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Research Article

Expression Profiles of Long Noncoding RNAs in Cutaneous Squamous Cell Carcinoma

, , , , , , & show all
Pages 501-518 | Received 11 Dec 2015, Accepted 21 Jan 2016, Published online: 12 Apr 2016

References

  • Mattick JS . Non-coding RNAs: the architects of Eukaryotic complexity . EMBO Rep.2 ( 11 ), 986 – 991 ( 2001 ).
  • Pertea M , SalzbergSL . Between a chicken and a grape: estimating the number of human genes . Genome Biol.11 ( 5 ), 206 ( 2010 ).
  • Mathiyalagan P , KeatingST , DuXJ , El-OstaA . Interplay of chromatin modifications and non-coding RNAs in the heart . Epigenetics9 ( 1 ), 101 – 112 ( 2014 ).
  • Hombach S , KretzM . The non-coding skin: exploring the roles of long non-coding RNAs in epidermal homeostasis and disease . Bioessays35 ( 12 ), 1093 – 1100 ( 2013 ).
  • Guo X , GaoL , WangY , ChiuDK , WangT , DengY . Advances in long noncoding RNAs: identification, structure prediction and function annotation . Brief. Funct. Genomics15 ( 1 ), 38 – 46 ( 2015 ).
  • Sand M , GambichlerT , SandD , SkryganM , AltmeyerP , BecharaFG . MicroRNAs and the skin: tiny players in the body’s largest organ . J. Dermatol. Sci.53 ( 3 ), 169 – 175 ( 2009 ).
  • Sand M , SandD , AltmeyerP , BecharaFG . MicroRNA in non-melanoma skin cancer . Cancer Biomarkers11 ( 6 ), 253 – 257 ( 2012 ).
  • Sand M . The pathway of miRNA maturation . Methods Mol. Biol.1095 , 3 – 10 ( 2014 ).
  • Sand M , SkryganM , GeorgasDet al. Microarray analysis of microRNA expression in cutaneous squamous cell carcinoma . J. Dermatol. Sci.68 ( 3 ), 119 – 126 ( 2012 ).
  • Sand M , GambichlerT , SkryganMet al. Expression levels of the microRNA processing enzymes Drosha and dicer in epithelial skin cancer . Cancer Invest.28 ( 6 ), 649 – 653 ( 2010 ).
  • Sand M , SkryganM , GeorgasDet al. Expression levels of the microRNA maturing microprocessor complex component DGCR8 and the RNA-induced silencing complex (RISC) components argonaute-1, argonaute-2, PACT, TARBP1, and TARBP2 in epithelial skin cancer . Mol. Carcinogen.51 ( 11 ), 916 – 922 ( 2012 ).
  • Lalevee S , FeilR . Long noncoding RNAs in human disease: emerging mechanisms and therapeutic strategies . Epigenomics7 ( 6 ), 877 – 879 ( 2015 ).
  • Kretz M , WebsterDE , FlockhartRJet al. Suppression of progenitor differentiation requires the long noncoding RNA ANCR . Genes Dev.26 ( 4 ), 338 – 343 ( 2012 ).
  • Lopez-Pajares V , QuK , ZhangJet al. A LncRNA-MAF:MAFB transcription factor network regulates epidermal differentiation . Dev. Cell32 ( 6 ), 693 – 706 ( 2015 ).
  • Orom UA , DerrienT , BeringerMet al. Long noncoding RNAs with enhancer-like function in human cells . Cell143 ( 1 ), 46 – 58 ( 2010 ).
  • Mazar J , SinhaS , DingerME , MattickJS , PereraRJ . Protein-coding and non-coding gene expression analysis in differentiating human keratinocytes using a three-dimensional epidermal equivalent . Mol. Genet. Genom.284 ( 1 ), 1 – 9 ( 2010 ).
  • Zou AE , KuJ , HondaTKet al. Transcriptome sequencing uncovers novel long noncoding and small nucleolar RNAs dysregulated in head and neck squamous cell carcinoma . RNA21 ( 6 ), 1122 – 1134 ( 2015 ).
  • Zhang S , TianL , MaPet al. Potential role of differentially expressed lncRNAs in the pathogenesis of oral squamous cell carcinoma . Arch. Oral. Biol.60 ( 10 ), 1581 – 1587 ( 2015 ).
  • Shahryari A , JaziMS , SamaeiNM , MowlaSJ . Long non-coding RNA SOX2OT: expression signature, splicing patterns, and emerging roles in pluripotency and tumorigenesis . Front. Genet.6 , 196 ( 2015 ).
  • Huang L , LiaoLM , LiuAWet al. Overexpression of long noncoding RNA HOTAIR predicts a poor prognosis in patients with cervical cancer . Arch. Gynecol. Obstet.290 ( 4 ), 717 – 723 ( 2014 ).
  • Table Browser . http://genome.ucsc.edu/cgi-bin/hgTables .
  • RefSeq: NCBI Reference Sequence Database . www.ncbi.nlm.nih.gov/refseq/ .
  • RNAdb 2.0 - A database of mammalian noncoding RNAs . http://research.imb.uq.edu.au/rnadb/ .
  • ncRNA Expression Database . http://jsm-research.imb.uq.edu.au/nred/cgi-bin/ncrnadb.pl .
  • Science 2204 Paper Supplement . https://users.soe.ucsc.edu/~jill/ultra.html .
  • Long Noncoding RNA Database v2.0: The Reference Database For Functional Long Noncoding RNAs . http://lncrnadb.com .
  • Amaral PP , ClarkMB , GascoigneDK , DingerME , MattickJS . lncRNAdb: a reference database for long noncoding RNAs . Nucleic Acids Res.39 , D146 – D151 ( 2011 ).
  • Bejerano G , PheasantM , MakuninIet al. Ultraconserved elements in the human genome . Science304 ( 5675 ), 1321 – 1325 ( 2004 ).
  • Cabili MN , TrapnellC , GoffLet al. Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses . Genes Dev.25 ( 18 ), 1915 – 1927 ( 2011 ).
  • Dinger ME , PangKC , MercerTR , CroweML , GrimmondSM , MattickJS . NRED: a database of long noncoding RNA expression . Nucleic Acids Res.37 , D122 – D126 ( 2009 ).
  • Harrow J , DenoeudF , FrankishAet al. GENCODE: producing a reference annotation for ENCODE . Genome Biol.7 ( Suppl. 1 ), S4.1 – S9 ( 2006 ).
  • Hsu F , KentWJ , ClawsonH , KuhnRM , DiekhansM , HausslerD . The UCSC known genes . Bioinformatics22 ( 9 ), 1036 – 1046 ( 2006 ).
  • Khalil AM , GuttmanM , HuarteMet al. Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression . Proc. Natl Acad. Sci. USA106 ( 28 ), 11667 – 11672 ( 2009 ).
  • Pang KC , StephenS , DingerME , EngstromPG , LenhardB , MattickJS . RNAdb 2.0 – an expanded database of mammalian non-coding RNAs . Nucleic Acids Res.35 , D178 – D182 ( 2007 ).
  • Pruitt KD , TatusovaT , BrownGR , MaglottDR . NCBI reference sequences (RefSeq): current status, new features and genome annotation policy . Nucleic Acids Res.40 , D130 – D135 ( 2012 ).
  • Rinn JL , KerteszM , WangJKet al. Functional demarcation of active and silent chromatin domains in human HOX loci by noncoding RNAs . Cell129 ( 7 ), 1311 – 1323 ( 2007 ).
  • Luo X , ShiQ , GuYet al. LncRNA pathway involved in premature preterm rupture of membrane (PPROM): an epigenomic approach to study the pathogenesis of reproductive disorders . PLoS ONE8 ( 11 ), e79897 ( 2013 ).
  • Primer-BLAST . www.ncbi.nlm.nih.gov/tools/primer-blast/ .
  • GEO Accession viewer . www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE74859 .
  • The R Project for Statistical Computing . www.r-project.org/ .
  • Gene Ontology Consortium . www.geneontology.org .
  • Gene Ontology C . Gene Ontology Consortium: going forward . Nucleic Acids Res.43 , D1049 – D1056 ( 2015 ).
  • Consortium TGO . Gene Ontology Consortium: going forward . Nucleic Acids Res.43 ( D1 ), D1049 – D1056 ( 2015 ).
  • Benjamini Y , DraiD , ElmerG , KafkafiN , GolaniI . Controlling the false discovery rate in behavior genetics research . Behav. Brain. Res.125 ( 1–2 ), 279 – 284 ( 2001 ).
  • Various R Programming Tools for Plotting Data . https://cran.r-project.org/web/packages/gplots/gplots.pdf .
  • Quackenbush J . Computational analysis of microarray data . Nat. Rev. Genet.2 ( 6 ), 418 – 427 ( 2001 ).
  • Sokal RR , MichenerCD . A statistical method for evaluating systematic relationships . Univ. Kansas Sci. Bull.28 , 1409 – 1438 ( 1958 ).
  • Gutschner T , DiederichsS . The hallmarks of cancer: a long non-coding RNA point of view . RNA Biol.9 ( 6 ), 703 – 719 ( 2012 ).
  • Kumar V , WestraHJ , KarjalainenJet al. Human disease-associated genetic variation impacts large intergenic non-coding RNA expression . PLoS Genet.9 ( 1 ), e1003201 ( 2013 ).
  • Binstock M , HafeezF , MetchnikoffC , ArronST . Single-nucleotide polymorphisms in pigment genes and nonmelanoma skin cancer predisposition: a systematic review . Br. J. Dermatol.171 ( 4 ), 713 – 721 ( 2014 ).
  • Xing Z , LinA , LiCet al. lncRNA directs cooperative epigenetic regulation downstream of chemokine signals . Cell159 ( 5 ), 1110 – 1125 ( 2014 ).
  • Kallini JR , HamedN , KhachemouneA . Squamous cell carcinoma of the skin: epidemiology, classification, management, and novel trends . Int. J. Dermatol.54 ( 2 ), 130 – 140 ( 2015 ).
  • Leiter U , EigentlerT , GarbeC . Epidemiology of skin cancer . Adv. Exp. Med. Biol810 , 120 – 140 ( 2014 ).
  • Wollina U . Cetuximab in non-melanoma skin cancer . Expert Opin. Biol. Ther.12 ( 7 ), 949 – 956 ( 2012 ).
  • Cranmer LD , EngelhardtC , MorganSS . Treatment of unresectable and metastatic cutaneous squamous cell carcinoma . Oncologist15 ( 12 ), 1320 – 1328 ( 2010 ).
  • Panagopoulos I , GorunovaL , DavidsonB , HeimS . Novel TNS3–MAP3K3 and ZFPM2–ELF5 fusion genes identified by RNA sequencing in multicystic mesothelioma with t(7;17)(p12;q23) and t(8;11)(q23;p13) . Cancer Lett.357 ( 2 ), 502 – 509 ( 2015 ).
  • Tsang SY , MeiL , WanWet al. Glioma association and balancing selection of ZFPM2 . PLoS ONE10 ( 7 ), e0133003 ( 2015 ).
  • Luo D , LuML , ZhaoGFet al. Reduced Popdc3 expression correlates with high risk and poor survival in patients with gastric cancer . World J. Gastroenterol.18 ( 19 ), 2423 – 2429 ( 2012 ).
  • Mills E , O’NeillLA . Succinate: a metabolic signal in inflammation . Trends Cell Biol.24 ( 5 ), 313 – 320 ( 2014 ).
  • Gu W , GaoT , SunYet al. LncRNA expression profile reveals the potential role of lncRNAs in gastric carcinogenesis . Cancer Biomarkers15 ( 3 ), 249 – 258 ( 2015 ).
  • Kar SP , TyrerJP , LiQet al. Network-Based integration of GWAS and gene expression identifies a HOX-centric network associated with serous ovarian cancer risk . Cancer Epidemiol. Biomarkers Prev.24 ( 10 ), 1574 – 1584 ( 2015 ).
  • Huang T , YangJ , CaiYD . Novel candidate key drivers in the integrative network of genes, microRNAs, methylations, and copy number variations in squamous cell lung carcinoma . Biomed Res. Int.2015 , 358125 ( 2015 ).
  • Song W , LiuYY , PengJJet al. Identification of differentially expressed signatures of long non-coding RNAs associated with different metastatic potentials in gastric cancer . J. Gastroenterol.51 ( 2 ), 119 – 129 ( 2016 ).
  • Liu Y , LiY , GuoFet al. Identification of HTA as a novel-specific marker for human hepatocellular carcinoma . J. Cancer Res. Clin. Oncol.136 ( 8 ), 1187 – 1192 ( 2010 ).
  • Su X , MaloufGG , ChenYet al. Comprehensive analysis of long non-coding RNAs in human breast cancer clinical subtypes . Oncotarget5 ( 20 ), 9864 – 9876 ( 2014 ).
  • Wan DC , WangKC . Long noncoding RNA: significance and potential in skin biology . Cold Spring Harb. Perspect. Med.4 ( 5 ), pii: a015404 ( 2014 ).
  • Jiang YJ , BikleDD . LncRNA profiling reveals new mechanism for VDR protection against skin cancer formation . J. Steroid Biochem. Mol. Biol.144 ( Pt A ), 87 – 90 ( 2014 ).
  • Thyssen JP , Godoy-GijonE , EliasPM . Ichthyosis vulgaris: the filaggrin mutation disease . Br. J. Dermatol.168 ( 6 ), 1155 – 1166 ( 2013 ).
  • Kretz M , SiprashviliZ , ChuCet al. Control of somatic tissue differentiation by the long non-coding RNA TINCR . Nature493 ( 7431 ), 231 – 235 ( 2013 ).
  • Kretz M . TINCR, staufen1, and cellular differentiation . RNA Biol.10 ( 10 ), 1597 – 1601 ( 2013 ).
  • Szegedi K , SonkolyE , NagyNet al. The anti-apoptotic protein G1P3 is overexpressed in psoriasis and regulated by the non-coding RNA, PRINS . Exp. Dermatol.19 ( 3 ), 269 – 278 ( 2010 ).
  • Yu X , LiZ . Long non-coding RNA HOTAIR: a novel oncogene (Review) . Mol. Med. Rep.12 ( 4 ), 5611 – 5618 ( 2015 ).
  • Kong L , ZhouX , WuYet al. Targeting HOTAIR induces mitochondria related apoptosis and inhibits tumor growth in head and neck squamous cell carcinoma in vitro and in vivo . Curr. Mol. Med.15 ( 10 ), 952 – 960 ( 2015 ).
  • Xu ZY , YuQM , DuYAet al. Knockdown of long non-coding RNA HOTAIR suppresses tumor invasion and reverses epithelial-mesenchymal transition in gastric cancer . Int. J. Biol. Sci.9 ( 6 ), 587 – 597 ( 2013 ).
  • Fayda M , IsinM , TambasMet al. Do circulating long non-coding RNAs (lncRNAs) (LincRNA-p21, GAS 5, HOTAIR) predict the treatment response in patients with head and neck cancer treated with chemoradiotherapy? Tumour Biol. doi:10.1007/s13277-015-4189-1 ( 2015 ) ( Epub ahead of print ).
  • Prensner JR , ChinnaiyanAM . The emergence of lncRNAs in cancer biology . Cancer Discov.1 ( 5 ), 391 – 407 ( 2011 ).
  • Gao W , ChanJY , WongTS . Long non-coding RNA deregulation in tongue squamous cell carcinoma . Biomed. Res. Int.2014 , 405860 ( 2014 ).
  • Romano RA , SinhaS . Family matters: sibling rivalry and bonding between p53 and p63 in cancer . Exp. Dermatol.23 ( 4 ), 238 – 239 ( 2014 ).
  • Duperret EK , RidkyTW . Focal adhesion complex proteins in epidermis and squamous cell carcinoma . Cell Cycle12 ( 20 ), 3272 – 3285 ( 2013 ).
  • Zhao D , TangXF , YangK , LiuJY , MaXR . Over-expression of integrin-linked kinase correlates with aberrant expression of snail, E-cadherin and N-cadherin in oral squamous cell carcinoma: implications in tumor progression and metastasis . Clin. Exp. Metastasis29 ( 8 ), 957 – 969 ( 2012 ).
  • Guasch G , SchoberM , PasolliHA , ConnEB , PolakL , FuchsE . Loss of TGFbeta signaling destabilizes homeostasis and promotes squamous cell carcinomas in stratified epithelia . Cancer Cell12 ( 4 ), 313 – 327 ( 2007 ).
  • Yan W , ZhangLL , YanLet al. Transcriptome analysis of skin photoaging in chinese females reveals the involvement of skin homeostasis and metabolic changes . PLoS ONE8 ( 4 ), e61946 ( 2013 ).
  • Bito T , SumitaN , AshidaMet al. Inhibition of epidermal growth factor receptor and PI3K/Akt signaling suppresses cell proliferation and survival through regulation of Stat3 activation in human cutaneous squamous cell carcinoma . J. Skin Cancer2011 , 874571 ( 2011 ).
  • Fagard R , MetelevV , SouissiI , Baran-MarszakF . STAT3 inhibitors for cancer therapy: have all roads been explored?JAKSTAT2 ( 1 ), e22882 ( 2013 ).
  • Chai EZ , ShanmugamMK , ArfusoFet al. Targeting transcription factor STAT3 for cancer prevention and therapy . Pharmacol. Ther. doi:10.1016/j.pharmthera.2015.10.004 ( 2015 ) ( Epub ahead of print ).

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