High throughput RNA sequencing utility for diagnosis and prognosis in colon diseases
详细信息    查看全文 | 推荐本文 |
  • 英文篇名:High throughput RNA sequencing utility for diagnosis and prognosis in colon diseases
  • 作者:Mamie ; Gao ; Allen ; Zhong ; Neil ; Patel ; Chiraag ; Alur ; Dinesh ; Vyas
  • 英文作者:Mamie Gao;Allen Zhong;Neil Patel;Chiraag Alur;Dinesh Vyas;Department of Surgery, Texas Tech University;
  • 英文关键词:Colon;;RNA sequencing;;Colon cancer;;Transcriptome;;Next generation sequencing;;high throughput
  • 中文刊名:ZXXY
  • 英文刊名:世界胃肠病学杂志(英文版)
  • 机构:Department of Surgery, Texas Tech University;
  • 出版日期:2017-04-28
  • 出版单位:World Journal of Gastroenterology
  • 年:2017
  • 期:v.23
  • 语种:英文;
  • 页:ZXXY201716002
  • 页数:7
  • CN:16
  • 分类号:15-21
摘要
RNA sequencing is the use of hight hroughput next generation sequencing technology to survey, characterize, and quantify the transcriptome of a genome. RNA sequencing has been used to analyze the pathogenesis of several malignancies such melanoma, lung cancer, and colorectal cancer. RNA sequencing can identify differential expression of genes(DEG's), mutated genes, fusion genes, and gene isoforms in disease states. RNA sequencing has been used in the investigation of several colorectal diseases such as colorectal cancer, inflammatory bowel disease(ulcerative colitis and Crohn's disease), and irritable bowel syndrome.
        RNA sequencing is the use of hight hroughput next generation sequencing technology to survey, characterize, and quantify the transcriptome of a genome. RNA sequencing has been used to analyze the pathogenesis of several malignancies such melanoma, lung cancer, and colorectal cancer. RNA sequencing can identify differential expression of genes(DEG's), mutated genes, fusion genes, and gene isoforms in disease states. RNA sequencing has been used in the investigation of several colorectal diseases such as colorectal cancer, inflammatory bowel disease(ulcerative colitis and Crohn's disease), and irritable bowel syndrome.
引文
1 Morin R,Bainbridge M,Fejes A,Hirst M,Krzywinski M,Pugh T,Mc Donald H,Varhol R,Jones S,Marra M.Profiling the He La S3 transcriptome using randomly primed c DNA and massively parallel short-read sequencing.Biotechniques 2008;45:81-94[PMID:18611170 DOI:10.2144/000112900]
    2 Wang Z,Gerstein M,Snyder M.RNA-Seq:a revolutionary tool for transcriptomics.Nat Rev Genet 2009;10:57-63[PMID:19015660 DOI:10.1038/nrg2484]
    3 Kolodziejczyk AA,Kim JK,Svensson V,Marioni JC,Teichmann SA.The technology and biology of single-cell RNA sequencing.Mol Cell 2015;58:610-620[PMID:26000846 DOI:10.1016/j.molcel.2015.04.005]
    4 Beane J,Vick J,Schembri F,Anderlind C,Gower A,Campbell J,Luo L,Zhang XH,Xiao J,Alekseyev YO,Wang S,Levy S,Massion PP,Lenburg M,Spira A.Characterizing the impact of smoking and lung cancer on the airway transcriptome using RNA-Seq.Cancer Prev Res(Phila)2011;4:803-817[PMID:21636547DOI:10.1158/1940-6207.CAPR-11-0212]
    5 Nalpas NC,Magee DA,Conlon KM,Browne JA,Healy C,Mc Loughlin KE,Rue-Albrecht K,Mc Gettigan PA,Killick KE,Gormley E,Gordon SV,Mac Hugh DE.RNA sequencing provides exquisite insight into the manipulation of the alveolar macrophage by tubercle bacilli.Sci Rep 2015;5:13629[PMID:26346536 DOI:10.1038/srep13629]
    6 Chu Y,Corey DR.RNA sequencing:platform selection,experimental design,and data interpretation.Nucleic Acid Ther2012;22:271-274[PMID:22830413 DOI:10.1089/nat.2012.0367]
    7 Tuch BB,Laborde RR,Xu X,Gu J,Chung CB,Monighetti CK,Stanley SJ,Olsen KD,Kasperbauer JL,Moore EJ,Broomer AJ,Tan R,Brzoska PM,Muller MW,Siddiqui AS,Asmann YW,Sun Y,Kuersten S,Barker MA,De La Vega FM,Smith DI.Tumor transcriptome sequencing reveals allelic expression imbalances associated with copy number alterations.PLo S One 2010;5:e9317[PMID:20174472 DOI:10.1371/journal.pone.0009317]
    8 Han Y,Gao S,Muegge K,Zhang W,Zhou B.Advanced Applications of RNA Sequencing and Challenges.Bioinform Biol Insights 2015;9:29-46[PMID:26609224 DOI:10.4137/BBI.S28991]
    9 Burroughs AM,Ando Y,Aravind L.New perspectives on the diversification of the RNA interference system:insights from comparative genomics and small RNA sequencing.Wiley Interdiscip Rev RNA 2013;5:141-181[PMID:24311560 DOI:10.1002/wrna.1210]
    10 de Klerk E,‘t Hoen PA.Alternative m RNA transcription,processing,and translation:insights from RNA sequencing.Trends Genet 2015;31:128-139[PMID:25648499 DOI:10.1016/j.tig.2015.01.001]
    11 Scarpato M,Federico A,Ciccodicola A,Costa V.Novel transcription factor variants through RNA-sequencing:the importance of being“alternative”.Int J Mol Sci 2015;16:1755-1771[PMID:25590302 DOI:10.3390/ijms16011755]
    12 de Klerk E,den Dunnen JT,‘t Hoen PA.RNA sequencing:from tag-based profiling to resolving complete transcript structure.Cell Mol Life Sci 2014;71:3537-3551[PMID:24827995 DOI:10.1007/s00018-014-1637-9]
    13 Derks KW,Misovic B,van den Hout MC,Kockx CE,Gomez CP,Brouwer RW,Vrieling H,Hoeijmakers JH,van IJcken WF,Pothof J.Deciphering the RNA landscape by RNAome sequencing.RNABiol 2015;12:30-42[PMID:25826412 DOI:10.1080/15476286.2015.1017202]
    14 Nome T,Thomassen GO,Bruun J,Ahlquist T,Bakken AC,Hoff AM,Rognum T,Nesbakken A,Lorenz S,Sun J,Barros-Silva JD,Lind GE,Myklebost O,Teixeira MR,Meza-Zepeda LA,Lothe RA,Skotheim RI.Common fusion transcripts identified in colorectal cancer cell lines by high-throughput RNA sequencing.Transl Oncol 2013;6:546-553[PMID:24151535 DOI:10.1593/tlo.13457]
    15 Peltekova VD,Lemire M,Qazi AM,Zaidi SH,Trinh QM,Bielecki R,Rogers M,Hodgson L,Wang M,D’Souza DJ,Zandi S,Chong T,Kwan JY,Kozak K,De Borja R,Timms L,Rangrej J,Volar M,Chan-Seng-Yue M,Beck T,Ash C,Lee S,Wang J,Boutros PC,Stein LD,Dick JE,Gryfe R,Mc Pherson JD,Zanke BW,Pollett A,Gallinger S,Hudson TJ.Identification of genes expressed by immune cells of the colon that are regulated by colorectal cancerassociated variants.Int J Cancer 2014;134:2330-2341[PMID:24154973 DOI:10.1002/ijc.28557]
    16 Liu F,Ji F,Ji Y,Jiang Y,Sun X,Lu Y,Zhang L,Han Y,Liu X.Dissecting the mechanism of colorectal tumorigenesis based on RNA-sequencing data.Exp Mol Pathol 2015;98:246-253[PMID:25576648 DOI:10.1016/j.yexmp.2015.01.004]
    17 L?vf M,Nome T,Bruun J,Eknaes M,Bakken AC,Mpindi JP,Kilpinen S,Rognum TO,Nesbakken A,Kallioniemi O,Lothe RA,Skotheim RI.A novel transcript,VNN1-AB,as a biomarker for colorectal cancer.Int J Cancer 2014;135:2077-2084[PMID:24687856 DOI:10.1002/ijc.28855]
    18 Ji H,Chen M,Greening DW,He W,Rai A,Zhang W,Simpson RJ.Deep sequencing of RNA from three different extracellular vesicle(EV)subtypes released from the human LIM1863 colon cancer cell line uncovers distinct mi RNA-enrichment signatures.PLo SOne 2014;9:e110314[PMID:25330373 DOI:10.1371/journal.pone.0110314]
    19 Lin J,Welker NC,Zhao Z,Li Y,Zhang J,Reuss SA,Zhang X,Lee H,Liu Y,Bronner MP.Novel specific micro RNA biomarkers in idiopathic inflammatory bowel disease unrelated to disease activity.Mod Pathol 2014;27:602-608[PMID:24051693 DOI:10.1038/modpathol.2013.152]
    20 Holgersen K,Kutlu B,Fox B,Serikawa K,Lord J,Hansen AK,Holm TL.High-resolution gene expression profiling using RNAsequencing in patients with inflammatory bowel disease and in mouse models of colitis.J Crohns Colitis 2015;9:492-506[PMID:25795566 DOI:10.1093/ecco-jcc/jjv050]
    21 Lopes-Ramos C,Koyama FC,Habr-Gama A,Salim AC,Bettoni F,Asprino PF,Fran?a GS,Gama-Rodrigues J,Parmigiani RB,Perez RO,Galante PA,Camargo AA.Comprehensive evaluation of the effectiveness of gene expression signatures to predict complete response to neoadjuvant chemoradiotherapy and guide surgical intervention in rectal cancer.Cancer Genet 2015;208:319-326[PMID:25963525 DOI:10.1016/j.cancergen.2015.03.010]
    22 Camilleri M,Carlson P,Acosta A,Busciglio I,Nair AA,Gibbons SJ,Farrugia G,Klee EW.RNA sequencing shows transcriptomic changes in rectosigmoid mucosa in patients with irritable bowel syndrome-diarrhea:a pilot case-control study.Am J Physiol Gastrointest Liver Physiol 2014;306:G1089-G1098[PMID:24763552 DOI:10.1152/ajpgi.00068.2014]
    23 Vyas D,Garthe CC,Vyas A.Limitations of current timing and frequency of screening colonoscopy and possible future direction.J Laparoendosc Adv Surg Tech A 2013;23:271-275[PMID:23272724 DOI:10.1089/lap.2012.0428]
    24 Gambhir S,Vyas D,Hollis M,Aekka A,Vyas A.Nuclear factor kappa B role in inflammation associated gastrointestinal malignancies.World J Gastroenterol 2015;21:3174-3183[PMID:25805923 DOI:10.3748/wjg.v21.i11.3174]
    25 Siegel R,Desantis C,Jemal A.Colorectal cancer statistics,2014.CA Cancer J Clin 2014;64:104-117[PMID:24639052 DOI:10.3322/caac.21220]
    26 Joshi SS,Vyas AK,Vyas D,Kalla R.Reclassifying inflammatory bowel disease with capsule endoscopy in children.J Pediatr(Rio J)2013;89:514-515[PMID:23891118 DOI:10.1016/j.jped.2013.07.002]
    27 Malik TA.Inflammatory Bowel Disease:Historical Perspective,Epidemiology,and Risk Factors.Surg Clin North Am 2015;95:1105-1122,v[PMID:26596917 DOI:10.1016/j.suc.2015.07.006]
    28 Sayuk GS,Gyawali CP.Irritable bowel syndrome:modern concepts and management options.Am J Med 2015;128:817-827[PMID:25731138 DOI:10.1016/j.amjmed.2015.01.036]
    29 Hollis M,Nair K,Vyas A,Chaturvedi LS,Gambhir S,Vyas D.Micro RNAs potential utility in colon cancer:Early detection,prognosis,and chemosensitivity.World J Gastroenterol 2015;21:8284-8292[PMID:26217080 DOI:10.3748/wjg.v21.i27.8284]
    30 Balakrishnan A,Vyas A,Deshpande K,Vyas D.Pharmacological cyclin dependent kinase inhibitors:Implications for colorectal cancer.World J Gastroenterol 2016;22:2159-2164[PMID:26900281 DOI:10.3748/wjg.v22.i7.2159]
    31 Vyas D,Laput G,Vyas AK.Chemotherapy-enhanced inflammation may lead to the failure of therapy and metastasis.Onco Targets Ther 2014;7:1015-1023[PMID:24959088 DOI:10.2147/OTT.S60114]
    32 Wang J,Song YX,Ma B,Wang JJ,Sun JX,Chen XW,Zhao JH,Yang YC,Wang ZN.Regulatory Roles of Non-Coding RNAs in Colorectal Cancer.Int J Mol Sci 2015;16:19886-19919[PMID:26307974 DOI:10.3390/ijms160819886]
    33 Yang F,Xie YQ,Tang SQ,Wu XB,Zhu HY.mi R-143 regulates proliferation and apoptosis of colorectal cancer cells and exhibits altered expression in colorectal cancer tissue.Int J Clin Exp Med2015;8:15308-15312[PMID:26629019]
    34 Yau TO,Wu CW,Tang CM,Chen Y,Fang J,Dong Y,Liang Q,Ng SS,Chan FK,Sung JJ,Yu J.Micro RNA-20a in human faeces as a non-invasive biomarker for colorectal cancer.Oncotarget 2016;7:1559-1568[PMID:26621842 DOI:10.18632/oncotarget.6403]
    35 Sun G,Cheng YW,Lai L,Huang TC,Wang J,Wu X,Wang Y,Huang Y,Wang J,Zhang K,Hu S,Yang JR,Yen Y.Signature mi RNAs in colorectal cancers were revealed using a bias reduction small RNA deep sequencing protocol.Oncotarget 2016;7:3857-3872[PMID:26646696 DOI:10.18632/oncotarget.6460]
    36 Qin J,Ke J,Xu J,Wang F,Zhou Y,Jiang Y,Wang Z.Downregulation of micro RNA-132 by DNA hypermethylation is associated with cell invasion in colorectal cancer.Onco Targets Ther 2015;8:3639-3648[PMID:26675712 DOI:10.2147/OTT.S91560]
    37 Xu T,Jing C,Shi Y,Miao R,Peng L,Kong S,Ma Y,Li L.micro RNA-20a enhances the epithelial-to-mesenchymal transition of colorectal cancer cells by modulating matrix metalloproteinases.Exp Ther Med 2015;10:683-688[PMID:26622375 DOI:10.3892/etm.2015.2538]
    38 Liu Y,Zhang M,Liang L,Li J,Chen YX.Over-expression of lnc RNA DANCR is associated with advanced tumor progression and poor prognosis in patients with colorectal cancer.Int J Clin Exp Pathol 2015;8:11480-11484[PMID:26617879]
    39 Hu J,Xu Y,Cai S.Specific micro RNAs as novel biomarkers for combination chemotherapy resistance detection of colon adenocarcinoma.Eur J Med Res 2015;20:95[PMID:26626874DOI:10.1186/s40001-015-0183-8]
    40 Polytarchou C,Hommes DW,Palumbo T,Hatziapostolou M,Koutsioumpa M,Koukos G,van der Meulen-de Jong AE,Oikonomopoulos A,van Deen WK,Vorvis C,Serebrennikova OB,Birli E,Choi J,Chang L,Anton PA,Tsichlis PN,Pothoulakis C,Verspaget HW,Iliopoulos D.Micro RNA214 Is Associated With Progression of Ulcerative Colitis,and Inhibition Reduces Development of Colitis and Colitis-Associated Cancer in Mice.Gastroenterology 2015;149:981-92.e11[PMID:26055138 DOI:10.1053/j.gastro.2015.05.057]
    41 Deshpande K,Vyas A,Balakrishnan A,Vyas D.Clustered Regularly Interspaced Short Palindromic Repeats/Cas9 Genetic Engineering:Robotic Genetic Surgery.Am J Robot Surg 2015;2:49-52[PMID:27453936 DOI:10.1166/ajrs.2015.1023]
    42 Wang J,Lei ZJ,Guo Y,Wang T,Qin ZY,Xiao HL,Fan LL,Chen DF,Bian XW,Liu J,Wang B.mi RNA-regulated delivery of linc RNA-p21 suppressesβ-catenin signaling and tumorigenicity of colorectal cancer stem cells.Oncotarget 2015;6:37852-37870[PMID:26497997 DOI:10.18632/oncotarget.5635]
    43 Davis ME,Zuckerman JE,Choi CH,Seligson D,Tolcher A,Alabi CA,Yen Y,Heidel JD,Ribas A.Evidence of RNAi in humans from systemically administered si RNA via targeted nanoparticles.Nature 2010;464:1067-1070[PMID:20305636 DOI:10.1038/nature08956]
    44 Ji Q,Liu X,Fu X,Zhang L,Sui H,Zhou L,Sun J,Cai J,Qin J,Ren J,Li Q.Resveratrol inhibits invasion and metastasis of colorectal cancer cells via MALAT1 mediated Wnt/β-catenin signal pathway.PLo S One 2013;8:e78700[PMID:24244343DOI:10.1371/journal.pone.0078700]
    45 Burnett JC,Rossi JJ,Tiemann K.Current progress of si RNA/sh RNA therapeutics in clinical trials.Biotechnol J 2011;6:1130-1146[PMID:21744502 DOI:10.1002/biot.201100054]
    46 Lanford RE,Hildebrandt-Eriksen ES,Petri A,Persson R,Lindow M,Munk ME,Kauppinen S,?rum H.Therapeutic silencing of micro RNA-122 in primates with chronic hepatitis C virus infection.Science 2010;327:198-201[PMID:19965718 DOI:10.1126/science.1178178]
    47 Watts JK,Corey DR.Silencing disease genes in the laboratory and the clinic.J Pathol 2012;226:365-379[PMID:22069063DOI:10.1002/path.2993]
    48 Modarresi F,Faghihi MA,Lopez-Toledano MA,Fatemi RP,Magistri M,Brothers SP,van der Brug MP,Wahlestedt C.Inhibition of natural antisense transcripts in vivo results in genespecific transcriptional upregulation.Nat Biotechnol 2012;30:453-459[PMID:22446693 DOI:10.1038/nbt.2158]
    49 Mizrahi A,Czerniak A,Levy T,Amiur S,Gallula J,Matouk I,Abu-lail R,Sorin V,Birman T,de Groot N,Hochberg A,Ohana P.Development of targeted therapy for ovarian cancer mediated by a plasmid expressing diphtheria toxin under the control of H19regulatory sequences.J Transl Med 2009;7:69[PMID:19656414DOI:10.1186/1479-5876-7-69]
    50 Liu D,Graber JH.Quantitative comparison of EST libraries requires compensation for systematic biases in c DNA generation.BMC Bioinformatics 2006;7:77[PMID:16503995 DOI:10.1186/1471-2105-7-77]
    51 Raabe CA,Tang TH,Brosius J,Rozhdestvensky TS.Biases in small RNA deep sequencing data.Nucleic Acids Res 2014;42:1414-1426[PMID:24198247 DOI:10.1093/nar/gkt1021]
    52 Vyas D,Balakrishnan A,Vyas A.The Value of the P Value.Am J Robot Surg 2015;2:53-56[PMID:27430018 DOI:10.1166/ajrs.2015.1017]
    53 Cohen JE,Cohen Y,Peretz T,Hubert A.Retrospective Study of the Predictive Value of Target Now in Systemic Therapy for Metastatic Colorectal and Gastric Carcinomas.Isr Med Assoc J2015;17:612-615[PMID:26665314]
    54 Tiemann K,H?hn B,Ehsani A,Forman SJ,Rossi JJ,Saetrom P.Dual-targeting si RNAs.RNA 2010;16:1275-1284[PMID:20410240 DOI:10.1261/rna.2005710]
    55 van de Water FM,Boerman OC,Wouterse AC,Peters JG,Russel FG,Masereeuw R.Intravenously administered short interfering RNA accumulates in the kidney and selectively suppresses gene function in renal proximal tubules.Drug Metab Dispos 2006;34:1393-1397[PMID:16714375 DOI:10.1124/dmd.106.009555]
NGLC 2004-2010.National Geological Library of China All Rights Reserved.
Add:29 Xueyuan Rd,Haidian District,Beijing,PRC. Mail Add: 8324 mailbox 100083
For exchange or info please contact us via email.