358
Views
0
CrossRef citations to date
0
Altmetric
Research Article

Screening Key Long Non-Coding RNAs in Early-Stage Colon Adenocarcinoma by RNA-Sequencing

, , , &
Pages 1215-1228 | Received 27 Nov 2017, Accepted 18 May 2018, Published online: 05 Sep 2018

References

  • Wang Y , ZhangJ , LiLet al. Identification of molecular targets for predicting colon adenocarcinoma . Med. Sci. Monit.22 , 460 ( 2016 ).
  • Chang W , WuL , CaoFet al. Development of autoantibody signatures as biomarkers for early detection of colorectal carcinoma . Clin. Cancer Res.17 ( 17 ), 5715 ( 2011 ).
  • Xi WD , LiuYJ , SunXB , ShanJ , YiL , ZhangTT . Bioinformatics analysis of RNA-seq data revealed critical genes in colon adenocarcinoma . Eur. Rev. Med. Pharmacol. Sci.21 ( 13 ), 3012 – 3020 ( 2017 ).
  • Wang Y , ZhangJ , LiLet al. Identification of molecular targets for predicting colon adenocarcinoma . Med. Sci. Monit.22 , 460 – 468 ( 2016 ).
  • Zhang MX , CaiH , WangJS , HuangC , WuWA , MaRQ . Expression profiles of microRNA in colon adenocarcinoma . Xi Bao Yu Fen Zi Mian Yi Xue Za Zhi.26 ( 10 ), 959 – 961 ( 2010 ).
  • Guo XB , HuaZ , LiCet al. Biological significance of long non-coding RNA FTX expression in human colorectal cancer . Int. J. Clin. Exp. Med.8 ( 9 ), 15591 ( 2015 ).
  • Zeng JH , LiangL , HeRQet al. Comprehensive investigation of a novel differentially expressed lncRNA expression profile signature to assess the survival of patients with colorectal adenocarcinoma . Oncotarget8 ( 10 ), 16811 – 16828 ( 2017 ).
  • Vafaee F , ColvinEK , MokSC , HowellVM . Functional prediction of long non-coding RNAs in ovarian cancer-associated fibroblasts indicate a potential role in metastasis . Sci. Rep.7 ( 1 ), 10374 ( 2017 ).
  • Lu X , HuangC , HeXet al. A novel long non-coding RNA, SOX21-AS1, indicates a poor prognosis and promotes lung adenocarcinoma proliferation . Cell. Physiol. Biochem.42 ( 5 ), 1857 – 1869 ( 2017 ).
  • Wang L , ZhaoZ , FengWet al. Long non-coding RNA TUG1 promotes colorectal cancer metastasis via EMT pathway . Oncotarget7 ( 32 ), 51713 – 51719 ( 2016 ).
  • Liu J , LiuF , LiX , SongX , ZhouL , JieJ . Screening key genes and miRNAs in early-stage colon adenocarcinoma by RNA-sequencing . Tumour Biol.39 ( 7 ), 1010428317714899 ( 2017 ).
  • Trapnell C , RobertsA , GoffLet al. Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks . Nat. Protoc.7 ( 3 ), 562 – 578 ( 2012 ).
  • Lister R , PelizzolaM , KidaYSet al. Hotspots of aberrant epigenomic reprogramming in human induced pluripotent stem cells . Nature471 ( 7336 ), 68 – 73 ( 2011 ).
  • Graveley BR , BrooksAN , CarlsonJWet al. The developmental transcriptome of Drosophila melanogaster . Nature471 ( 7339 ), 473 – 479 ( 2011 ).
  • Twine NA , JanitzK , WilkinsMR , JanitzM . Whole transcriptome sequencing reveals gene expression and splicing differences in brain regions affected by Alzheimer’s disease . PLoS ONE6 ( 1 ), e16266 ( 2011 ).
  • Ruizorera J , MesseguerX , SubiranaJA , AlbaMM . Long non-coding RNAs as a source of new peptides . Elife3 ( e03523 ), e03523 ( 2014 ).
  • Hung T , ChangHY . Long noncoding RNA in genome regulation: prospects and mechanisms . RNA Biol.7 ( 5 ), 582 – 585 ( 2010 ).
  • Ponting CP , OliverPL , ReikW . Evolution and functions of long noncoding RNAs . Cell136 ( 4 ), 629 – 641 ( 2009 ).
  • Maoz R , GarfinkelBP , SoreqH . Alzheimer’s disease and ncRNAs . Adv. Exp. Med. Biol.978 , 337 – 361 ( 2017 ).
  • Liao Q , LiuC , YuanXet al. Large-scale prediction of long non-coding RNA functions in a coding-non-coding gene co-expression network . Nucleic Acids Res.39 ( 9 ), 3864 – 3878 ( 2011 ).
  • Da Sacco L , BaldassarreA , MasottiA . Bioinformatics tools and novel challenges in long non-coding RNAs (lncRNAs) functional analysis . Int. J. Mol. Sci.13 ( 1 ), 97 – 114 ( 2012 ).
  • Guo Q , ChengY , LiangTet al. Comprehensive analysis of lncRNA-mRNA co-expression patterns identifies immune-associated lncRNA biomarkers in ovarian cancer malignant progression . Sci. Rep.5 , 17683 ( 2015 ).
  • Fang L , WangH , LiP . Systematic analysis reveals a lncRNA-mRNA co-expression network associated with platinum resistance in high-grade serous ovarian cancer . Invest. New Drugs36 ( 2 ), 187 – 194 ( 2018 ).
  • Du Y , XiaW , ZhangJ , WanD , YangZ , LiX . Comprehensive analysis of long noncoding RNA-mRNA co-expression patterns in thyroid cancer . Mol. Biosyst.13 ( 10 ), 2107 – 2115 ( 2017 ).
  • Yang L , YiK , WangH , ZhaoY , XiM . Comprehensive analysis of lncRNAs microarray profile and mRNA-lncRNA co-expression in oncogenic HPV-positive cervical cancer cell lines . Oncotarget7 ( 31 ), 49917 – 49929 ( 2016 ).
  • Martens JA , LapradeL , WinstonF . Intergenic transcription is required to repress the Saccharomyces cerevisiae SER3 gene . Nature429 ( 6991 ), 571 – 574 ( 2004 ).
  • Feng J , BiC , ClarkBS , MadyR , ShahP , KohtzJD . The Evf-2 noncoding RNA is transcribed from the Dlx-5/6 ultraconserved region and functions as a Dlx-2 transcriptional coactivator . Genes Dev.20 ( 11 ), 1470 – 1484 ( 2006 ).
  • Lang UE , KocabayogluP , ChengGZet al. GSK3β phosphorylation of the KLF6 tumor suppressor promotes its transactivation of p21 . Oncogene32 ( 38 ), 4557 – 4564 ( 2013 ).
  • Cho YG , ChoiBJ , SongJWet al. Aberrant expression of krUppel-like factor 6 protein in colorectal cancers . World J. Gastroenterol.12 ( 14 ), 2250 – 2253 ( 2006 ).
  • Zhang Q , TanXP , YuanYSet al. Decreased expression of KLF6 and its significance in gastric carcinoma . Med. Oncol.27 ( 4 ), 1295 – 1302 ( 2010 ).
  • Kong LM , LiY , NingLet al. Interaction of KLF6 and Sp1 regulates basigin-2 expression mediated proliferation, invasion and metastasis in hepatocellular carcinoma . Oncotarget7 ( 19 ), 27975 – 27987 ( 2016 ).
  • Difeo A , FeldL , RodriguezEet al. A functional role for KLF6-SV1 in lung adenocarcinoma prognosis and chemotherapy response . Cancer Res.68 ( 4 ), 965 – 970 ( 2008 ).
  • Mukai S , HiyamaT , TanakaSet al. Involvement of Krüippel-like factor 6 (KLF6) mutation in the development of nonpolypoid colorectal carcinoma . World J. Gastroenterol.13 ( 29 ), 3932 – 3938 ( 2007 ).
  • Hussain MR , NasirJ , Al-AamaJY . Clinically significant missense variants in human GALNT3, GALNT8, GALNT12, and GALNT13 genes: intriguing in silico findings . J. Cell. Biochem.115 ( 2 ), 313 ( 2014 ).
  • Mildelangosch K , SchützeD , OliveiraferrerLet al. Relevance of βGal-βGalNAc-containing glycans and the enzymes involved in their synthesis for invasion and survival in breast cancer patients . Breast Cancer Res. Treat.151 ( 3 ), 515 – 528 ( 2015 ).
  • Polev DE , KarnaukhovaIK , KrukovskayaLL , KozlovAP . ELFN1-AS1: a novel primate gene with possible microRNA function expressed predominantly in human tumors . Biomed. Res. Int.2014 ( 1 ), 398097 ( 2014 ).
  • Wang X , ZhangL , LiH , SunWJ , ZhangH , LaiM . THBS2 is a potential prognostic biomarker in colorectal cancer . Sci. Rep.6 , 33366 ( 2016 ).
  • Kawasaki T , NoshoK , OhnishiMet al. IGFBP3 promoter methylation in colorectal cancer: relationship with microsatellite instability, CpG island methylator phenotype, and p53 . Neoplasia9 ( 12 ), 1091 ( 2007 ).
  • Williams AC , CollardTJ , PerksCMet al. Increased p53-dependent apoptosis by the insulin-like growth factor binding protein IGFBP-3 in human colonic adenoma-derived cells . Cancer Res.60 ( 1 ), 22 ( 2000 ).
  • Han Y , YangYN , YuanHHet al. UCA1, a long non-coding RNA up-regulated in colorectal cancer influences cell proliferation, apoptosis and cell cycle distribution . Pathology46 ( 5 ), 396 – 401 ( 2014 ).
  • Bian Z , JinL , ZhangJet al. LncRNA – UCA1 enhances cell proliferation and 5-fluorouracil resistance in colorectal cancer by inhibiting miR-204-5p . Sci. Rep.6 , 23892 ( 2016 ).
  • Gu J , LiY , FanLet al. Identification of aberrantly expressed long non-coding RNAs in stomach adenocarcinoma . Oncotarget8 ( 30 ), 49201 – 49216 ( 2017 ).
  • Guo W , WangQ , ZhanYet al. Transcriptome sequencing uncovers a three-long noncoding RNA signature in predicting breast cancer survival . Sci. Rep.6 , 27931 ( 2016 ).
  • Zhang L , PickardK , JeneiVet al. miR-153 supports colorectal cancer progression via pleiotropic effects that enhance invasion and chemotherapeutic resistance . Cancer Res.73 ( 21 ), 6435 ( 2013 ).
  • Kai K , PlaksV , WerbZ . Matrix metalloproteinases: regulators of the tumor microenvironment . Cell141 ( 1 ), 52 – 67 ( 2010 ).
  • Li C , GaoY , LiY , DingD . TUG1 mediates methotrexate resistance in colorectal cancer via miR-186/CPEB2 axis . Biochem. Biophys. Res. Commun.491 ( 2 ), 552 – 557 ( 2017 ).

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.