|
1.
|
Jemal A, Siegel R, Xu J and Ward E: Cancer
statistics, 2010. CA Cancer J Clin. 60:277–300. 2010. View Article : Google Scholar
|
|
2.
|
Molina JR, Yang P, Cassivi SD, Schild SE
and Adjei AA: Non-small cell lung cancer: epidemiology, risk
factors, treatment, and survivorship. Mayo Clin Proc. 83:584–594.
2008. View Article : Google Scholar : PubMed/NCBI
|
|
3.
|
Nagamachi Y, Tani M, Shimizu K, Tsuda H,
Niitsu Y and Yokota J: Orthotopic growth and metastasis of human
non-small cell lung carcinoma cell injected into the pleural cavity
of nude mice. Cancer Lett. 127:203–209. 1998. View Article : Google Scholar : PubMed/NCBI
|
|
4.
|
Wang Y, Yang H, Liu H, Huang J and Song X:
Effect of staurosporine on the mobility and invasiveness of lung
adenocarcinoma A549 cells: an in vitro study. BMC Cancer.
9:1742009. View Article : Google Scholar : PubMed/NCBI
|
|
5.
|
Ji P, Diederichs S, Wang W, et al:
MALAT-1, a novel noncoding RNA, and thymosin beta4 predict
metastasis and survival in early-stage non-small cell lung cancer.
Oncogene. 22:8031–8041. 2003. View Article : Google Scholar : PubMed/NCBI
|
|
6.
|
Schmidt LH, Spieker T, Koschmieder S, et
al: The long noncoding MALAT-1 RNA indicates a poor prognosis in
non-small cell lung cancer and induces migration and tumor growth.
J Thorac Oncol. 6:1984–1992. 2011. View Article : Google Scholar : PubMed/NCBI
|
|
7.
|
Lee J, Yoo J, Yoo H, et al: The novel
miRNA hc-smR-S2-5 decrease the proliferation and migration of human
lung cancer cells by targeting c-Met. Mol Cancer Res. 11:43–53.
2013. View Article : Google Scholar : PubMed/NCBI
|
|
8.
|
Liu J, Lu KH, Liu ZL, Sun M, De W and Wang
ZX: MicroRNA-100 is a potential molecular marker of non-small cell
lung cancer and functions as a tumor suppressor by targeting
polo-like kinase 1. BMC Cancer. 12:5192012. View Article : Google Scholar : PubMed/NCBI
|
|
9.
|
Enfield KS, Pikor LA, Martinez VD and Lam
WL: Mechanistic roles of noncoding RNAs in lung cancer biology and
their clinical implications. Genet Res Int.
2012:7374162012.PubMed/NCBI
|
|
10.
|
Prasanth KV and Spector DL: Eukaryotic
regulatory RNAs: an answer to the ‘genome complexity’ conundrum.
Genes Dev. 21:11–42. 2007.
|
|
11.
|
Gutschner T and Diederichs S: The
hallmarks of cancer: a long non-coding RNA point of view. RNA Biol.
9:703–719. 2012. View Article : Google Scholar : PubMed/NCBI
|
|
12.
|
Chiang AC and Massague J: Molecular basis
of metastasis. N Engl J Med. 359:2814–2823. 2008. View Article : Google Scholar
|
|
13.
|
Hanahan D and Weinberg RA: Hallmarks of
cancer: the next generation. Cell. 144:646–674. 2011. View Article : Google Scholar : PubMed/NCBI
|
|
14.
|
Ovcharenko I, Nobrega MA, Loots GG and
Stubbs L: ECR Browser: a tool for visualizing and accessing data
from comparisons of multiple vertebrate genomes. Nucleic Acids Res.
32:W280–W286. 2004. View Article : Google Scholar : PubMed/NCBI
|
|
15.
|
Larkin MA, Blackshields G, Brown NP, et
al: Clustal W and Clustal X version 2.0. Bioinformatics.
23:2947–2948. 2007. View Article : Google Scholar : PubMed/NCBI
|
|
16.
|
Kong L, Zhang Y, Ye ZQ, et al: CPC: assess
the protein-coding potential of transcripts using sequence features
and support vector machine. Nucleic Acids Res. 35:W345–W349. 2007.
View Article : Google Scholar : PubMed/NCBI
|
|
17.
|
Kohany O, Gentles AJ, Hankus L and Jurka
J: Annotation, submission and screening of repetitive elements in
Repbase: RepbaseSubmitter and Censor. BMC Bioinformatics.
7:4742006. View Article : Google Scholar : PubMed/NCBI
|
|
18.
|
Lai J, Lehman ML, Dinger ME, et al: A
variant of the KLK4 gene is expressed as a cis sense-antisense
chimeric transcript in prostate cancer cells. RNA. 16:1156–1166.
2010. View Article : Google Scholar : PubMed/NCBI
|
|
19.
|
Fung JN, Seim I, Wang D, Obermair A,
Chopin LK and Chen C: Expression and in vitro functions of the
ghrelin axis in endometrial cancer. Horm Cancer. 1:245–255. 2010.
View Article : Google Scholar : PubMed/NCBI
|
|
20.
|
Livak KJ and Schmittgen TD: Analysis of
relative gene expression data using real-time quantitative PCR and
the 2(−Delta Delta C(T)) method. Methods. 25:402–408. 2001.
|
|
21.
|
Mituyama T, Yamada K, Hattori E, et al:
The functional RNA database 3.0: databases to support mining and
annotation of functional RNAs. Nucleic Acids Res. 37:D89–D92. 2009.
View Article : Google Scholar : PubMed/NCBI
|
|
22.
|
Bertino EM, Confer PD, Colonna JE, Ross P
and Otterson GA: Pulmonary neuroendocrine/carcinoid tumors: a
review article. Cancer. 115:4434–4441. 2009. View Article : Google Scholar : PubMed/NCBI
|
|
23.
|
Nakaya HI, Amaral PP, Louro R, et al:
Genome mapping and expression analyses of human intronic noncoding
RNAs reveal tissue-specific patterns and enrichment in genes
related to regulation of transcription. Genome Biol. 8:R432007.
View Article : Google Scholar
|
|
24.
|
Wobbe CR and Struhl K: Yeast and human
TATA-binding proteins have nearly identical DNA sequence
requirements for transcription in vitro. Mol Cell Biol.
10:3859–3867. 1990.PubMed/NCBI
|
|
25.
|
Jurka J: Novel families of interspersed
repetitive elements from the human genome. Nucleic Acids Res.
18:137–141. 1990. View Article : Google Scholar : PubMed/NCBI
|
|
26.
|
Tsuritani K, Irie T, Yamashita R, et al:
Distinct class of putative ‘non-conserved’ promoters in humans:
comparative studies of alternative promoters of human and mouse
genes. Genome Res. 17:1005–1014. 2007.
|
|
27.
|
Segal E and Widom J: Poly(dA:dT) tracts:
major determinants of nucleosome organization. Curr Opin Struct
Biol. 19:65–71. 2009. View Article : Google Scholar : PubMed/NCBI
|
|
28.
|
Dinger ME, Pang KC, Mercer TR and Mattick
JS: Differentiating protein-coding and noncoding RNA: challenges
and ambiguities. PLoS Comput Biol. 4:e10001762008. View Article : Google Scholar : PubMed/NCBI
|
|
29.
|
Kozak M: An analysis of 5′-noncoding
sequences from 699 vertebrate messenger RNAs. Nucleic Acids Res.
15:8125–8148. 1987.
|
|
30.
|
Taft R, Pang K, Mercer T, Dinger M and
Mattick J: Non-coding RNAs: regulators of disease. J Pathol.
220:126–139. 2010. View Article : Google Scholar : PubMed/NCBI
|
|
31.
|
Kondo T, Hashimoto Y, Kato K, Inagaki S,
Hayashi S and Kageyama Y: Small peptide regulators of actin-based
cell morphogenesis encoded by a polycistronic mRNA. Nat Cell Biol.
9:660–665. 2007. View Article : Google Scholar : PubMed/NCBI
|
|
32.
|
Kondo T, Plaza S, Zanet J, et al: Small
peptides switch the transcriptional activity of Shavenbaby during
Drosophila embryogenesis. Science. 329:336–339. 2010.
View Article : Google Scholar : PubMed/NCBI
|
|
33.
|
Slavoff SA, Mitchell AJ, Schwaid AG, et
al: Peptidomic discovery of short open reading frame-encoded
peptides in human cells. Nat Chem Biol. 9:59–64. 2013. View Article : Google Scholar : PubMed/NCBI
|
|
34.
|
Makawita S and Diamandis EP: The
bottleneck in the cancer biomarker pipeline and protein
quantification through mass spectrometry-based approaches: current
strategies for candidate verification. Clin Chem. 56:212–222. 2010.
View Article : Google Scholar
|
|
35.
|
Jacquot C, Carbonnelle D, Tomasoni C,
Papaconstadinou A, Roussis V and Roussakis C: Identification of a
novel putative non-coding RNA involved in proliferation arrest of a
non-small cell lung carcinoma cell line treated with an original
chemical substance, methyl-4-methoxy-3-(3-methyl-2-butanoyl)
benzoate. Int J Oncol. 25:519–527. 2004.
|
|
36.
|
Chen LL and Carmichael GG: Long noncoding
RNAs in mammalian cells: what, where, and why? Wiley Interdiscip
Rev RNA. 1:2–21. 2010.PubMed/NCBI
|
|
37.
|
Moh MC, Lee LH, Yang X and Shen S:
Identification of a novel gene HEPT3 that is overexpressed in human
hepatocellular carcinoma and may function through its noncoding
RNA. Int J Oncol. 31:293–301. 2007.PubMed/NCBI
|
|
38.
|
Panzitt K, Tschernatsch MM, Guelly C, et
al: Characterization of HULC, a novel gene with striking
up-regulation in hepatocellular carcinoma, as noncoding RNA.
Gastroenterology. 132:330–342. 2007. View Article : Google Scholar : PubMed/NCBI
|
|
39.
|
Sonkoly E, Bata-Csorgo Z, Pivarcsi A, et
al: Identification and characterization of a novel, psoriasis
susceptibility-related noncoding RNA gene, PRINS. J Biol Chem.
280:24159–24167. 2005. View Article : Google Scholar : PubMed/NCBI
|
|
40.
|
Amaral PP, Neyt C, Wilkins SJ, et al:
Complex architecture and regulated expression of the Sox2ot locus
during vertebrate development. RNA. 15:2013–2027. 2009. View Article : Google Scholar : PubMed/NCBI
|
|
41.
|
Conley AB, Miller WJ and Jordan IK: Human
cis natural antisense transcripts initiated by transposable
elements. Trends Genet. 24:53–56. 2008. View Article : Google Scholar : PubMed/NCBI
|
|
42.
|
Pheasant M and Mattick JS: Raising the
estimate of functional human sequences. Genome Res. 17:1245–1253.
2007. View Article : Google Scholar : PubMed/NCBI
|
|
43.
|
Reis EM, Louro R, Nakaya HI and
Verjovski-Almeida S: As antisense RNA gets intronic. Omics. 9:2–12.
2005. View Article : Google Scholar : PubMed/NCBI
|
|
44.
|
Louro R, Smirnova AS and Verjovski-Almeida
S: Long intronic noncoding RNA transcription: expression noise or
expression choice? Genomics. 93:291–298. 2009. View Article : Google Scholar : PubMed/NCBI
|
|
45.
|
Louro R, Nakaya HI, Amaral PP, et al:
Androgen responsive intronic non-coding RNAs. BMC Biol. 5:42007.
View Article : Google Scholar : PubMed/NCBI
|
|
46.
|
Michael DR, Phillips AO, Krupa A, et al:
The human hyaluronan synthase 2 (HAS2) gene and its natural
antisense RNA exhibit coordinated expression in the renal proximal
tubular epithelial cell. J Biol Chem. 286:19523–19532. 2011.
View Article : Google Scholar : PubMed/NCBI
|
|
47.
|
Khaitan D, Dinger ME, Mazar J, et al: The
melanoma-upregulated long noncoding RNA SPRY4-IT1 modulates
apoptosis and invasion. Cancer Res. 71:3852–3862. 2011. View Article : Google Scholar : PubMed/NCBI
|
|
48.
|
Lonergan KM, Chari R, Coe BP, et al:
Transcriptome profiles of carcinoma-in-situ and invasive non-small
cell lung cancer as revealed by SAGE. PLoS One. 5:e91622010.
View Article : Google Scholar : PubMed/NCBI
|
|
49.
|
Dempsey EC, Cool CD and Littler CM: Lung
disease and PKCs. Pharmacol Res. 55:545–559. 2007. View Article : Google Scholar : PubMed/NCBI
|
|
50.
|
Espina V, Wulfkuhle JD, Calvert VS, et al:
Laser-capture microdissection. Nat Protoc. 1:586–603. 2006.
View Article : Google Scholar
|
|
51.
|
Edwards RA: Laser capture microdissection
of mammalian tissue. J Vis Exp. 2007:3092007.PubMed/NCBI
|
|
52.
|
Gupta RA, Shah N, Wang KC, et al: Long
non-coding RNA HOTAIR reprograms chromatin state to promote cancer
metastasis. Nature. 464:1071–1076. 2010. View Article : Google Scholar : PubMed/NCBI
|
|
53.
|
Gutschner T, Hammerle M, Eissmann M, et
al: The non-coding RNA MALAT1 is a critical regulator of the
metastasis phenotype of lung cancer cells. Cancer Res.
73:1180–1189. 2013. View Article : Google Scholar : PubMed/NCBI
|
|
54.
|
Xu C, Yang M, Tian J, Wang X and Li Z:
MALAT-1: a long non-coding RNA and its important 3′ end functional
motif in colorectal cancer metastasis. Int J Oncol. 39:169–175.
2011.
|
|
55.
|
Ying L, Chen Q, Wang Y, Zhou Z, Huang Y
and Qiu F: Upregulated MALAT-1 contributes to bladder cancer cell
migration by inducing epithelial-to-mesenchymal transition. Mol
Biosyst. 8:2289–2294. 2012. View Article : Google Scholar : PubMed/NCBI
|
|
56.
|
Tano K, Mizuno R, Okada T, et al: MALAT-1
enhances cell motility of lung adenocarcinoma cells by influencing
the expression of motility-related genes. FEBS Lett. 584:4575–4580.
2010. View Article : Google Scholar : PubMed/NCBI
|
|
57.
|
Guffanti A, Iacono M, Pelucchi P, et al: A
transcriptional sketch of a primary human breast cancer by 454 deep
sequencing. BMC Genomics. 10:1632009. View Article : Google Scholar : PubMed/NCBI
|
|
58.
|
Lai MC, Yang Z, Zhou L, et al: Long
non-coding RNA MALAT-1 overexpression predicts tumor recurrence of
hepatocellular carcinoma after liver transplantation. Med Oncol.
29:1810–1816. 2012. View Article : Google Scholar : PubMed/NCBI
|
|
59.
|
Yamada K, Kano J, Tsunoda H, et al:
Phenotypic characterization of endometrial stromal sarcoma of the
uterus. Cancer Sci. 97:106–112. 2006. View Article : Google Scholar : PubMed/NCBI
|
|
60.
|
Lin R, Maeda S, Liu C, Karin M and
Edgington T: A large noncoding RNA is a marker for murine
hepatocellular carcinomas and a spectrum of human carcinomas.
Oncogene. 26:851–858. 2007. View Article : Google Scholar : PubMed/NCBI
|
|
61.
|
Lottin S, Adriaenssens E, Dupressoir T, et
al: Overexpression of an ectopic H19 gene enhances the tumorigenic
properties of breast cancer cells. Carcinogenesis. 23:1885–1895.
2002. View Article : Google Scholar : PubMed/NCBI
|
|
62.
|
Matouk IJ, DeGroot N, Mezan S, et al: The
H19 non-coding RNA is essential for human tumor growth. PLoS One.
2:e8452007. View Article : Google Scholar : PubMed/NCBI
|
|
63.
|
Yoshimizu T, Miroglio A, Ripoche MA, et
al: The H19 locus acts in vivo as a tumor suppressor. Proc Natl
Acad Sci USA. 105:12417–12422. 2008. View Article : Google Scholar : PubMed/NCBI
|
|
64.
|
Barsyte-Lovejoy D, Lau SK, Boutros PC, et
al: The c-Myc oncogene directly induces the H19 noncoding RNA by
allele-specific binding to potentiate tumorigenesis. Cancer Res.
66:5330–5337. 2006. View Article : Google Scholar : PubMed/NCBI
|
|
65.
|
Yang F, Bi J, Xue X, et al: Up-regulated
long non-coding RNA H19 contributes to proliferation of gastric
cancer cells. FEBS J. 279:3159–3165. 2012. View Article : Google Scholar : PubMed/NCBI
|
|
66.
|
Kaplan R, Luettich K, Heguy A, Hackett NR,
Harvey BG and Crystal RG: Monoallelic up-regulation of the
imprinted H19 gene in airway epithelium of phenotypically normal
cigarette smokers. Cancer Res. 63:1475–1482. 2003.PubMed/NCBI
|
|
67.
|
Cai X and Cullen BR: The imprinted H19
noncoding RNA is a primary microRNA precursor. RNA. 13:313–316.
2007. View Article : Google Scholar : PubMed/NCBI
|
|
68.
|
Keniry A, Oxley D, Monnier P, et al: The
H19 lincRNA is a developmental reservoir of miR-675 that suppresses
growth and Igf1r. Nat Cell Biol. 14:659–665. 2012. View Article : Google Scholar : PubMed/NCBI
|
|
69.
|
Huarte M, Guttman M, Feldser D, et al: A
large intergenic noncoding RNA induced by p53 mediates global gene
repression in the p53 response. Cell. 142:409–419. 2010. View Article : Google Scholar : PubMed/NCBI
|
|
70.
|
Yoon JH, Abdelmohsen K, Srikantan S, et
al: LincRNA-p21 suppresses target mRNA translation. Mol Cell.
47:648–655. 2012. View Article : Google Scholar : PubMed/NCBI
|
|
71.
|
Gebeshuber CA, Zatloukal K and Martinez J:
miR-29a suppresses tristetraprolin, which is a regulator of
epithelial polarity and metastasis. EMBO Rep. 10:400–405. 2009.
View Article : Google Scholar : PubMed/NCBI
|
|
72.
|
Krol M, Polanska J, Pawlowski KM, et al:
Transcriptomic signature of cell lines isolated from canine mammary
adenocarcinoma metastases to lungs. J Appl Genet. 51:37–50. 2010.
View Article : Google Scholar : PubMed/NCBI
|
|
73.
|
Mattick JS and Makunin IV: Non-coding RNA.
Hum Mol Genet 15 Spec No. 1:R17–R29. 2006. View Article : Google Scholar
|
|
74.
|
Ulveling D, Francastel C and Hube F: When
one is better than two: RNA with dual functions. Biochimie.
93:633–644. 2011. View Article : Google Scholar : PubMed/NCBI
|
|
75.
|
Cesana M, Cacchiarelli D, Legnini I, et
al: A long noncoding RNA controls muscle differentiation by
functioning as a competing endogenous RNA. Cell. 147:358–369. 2011.
View Article : Google Scholar : PubMed/NCBI
|
|
76.
|
Wang J, Liu X, Wu H, et al: CREB
up-regulates long non-coding RNA, HULC expression through
interaction with microRNA-372 in liver cancer. Nucleic Acids Res.
38:5366–5383. 2010. View Article : Google Scholar : PubMed/NCBI
|
|
77.
|
Franco-Zorrilla JM, Valli A, Todesco M, et
al: Target mimicry provides a new mechanism for regulation of
microRNA activity. Nat Genet. 39:1033–1037. 2007. View Article : Google Scholar : PubMed/NCBI
|
