. Bmi-1 is a novel molecular marker of nasopharyngeal carcinoma progression and immortalizes primary human nasopharyngeal epithelial cells. Cancer Res 66, 6225-6232, doi: 10.1158/0008-5472.CAN-06-0094 (2006).
13. Wu, T., et al. HMGB1 overexpression as a prognostic factor for survival in cancer: a meta-Analysis and systematic review. Oncotarget, doi: 10.18632/oncotarget.10413 (2016).
14. Lian, Y. F., et al. Upregulation of KLHDC4 Predicts a Poor Prognosis in Human Nasopharyngeal Carcinoma. PLoS One 11, e0152820, doi: 10.1371/journal.pone.0152820 (2016).
15. Xiao, L., Xiao, T., Wang, Z. M., Cho, W. C. & Xiao, Z. Q. Biomarker discovery of nasopharyngeal carcinoma by proteomics. Expert Rev Proteomics 11, 215-225, doi: 10.1586/14789450.2014.897613 (2014).
16. Chen, Z., et al. Identification of nasopharyngeal carcinoma metastasis-related biomarkers by iTRAQ combined with 2D-LC-MS/MS. Oncotarget 7, 34022-34037, doi: 10.18632/oncotarget.9067 (2016).
17. Omenn, G. S., et al. Metrics for the Human Proteome Project 2015: Progress on the Human Proteome and Guidelines for High-Confidence Protein Identification. J Proteome Res 14, 3452-3460, doi: 10.1021/acs.jproteome.5b00499 (2015).
18. Gillet, L. C., et al. Targeted data extraction of the MS/MS spectra generated by data-independent acquisition: a new concept for consistent and accurate proteome analysis. Mol Cell Proteomics 11, O111 016717, doi: 10.1074/mcp.O111.016717 (2012).
19. Aebersold, R., Bensimon, A., Collins, B. C., Ludwig, C. & Sabido, E. Applications and Developments in Targeted Proteomics: From SRM to DIA/SWATH. Proteomics 16, 2065-2067, doi: 10.1002/pmic.201600203 (2016).
20. Lange, V., Picotti, P., Domon, B. & Aebersold, R. Selected reaction monitoring for quantitative proteomics: a tutorial. Mol Syst Biol 4, 222, doi: 10.1038/msb.2008.61 (2008).
21. Picotti, P. & Aebersold, R. Selected reaction monitoring-based proteomics: workflows, potential, pitfalls and future directions. Nat Methods 9, 555-566, doi: 10.1038/nmeth.2015 (2012).
22. Liu, Y., et al. Glycoproteomic analysis of prostate cancer tissues by SWATH mass spectrometry discovers N-Acylethanolamine acid amidase and protein tyrosine kinase 7 as signatures for tumor aggressiveness. Mol Cell Proteomics 13, 1753-1768, doi: 10.1074/mcp. M114.038273 (2014).
23. Lin, Q., et al. Analysis of colorectal cancer glyco-secretome identifies laminin beta-1 (LAMB1) as a potential serological biomarker for colorectal cancer. Proteomics 15, 3905-3920, doi: 10.1002/pmic.201500236 (2015).
24. Wu, W., Yong, W. W. & Chung, M. C. A simple biomarker scoring matrix for early gastric cancer detection. Proteomics, doi: 10.1002/pmic.201600194 (2016).
25. Ortea, I., Rodriguez-Ariza, A., Chicano-Galvez, E., Arenas Vacas, M. S. & Jurado Gamez, B. Discovery of potential protein biomarkers of lung adenocarcinoma in bronchoalveolar lavage fluid by SWATH MS data-independent acquisition and targeted data extraction. J Proteomics 138, 106-114, doi: 10.1016/j.jprot.2016.02.010 (2016).
26. Pavelka, N., et al. A power law global error model for the identification of differentially expressed genes in microarray data. BMC Bioinformatics 5, 203, doi: 10.1186/1471-2105-5-203 (2004).
27. Pavelka, N., et al. Statistical similarities between transcriptomics and quantitative shotgun proteomics data. Mol Cell Proteomics 7, 631-644, doi: 10.1074/mcp.M700240-MCP200 (2008).
28. Chen, Z., et al. Cytoskeleton-centric protein transportation by exosomes transforms tumor-favorable macrophages. Oncotarget, doi: 10.18632/oncotarget.11794 (2016).
29. Wu, C. C., et al. Identification of potential serum markers for nasopharyngeal carcinoma from a xenografted mouse model using Cy-dye labeling combined with three-dimensional fractionation. Proteomics 8, 3605-3620, doi: 10.1002/pmic.200701034 (2008).
30. Wang, T., et al. Translating mRNAs strongly correlate to proteins in a multivariate manner and their translation ratios are phenotype specific. Nucleic Acids Res 41, 4743-4754, doi: 10.1093/nar/gkt178 (2013).
31. Guo, J., Lian, X., Zhong, J., Wang, T. & Zhang, G. Length-dependent translation initiation benefits the functional proteome of human cells. Mol Biosyst 11, 370-378, doi: 10.1039/c4mb00462k (2015).
32. Huang, Q., et al. SWATH enables precise label-free quantification on proteome scale. Proteomics 15, 1215-1223, doi: 10.1002/pmic.201400270 (2015).
33. Wykoff, C. C., et al. Hypoxia-inducible expression of tumor-Associated carbonic anhydrases. Cancer Res 60, 7075-7083 (2000).
34. Supuran, C. T. Carbonic anhydrases: novel therapeutic applications for inhibitors and activators. Nat Rev Drug Discov 7, 168-181, doi: 10.1038/nrd2467 (2008).
35. Viikila, P., et al. Carbonic anhydrase enzymes II, VII, IX and XII in colorectal carcinomas. World J Gastroenterol 22, 8168-8177, doi: 10.3748/wjg.v22.i36.8168 (2016).
36. Kurono, S., et al. Identification of potential breast cancer markers in nipple discharge by protein profile analysis using twodimensional nano-liquid chromatography/nanoelectrospray ionization-mass spectrometry. Proteomics Clin Appl 10, 605-613, doi: 10.1002/prca.201500016 (2016).
37. Henry, E. K., et al. Carbonic anhydrase enzymes regulate mast cell-mediated inflammation. J Exp Med 213, 1663-1673, doi: 10.1084/jem.20151739 (2016).
38. Gordon, S. C., et al. Antibodies to carbonic anhydrase in patients with immune cholangiopathies. Gastroenterology 108, 1802-1809 (1995).
39. Alver, A., et al. Carbonic anhydrase II autoantibody and oxidative stress in rheumatoid arthritis. Clin Biochem 44, 1385-1389, doi: 10.1016/j.clinbiochem.2011.09.014 (2011).
40. Hornef, M. W., Wagner, H. J., Kruse, A. & Kirchner, H. Cytokine production in a whole-blood assay after Epstein-Barr virus infection in vivo. Clin Diagn Lab Immunol 2, 209-213 (1995).
41. Fang, W., et al. EBV-driven LMP1 and IFN-gamma up-regulate PD-L1 in nasopharyngeal carcinoma: Implications for oncotargeted therapy. Oncotarget 5, 12189-12202, doi: 10.18632/oncotarget.2608 (2014).
42. Wu, M., Li, X., Li, X. & Li, G. Signaling Transduction Network Mediated by Tumor Suppressor/Susceptibility Genes in NPC. Curr Genomics 10, 216-222, doi: 10.2174/138920209788488481 (2009).
43. Ma, J., et al. Role of a novel EGF-like domain-containing gene NGX6 in cell adhesion modulation in nasopharyngeal carcinoma cells. Carcinogenesis 26, 281-291, doi: 10.1093/carcin/bgh312 (2005).
44. Li, Z., et al. Macrophage migration inhibitory factor enhances neoplastic cell invasion by inducing the expression of matrix metalloproteinase 9 and interleukin-8 in nasopharyngeal carcinoma cell lines. Chin Med J (Engl) 117, 107-114 (2004).
45. Lo, M. C., et al. Role of MIF/CXCL8/CXCR2 signaling in the growth of nasopharyngeal carcinoma tumor spheres. Cancer Lett 335, 81-92, doi: 10.1016/j.canlet.2013.01.052 (2013).
46. Chen Y., et al. Identification of Missing Proteins Defined by Chromosome-Centric Proteome Project in the Cytoplasmic Detergent-Insoluble Proteins. J Proteome Res 14, 3693-3709, doi: 10.1021/pr501103r (2015).
47. Geiger, T., et al. Use of stable isotope labeling by amino acids in cell culture as a spike-in standard in quantitative proteomics. Nat Protoc 6, 147-157, doi: 10.1038/nprot.2010.192 (2011).
48. Yang, L., et al. Finding Missing Proteins from the Epigenetically Manipulated Human Cell with Stringent Quality Criteria. J Proteome Res 14, 3645-3657, doi: 10.1021/acs.jproteome.5b00480 (2015).
49. Wisniewski, J. R., Zougman, A., Nagaraj, N. & Mann, M. Universal sample preparation method for proteome analysis. Nat Methods 6, 359-362, doi: 10.1038/nmeth.1322 (2009).
50. Guo, J., et al. Phosphoproteome Characterization of Human Colorectal Cancer SW620 Cell-Derived Exosomes and New Phosphosite Discovery for C-HPP. J Proteome Res 15, 4060-4072, doi: 10.1021/acs.jproteome.6b00391 (2016).
51. Shen, S., et al. Functional proteomics revealed IL-1beta amplifies TNF downstream protein signals in human synoviocytes in a TNFindependent manner. Biochem Biophys Res Commun 450, 538-544, doi: 10.1016/j.bbrc.2014.06.008 (2014).