Abstract
The fact that lung cancer is a heterogeneous disease suggests that there is a high likelihood that effective lung cancer biomarkers will need to address patient-specific molecular defects, clinical characters, and aspects of the tumor microenvironment. In this transition, clinical bioinformatics tools and resources are the most appropriate means to improve the analysis, as major biological databases are now containing clinical data alongside genomics, proteomics, and other biological data. Clinical bioinformatics comprises a series of concepts and approaches that have been used successfully both to delineate novel biological mechanisms and to drive translational advances in individualized healthcare. In this article, we outline several of emerging clinical bioinformatics-based strategies as they apply specifically to lung cancer.
Similar content being viewed by others
References
Jemal, A., Bray, F., Center, M. M., Ferlay, J., Ward, E., & Forman, D. (2011). Global cancer statistics. CA: A Cancer Journal for Clinicians, 61(2), 69–90.
Chen, Z., Fillmore, C. M., Hammerman, P. S., Kim, C. F., & Wong, K. K. (2014). Non-small-cell lung cancers: a heterogeneous set of diseases. Nature Reviews Cancer, 14(8), 535–546.
Nana-Sinkam, S. P., & Powell, C. A. (2013). Molecular biology of lung cancer: diagnosis and management of lung cancer, 3rd ed: American College of Chest Physicians evidence-based clinical practice guidelines. Chest, 143(5 Suppl), e30S–e39S.
Cagle, P. T., Allen, T. C., & Olsen, R. J. (2013). Lung cancer biomarkers: present status and future developments. Archives of Pathology and Laboratory Medicine, 137(9), 1191–1198.
Kelloff, G. J., & Sigman, C. C. (2012). Cancer biomarkers: selecting the right drug for the right patient. Nature Reviews Drug Discovery, 11(3), 201–214.
Zer, A., & Leighl, N. (2014). Promising targets and current clinical trials in metastatic non-squamous NSCLC. Frontiers Oncology, 4, 329.
Kim, E. S., Hirsh, V., Mok, T., Socinski, M. A., Gervais, R., Wu, Y. L., et al. (2008). Gefitinib versus docetaxel in previously treated non-small-cell lung cancer (INTEREST): a randomised phase III trial. Lancet, 372(9652), 1809–1818.
Korpanty, G. J., Graham, D. M., Vincent, M. D., & Leighl, N. B. (2014). Biomarkers that currently affect clinical practice in lung cancer: EGFR, ALK, MET, ROS-1, and KRAS. Frontiers Oncology, 4, 204.
Mok, T. S. (2011). Personalized medicine in lung cancer: what we need to know. Nature Reviews Clinical Oncology, 8(11), 661–668.
Shigematsu, H., Lin, L., Takahashi, T., Nomura, M., Suzuki, M., Wistuba, I. I., et al. (2005). Clinical and biological features associated with epidermal growth factor receptor gene mutations in lung cancers. Journal of the National Cancer Institute, 97(5), 339–346.
Giaccone, G., & Rodriguez, J. A. (2005). EGFR inhibitors: what have we learned from the treatment of lung cancer? Nature Clinical Practice Oncology, 2(11), 554–561.
da Cunha Santos, G., Shepherd, F. A., & Tsao, M. S. (2011). EGFR mutations and lung cancer. Annual Review of Pathology, 6, 49–69.
Wang, X., & Liotta, L. (2011). Clinical bioinformatics: a new emerging science. Journal of Clinical Bioinformatics, 1(1), 1. doi:10.1186/2043-9113-1-1.
Weinstein, J. N., Collisson, E. A., Mills, G. B., Shaw, K. R., Ozenberger, B. A., Ellrott, K., et al. (2013). The Cancer Genome Atlas pan-cancer analysis project. Nature Genetics, 45(10), 1113–1120.
Akbani, R., Ng, P. K., Werner, H. M., Shahmoradgoli, M., Zhang, F., Ju, Z., et al. (2014). A pan-cancer proteomic perspective on The Cancer Genome Atlas. Nature Communications, 5, 3887. doi:10.1038/ncomms4887.
Schwarz, E., Leweke, F. M., Bahn, S., & Liò, P. (2009). Clinical bioinformatics for complex disorders: a schizophrenia case study. BMC Bioinformatics, 10(Suppl 12), S6. doi:10.1186/1471-2105-10-S12-S6.
Nishino, M., Jackman, D. M., Hatabu, H., Yeap, B. Y., Cioffredi, L. A., Yap, J. T., et al. (2010). New Response Evaluation Criteria in Solid Tumors (RECIST) guidelines for advanced non-small cell lung cancer: comparison with original RECIST and impact on assessment of tumor response to targeted therapy. AJR. American Journal of Roentgenology, 195(3), W221–w228.
Lee, H. Y., Lee, K. S., Ahn, M. J., Hwang, H. S., Lee, J. W., Park, K., et al. (2011). New CT response criteria in non-small cell lung cancer: proposal and application in EGFR tyrosine kinase inhibitor therapy. Lung Cancer, 73(1), 63–69.
Imai, K., Minamiya, Y., Saito, H., Motoyama, S., Sato, Y., Ito, A., et al. (2014). Diagnostic imaging in the preoperative management of lung cancer. Surgery Today, 44(7), 1197–1206.
Peng, H. (2008). Bioimage informatics: a new area of engineering biology. Bioinformatics, 24(17), 1827–1836.
Bauer, S., Wiest, R., Nolte, L. P., & Reyes, M. (2013). A survey of MRI-based medical image analysis for brain tumor studies. Physics in Medicine and Biology, 58(13), R97–R129.
Eklund, A., Dufort, P., Forsberg, D., & LaConte, S. M. (2013). Medical image processing on the GPU—past, present and future. Medical Image Analysis, 17(8), 1073–1094.
Caon, M., Sedlář, J., Bajger, M., & Lee, G. (2014). Computer-assisted segmentation of CT images by statistical region merging for the production of voxel models of anatomy for CT dosimetry. Australasian Physical and Engineering Sciences in Medicine, 37(2), 393–403.
Kipli, K., Kouzani, A. Z., & Williams, L. J. (2013). Towards automated detection of depression from brain structural magnetic resonance images. Neuroradiology, 55(5), 567–584.
Shi, P., Huang, Y., & Hong, J. (2014). Automated three-dimensional reconstruction and morphological analysis of dendritic spines based on semi-supervised learning. Biomedical Optics Express, 5(5), 1541–1553.
Meyer, C., Ma, B., Kunju, L. P., Davenport, M., & Piert, M. (2013). Challenges in accurate registration of 3-D medical imaging and histopathology in primary prostate cancer. European Journal of Nuclear Medicine and Molecular Imaging, 40(Suppl 1), S72–S78. doi:10.1007/s00259-013-2382-2.
Yeh, F. C., Ye, Q., Hitchens, T. K., Wu, Y. L., Parwani, A. V., & Ho, C. (2014). Mapping stain distribution in pathology slides using whole slide imaging. Journal of Pathology Informatics, 5, 1. doi:10.4103/2153-3539.126140.
Kovarik, M., Hronek, M., & Zadak, Z. (2014). Clinically relevant determinants of body composition, function and nutritional status as mortality predictors in lung cancer patients. Lung Cancer, 84(1), 1–6.
Sánchez-Lara, K., Turcott, J. G., Juárez, E., Guevara, P., Núñez-Valencia, C., Oñate-Ocaña, L. F., et al. (2012). Association of nutrition parameters including bioelectrical impedance and systemic inflammatory response with quality of life and prognosis in patients with advanced non-small-cell lung cancer: a prospective study. Nutrition and Cancer, 64(4), 526–534.
Prado, C. M., Lieffers, J. R., McCargar, L. J., Reiman, T., Sawyer, M. B., Martin, L., et al. (2008). Prevalence and clinical implications of sarcopenic obesity in patients with solid tumours of the respiratory and gastrointestinal tracts: a population-based study. The Lancet Oncology, 9(7), 629–635.
Jafri, S. H., Shi, R., & Mills, G. (2013). Advance lung cancer inflammation index (ALI) at diagnosis is a prognostic marker in patients with metastatic non-small cell lung cancer (NSCLC): a retrospective review. BMC Cancer, 13, 158. doi:10.1186/1471-2407-13-158.
Piskorz, L., Lesiak, T., Brocki, M., Klimek-Piskorz, E., Smigielski, J., Misiak, P., et al. (2011). Biochemical and functional indices of malnutrition in patients with operable, non-microcelullar lung cancer. Nutrición Hospitalaria, 26(5), 1025–1032. doi:10.1590/S0212-16112011000500016.
Barbosa-Silva, M. C., & Barros, A. J. (2005). Bioelectrical impedance analysis in clinical practice: a new perspective on its use beyond body composition equations. Current Opinion in Clinical Nutrition and Metabolic Care, 8(3), 311–317.
Chen, H., Song, Z., Qian, M., Bai, C., & Wang, X. (2012). Selection of disease-specific biomarkers by integrating inflammatory mediators with clinical informatics in AECOPD patients: a preliminary study. Journal of Cellular and Molecular Medicine, 16(6), 1286–1297.
Chen, H., Wang, Y., Bai, C., & Wang, X. (2012). Alterations of plasma inflammatory biomarkers in the healthy and chronic obstructive pulmonary disease patients with or without acute exacerbation. Journal of Proteomics, 75(10), 2835–2843.
Chen, H., & Wang, X. (2011). Significance of bioinformatics in research of chronic obstructive pulmonary disease. Journal of Clinical Bioinformatics, 1, 35. doi:10.1186/2043-9113-1-35.
Gottlieb, L. M., Tirozzi, K. J., Manchanda, R., Burns, A. R., & Sandel, M. T. (2015). Moving electronic medical records upstream: incorporating social determinants of health. American Journal of Preventive Medicine, 48(2), 215–218.
Amberger, J., Bocchini, C. A., Scott, A. F., & Hamosh, A. (2009). McKusick’s Online Mendelian Inheritance in Man (OMIM). Nucleic Acids Research, 37(Database issue), D793–D796.
Junttila, M. R., & de Sauvage, F. J. (2013). Influence of tumour micro-environment heterogeneity on therapeutic response. Nature, 501(7467), 346–354.
Goldstein, D. B. (2009). Common genetic variation and human traits. The New England Journal of Medicine, 360(17), 1696–1698.
Schadt, E. E. (2009). Molecular networks as sensors and drivers of common human diseases. Nature, 461(7261), 218–223.
Barabasi, A. L., & Albert, R. (1999). Emergence of scaling in random networks. Science, 286(5439), 509–512.
Xu, J., & Li, Y. (2006). Discovering disease-genes by topological features in human protein-protein interaction network. Bioinformatics, 22(22), 2800–2805.
Wang, J., Peng, X., Peng, W., & Wu, F. X. (2014). Dynamic protein interaction network construction and applications. Proteomics, 14(4–5), 338–352.
Wu, X., Chen, L., & Wang, X. (2014). Network biomarkers, interaction networks and dynamical network biomarkers in respiratory diseases. Clinical and Translational Medicine, 3, 16. doi:10.1186/2001-1326-3-16.
Acknowledgments
This work was supported by the National Natural Science Foundation of China (81100534,91230204, 81270099, 81320108001, 81270131, 81300010), the Shanghai Rising Star Program (13QA1400800). The work was also supported by Zhongshan Distinguished Professor Grant (XDW), The Shanghai Committee of Science and Technology (12JC1402200, 12431900207, 11410708600, 14431905100), Zhejiang Provincial Natural Science Foundation (Z2080988), Zhejiang Provincial Science Technology Department Foundation (2010C14011), and Ministry of Education, Academic Special Science and Research Foundation for PhD Education (20130071110043). The authors have no commercial or other associations that might pose a conflict of interest in connection with the submitted material.
Author information
Authors and Affiliations
Corresponding author
Rights and permissions
About this article
Cite this article
Wu, D., Wang, X. Application of clinical bioinformatics in lung cancer-specific biomarkers. Cancer Metastasis Rev 34, 209–216 (2015). https://doi.org/10.1007/s10555-015-9564-2
Published:
Issue Date:
DOI: https://doi.org/10.1007/s10555-015-9564-2