Table of Contents Author Guidelines Submit a Manuscript
BioMed Research International
Volume 2017 (2017), Article ID 2563085, 9 pages
https://doi.org/10.1155/2017/2563085
Research Article

Diagnostic MicroRNA Biomarker Discovery for Non-Small-Cell Lung Cancer Adenocarcinoma by Integrative Bioinformatics Analysis

Department of Respiratory Medicine, Shandong Provincial Hospital Affiliated to Shandong University, Jinan, Shandong 250021, China

Correspondence should be addressed to Shu-Juan Jiang; moc.361@gnaij-naujuhs

Received 3 March 2017; Accepted 10 April 2017; Published 15 June 2017

Academic Editor: Xingming Zhao

Copyright © 2017 Yang Shao et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Linked References

  1. R. L. Siegel, K. D. Miller, and A. Jemal, “Cancer statistics, 2017,” CA: A Cancer Journal for Clinicians, vol. 67, no. 1, pp. 7–30, 2017. View at Publisher · View at Google Scholar
  2. L. A. Torre, R. L. Siegel, and A. Jemal, “Lung cancer statistics,” Advances in Experimental Medicine and Biology, vol. 893, pp. 1–19, 2016. View at Publisher · View at Google Scholar · View at Scopus
  3. M. Saito, K. Shiraishi, H. Kunitoh, S. Takenoshita, J. Yokota, and T. Kohno, “Gene aberrations for precision medicine against lung adenocarcinoma,” Cancer Science, vol. 107, no. 6, pp. 713–720, 2016. View at Publisher · View at Google Scholar · View at Scopus
  4. Y. Zhang, H. Wang, J. Wang et al., “Global analysis of chromosome 1 genes among patients with lung adenocarcinoma, squamous carcinoma, large-cell carcinoma, small-cell carcinoma, or non-cancer,” Cancer and Metastasis Reviews, vol. 34, no. 2, pp. 249–264, 2015. View at Publisher · View at Google Scholar · View at Scopus
  5. C.-W. Xu, X.-Y. Cai, Y. Shao et al., “A case of lung adenocarcinoma with a concurrent EGFR mutation and ALK rearrangement: a case report and literature review,” Molecular Medicine Reports, vol. 12, no. 3, pp. 4370–4375, 2015. View at Publisher · View at Google Scholar · View at Scopus
  6. G. Roviello, “The distinctive nature of adenocarcinoma of the lung,” OncoTargets and Therapy, vol. 8, pp. 2399–2406, 2015. View at Publisher · View at Google Scholar · View at Scopus
  7. P. T. Cagle, K. Raparia, and B. P. Portier, “Emerging biomarkers in personalized therapy of lung cancer,” Advances in Experimental Medicine and Biology, vol. 890, pp. 25–36, 2016. View at Publisher · View at Google Scholar · View at Scopus
  8. F. L. Wang, “Analysis of risk factors for female lung adenocarcinoma in haerbin: indoor air pollution,” Zhonghua Yu Fang Yi Xue Za Zhi, vol. 23, no. 5, pp. 270–273, 1989. View at Google Scholar · View at Scopus
  9. L. M. Butler, J. A. Montague, W.-P. Koh, R. Wang, M. C. Yu, and J.-M. Yuan, “Fried meat intake is a risk factor for lung adenocarcinoma in a prospective cohort of Chinese men and women in Singapore,” Carcinogenesis, vol. 34, no. 8, pp. 1794–1799, 2013. View at Publisher · View at Google Scholar · View at Scopus
  10. C. Paris, C. Clement-Duchene, J. M. Vignaud et al., “Relationships between lung adenocarcinoma and gender, age, smoking and occupational risk factors: a case-case study,” Lung Cancer, vol. 68, no. 2, pp. 146–153, 2010. View at Publisher · View at Google Scholar · View at Scopus
  11. J. Jiang, P. Jia, Z. Zhao, and B. Shen, “Key regulators in prostate cancer identified by co-expression module analysis,” BMC Genomics, vol. 15, no. 1, article 1015, 2014. View at Publisher · View at Google Scholar · View at Scopus
  12. H. C. Jeong, “Clinical aspect of MicroRNA in lung cancer,” Tuberculosis and Respiratory Diseases, vol. 77, no. 2, pp. 60–64, 2014. View at Publisher · View at Google Scholar · View at Scopus
  13. M. K. Kim, S. B. Jung, J.-S. Kim et al., “Expression of microRNA miR-126 and miR-200c is associated with prognosis in patients with non-small cell lung cancer,” Virchows Archiv, vol. 465, no. 4, pp. 463–471, 2014. View at Publisher · View at Google Scholar · View at Scopus
  14. S. Shen, Y. Lin, X. Yuan et al., “Biomarker microRNAs for Diagnosis, prognosis and treatment of hepatocellular carcinoma: a functional survey and comparison,” Scientific Reports, vol. 6, article 38311, 2016. View at Publisher · View at Google Scholar
  15. L. Shen, Y. Lin, Z. Sun, X. Yuan, L. Chen, and B. Shen, “Knowledge-guided bioinformatics model for identifying autism spectrum disorder diagnostic microrna biomarkers,” Scientific Reports, vol. 6, article 39663, 2016. View at Publisher · View at Google Scholar
  16. Y. Zhu, Y. Lin, W. Yan et al., “Novel biomarker micrornas for subtyping of acute coronary syndrome: a bioinformatics approach,” BioMed Research International, vol. 2016, Article ID 4618323, 11 pages, 2016. View at Publisher · View at Google Scholar
  17. Y. Hu, J. Li, W. Yan et al., “Identifying novel glioma associated pathways based on systems biology level meta-analysis,” BMC Systems Biology, vol. 7, supplement 2, p. S9, 2013. View at Publisher · View at Google Scholar
  18. B. Shen, Shen H. -B., Tian T., Lü Q., and Hu G., “Translational bioinformatics and computational systems medicine,” Computational and Mathematical Methods in Medicine, vol. 2013, Article ID 375641, 2 pages, 2013. View at Publisher · View at Google Scholar
  19. H. A. Mattison, T. Stewart, and J. Zhang, “Applying bioinformatics to proteomics: is machine learning the answer to biomarker discovery for PD and MSA?” Movement Disorders, vol. 27, no. 13, pp. 1595–1597, 2012. View at Publisher · View at Google Scholar · View at Scopus
  20. V. A. Huynh-Thu, Y. Saeys, L. Wehenkel, and P. Geurts, “Statistical interpretation of machine learning-based feature importance scores for biomarker discovery,” Bioinformatics, vol. 28, no. 13, Article ID bts238, pp. 1766–1774, 2012. View at Publisher · View at Google Scholar · View at Scopus
  21. X. M. Zhao, K. Q. Liu, G. Zhu et al., “Identifying cancer-related microRNAs based on gene expression data,” Bioinformatics, vol. 31, no. 8, pp. 1226–1234, 2015. View at Publisher · View at Google Scholar
  22. T. Barrett, T. O. Suzek, D. B. Troup et al., “NCBI GEO: mining millions of expression profiles—database and tools,” Nucleic Acids Research, vol. 35, pp. D760–D765, 2007. View at Publisher · View at Google Scholar · View at Scopus
  23. G. K. Smyth, “Linear models and empirical Bayes methods for assessing differential expression in microarray experiments,” Statistical Applications in Genetics and Molecular Biology, vol. 3, no. 1, article 3, 2004. View at Publisher · View at Google Scholar · View at MathSciNet
  24. M. E. Ritchie, B. Phipson, D. Wu et al., “limma powers differential expression analyses for RNA-sequencing and microarray studies,” Nucleic Acids Research, vol. 43, no. 7, 2015. View at Publisher · View at Google Scholar
  25. J. Huang, Z. Sun, W. Yan et al., “Identification of MicroRNA as sepsis biomarker based on miRNAs regulatory network analysis,” BioMed Research International, vol. 2014, Article ID 594350, 12 pages, 2014. View at Publisher · View at Google Scholar · View at Scopus
  26. W. Yan, L. Xu, Z. Sun et al., “MicroRNA biomarker identification for pediatric acute myeloid leukemia based on a novel bioinformatics model,” Oncotarget, vol. 6, no. 28, pp. 26424–26436, 2015. View at Publisher · View at Google Scholar · View at Scopus
  27. F. Gao, J. Chang, H. Wang, and G. Zhang, “Potential diagnostic value of miR-155 in serum from lung adenocarcinoma patients,” Oncology Reports, vol. 31, no. 1, pp. 351–357, 2014. View at Publisher · View at Google Scholar · View at Scopus
  28. F. Tian, R. Li, Z. Chen et al., “Differentially expressed miRNAs in tumor, adjacent, and normal tissues of lung adenocarcinoma,” BioMed Research International, vol. 2016, Article ID 1428271, 2016. View at Publisher · View at Google Scholar · View at Scopus
  29. X. L. Zeng, S. Y. Zhang, J. F. Zheng, H. Yuan, and Y. Wang, “Altered miR-143 and miR-150 expressions in peripheral blood mononuclear cells for diagnosis of non-small cell lung cancer,” Chinese Medical Journal, vol. 126, no. 23, pp. 4510–6, 2013 (English). View at Google Scholar
  30. W. C. Cho, A. S. Chow, and J. S. Au, “Restoration of tumour suppressor hsa-miR-145 inhibits cancer cell growth in lung adenocarcinoma patients with epidermal growth factor receptor mutation,” European Journal of Cancer, vol. 45, no. 12, pp. 2197–2206, 2009. View at Publisher · View at Google Scholar · View at Scopus
  31. Huang J. Y., Cui S. Y., Chen Y. T. et al., “MicroRNA-650 was a prognostic factor in human lung adenocarcinoma and confers the docetaxel chemoresistance of lung adenocarcinoma cells via regulating Bcl-2/Bax expression,” PLoS ONE, vol. 8, no. 8, Article ID e72615, 2013. View at Publisher · View at Google Scholar · View at Scopus
  32. X. Zhang, P. Li, M. Rong et al., “MicroRNA-141 is a biomarker for progression of squamous cell carcinoma and adenocarcinoma of the lung: clinical analysis of 125 patients,” The Tohoku Journal of Experimental Medicine, vol. 235, no. 3, pp. 161–169, 2015. View at Publisher · View at Google Scholar
  33. L. Liu, N. Bi, L. Wu et al., “MicroRNA-29c functions as a tumor suppressor by targeting VEGFA in lung adenocarcinoma,” Molecular Cancer, vol. 16, article 50, no. 1, 2017. View at Publisher · View at Google Scholar
  34. Q. Liu, Z. Yu, S. Yuan et al., “Circulating exosomal microRNAs as prognostic biomarkers for non-small-cell lung cancer,” Oncotarget, vol. 8, no. 8, pp. 13048–13058, 2017. View at Publisher · View at Google Scholar
  35. Q. Chen, H. Hu, D. Jiao et al., “miR-126-3p and miR-451a correlate with clinicopathological features of lung adenocarcinoma: The underlying molecular mechanisms,” Oncology Reports, vol. 36, no. 2, pp. 209–917, 2016. View at Google Scholar
  36. S.-B. Shi, M. Wang, J. Tian, R. Li, C.-X. Chang, and J.-L. Qi, “MicroRNA 25, microRNA 145, and microRNA 210 as biomarkers for predicting the efficacy of maintenance treatment with pemetrexed in lung adenocarcinoma patients who are negative for epidermal growth factor receptor mutations or anaplastic lymphoma kinase translocations,” Translational Research, vol. 170, pp. 1–7, 2016. View at Publisher · View at Google Scholar · View at Scopus
  37. S. Kaduthanam, S. Gade, M. Meister et al., “Serum miR-142-3p is associated with early relapse in operable lung adenocarcinoma patients,” Lung Cancer, vol. 80, no. 2, pp. 223–227, 2013. View at Google Scholar
  38. S. I. Rothschild, M. P. Tschan, E. A. Federzoni et al., “MicroRNA-29b is involved in the Src-ID1 signaling pathway and is dysregulated in human lung adenocarcinoma,” Oncogene, vol. 31, no. 38, pp. 4221–4232, 2012. View at Publisher · View at Google Scholar · View at Scopus
  39. Y. Liu, F. Wang, and P. Xu, “miR-590 accelerates lung adenocarcinoma migration and invasion through directly suppressing functional target OLFM4,” Biomedicine & Pharmacotherapy, vol. 86, pp. 466–474, 2017. View at Publisher · View at Google Scholar
  40. J. Zhu, S. Wang, W. Zhang et al., “Screening key microRNAs for castration-resistant prostate cancer based on miRNA/mRNA functional synergistic network,” Oncotarget, vol. 6, no. 41, pp. 43819–43830, 2015. View at Publisher · View at Google Scholar · View at Scopus
  41. W. Zhang, J. Zang, X. Jing et al., “Identification of candidate miRNA biomarkers from miRNA regulatory network with application to prostate cancer,” Journal of Translational Medicine, vol. 12, p. 12, 2014. View at Publisher · View at Google Scholar · View at Scopus
  42. J. Chen, D. Zhang, W. Zhang et al., “Clear cell renal cell carcinoma associated microRNA expression signatures identified by an integrated bioinformatics analysis,” Journal of Translational Medicine, vol. 11, article 169, 2013. View at Publisher · View at Google Scholar
  43. G. Dennis Jr., B. T. Sherman, D. A. Hosack et al., “DAVID: database for annotation, visualization, and integrated discovery,” Genome Biology, vol. 4, no. 5, p. P3, 2003. View at Google Scholar
  44. Z. Timsah, Z. Ahmed, C.-C. Lin et al., “Competition between Grb2 and Plcγ1 for FGFR2 regulates basal phospholipase activity and invasion,” Nature Structural and Molecular Biology, vol. 21, no. 2, pp. 180–188, 2014. View at Publisher · View at Google Scholar · View at Scopus
  45. L. Li, L. Wang, K. M. Prise et al., “Akt/mTOR mediated induction of bystander effect signaling in a nucleus independent manner in irradiated human lung adenocarcinoma epithelial cells,” Oncotarget, 2017. View at Publisher · View at Google Scholar
  46. Z. Su, K. Wang, R. Li et al., “Overexpression of RBM5 induces autophagy in human lung adenocarcinoma cells,” World Journal of Surgical Oncology, vol. 14, no. 1, article 57, 2016. View at Publisher · View at Google Scholar · View at Scopus
  47. E. Y. P. Lee, P.-L. Khong, V. H. F. Lee, W. Qian, X. Yu, and M. P. Wong, “Metabolic phenotype of stage IV lung adenocarcinoma: relationship with epidermal growth factor receptor mutation,” Clinical Nuclear Medicine, vol. 40, no. 3, pp. e190–e195, 2015. View at Publisher · View at Google Scholar · View at Scopus
  48. D. D. Becker-Santos, K. L. Thu, J. C. English et al., “Developmental transcription factor NFIB is a putative target of oncofetal miRNAs and is associated with tumour aggressiveness in lung adenocarcinoma,” The Journal of Pathology, vol. 240, no. 2, pp. 161–172, 2016. View at Google Scholar
  49. X. Wang, M. Long, K. Dong et al., “Chemotherapy agents-induced immunoresistance in lung cancer cells could be reversed by trop-2 inhibition in vitro and in vivo by interaction with MAPK signaling pathway,” Cancer Biology & Therapy, vol. 14, no. 12, pp. 1123–1132, 2013. View at Publisher · View at Google Scholar
  50. G. M. Dancik and D. Theodorescu, “Robust prognostic gene expression signatures in bladder cancer and lung adenocarcinoma depend on cell cycle related genes,” PLoS ONE, vol. 9, no. 1, Article ID e85249, 2014. View at Publisher · View at Google Scholar · View at Scopus
  51. J. M. Kim, D. W. Kang, L. Z. Long et al., “Differential expression of Yes-associated protein is correlated with expression of cell cycle markers and pathologic TNM staging in non-small-cell lung carcinoma,” Human Pathology, vol. 42, no. 3, pp. 315–323, 2011. View at Publisher · View at Google Scholar
  52. R. L. Toonkel, A. C. Borczuk, and C. A. Powell, “TGF-β signaling pathway in lung adenocarcinoma invasion,” Journal of Thoracic Oncology, vol. 5, no. 2, pp. 153–157, 2010. View at Publisher · View at Google Scholar · View at Scopus
  53. Y. Kusano, Y. Yoshitomi, S. Munesue, M. Okayama, and K. Oguri, “Cooperation of syndecan-2 and syndecan-4 among cell surface heparan sulfate proteoglycans in the actin cytoskeletal organization of Lewis lung carcinoma cells,” Journal of Biochemistry, vol. 135, no. 1, pp. 129–137, 2004. View at Publisher · View at Google Scholar · View at Scopus