Oncology
Laboratory/Clinical Translational Research
An Ultrasensitive New DNA Microarray Chip Provides Gene Expression Profiles for Preoperative Esophageal Cancer Biopsies without RNA AmplificationIto T.a, b · Tanaka E.b · Kadowaki T.e · Kan T.a · Higashiyama M.b · Shiojima S.e · Tomoda S.f · Myoumoto A.f · Akiyama H.f · Nobumasa H.f · Matsumoto S.c · Miyamoto S.c · Mitsumori M.d · Sato F.a · Watanabe G.b · Itami A.b · Meltzer S.J.a · Tsujimoto G.e · Shimada Y.b, gaDivision of Gastroenterology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Md., USA; Departments of bSurgery, cGastroenterology and Hepatology and dTherapeutic Radiology and Oncology, Graduate School of Medicine and eDepartment of Genomic Drug Discovery Science, Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, fNew Frontiers Research Laboratories, Toray Industries Inc., Kanagawa, and gDepartment of Surgery and Science, Graduate School of Medicine and Pharmaceutical Sciences Research, University of Toyama, Toyama, Japan
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Article / Publication Details
Received: February 07, 2007
Accepted: August 09, 2007
Published online: May 30, 2008
Issue release date: June 2008
Number of Print Pages: 10
Number of Figures: 4
Number of Tables: 3
ISSN: 0030-2414 (Print)
eISSN: 1423-0232 (Online)
For additional information: https://www.karger.com/OCL
Abstract
Objectives: Gene expression profiling using pretreatment biopsies has been limited due to their small sample sizes. This study evaluated the usefulness of an ultrasensitive new DNA microarray chip, which has a unique array structure, for the clinical diagnosis of esophageal cancer using preoperative biopsies. Methods: Paired cancer and normal esophageal epithelial tissues from 56 patients who underwent esophagectomy and from 48 patients who underwent preoperative endoscopy were studied. Among 2 feature gene sets selected by a reference DNA chip discriminating malignant status of samples, 20 feature genes were selected for the development of the new DNA chip. The new DNA chip was hybridized with 0.1 µg of total RNA per slide without RNA amplification. Results: Twenty feature genes, including RRM-2 and XRCC-3, for the new DNA chip could discriminate cancer from noncancer at a 95.2% rate of accuracy in 42 biopsies (sensitivity 95.7%, specificity 94.7%). A receiver operating characteristic (ROC) curve analysis showed that the area under ROC curve for the prediction was 0.966. Conclusions: The gene expression profiles from the preoperative biopsies could diagnose esophageal cancer accurately, using the ultrasensitive DNA chip without RNA amplification. This new DNA chip technology might contribute further to the development of customized therapeutic strategies for various cancer patients.
© 2008 S. Karger AG, Basel
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References
- Parkin DM, Bray FI, Devesa SS: Cancer burden in the year 2000. The global picture. Eur J Cancer 2001;37(suppl 8):S4–S66.
- Lerut T, Coosemans W, Decker G, De Leyn P, Nafteux P, Van Raemdonck D: Cancer of the esophagus and gastro-esophageal junction: potentially curative therapies. Surg Oncol 2001;10:113–122.
- Visbal AL, Allen MS, Miller DL, Deschamps C, Trastek VF, Pairolero PC: Ivor Lewis esophagogastrectomy for esophageal cancer. Ann Thorac Surg 2001;71:1803–1808.
- Sweet-Cordero A, Mukherjee S, Subramanian A, You H, Roix JJ, Ladd-Acosta C, Mesirov J, Golub TR, Jacks T: An oncogenic KRAS2 expression signature identified by cross-species gene-expression analysis. Nat Genet 2005;37:48–55.
- van de Vijver MJ, He YD, van’t Veer LJ, Dai H, Hart AA, Voskuil DW, Schreiber GJ, Peterse JL, Roberts C, Marton MJ, Parrish M, Atsma D, Witteveen A, Glas A, Delahaye L, van der Velde T, Bartelink H, Rodenhuis S, Rutgers ET, Friend SH, Bernards R: A gene-expression signature as a predictor of survival in breast cancer. N Engl J Med 2002;347:1999–2009.
- Bild AH, Yao G, Chang JT, Wang Q, Potti A, Chasse D, Joshi MB, Harpole D, Lancaster JM, Berchuck A, Olson JA Jr, Marks JR, Dressman HK, West M, Nevins JR: Oncogenic pathway signatures in human cancers as a guide to targeted therapies. Nature 2006;439:353–357.
- Iscove NN, Barbara M, Gu M, Gibson M, Modi C, Winegarden N: Representation is faithfully preserved in global cDNA amplified exponentially from sub-picogram quantities of mRNA. Nat Biotechnol 2002;20:940–943.
- Puskas LG, Zvara A, Hackler L Jr, Van Hummelen P: RNA amplification results in reproducible microarray data with slight ratio bias. Biotechniques 2002;32:1330–1334, 1336, 1338, 1340.
- Spiess AN, Mueller N, Ivell R: Amplified RNA degradation in T7-amplification methods results in biased microarray hybridizations. BMC Genomics 2003;4:44.
- Nagino K, Nomura O, Takii Y, Myomoto A, Ichikawa M, Nakamura F, Higasa M, Akiyama H, Nobumasa H, Shiojima S, Tsujimoto G: Ultrasensitive DNA chip: gene expression profile analysis without RNA amplification. J Biochem (Tokyo) 2006;139:697–703.
-
Sobin L, Wittekind C: TNM Classification of Malignant Tumours, ed 6. New York, Wiley-Liss, 2002, pp 60–64.
- Centeno BA, Enkemann SA, Coppola D, Huntsman S, Bloom G, Yeatman TJ: Classification of human tumors using gene expression profiles obtained after microarray analysis of fine-needle aspiration biopsy samples. Cancer 2005;105:101–109.
- Braga-Neto UM, Dougherty ER: Is cross-validation valid for small-sample microarray classification? Bioinformatics 2004;20:374–380.
- Abraham JM, Wang S, Suzuki H, Jiang HY, Rosenblum-Vos LS, Yin J, Meltzer SJ: Esophagin cDNA cloning and characterization: a tissue-specific member of the small proline-rich protein family that is not expressed in esophageal tumors. Cell Growth Differ 1996;7:855–860.
- Kimos MC, Wang S, Borkowski A, Yang GY, Yang CS, Perry K, Olaru A, Deacu E, Sterian A, Cottrell J, Papadimitriou J, Sisodia L, Selaru FM, Mori Y, Xu Y, Yin J, Abraham JM, Meltzer SJ: Esophagin and proliferating cell nuclear antigen (PCNA) are biomarkers of human esophageal neoplastic progression. Int J Cancer 2004;111:415–417.
- Smolinski KN, Abraham JM, Souza RF, Yin J, Wang S, Xu Y, Zou TT, Kong D, Fleisher AS, Meltzer SJ: Activation of the esophagin promoter during esophageal epithelial cell differentiation. Genomics 2002;79:875–880.
- Kan T, Shimada Y, Sato F, Maeda M, Kawabe A, Kaganoi J, Itami A, Yamasaki S, Imamura M: Gene expression profiling in human esophageal cancers using cDNA microarray. Biochem Biophys Res Commun 2001;286:792–801.
- Ramaswamy S, Ross KN, Lander ES, Golub TR: A molecular signature of metastasis in primary solid tumors. Nat Genet 2003;33:49–54.
- Kan T, Shimada Y, Sato F, Ito T, Kondo K, Watanabe G, Maeda M, Yamasaki S, Meltzer SJ, Imamura M: Prediction of lymph node metastasis with use of artificial neural networks based on gene expression profiles in esophageal squamous cell carcinoma. Ann Surg Oncol 2004;11:1070–1078.
- van’t Veer LJ, Dai H, van de Vijver MJ, He YD, Hart AA, Mao M, Peterse HL, van der Kooy K, Marton MJ, Witteveen AT, Schreiber GJ, Kerkhoven RM, Roberts C, Linsley PS, Bernards R, Friend SH: Gene expression profiling predicts clinical outcome of breast cancer. Nature 2002;415:530–536.
- Lin DW, Coleman IM, Hawley S, Dumpit R, Gifford D, Kezele P, Hung H, Knudsen BS, Kristal AR, Nelson PS: Influence of surgical manipulation on prostate gene expression: implications for molecular correlates of treatment effects and disease prognosis. J Clin Oncol 2006;24:3763–3770.
- Lin YM, Furukawa Y, Tsunoda T, Yue CT, Yang KC, Nakamura Y: Molecular diagnosis of colorectal tumors by expression profiles of 50 genes expressed differentially in adenomas and carcinomas. Oncogene 2002;21:4120–4128.
Article / Publication Details
Received: February 07, 2007
Accepted: August 09, 2007
Published online: May 30, 2008
Issue release date: June 2008
Number of Print Pages: 10
Number of Figures: 4
Number of Tables: 3
ISSN: 0030-2414 (Print)
eISSN: 1423-0232 (Online)
For additional information: https://www.karger.com/OCL
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