Bioinformatics Analyses of Significant Prognostic Risk Markers for Thyroid Papillary Carcinoma

Overview

Journal Tumour Biol

Publisher Sage Publications

Specialty Oncology

Date 2015 Apr 25

PMID 25908172

Citations 10

Authors

Xiao-Shan Min

Peng Huang

Xu Liu

Chao Dong

Xiao-Lin Jiang

Zheng-Tai Yuan

Lin-Feng Mao

Shi Chang

Affiliations

Soon will be listed here.

Abstract

This study was aimed to identify the prognostic risk markers for thyroid papillary carcinoma (TPC) by bioinformatics. The clinical data of TPC and their microRNAs (miRNAs) and genes expression profile data were downloaded from The Cancer Genome Atlas. Elastic net-Cox's proportional regression hazards model (EN-COX) was used to identify the prognostic associated factors. The receiver operating characteristic (ROC) curve and Kaplan-Meier (KM) curve were used to screen the significant prognostic risk miRNA and genes. Then, the target genes of the obtained miRNAs were predicted followed by function prediction. Finally, the significant risk genes were performed literature mining and function analysis. Total 1046 miRNAs and 20531 genes in 484 cases samples were identified after data preprocessing. From the EN-COX model, 30 prognostic risk factors were obtained. Based on the 30 risk factors, 3 miRNAs and 11 genes were identified from the ROC and KM curves. The target genes of miRNA-342 such as B-cell CLL/lymphoma 2 (BCL2) were mainly enriched in the biological process related to cellular metabolic process and Disease Ontology terms of lymphoma. The target genes of miRNA-93 were mainly enriched in the pathway of G1 phase. Among the 11 prognostic risk genes, v-maf avian musculoaponeurotic fibrosarcoma oncogene homologue F (MAFF), SRY (sex-determining region Y)-box 4 (SOX4), and retinoic acid receptor, alpha (RARA) encoded transcription factors. Besides, RARA was enriched in four pathways. These prognostic markers such as miRNA-93, miRNA-342, RARA, MAFF, SOX4, and BCL2 may be used as targets for TPC chemoprevention.

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References

Croft D, OKelly G, Wu G, Haw R, Gillespie M, Matthews L . Reactome: a database of reactions, pathways and biological processes. Nucleic Acids Res. 2010; 39(Database issue):D691-7. PMC: 3013646. DOI: 10.1093/nar/gkq1018. View

Allegretto E, McClurg M, Lazarchik S, Clemm D, Kerner S, Elgort M . Transactivation properties of retinoic acid and retinoid X receptors in mammalian cells and yeast. Correlation with hormone binding and effects of metabolism. J Biol Chem. 1993; 268(35):26625-33. View

Kimura T, TANIZAWA O, Mori K, Brownstein M, Okayama H . Structure and expression of a human oxytocin receptor. Nature. 1992; 356(6369):526-9. DOI: 10.1038/356526a0. View

Kanehisa M, Goto S . KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Res. 1999; 28(1):27-30. PMC: 102409. DOI: 10.1093/nar/28.1.27. View

Bovolenta L, Acencio M, Lemke N . HTRIdb: an open-access database for experimentally verified human transcriptional regulation interactions. BMC Genomics. 2012; 13:405. PMC: 3472291. DOI: 10.1186/1471-2164-13-405. View

Lufkin T, Lohnes D, Mark M, Dierich A, Gorry P, Gaub M . High postnatal lethality and testis degeneration in retinoic acid receptor alpha mutant mice. Proc Natl Acad Sci U S A. 1993; 90(15):7225-9. PMC: 47109. DOI: 10.1073/pnas.90.15.7225. View

Wagner G, Kin K, Lynch V . Measurement of mRNA abundance using RNA-seq data: RPKM measure is inconsistent among samples. Theory Biosci. 2012; 131(4):281-5. DOI: 10.1007/s12064-012-0162-3. View

Lohnes D, Kastner P, Dierich A, Mark M, Lemeur M, Chambon P . Function of retinoic acid receptor gamma in the mouse. Cell. 1993; 73(4):643-58. DOI: 10.1016/0092-8674(93)90246-m. View

Friedman J, Hastie T, Tibshirani R . Regularization Paths for Generalized Linear Models via Coordinate Descent. J Stat Softw. 2010; 33(1):1-22. PMC: 2929880. View

10.

Grady W, Parkin R, Mitchell P, Lee J, Kim Y, Tsuchiya K . Epigenetic silencing of the intronic microRNA hsa-miR-342 and its host gene EVL in colorectal cancer. Oncogene. 2008; 27(27):3880-8. DOI: 10.1038/onc.2008.10. View

11.

Xiao F, Zuo Z, Cai G, Kang S, Gao X, Li T . miRecords: an integrated resource for microRNA-target interactions. Nucleic Acids Res. 2008; 37(Database issue):D105-10. PMC: 2686554. DOI: 10.1093/nar/gkn851. View

12.

Kimura T, Takemura M, Nomura S, Nobunaga T, Kubota Y, Inoue T . Expression of oxytocin receptor in human pregnant myometrium. Endocrinology. 1996; 137(2):780-5. DOI: 10.1210/endo.137.2.8593830. View

13.

Huang Y, Prasad M, Lemon W, Hampel H, Wright F, Kornacker K . Gene expression in papillary thyroid carcinoma reveals highly consistent profiles. Proc Natl Acad Sci U S A. 2001; 98(26):15044-9. PMC: 64980. DOI: 10.1073/pnas.251547398. View

14.

Zeng Q, Chen G, Vlantis A, van Hasselt C . Oestrogen mediates the growth of human thyroid carcinoma cells via an oestrogen receptor-ERK pathway. Cell Prolif. 2007; 40(6):921-35. PMC: 6495898. DOI: 10.1111/j.1365-2184.2007.00471.x. View

15.

Shannon P, Markiel A, Ozier O, Baliga N, Wang J, Ramage D . Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res. 2003; 13(11):2498-504. PMC: 403769. DOI: 10.1101/gr.1239303. View

16.

Cahill D, Kinzler K, Vogelstein B, Lengauer C . Genetic instability and darwinian selection in tumours. Trends Cell Biol. 1999; 9(12):M57-60. View

17.

Pramoonjago P, Baras A, Moskaluk C . Knockdown of Sox4 expression by RNAi induces apoptosis in ACC3 cells. Oncogene. 2006; 25(41):5626-39. DOI: 10.1038/sj.onc.1209566. View

18.

Vervoort S, van Boxtel R, Coffer P . The role of SRY-related HMG box transcription factor 4 (SOX4) in tumorigenesis and metastasis: friend or foe?. Oncogene. 2012; 32(29):3397-409. DOI: 10.1038/onc.2012.506. View

19.

Tavazoie S, Alarcon C, Oskarsson T, Padua D, Wang Q, Bos P . Endogenous human microRNAs that suppress breast cancer metastasis. Nature. 2008; 451(7175):147-52. PMC: 2782491. DOI: 10.1038/nature06487. View

20.

Haugen B, Larson L, Pugazhenthi U, Hays W, Klopper J, Kramer C . Retinoic acid and retinoid X receptors are differentially expressed in thyroid cancer and thyroid carcinoma cell lines and predict response to treatment with retinoids. J Clin Endocrinol Metab. 2004; 89(1):272-80. DOI: 10.1210/jc.2003-030770. View