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http://dx.doi.org/10.5626/JCSE.2017.11.4.111

Identifying Post-translational Modification Crosstalks for Breast Cancer  

Tung, Chi-Hua (Department of Bioinformatics, Chung-Hua University)
Shueng, Pei-Wei (Division of Radiation Oncology, Far Eastern Memorial Hospital)
Chu, Yen-Wei (Institute of Genomics and Bioinformatics, Biotechnology Center, and Agricultural Biotechnology Center)
Chu, Yen-Wei (Institute of Genomics and Bioinformatics)
Chen, Chian-Ying (Institute of Genomics and Bioinformatics)
Publication Information
Journal of Computing Science and Engineering / v.11, no.4, 2017 , pp. 111-120 More about this Journal
Abstract
Post-translational modifications (PTMs) of proteins play substantial roles in the gene regulation of cell physiological functions and in the generation of major diseases. However, the majority of existing studies only explored a certain PTM of proteins, while very few have investigated the PTMs of two or more domains and the effects of their interactions. In this study, after collecting data regarding a large number of breast cancer-related and validated PTMs, a sequence and domain analysis of breast cancer proteins was carried out using bioinformatics methods. Then, protein-protein interaction network-related tools were applied in order to determine the crosstalks between the PTMs of the proteins. Finally, statistical and functional analyses were conducted to identify more modification sites of domains and proteins that may interact with at least two or more PTMs. In addition to exploring the associations between the interactive effects of PTMs, the present study also provides important information that would allow biologists to further explore the regulatory pathways of biological functions and related diseases.
Keywords
Post-translational modification; Crosstalk; Sequence analysis; Breast cancer;
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1 J. Seo and K. J. Lee, "Post-translational modifications and their biological functions: proteomic analysis and systematic approaches," Journal of Biochemistry and Molecular Biology, vol. 37, no. 1, pp. 35-44, 2004.
2 M. A. Daniels, K. A. Hogquist, and S. C. Jameson, "Sweet 'n' sour: the impact of differential glycosylation on T cell responses," Nature immunology, vol. 3, no. 10, pp. 903-910, 2002.   DOI
3 D. Hanahan and R. A. Weinberg, "The hallmarks of cancer," Cell, vol. 100, no. 1, pp. 57-70, 2000.   DOI
4 S. I. Hayashi, H. Eguchi, K. Tanimoto, T. Yoshida, Y. Omoto, A. Inoue, N. Yoshida, and Y. Yamaguchi, "The expression and function of estrogen receptor alpha and beta in human breast cancer and its clinical application," Endocrine-Related Cancer, vol. 10, no. 2, pp. 193-202, 2003.   DOI
5 A. S. Venne, L. Kollipara, and R. P. Zahedi, "The next level of complexity: crosstalk of posttranslational modifications," Proteomics, vol. 14, no. 4-5, pp. 513-524, 2014.   DOI
6 M. R. Fernandes, D. C. de Carvalho, A. K. dos Santos, S. E. dos Santos, P. P. de Assumpcao, R. M. Burbano, and N. P. dos Santos, "Association of slow acetylation profile of NAT2 with breast and gastric cancer risk in Brazil," Anticancer Research, vol. 33, no. 9, pp. 3683-3689, 2013.
7 P. O. Esteve, Y. Chang, M. Samaranayake, A. K. Upadhyay, J. R. Horton, G. R. Feehery, X. Cheng and S. Pradhan, "A methylation and phosphorylation switch between an adjacent lysine and serine determines human DNMT1 stability," Nature Structural & Molecular Biology, vol. 18, no. 1, pp. 42-48, 2011.   DOI
8 F. Hochgrafe, L. Zhang, S. A. O'Toole, B. C. Browne, M. Pinese, A. Porta Cubas, G. M. Lehrbach, D. R. Croucher, D. Rickwood, A. Boulghourjian, et al., "Tyrosine phosphorylation profiling reveals the signaling network characteristics of Basal breast cancer cells," Cancer Research, vol. 70, no. 22, pp. 9391-9401, 2010.   DOI
9 N. Blom, S. Gammeltoft, and S. Brunak, "Sequence and structure-based prediction of eukaryotic protein phosphorylation sites," Journal of Molecular Biology, vol. 294, no. 5, pp. 1351-1362, 1999.   DOI
10 H. Tang and E. Goldberg, "Homo sapiens lactate dehydrogenase c (Ldhc) gene expression in cancer cells is regulated by transcription factor Sp1, CREB, and CpG island methylation," Journal of Andrology, vol. 30, no. 2, pp. 157-167, 2009.   DOI
11 L. Yan, X. Yang, and N. E. Davidson, "Role of DNA methylation and histone acetylation in steroid receptor expression in breast cancer," Journal of Mammary Gland Biology and Neoplasia, vol. 6, no. 2, pp. 183-192, 2001.   DOI
12 R. Gupta and S. Brunak, "Prediction of glycosylation across the human proteome and the correlation to protein function," Pacific Symposium on Biocomputing, vol. 7, pp. 310-322, 2002.
13 M. V. Dwek, H. A. Ross, and A. J. Leathem, "Proteome and glycosylation mapping identifies post-translational modifications associated with aggressive breast cancer," Proteomics, vol. 1, no. 6, pp. 756-762, 2001.   DOI
14 T. van Agthoven, J. Veldscholte, M. Smid, T. L. van Agthoven, L. Vreede, M. Broertjes, I. de Vries, D. de Jong, R. Sarwari, and L. C. Dorssers, "Functional identification of genes causing estrogen independence of human breast cancer cells," Breast Cancer Research and Treatment, vol. 114, no. 1, pp. 23-30, 2009.   DOI
15 C. Steentoft, S. Y. Vakhrushev, H. J. Joshi, Y. Kong, M. B. Vester-Christensen, K. T. Schjoldager, K. Lavrsen, S. Dabelsteen, N. B. Pedersen, L. Marcos-Silva, et al., "Precision mapping of the human O-GalNAc glycoproteome through SimpleCell technology," The EMBO Journal, vol. 32, no. 10, pp. 1478-1488, 2013.   DOI
16 P. N. Munster, T. Troso-Sandoval, N. Rosen, R. Rifkind, P. A. Marks, and V. M. Richon, "The histone deacetylase inhibitor suberoylanilide hydroxamic acid induces differentiation of human breast cancer cells," Cancer Research, vol. 61, no. 23, pp. 8492-8497, 2001.
17 J. Song, W. Yang, M. Shih Ie, Z. Zhang, and J. Bai, "Identification of BCOX1, a novel gene overexpressed in breast cancer," Biochimica et Biophysica Acta (BBA)-General Subjects, vol. 1760, no. 1, pp. 62-69, 2006.   DOI
18 M. J. Scanlan, I. Gout, C. M. Gordon, B. Williamson, E. Stockert, A. O. Gure, D. Jager, Y. T. Chen, A. Mackay, M. J. O'Hare, et al., "Humoral immunity to human breast cancer: antigen definition and quantitative analysis of mRNA expression," Cancer Immunity Archive, vol. 1, article no. 4, 2001.
19 L. H. Low, Y. L. Chow, Y. Li, C. P. Goh, U. Putz, J. Silke, T. Ouchi, J. Howitt, and S. S. Tan, "Nedd4 family interacting protein 1 (Ndfip1) is required for ubiquitination and nuclear trafficking of BRCA1-associated ATM activator 1 (BRAT1) during the DNA damage response," Journal of Biological Chemistry, vol. 290, no. 11, pp. 7141-7150, 2015.   DOI
20 W. Jiang, Y. Zhang, F. Meng, B. Lian, X. Chen, X. Yu, E. Dai, S. Wang, X. Liu, X. Li, et al., "Identification of active transcription factor and miRNA regulatory pathways in Alzheimer's disease," Bioinformatics, vol. 29, no. 20, pp. 2596-2602, 2013.   DOI
21 G. W. Hart, C. Slawson, G. Ramirez-Correa, and O. Lagerlof, "Cross talk between O-GlcNAcylation and phosphorylation: roles in signaling, transcription, and chronic disease," Annual Review of Biochemistry, vol. 80, pp. 825-858, 2011.   DOI
22 J. Mohandass, S. Ravichandran, K. Srilakshmi, C. P. Rajadurai, S. Sanmugasamy, and G. R. Kumar, "BCDB: a database for breast cancer research and information," Bioinformation, vol. 5, no. 1, pp. 1-3, 2010.   DOI
23 R. A. Baasiri, S. R. Glasser, D. L. Steffen, and D. A. Wheeler, "The breast cancer gene database: a collaborative information resource," Oncogene, vol. 18, no. 56, pp. 7958-7965, 1999.   DOI
24 A. M. Butt, D. Feng, M. Idrees, Y. Tong, and J. Lu, "Computational identification and modeling of crosstalk between phosphorylation, O-beta-glycosylation and methylation of FoxO3 and implications for cancer therapeutics," International Journal of Molecular Sciences, vol. 13, no. 3, pp. 2918-2938, 2012.   DOI
25 A. M. Butt, D. Feng, I. Nasrullah, S. Tahir, M. Idrees, Y. Tong, and J. Lu, "Computational identification of interplay between phosphorylation and O-beta-glycosylation of human occludin as potential mechanism to impair hepatitis C virus entry," Infection, Genetics and Evolution, vol. 12, no. 6, pp. 1235-1245, 2012.   DOI
26 R. Rao, D. Xu, J. J. Thelen, and J. A. Miernyk, "Circles within circles: crosstalk between protein Ser/Thr/Tyrphosphorylation and Met oxidation," BMC Bioinformatics, vol. 14(Suppl 14), article no. S14, 2013.
27 J. S. Chauhan, A. Rao, and G. P. Raghava, "In silico platform for prediction of N-, O- and C-glycosites in eukaryotic protein sequences," PLoS One, vol. 8, no. 6, article no. e67008, 2013.   DOI
28 J. L. McLarty, S. A. Marsh, and J. C. Chatham, "Posttranslational protein modification by O-linked N-acetylglucosamine: its role in mediating the adverse effects of diabetes on the heart," Life Sciences, vol. 92, no. 11, pp. 621-627, 2013.   DOI
29 Z. Lu, Z. Cheng, Y. Zhao, and S. L. Volchenboum, "Bioinformatic analysis and post-translational modification crosstalk prediction of lysine acetylation," PLoS One, vol. 6, no. 12, article no. e28228, 2011.   DOI
30 G. Alves, A. Tatro, and T. Fanning, "Differential methylation of human LINE-1 retrotransposons in malignant cells," Gene, vol. 176, no. 1-2, pp. 39-44, 1996.   DOI
31 U. Omasits, C. H. Ahrens, S. Muller and B. Wollscheid, "Protter: interactive protein feature visualization and integration with experimental proteomic data," Bioinformatics, vol. 30, no. 6, pp. 884-886, 2014.   DOI
32 R. D. Finn, T. K. Attwood, P. C. Babbitt, A. Bateman, P. Bork, A. J. Bridge, H. Y. Chang, Z. Dosztanyi, S. El-Gebali, M. Fraser, et al., "InterPro in 2017: beyond protein family and domain annotations," Nucleic Acids Researchg, vol. 45(D1), pp. D190-D199, 2017.   DOI
33 A. Mitchell, H. Y. Chang, L. Daugherty, M. Fraser, S. Hunter, R. Lopez, C. McAnulla, C. McMenamin, G. Nuka, S. Pesseat, et al., "The InterPro protein families database: the classification resource after 15 years," Nucleic Acids Research, vol. 43(D1), pp. D213-D221, 2015.   DOI
34 P. Minguez, I. Letunic, L. Parca, and P. Bork, "PTMcode: a database of known and predicted functional associations between post-translational modifications in proteins," Nucleic Acids Research, vol. 41(D1), pp. D306-D311, 2013.
35 R. Mosca, A. Ceol, A. Stein, R. Olivella, and P. Aloy, "3did: a catalog of domain-based interactions of known threedimensional structure," Nucleic Acids Research, vol. 42(D1), pp. D374-D379, 2014.   DOI
36 P. Minguez, L. Parca, F. Diella, D. R. Mende, R. Kumar, M. Helmer-Citterich, A. C. Gavin, V. van Noort, and P. Bork, "Deciphering a global network of functionally associated post-translational modifications," Molecular Systems Biology, vol. 8, article no. 599, 2012.
37 C. Slawson and G. W. Hart, "O-GlcNAc signalling: implications for cancer cell biology," Nature Reviews Cancer, vol. 11, no. 9, pp. 678-684, 2011.   DOI