Screening of Long Non-coding RNA in Colon Cancer by Bioinformatics

ZHANG Xinli; ZHAO Yanhua; LI Shu'na; ZHANG Wenling

doi:10.3971/j.issn.1000-8578.2015.05.005

Cancer Research on Prevention and Treatment > 2015 > 42(05): 446-449. > DOI: 10.3971/j.issn.1000-8578.2015.05.005

ZHANG Xinli, ZHAO Yanhua, LI Shu'na, ZHANG Wenling. Screening of Long Non-coding RNA in Colon Cancer by Bioinformatics[J]. Cancer Research on Prevention and Treatment, 2015, 42(05): 446-449. DOI: 10.3971/j.issn.1000-8578.2015.05.005

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Screening of Long Non-coding RNA in Colon Cancer by Bioinformatics

Department of Medical Laboratory, Xiangya School of Medicine, Central South University,Changsha 410013, China

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Received Date: August 13, 2014
Revised Date: October 26, 2014

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Abstract

Objective To screen the differentially-expressed lncRNA and analyze its expression in colon cancer. Methods The publicly available gene chip data GSE413268, which consists of 10 paired colon cancers and normal tissues, were downloaded from the Gene Expression Omnibus (GEO) of National Center for Biotechnology Information (NCBI) . The data were analyzed by SAM software, which generated some differentially-expressed gene probes. Then we re-annotated the probes in some online websites and used the Gene Cluster and TreeView software to further validate the expression of lncRNA. Results There were 66 differentially-expressed lncRNA in colon cancer tissues compared with normal tissues, among which 22 were up-regulated and 44 were down-regulated. All lncRNA showed notably differential expression and the foldchange of gene expression was all more than 2 or less than 0.5. Conclusion The bioinformatics applied to screen cancer-related lncRNA provide a novel way to find new biomarkers, but further study is needed to validate the results.
- Long non-coding RNA(lncRNA),
- Colon cancer,
- Gene microarray

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References

[1]	Jemal A, Bray F, Center MM, et al. Global cancer statistics[J]. CA Cancer J Clin, 2011, 61(2): 69-90.
[2]	Nie L, Wu H J, Hsu J M, et al. Long non-coding RNAs: versatile master regulators of gene expression and crucial players in cancer[J]. Am J Transl Res, 2012, 4(2): 127-50.
[3]	Da Sacco L, Baldassarre A, Masotti A. Bioinformatics tools and novel challenges in long non-coding RNAs (lncRNAs) functional analysis[J]. Int J Mol Sci, 2012, 13(1): 97-114.
[4]	Cao WJ, Wu HL, He BS, et al. Analysis of long non-coding RNA expression profiles in gastric cancer[J]. World J Gastroenterol, 20 13, 19(23): 3658-64.
[5]	Maruyama R, Suzuki H. Long noncoding RNA involvement in cancer[J]. BMB Rep, 2012, 45(11): 604-11.
[6]	Guttman M, Rinn JL. Modular regulatory principles of large noncoding RNAs[J]. Nature, 2012, 482(7385): 339-46.
[7]	Nagano T, Fraser P. No-nonsense functions for long noncoding RNAs[J]. Cell, 2011, 145(2): 178-81.
[8]	Derrien T, Johnson R, Bussotti G, et al. The GENCODE v7 catalog of human long noncoding RNAs: analysis of their gene structure, evolution, and expression[J]. Genome Res, 2012, 22(9): 1775-89.
[9]	Yang G, Lu X, Yuan L. LncRNA: A link between RNA and cancer[J]. Biochim Biophys Acta, 2014, 1839(11): 1097-109.
[10]	Wang N, Luo YH, Deng JC, et al. LncRNAs and cardiovascular diseases[J]. Sheng Li Ke Xue Jin Zhan, 2014, 45(3): 172-6. [王楠, 罗雨虹, 邓嘉成, 等. 长非编码RNA(lncRNA)与心血管疾病生理科学进展[J]. 2014, 45(3): 172-6.]
[11]	Wang H, Cao Q, Ge J, et al. LncRNA-regulated Infection and Inflammation Pathways Associated with Pregnancy Loss: Genome Wide Differential Expression of lncRNAs in Early Spontaneous Abortion[J]. Am J Reprod Immunol, 2014, 72(4): 359-75.
[12]	Mirza AH, Kaur S, Brorsson CA, et al. Effects of GWASAssociated Genetic Variants on lncRNAs within IBD and T1D Candidate Loci[J]. PLoS One, 2014, 9(8): e105723.
[13]	Gutschner T, Hämmerle M, Diederichs S. MALAT1 -- a paradigm for long noncoding RNA function in cancer[J]. J Mol Med (Berl), 20 13, 91(7): 791-801.
[14]	Wu Y, Zhang L, Wang Y, et al. Long noncoding RNA HOTAIR involvement in cancer[J]. Tumour Biol, 2014, 35(10): 9531-8.
[15]	ChalignéR, Heard E. X-chromosome inactivation in development and cancer[J]. FEBS Lett, 2014, 588(15): 2514-22.
[16]	Pérot P, Cheynet V, Decaussin-Petrucci M, et al. Microarray-based identification of individual HERV loci expression: application to biomarker discovery in prostate cancer[J]. J Vis Exp, 2013, (81): e50713.
[17]	Michelhaugh SK, Lipovich L, Blythe J, et al. Mining Affymetrix microarray data for long non-coding RNAs: altered expression in the nucleus accumbens of heroin abusers[J]. J Neurochem, 2011, 11 6(3): 459-66.
[18]	Ellis B C, Molloy P L, Graham L D. CRNDE: A Long Non-Coding RNA Involved in CanceR, Neurobiology, and DEvelopment[J]. Front Genet, 2012, 3: 270.
[19]	Graham LD, Pedersen S K, Brown G S, et al. Colorectal Neoplasia Differentially Expressed (CRNDE), a Novel Gene with Elevated Expression in Colorectal Adenomas and Adenocarcinomas[J]. Genes Cancer, 2011, 2(8): 829-40.
[20]	Ellis BC, Graham LD, Molloy PL. CRNDE, a long non-coding RNA responsive to insulin/IGF signaling, regulates genes involved in central metabolism[J]. Biochim Biophys Acta, 2014, 18 43(2): 372-86.
[21]	Wang F, Yuan JH, Wang SB, et al. Oncofetal long noncoding RNA PVT1 promotes proliferation and stem cell-like property of hepatocellular carcinoma cells by stabilizing NOP2[J]. Hepatology, 2014, 60(4): 1278-90.
[22]	Ding J, Li D, Gong M, et al. Expression and clinical significance of the long non-coding RNA PVT1 in human gastric cancer[J]. Onco Targets Ther, 2014, 7: 1625-30.
[23]	Takahashi Y, Sawada G, Kurashige J, et al. Amplification of PVT-1 is involved in poor prognosis via apoptosis inhibition in colorectal cancers[J]. Br J Cancer, 2014, 110(1): 164-71.
[24]	Zhang Z, Zhu Z, Zhang B, et al. Frequent mutation of rs13281615 and its association with PVT1 expression and cell proliferation in breast cancer[J]. J Genet Genomics, 2014, 41(4): 187-95.
[25]	Riquelme E, Suraokar MB, Rodriguez J, et al. Frequent coamplification and cooperation between C-MYC and PVT1 oncogenes promote malignant pleural mesothelioma[J]. J Thorac Oncol, 2014, 9(7): 998-1007.
[26]	Pang Q, Ge J, Shao Y, et al. Increased expression of long intergenic non-coding RNA LINC00152 in gastric cancer and its clinical significance[J]. Tumour Biol, 2014, 35(6): 5441-7.

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