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Article

Decision tree‑based classifiers for lung cancer diagnosis and subtyping using TCGA miRNA expression data

  • Authors:
    • Masih Sherafatian
    • Fateme Arjmand
  • View Affiliations / Copyright

    Affiliations: Department of Molecular Genetics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran 14115‑111, Iran, Department of Genetics and Molecular Medicine, Zanjan University of Medical Sciences, Zanjan 45139‑56184, Iran
  • Pages: 2125-2131
    |
    Published online on: June 10, 2019
       https://doi.org/10.3892/ol.2019.10462
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Abstract

Lung cancer has the world's highest cancer‑​associated mortality rate, making biomarker discovery for this cancer a pressing issue. Machine learning approaches to identify molecular biomarkers are not as prevalent as screening of potential biomarkers by differential expression analysis. However, several differentially expressed miRNAs involved in cancer have been identified using this approach. The availability of The Cancer Genome Atlas (TCGA) allows the use of machine‑learning methods for the molecular profiling of tumors. The present study employed empirical negative control microRNAs (miRs) in lung cancer to normalize lung adenocarcinoma (LUAD) and lung squamous cell carcinoma (LUSC) datasets from TCGA to model decision trees in order to classify lung cancer status and subtype. The two primary classification models consisted of four miRNAs for lung cancer diagnosis and subtyping. hsa‑miR‑183 and hsa‑miR‑135b were used to distinguish lung tumors from normal samples taken from tissues adjacent to the tumor site, and hsa‑miR‑944 and hsa‑miR‑205 to further classify the tumors into LUAD and LUSC major subtypes. Specific cancer status classification models were also presented for each subtype.
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1 

Ridge CA, McErlean AM and Ginsberg MS: Epidemiology of lung cancer. Semin Intervent Radiol. 30:93–98. 2013. View Article : Google Scholar : PubMed/NCBI

2 

MacDonagh L, Gray SG, Finn SP, Cuffe S, O'Byrne KJ and Barr MP: The emerging role of microRNAs in resistance to lung cancer treatments. Cancer Trea Rev. 41:160–169. 2015. View Article : Google Scholar

3 

Landi MT, Zhao Y, Rotunno M, Koshiol J, Liu H, Bergen AW, Rubagotti M, Goldstein AM, Linnoila I, Marincola FM, et al: MicroRNA expression differentiates histology and predicts survival of lung cancer. Clin Cancer Res. 16:430–441. 2010. View Article : Google Scholar : PubMed/NCBI

4 

Leidinger P, Brefort T, Backes C, Krapp M, Galata V, Beier M, Kohlhaas J, Huwer H, Meese E and Keller A: High-throughput qRT-PCR validation of blood microRNAs in non-small cell lung cancer. Oncotarget. 26:4611–4616. 2016.

5 

Inamura K and Ishikawa Y: MicroRNA in lung cancer: Novel biomarkers and potential tools for treatment. J Clin Med. 5:E362016. View Article : Google Scholar : PubMed/NCBI

6 

Anglicheau D, Muthukumar T and Suthanthiran M: MicroRNAs: Small RNAs with big effects. Transplantation. 90:105–112. 2010. View Article : Google Scholar : PubMed/NCBI

7 

Takamizawa J, Konishi H, Yanagisawa K, Tomida S, Osada H, Endoh H, Harano T, Yatabe Y, Nagino M, Nimura Y, et al: Reduced expression of the let-7 microRNAs in human lung cancers in association with shortened postoperative survival. Cancer Res. 64:3753–3756. 2004. View Article : Google Scholar : PubMed/NCBI

8 

Iorio MV and Croce CM: MicroRNA dysregulation in cancer: Diagnostics, monitoring and therapeutics. A comprehensive review. EMBO Mol Med. 4:143–159. 2012. View Article : Google Scholar : PubMed/NCBI

9 

Yanaihara N, Caplen N, Bowman E, Seike M, Kumamoto K, Yi M, Stephens RM, Okamoto A, Yokota J, Tanaka T, et al: Unique microRNA molecular profiles in lung cancer diagnosis and prognosis. Cancer Cell. 9:189–198. 2006. View Article : Google Scholar : PubMed/NCBI

10 

Del Vescovo V, Cantaloni C, Cucino A, Girlando S, Silvestri M, Bragantini E, Fasanella S, Cuorvo LV, Palma PD, Rossi G, et al: miR-205 Expression levels in nonsmall cell lung cancerdo not always distinguish adenocarcinomas from squamous cell carcinomas. Am J Surg Pathol. 35:268–275. 2011. View Article : Google Scholar : PubMed/NCBI

11 

Geurts P, Irrthum A and Wehenkel L: Supervised learning with decision tree-based methods in computational and systems biology. Mol Biosyst. 5:1593–1605. 2009. View Article : Google Scholar : PubMed/NCBI

12 

Safavian SR and Landgrebe DA: A survey of decision tree classifier methodology. IEEE Trans Systems Man Cybernetics. 3:660–674. 1991. View Article : Google Scholar

13 

ENCODE Project Consortium, Birney E, Stamatoyannopoulos JA, Dutta A, Guigó R, Gingeras TR, Margulies EH, Weng Z, Snyder M, Dermitzakis ET, et al: Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature. 447:799–816. 2007. View Article : Google Scholar : PubMed/NCBI

14 

Rosenfeld N, Aharonov R, Meiri E, Rosenwald S, Spector Y, Zepeniuk M, Benjamin H, Shabes N, Tabak S, Levy A, et al: MicroRNAs accurately identify cancer tissue origin. Nat Biotechnol. 26:462–469. 2008. View Article : Google Scholar : PubMed/NCBI

15 

Rosenwald S, Gilad S, Benjamin S, Lebanony D, Dromi N, Faerman A, Benjamin H, Tamir R, Ezagouri M, Goren E, et al: Validation of a microRNA-based qRT-PCR test for accurate identification of tumor tissue origin. Mod Pathol. 23:814–823. 2010. View Article : Google Scholar : PubMed/NCBI

16 

Jeong Y, Xie Y, Xiao G, Behrens C, Girard L, Wistuba II, Minna JD and Mangelsdorf DJ: Nuclear receptor expression defines a set of prognostic biomarkers for lung cancer. PLoS Med. 7:e10003782010. View Article : Google Scholar : PubMed/NCBI

17 

Lu Y and Han J: Cancer classification using gene expression data. Information Systems. 28:243–268. 2003. View Article : Google Scholar

18 

Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, et al: Bioconductor: Open software development for computational biology and bioinformatics. Genome Biol. 5:R802004. View Article : Google Scholar : PubMed/NCBI

19 

Sherafatian M: Tree-based machine learning algorithms identified minimal set of miRNA biomarkers for breast cancer diagnosis and molecular subtyping. Gene. 667:111–118. 2018. View Article : Google Scholar

20 

Colaprico A, Silva TC, Olsen C, Garofano L, Cava C, Garolini D, Sabedot TS, Malta TM, Pagnotta SM, Castiglioni I, et al: TCGAbiolinks: An R/Bioconductor package for integrative analysis of TCGA data. Nucleic Acids Res. 44:e712015. View Article : Google Scholar : PubMed/NCBI

21 

Cancer Genome Atlas Research Network, . Comprehensive molecular profiling of lung adenocarcinoma. Nature. 511:543–550. 2014. View Article : Google Scholar : PubMed/NCBI

22 

Cancer Genome Atlas Research Network, . Comprehensive genomic characterization of squamous cell lung cancers. Nature. 489:519–525. 2012. View Article : Google Scholar : PubMed/NCBI

23 

Gentleman R, Carey V, Huber W and Hahne F: Genefilter: Methods for filtering genes from microarray experiments. R package version 1(0) R package version 1.42.0.2011.

24 

Kuhn M: Building predictive models in R using the Caret package. J Stat Software. 28:1–26. 2008. View Article : Google Scholar

25 

Risso D: EDASeq: Exploratory data analysis and normalization for RNA-Seq. 2013.

26 

Risso D, Ngai J, Speed TP and Dudoit S: Normalization of RNA-seq data using factor analysis of control genes or samples. Nat Biotechnol. 32:896–902. 2014. View Article : Google Scholar : PubMed/NCBI

27 

Love MI, Huber W and Anders S: Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 15:5502014. View Article : Google Scholar : PubMed/NCBI

28 

Hao M, Wang Y and Bryant SH: An efficient algorithm coupled with synthetic minority over-sampling technique to classify imbalanced PubChem BioAssay data. Anal Chim Acta. 806:117–127. 2014. View Article : Google Scholar : PubMed/NCBI

29 

Torgo L: Data mining with R: Learning with case studies. 2016, CRC press; Boca Raton, FL, USA:

30 

Williams GJ: Rattle: A data mining GUI for R. R J. 1:45–55. 2009. View Article : Google Scholar

31 

Therneau TM, Atkinson B and Ripley MB: The rpart package. 2010.

32 

Robin X, Turck N, Hainard A, Tiberti N, Lisacek F, Sanchez JC and Müller M: pROC: An open-source package for R and S+ to analyze and compare ROC curves. BMC Bioinformatics. 12:772011. View Article : Google Scholar : PubMed/NCBI

33 

Wang Y, Zhang X, Liu L, Li H, Yu J, Wang C and Ren X: Clinical implication of microrna for lung cancer. Cancer Biother Radiopharm. 28:261–267. 2013. View Article : Google Scholar : PubMed/NCBI

34 

Feng B, Zhang K, Wang R and Chen L: Non-small-cell lung cancer and miRNAs: Novel biomarkers and promising tools for treatment. Clin Sci (Lond). 128:619–634. 2015. View Article : Google Scholar : PubMed/NCBI

35 

Sun Y, Bai Y, Zhang F, Wang Y, Guo Y and Guo L: miR-126 inhibits non-small cell lung cancer cells proliferation by targeting EGFL7. Biochem Biophys Res Commun. 391:1483–1489. 2010. View Article : Google Scholar : PubMed/NCBI

36 

Zhong M, Ma X, Sun C and Chen L: MicroRNAs reduce tumor growth and contribute to enhance cytotoxicity induced by gefitinib in non-small cell lung cancer. Chem Biol Interact. 184:431–438. 2010. View Article : Google Scholar : PubMed/NCBI

37 

Su Y, Guarnera MA, Fang H and Jiang F: Small non-coding RNA biomarkers in sputum for lung cancer diagnosis. Mol Cancer. 15:362016. View Article : Google Scholar : PubMed/NCBI

38 

Võsa U, Vooder T, Kolde R, Vilo J, Metspalu A and Annilo T: Meta-analysis of microRNA expression in lung cancer. Int J Cancer. 132:2884–2893. 2013. View Article : Google Scholar : PubMed/NCBI

39 

Boeri M, Verri C, Conte D, Roz L, Modena P, Facchinetti F, Calabrò E, Croce CM, Pastorino U and Sozzi G: MicroRNA signatures in tissues and plasma predict development and prognosis of computed tomography detected lung cancer. Proc Natl Acad Sci USA. 108:3713–3718. 2011. View Article : Google Scholar : PubMed/NCBI

40 

Lebanony D, Benjamin H, Gilad S, Ezagouri M, Dov A, Ashkenazi K, Gefen N, Izraeli S, Rechavi G, Pass H, et al: Diagnostic assay based on hsa-miR-205 expression distinguishes squamous from nonsquamous non-small-cell lung carcinoma. J Clin Oncol. 27:2030–2037. 2009. View Article : Google Scholar : PubMed/NCBI

41 

Lu Y, Govindan R, Wang L, Liu PY, Goodgame B, Wen W, Sezhiyan A, Pfeifer J, Li YF, Hua X, et al: MicroRNA profiling and prediction of recurrence/relapse-free survival in stage I lung cancer. Carcinogenesis. 33:1046–1054. 2012. View Article : Google Scholar : PubMed/NCBI

42 

Zhang JG, Wang JJ, Zhao F, Liu Q, Jiang K and Yang GH: MicroRNA-21 (miR-21) represses tumor suppressor PTEN and promotes growth and invasion in non-small cell lung cancer (NSCLC). Clin Chim Acta. 411:846–852. 2010. View Article : Google Scholar : PubMed/NCBI

43 

Hamamoto J, Soejima K, Yoda S, Naoki K, Nakayama S, Satomi R, Terai H, Ikemura S, Sato T, Yasuda H, et al: Identification of microRNAs differentially expressed between lung squamous cell carcinoma and lung adenocarcinoma. Mol Med Rep. 8:456–462. 2013. View Article : Google Scholar : PubMed/NCBI

44 

Gregory PA, Bert AG, Paterson EL, Barry SC, Tsykin A, Farshid G, Vadas MA, Khew-Goodall Y and Goodall GJ: The miR-200 family and miR-205 regulate epithelial to mesenchymal transition by targeting ZEB1 and SIP1. Nat Cell Biol. 10:593–601. 2008. View Article : Google Scholar : PubMed/NCBI

45 

Duan B, Guo T, Sun H, Cai R, Rui Q and Xi Z: miR-205 as a biological marker in non-small cell lung cancer. Biomed Pharmacother. 91:823–830. 2017. View Article : Google Scholar : PubMed/NCBI

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Copy and paste a formatted citation
Spandidos Publications style
Sherafatian M and Arjmand F: Decision tree‑based classifiers for lung cancer diagnosis and subtyping using TCGA miRNA expression data. Oncol Lett 18: 2125-2131, 2019.
APA
Sherafatian, M., & Arjmand, F. (2019). Decision tree‑based classifiers for lung cancer diagnosis and subtyping using TCGA miRNA expression data. Oncology Letters, 18, 2125-2131. https://doi.org/10.3892/ol.2019.10462
MLA
Sherafatian, M., Arjmand, F."Decision tree‑based classifiers for lung cancer diagnosis and subtyping using TCGA miRNA expression data". Oncology Letters 18.2 (2019): 2125-2131.
Chicago
Sherafatian, M., Arjmand, F."Decision tree‑based classifiers for lung cancer diagnosis and subtyping using TCGA miRNA expression data". Oncology Letters 18, no. 2 (2019): 2125-2131. https://doi.org/10.3892/ol.2019.10462
Copy and paste a formatted citation
x
Spandidos Publications style
Sherafatian M and Arjmand F: Decision tree‑based classifiers for lung cancer diagnosis and subtyping using TCGA miRNA expression data. Oncol Lett 18: 2125-2131, 2019.
APA
Sherafatian, M., & Arjmand, F. (2019). Decision tree‑based classifiers for lung cancer diagnosis and subtyping using TCGA miRNA expression data. Oncology Letters, 18, 2125-2131. https://doi.org/10.3892/ol.2019.10462
MLA
Sherafatian, M., Arjmand, F."Decision tree‑based classifiers for lung cancer diagnosis and subtyping using TCGA miRNA expression data". Oncology Letters 18.2 (2019): 2125-2131.
Chicago
Sherafatian, M., Arjmand, F."Decision tree‑based classifiers for lung cancer diagnosis and subtyping using TCGA miRNA expression data". Oncology Letters 18, no. 2 (2019): 2125-2131. https://doi.org/10.3892/ol.2019.10462
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