Identification of key genes and miRNAs markers of papillary thyroid cancer
Tóm tắt
Từ khóa
Tài liệu tham khảo
Lodewijk L, Prins AM, Kist JW, Valk GD, Kranenburg O, Rinkes IH, et al. The value of miRNA in diagnosing thyroid cancer: a systematic review. Cancer Biomark. 2012;11(6):229–38.
Geraldo MV, Kimura ET. Integrated analysis of thyroid cancer public datasets reveals role of post-transcriptional regulation on tumor progression by targeting of immune system mediators. PLoS ONE. 2015;10(11):e0141726.
Hay ID, Thompson GB, Grant CS, Bergstralh EJ, Dvorak CE, Gorman CA, et al. Papillary thyroid carcinoma managed at the Mayo Clinic during six decades (1940–1999): temporal trends in initial therapy and long-term outcome in 2444 consecutively treated patients. World J Surg. 2002;26(8):879–85.
Esin YE, Duygu T, Serkan T, Ezel UF, Ugur G, Nejat D. microRNA expression profiles in papillary thyroid carcinoma, benign thyroid nodules and healthy controls. J Cancer. 2016;7(7):803–9.
Vasko V, Espinosa AV, Scouten W, He H, Auer H, Liyanarachchi S, et al. Gene expression and functional evidence of epithelial-to-mesenchymal transition in papillary thyroid carcinoma invasion. Proc Natl Acad Sci. 2007;104(8):2803–8.
Cohen Y, Xing M, Mambo E, Guo Z, Wu G, Trink B, et al. BRAF mutation in papillary thyroid carcinoma. J Natl Cancer Inst. 2003;95(8):625.
Kimura ET, Nikiforova MN, Zhu Z, Knauf JA, Nikiforov YE, Fagin JA. High prevalence of BRAF mutations in thyroid cancer: genetic evidence for constitutive activation of the RET/PTC-RAS-BRAF signaling pathway in papillary thyroid carcinoma. Can Res. 2003;63(7):1454.
Grieco M, Santoro M, Berlingieri MT, Melillo RM, Donghi R, Bongarzone I, et al. PTC is a novel rearranged form of the ret proto-oncogene and is frequently detected in vivo in human thyroid papillary carcinomas. Cell. 1990;60(4):557–63.
Eszlinger M, Paschke R. Molecular fine-needle aspiration biopsy diagnosis of thyroid nodules by tumor specific mutations and gene expression patterns. Mol Cell Endocrinol. 2010;322(1–2):29–37.
Yano Y, Uematsu N, Yashiro T, Hara H, Ueno E, Miwa M, et al. Gene expression profiling identifies platelet-derived growth factor as a diagnostic molecular marker for papillary thyroid carcinoma. Clin Cancer Res. 2004;10(6):2035–43.
Sheils O. Molecular classification and biomarker discovery in papillary thyroid carcinoma [J]. Expert Rev Mol Diagn. 2005;5(6):927–46.
Liu X, He M, Hou Y, Liang B, Zhao L, Ma S, et al. Expression profiles of microRNAs and their target genes in papillary thyroid carcinoma. Oncol Rep. 2013;29(4):1415–20.
Pallante P, Visone R, Ferracin M, Ferraro A, Berlingieri M, Troncone G, et al. MicroRNA deregulation in human thyroid papillary carcinomas. Endocr Relat Cancer. 2006;13(2):497–508.
Liang RQ, Li W, Li Y, Tan C, Li JX, Jin YX, et al. An oligonucleotide microarray for microRNA expression analysis based on labeling RNA with quantum dot and nanogold probe. Nucleic Acids Res. 2005;33(2):e17.
Qiu J, Zhang W, Xia Q, Liu F, Li L, Zhao S, et al. RNA sequencing identifies crucial genes in papillary thyroid carcinoma (PTC) progression. Exp Mol Pathol. 2015;100(1):151.
Robinson MD, McCarthy DJ, Smyth GK. edgeR: a bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics. 2010;26(1):139–40. https://doi.org/10.1093/bioinformatics/btp616 .
Law CW, Chen Y, Shi W, Smyth GK. voom: precision weights unlock linear model analysis tools for RNA-seq read counts. Genome Biol. 2014;15(2):R29.
Smyth GK. Limma: linear models for microarray data, in Bioinformatics and computational biology solutions using R and bioconductor. New York: Springer; 2005. p. 397–420.
Szklarczyk D, Franceschini A, Wyder S, Forslund K, Heller D, Huerta-Cepas J, et al. STRING v10: protein–protein interaction networks, integrated over the tree of life. Nucleic Acids Res. 2015;43(Database issue):D447–52. https://doi.org/10.1093/nar/gku1003 .
Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, et al. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res. 2003;13(11):2498–504.
Tang Y, Li M, Wang J, Pan Y, Wu FX. CytoNCA: a cytoscape plugin for centrality analysis and evaluation of biological networks. BioSystems. 2014;11:005. https://doi.org/10.1016/j.biosystems .
He X, Zhang J. Why do hubs tend to be essential in protein networks? PLoS Genet. 2006;2(6):e88. https://doi.org/10.1371/journal.pgen.0020088 .
Breuer K, Foroushani AK, Laird MR, Chen C, Sribnaia A, Lo R, et al. InnateDB: systems biology of innate immunity and beyond—recent updates and continuing curation. Nucleic Acids Res. 2013;41(Database issue):D1228–33. https://doi.org/10.1093/nar/gks1147 .
Dweep H, Gretz N. miRWalk2. 0: a comprehensive atlas of microRNA-target interactions. Nat Methods. 2015;12(8):697.
Yu G, Wang LG, Han Y, He QY. clusterProfiler: an R package for comparing biological themes among gene clusters. OMICS. 2012;16(5):284–7.
Hirohashi S, Kanai Y. Cell adhesion system and human cancer morphogenesis. Cancer Sci. 2003;94(7):575–81.
Yang L, Froio RM, Sciuto TE, Dvorak AM, Alon R, Luscinskas FW. ICAM-1 regulates neutrophil adhesion and transcellular migration of TNF-alpha-activated vascular endothelium under flow. Blood. 2005;106(2):584.
Buitrago D, Keutgen X, Crowley M, Filicori F, Aldailami H, Hoda R, et al. Intercellular adhesion molecule-1 (ICAM-1) is upregulated in aggressive papillary thyroid carcinoma. Ann Surg Oncol. 2012;19(3):973–80.
Skelding KA, Barry RD, Shafren DR. Systemic targeting of metastatic human breast tumor xenografts by Coxsackievirus A21. Breast Cancer Res Treat. 2009;113(1):21–30.
Husmark J, Heldin NE, Nilsson M. N-cadherin-mediated adhesion and aberrant catenin expression in anaplastic thyroid-carcinoma cell lines. Int J Cancer. 1999;83(5):692–9.
Zhang X, Liu G, Kang Y, Dong Z, Qian Q, Ma X. N-cadherin expression is associated with acquisition of EMT phenotype and with enhanced invasion in erlotinib-resistant lung cancer cell lines. PLoS ONE. 2013;8(3):e57692.
Richards EJ, Zhang G, Li ZP, Permuth-Wey J, Challa S, Li Y, et al. Long non-coding RNAs (LncRNA) regulated by transforming growth factor (TGF) β: LncRNA-hit-mediated TGFβ-induced epithelial to mesenchymal transition in mammary epithelia. J Biol Chem. 2015;290(11):6857–67.
Ferraro A, Boni T, Pintzas A. EZH2 regulates cofilin activity and colon cancer cell migration by targeting ITGA2 gene. Plos ONE. 2014;9(12):e115276.
Prasad ML, Pellegata NS, Huang Y, Nagaraja HN, de la Chapell A, Kloos RT. Galectin-3, fibronectin-1, CITED-1, HBME1 and cytokeratin-19 immunohistochemistry is useful for the differential diagnosis of thyroid tumors. Mod Pathol. 2004;18(1):48–57.
Sugenoya A, Usuda N, Adachi W, Oohashi M, Nagata T, Iida F. Immunohistochemical studies on the localization of fibronectin in human thyroid neoplastic tissues. Endocrinol Jpn. 1988;35(1):111.
Sponziello M, Rosignolo F, Celano M, Maggisano V, Pecce V, De Rose RF, et al. Fibronectin-1 expression is increased in aggressive thyroid cancer and favors the migration and invasion of cancer cells. Mol Cell Endocrinol. 2016;431:123–32.
Lu P, Weaver VM, Werb Z. The extracellular matrix: a dynamic niche in cancer progression. J Cell Biol. 2012;196(4):395.
Martin DC, Sanchezsweatman OH, Ho AT, Inderdeo DS, Tsao MS, Khokha R. Transgenic TIMP-1 inhibits simian virus 40 T antigen-induced hepatocarcinogenesis by impairment of hepatocellular proliferation and tumor angiogenesis. Lab Invest. 1999;79(2):225–34.
Murphy G, Docherty AJP. The matrix metalloproteinases and their inhibitors. Am J Respir Cell Mol Biol. 1992;7(2):120.
Khokha R, Zimmer MJ, Graham CH, Lala PK, Waterhouse P. Suppression of invasion by inducible expression of tissue inhibitor of metalloproteinase-1 (TIMP-1) in B16-F10 melanoma cells. J Natl Cancer Inst. 1992;84(13):1017–22.
Tsuchiya Y, Sato H, Endo Y, Okada Y, Mai M, Sasaki T, et al. Tissue inhibitor of metalloproteinase 1 is a negative regulator of the metastatic ability of a human gastric cancer cell line, KKLS, in the chick embryo. Can Res. 1993;53(6):1397.
Talvensaari-Mattila A, Turpeenniemi-Hujanen T. High preoperative serum TIMP-1 is a prognostic indicator for survival in breast carcinoma. Breast Cancer Res Treat. 2005;89(1):29–34.
Tetzlaff MT, Liu A, Xu X, Master SR, Baldwin DA, Tobias JW, et al. Differential expression of miRNAs in papillary thyroid carcinoma compared to multinodular goiter using formalin fixed paraffin embedded tissues. Endocr Pathol. 2007;18(3):163–73.
Liu L, Wang J, Li X, Ma J, Shi C, Zhu H, et al. MiR-204-5p suppresses cell proliferation by inhibiting IGFBP5 in papillary thyroid carcinoma. Biochem Biophys Res Commun. 2015;457(4):621–6.
Tanaka K, Sonoo H, Kurebayashi J, Nomura T, Ohkubo S, Yamamoto Y, et al. Inhibition of infiltration and angiogenesis by thrombospondin-1 in papillary thyroid carcinoma. Clin Cancer Res. 2002;8(5):1125–31.
Brennan K, Offiah G, Mcsherry EA, Hopkins AM. Tight junctions: a barrier to the initiation and progression of breast cancer? J Biomed Biotechnol. 2010;2010(1):460607.
Wang X, Tang S, Le SY, Lu R, Rader JS, Meyers C, et al. Aberrant expression of oncogenic and tumor-suppressive microRNAs in cervical cancer is required for cancer cell growth. PLoS ONE. 2008;3(7):e2557.
Li N, Tang B, Zhu ED, Li BS, Zhuang Y, Yu S, et al. Increased miR-222 in H. pylori-associated gastric cancer correlated with tumor progression by promoting cancer cell proliferation and targeting RECK. FEBS Lett. 2012;586(6):722–8.
Chou CK, Chen RF, Chou FF, Chang HW, Chen YJ, Lee YF, et al. miR-146b is highly expressed in adult papillary thyroid carcinomas with high risk features including extrathyroidal invasion and the BRAF(V600E) mutation. Thyroid. 2010;20(5):489.
Chang WSW, Chou RH, Wu CW, Chang JY. Human tissue kallikreins as prognostic biomarkers and as potential targets for anticancer therapy. Expert Opin Ther Pat. 2007;17(10):1227–40.
Macewan M, Mehta V, Darr EA, Xie S, Nowicki TS, Iacob C, et al. Abstract 1502: increased expression of KLK7 and KLK10 in papillary thyroid cancer. Cancer Res. 2011;71(8 Supplement):1502.
Xu X, Cai N, Zhi T, Bao Z, Wang D, Liu Y, et al. MicroRNA-1179 inhibits glioblastoma cell proliferation and cell cycle progression via directly targeting E2F transcription factor 5. Am J Cancer Res. 2017;7(8):1680–92.