Deep sequencing analysis of microRNA expression in human melanocyte and melanoma cell lines

Gene - Tập 572 - Trang 135-145 - 2015
Nan Ding1,2, Shaobin Wang1, Qiong Yang1,2, Yongjun Li1, Hua Cheng3, Junyun Wang1,2, Dong Wang4, Youhui Deng1,2, Yadong Yang1, Songnian Hu1, Hua Zhao4, Xiangdong Fang1
1CAS Key Laboratory of Genome Science and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
2University of Chinese Academy of Sciences, Beijing, 100049, China
3Institute of Biology, Hebei Academy of Sciences, Shijiazhuang 050081, China
4Department of Dermatology, General Hospital of People's Liberation Army, Beijing 100853, China

Tài liệu tham khảo

Adyshev, 2014, Mechanical stress induces pre-B-cell colony-enhancing factor/NAMPT expression via epigenetic regulation by miR-374a and miR-568 in human lung endothelium, Am. J. Respir. Cell Mol. Biol., 50, 409, 10.1165/rcmb.2013-0292OC Aladowicz, 2013, Molecular networks in melanoma invasion and metastasis, Future Oncol., 9, 713, 10.2217/fon.13.9 Babchia, 2010, The PI3K/Akt and mTOR/P70S6K signaling pathways in human uveal melanoma cells: interaction with B-Raf/ERK, Invest. Ophthalmol. Vis. Sci., 51, 421, 10.1167/iovs.09-3974 Baek, 2006, Inactivation of TGF-beta signaling in lung cancer results in increased CDK4 activity that can be rescued by ELF, Biochem. Biophys. Res. Commun., 346, 1150, 10.1016/j.bbrc.2006.05.195 Ball, 1994, Ras mutations in human melanoma: a marker of malignant progression, J. Invest. Dermatol., 102, 285, 10.1111/1523-1747.ep12371783 Barcellos-Hoff, 2009, Transforming growth factor-beta in breast cancer: too much, too late, Breast Cancer Res., 11, 202, 10.1186/bcr2224 Bartel, 2004, MicroRNAs: genomics, biogenesis, mechanism, and function, Cell, 116, 281, 10.1016/S0092-8674(04)00045-5 Brandhagen, 2013, Cytostasis and morphological changes induced by mifepristone in human metastatic cancer cells involve cytoskeletal filamentous actin reorganization and impairment of cell adhesion dynamics, BMC Cancer, 13, 35, 10.1186/1471-2407-13-35 Calin, 2006, MicroRNA signatures in human cancers, Nat. Rev. Cancer, 6, 857, 10.1038/nrc1997 Ciruelos Gil, 2014, Targeting the PI3K/AKT/mTOR pathway in estrogen receptor-positive breast cancer, Cancer Treat. Rev., 40, 862, 10.1016/j.ctrv.2014.03.004 Cloonan, 2008, Stem cell transcriptome profiling via massive-scale mRNA sequencing, Nat. Methods, 5, 613, 10.1038/nmeth.1223 Fabricant, 1977, Nerve growth factor receptors on human melanoma cells in culture, Proc. Natl. Acad. Sci. U. S. A., 74, 565, 10.1073/pnas.74.2.565 Friedlander, 2012, miRDeep2 accurately identifies known and hundreds of novel microRNA genes in seven animal clades, Nucleic Acids Res., 40, 37, 10.1093/nar/gkr688 Fumarola, 2014, Targeting PI3K/AKT/mTOR pathway in non small cell lung cancer, Biochem. Pharmacol., 90, 197, 10.1016/j.bcp.2014.05.011 Giannelli, 2014, Transforming growth factor-beta as a therapeutic target in hepatocellular carcinoma, Cancer Res., 74, 1890, 10.1158/0008-5472.CAN-14-0243 Giard, 1973, In vitro cultivation of human tumors: establishment of cell lines derived from a series of solid tumors, J. Natl. Cancer Inst., 51, 1417, 10.1093/jnci/51.5.1417 Greenberg, 2011, Regulation of cancer aggressive features in melanoma cells by microRNAs, PLoS One, 6, 10.1371/journal.pone.0018936 Griffiths-Jones, 2006, miRBase: microRNA sequences, targets and gene nomenclature, Nucleic Acids Res., 34, D140, 10.1093/nar/gkj112 Han, 2013, A c-myc-microRNA functional feedback loop affects hepatocarcinogenesis, Hepatology, 57, 2378, 10.1002/hep.26302 Howell, 2010, MicroRNA in melanoma, Ochsner J, 10, 83 Humbert, 2013, TGF-beta inhibits human cutaneous melanoma cell migration and invasion through regulation of the plasminogen activator system, Cell. Signal., 25, 490, 10.1016/j.cellsig.2012.10.011 Javelaud, 2011, Efficient TGF-beta/SMAD signaling in human melanoma cells associated with high c-SKI/SnoN expression, Mol. Cancer, 10, 2, 10.1186/1476-4598-10-2 Jeon, 2010, TGF-beta signaling and the role of inhibitory Smads in non-small cell lung cancer, J. Thorac. Oncol., 5, 417, 10.1097/JTO.0b013e3181ce3afd Kozlowski, 1984, A human melanoma line heterogeneous with respect to metastatic capacity in athymic nude mice, J. Natl. Cancer Inst., 72, 913 Kozubek, 2013, In-depth characterization of microRNA transcriptome in melanoma, PLoS One, 8, 10.1371/journal.pone.0072699 Kruger, 2006, RNAhybrid: microRNA target prediction easy, fast and flexible, Nucleic Acids Res., 34, W451, 10.1093/nar/gkl243 Larkin, 2012, Identification of markers of prostate cancer progression using candidate gene expression, Br. J. Cancer, 106, 157, 10.1038/bjc.2011.490 Leidinger, 2010, High-throughput miRNA profiling of human melanoma blood samples, BMC Cancer, 10, 262, 10.1186/1471-2407-10-262 Lu, 2012, miRSystem: an integrated system for characterizing enriched functions and pathways of microRNA targets, PLoS One, 7, e42390, 10.1371/journal.pone.0042390 Metzker, 2010, Sequencing technologies — the next generation, Nat. Rev. Genet., 11, 31, 10.1038/nrg2626 Mortazavi, 2008, Mapping and quantifying mammalian transcriptomes by RNA-Seq, Nat. Methods, 5, 621, 10.1038/nmeth.1226 Muller, 2014, Exploring the miRNA–mRNA regulatory network in clear cell renal cell carcinomas by next-generation sequencing expression profiles, Biomed. Res. Int., 2014, 948408, 10.1155/2014/948408 Perlis, 2004, Recent advances in melanoma biology, Oncologist, 9, 182, 10.1634/theoncologist.9-2-182 Perrot, 2013, Insights into the transforming growth factor-beta signaling pathway in cutaneous melanoma, Ann. Dermatol., 25, 135, 10.5021/ad.2013.25.2.135 Scollen, 2011, TGF-beta signaling pathway and breast cancer susceptibility, Cancer Epidemiol. Biomarkers Prev., 20, 1112, 10.1158/1055-9965.EPI-11-0062 Tokunaga, 2006, Activation of PI3K/Akt signaling and hormone resistance in breast cancer, Breast Cancer, 13, 137, 10.2325/jbcs.13.137 Ulasov, 2013, Inhibition of MMP14 potentiates the therapeutic effect of temozolomide and radiation in gliomas, Cancer Med., 2, 457, 10.1002/cam4.104 Vlachos, 2012, DIANA miRPath v. 2.0: investigating the combinatorial effect of microRNAs in pathways, Nucleic Acids Res., 40, W498, 10.1093/nar/gks494 Wang, 2009, RNA-Seq: a revolutionary tool for transcriptomics, Nat. Rev. Genet., 10, 57, 10.1038/nrg2484 Wang, 2010, DEGseq: an R package for identifying differentially expressed genes from RNA-seq data, Bioinformatics, 26, 136, 10.1093/bioinformatics/btp612 Wu, 2014, Huaier suppresses proliferation and induces apoptosis in human pulmonary cancer cells via upregulation of miR-26b-5p, FEBS Lett., 588, 2107, 10.1016/j.febslet.2014.04.044 Xu, 2014, lncRNA-AC130710 targeting by miR-129-5p is upregulated in gastric cancer and associates with poor prognosis, Tumor Biol., 35, 9701, 10.1007/s13277-014-2274-5 Yin, 1999, TGF-beta signaling blockade inhibits PTHrP secretion by breast cancer cells and bone metastases development, J. Clin. Invest., 103, 197, 10.1172/JCI3523 Zbytek, 2008, Current concepts of metastasis in melanoma, Expert. Rev. Dermatol., 3, 569, 10.1586/17469872.3.5.569 Zhao, 2014, Whole transcriptome RNA-seq analysis: tumorigenesis and metastasis of melanoma, Gene, 548, 234, 10.1016/j.gene.2014.07.038