Optimized high-throughput microRNA expression profiling provides novel biomarker assessment of clinical prostate and breast cancer biopsies
Tóm tắt
Recent studies indicate that microRNAs (miRNAs) are mechanistically involved in the development of various human malignancies, suggesting that they represent a promising new class of cancer biomarkers. However, previously reported methods for measuring miRNA expression consume large amounts of tissue, prohibiting high-throughput miRNA profiling from typically small clinical samples such as excision or core needle biopsies of breast or prostate cancer. Here we describe a novel combination of linear amplification and labeling of miRNA for highly sensitive expression microarray profiling requiring only picogram quantities of purified microRNA. Comparison of microarray and qRT-PCR measured miRNA levels from two different prostate cancer cell lines showed concordance between the two platforms (Pearson correlation R2 = 0.81); and extension of the amplification, labeling and microarray platform was successfully demonstrated using clinical core and excision biopsy samples from breast and prostate cancer patients. Unsupervised clustering analysis of the prostate biopsy microarrays separated advanced and metastatic prostate cancers from pooled normal prostatic samples and from a non-malignant precursor lesion. Unsupervised clustering of the breast cancer microarrays significantly distinguished ErbB2-positive/ER-negative, ErbB2-positive/ER-positive, and ErbB2-negative/ER-positive breast cancer phenotypes (Fisher exact test, p = 0.03); as well, supervised analysis of these microarray profiles identified distinct miRNA subsets distinguishing ErbB2-positive from ErbB2-negative and ER-positive from ER-negative breast cancers, independent of other clinically important parameters (patient age; tumor size, node status and proliferation index). In sum, these findings demonstrate that optimized high-throughput microRNA expression profiling offers novel biomarker identification from typically small clinical samples such as breast and prostate cancer biopsies.
Tài liệu tham khảo
Bartel DP: MicroRNAs: genomics, biogenesis, mechanism, and function. Cell. 2004, 116: 281-297. 10.1016/S0092-8674(04)00045-5
Carrington JC, Ambros V: Role of MicroRNAs in Plant and Animal Development. Science. 2003, 301: 336-338. 10.1126/science.1085242
Lim LP, Lau NC, Weinstein EG, Abdelhakim A, Yekta S, Rhoades MW, Burge CB, Bartel DP: The microRNAs of Caenorhabditis elegans. Genes & Development. 2003, 17: 991-1008. 10.1101/gad.1074403
Lim LP, Glasner ME, Yekta S, Burge CB, Bartel DP: Vertebrate MicroRNA Genes. Science. 2003, 299: 1540- 10.1126/science.1080372
Ambros V: MicroRNA Pathways in Flies and Worms: Growth, Death, Fat, Stress, and Timing. Cell. 2003, 113: 673-676. 10.1016/S0092-8674(03)00428-8
Bartel B, Bartel DP: MicroRNAs: At the Root of Plant Development?. Plant Physiol. 2003, 132: 709-717. 10.1104/pp.103.023630
Ke XS, Liu CM, Liu DP, Liang CC: MicroRNAs: key participants in gene regulatory networks. Current Opinion in Chemical Biology. 2003, 7: 516-523. 10.1016/S1367-5931(03)00075-9
Moss E: . Molecular Biology and Molecular Medicine. 2003, 98-114. Eurekah.com.
Hutvagner G, McLachlan J, Pasquinelli AE, Balint E, Tuschl T, Zamore PD: A Cellular Function for the RNA-Interference Enzyme Dicer in the Maturation of the let-7 Small Temporal RNA. Science. 2001, 293: 834-838. 10.1126/science.1062961
Reinhart BJ, Slack FJ, Basson M, Pasquinelli AE, Bettinger JC, Rougvie AE, Horvitz HR, Ruvkun G: The 21-nucleotide let-7 RNA regulates developmental timing in Caenorhabditis elegans. Nature. 2000, 403: 901-906. 10.1038/35002607
Wightman B, Ha I, Ruvkun G: Posttranscriptional regulation of the heterochronic gene lin-14 by lin-4 mediates temporal pattern formation in C. elegans. Cell. 1993, 75: 855-862. 10.1016/0092-8674(93)90530-4
Olsen PH, Ambros V: The lin-4 Regulatory RNA Controls Developmental Timing in Caenorhabditis elegans by Blocking LIN-14 Protein Synthesis after the Initiation of Translation. Developmental Biology. 1999, 216: 671-680. 10.1006/dbio.1999.9523
Lu J, Getz G, Miska EA, Alvarez-Saavedra E, Lamb J, Peck D, Sweet-Cordero A, Ebert BL, Mak RH, Ferrando AA, Downing JR, Jacks T, Horvitz HR, Golub TR: MicroRNA expression profiles classify human cancers.[see comment]. Nature. 2005, 435: 834-838. 10.1038/nature03702
Iorio MV, Ferracin M, Liu CG, Veronese A, Spizzo R, Sabbioni S, Magri E, Pedriali M, Fabbri M, Campiglio M, Menard S, Palazzo JP, Rosenberg A, Musiani P, Volinia S, Nenci I, Calin GA, Querzoli P, Negrini M, Croce CM: MicroRNA gene expression deregulation in human breast cancer. Cancer Res. 2005, 65: 7065-7070. 10.1158/0008-5472.CAN-05-1783
Lau NC, Lim LP, Weinstein EG, Bartel DP: An abundant class of tiny RNAs with probable regulatory roles in Caenorhabditis elegans.[see comment]. Science. 2001, 294: 858-862. 10.1126/science.1065062
Lagos-Quintana M, Rauhut R, Lendeckel W, Tuschl T: Identification of Novel Genes Coding for Small Expressed RNAs. Science. 2001, 294: 853-858. 10.1126/science.1064921
Lee RC, Ambros V: An extensive class of small RNAs in Caenorhabditis elegans.[see comment]. Science. 2001, 294: 862-864. 10.1126/science.1065329
Barad O, Meiri E, Avniel A, Aharonov R, Barzilai A, Bentwich I, Einav U, Gilad S, Hurban P, Karov Y, Lobenhofer EK, Sharon E, Shiboleth YM, Shtutman M, Bentwich Z, Einat P: MicroRNA expression detected by oligonucleotide microarrays: System establishment and expression profiling in human tissues. Genome Res. 2004, 14: 2486-2494. 10.1101/gr.2845604
Liang RQ, Li W, Li Y, Tan CY, Li JX, Jin YX, Ruan KC: An oligonucleotide microarray for microRNA expression analysis based on labeling RNA with quantum dot and nanogold probe. Nucl Acids Res. 2005, 33: e17- 10.1093/nar/gni019
Miska E, Alvarez-Saavedra E, Townsend M, Yoshii A, Sestan N, Rakic P, Constantine-Paton M, Horvitz HR: Microarray analysis of microRNA expression in the developing mammalian brain. Genome Biology. 2004, 5: R68- 10.1186/gb-2004-5-9-r68
Nelson PT, Baldwin DA, Scearce LM, Oberholtzer JC, Tobias JW, Mourelatos Z: Microarray-based, high-throughput gene expression profiling of microRNAs.[see comment]. Nature Methods. 2004, 1: 155-161. 10.1038/nmeth717
Castoldi M, Schmidt S, Benes V, Noerholm M, Kulozik AE, Hentze MW, Muckenthaler MU: A sensitive array for microRNA expression profiling (miChip) based on locked nucleic acids (LNA). Rna. 2006, 12: 913-920. 10.1261/rna.2332406
Liu CG, Calin GA, Meloon B, Gamliel N, Sevignani C, Ferracin M, Dumitru CD, Shimizu M, Zupo S, Dono M, Alder H, Bullrich F, Negrini M, Croce CM: An oligonucleotide microchip for genome-wide microRNA profiling in human and mouse tissues. Proceedings of the National Academy of Sciences of the United States of America. 2004, 101: 9740-9744. 10.1073/pnas.0403293101
Goff LA, Bowers J, Schwalm J, Howerton K, Getts RC, Hart RP: Evaluation of sense-strand mRNA amplification by comparative quantitative PCR. BMC Genomics. 2004, 5: 76-80. 10.1186/1471-2164-5-76
Chen C, Ridzon DA, Broomer AJ, Zhou Z, Lee DH, Nguyen JT, Barbisin M, Xu NL, Mahuvakar VR, Andersen MR, Lao KQ, Livak KJ, Guegler KJ: Real-time quantification of microRNAs by stem-loop RT-PCR. Nucl Acids Res. 2005, 33: e179- 10.1093/nar/gni178
Sorlie T, Perou CM, Tibshirani R, Aas T, Geisler S, Johnsen H, Hastie T, Eisen MB, van de Rijn M, Jeffrey SS, Thorsen T, Quist H, Matese JC, Brown PO, Botstein D, Lonning PE, Borresen-Dale AL: Gene expression patterns of breast carcinomas distinguish tumor subclasses with clinical implications. PNAS. 2001, 98: 10869-10874. 10.1073/pnas.191367098
De Laurentiis M, Arpino G, Massarelli E, Ruggiero A, Carlomagno C, Ciardiello F, Tortora G, D'Agostino D, Caputo F, Cancello G, Montagna E, Malorni L, Zinno L, Lauria R, Bianco AR, De Placido S: A Meta-Analysis on the Interaction between HER-2 Expression and Response to Endocrine Treatment in Advanced Breast Cancer. Clin Cancer Res. 2005, 11: 4741-4748. 10.1158/1078-0432.CCR-04-2569
Southern E, Mir K, Schchepinov M: Molecular interactions on microarrays. Nat Genet. 1999, 21: 5-9. 10.1038/4429
Shchepinov MS, Case-Green SC, Southern EM: Steric factors influencing hybridisation of nucleic acids to oligonucleotide arrays. Nucl Acids Res. 1997, 25: 1155-1161. 10.1093/nar/25.6.1155
STEARS ROBINL, GETTS ROBERTC, GULLANS STEVENR: A novel, sensitive detection system for high-density microarrays using dendrimer technology. Physiol Genomics. 2000, 3: 93-99.
Hardiman G: Microarray platforms-comparisons and contrasts. Pharmacogenomics. 2004, 5: 487-502. 10.1517/14622416.5.5.487
Scott GK, Mattie MD, Berger CE, Benz SC, Benz CC: Rapid alteration of microRNA levels by histone deacetylase inhibition. Cancer Res. 2006, 66: 1277-1281. 10.1158/0008-5472.CAN-05-3632
RAYMOND CHRISTOPHERK, ROBERTS BRIANS, GARRETT-ENGELE PHIL, Lim LP, JOHNSON JASONM: Simple, quantitative primer-extension PCR assay for direct monitoring of microRNAs and short-interfering RNAs. Rna. 2005, 11: 1737-1744. 10.1261/rna.2148705
Valoczi A, Hornyik C, Varga N, Burgyan J, Kauppinen S, Havelda Z: Sensitive and specific detection of microRNAs by northern blot analysis using LNA-modified oligonucleotide probes. Nucl Acids Res. 2004, 32: e175- 10.1093/nar/gnh171
THOMSEN RUNE, NIELSEN PETERSTEIN, JENSEN TORBENHEICK: Dramatically improved RNA in situ hybridization signals using LNA-modified probes. Rna. 2005, 11: 1745-1748. 10.1261/rna.2139705
Microarrays.org. 2006, [http://derisilab.ucsf.edu/microarray/]
microRNA Registry. 2006, [http://www.sanger.ac.uk/Software/Rfam/mirna/]
Goff LA, Yang M, Bowers J, Getts RC, Padgett RW, Hart RP: Rational probe optimization and enhanced detection strategy for microRNAs using microarrays. RNA Biology. 2005, 2: E9-E16.
Genisphere Inc. 2006, [http://www.genisphere.com]
Eisen MB, Spellman PT, Brown PO, Botstein D: Cluster analysis and display of genome-wide expression patterns. PNAS. 1998, 95: 14863-14868. 10.1073/pnas.95.25.14863
Tusher VG, Tibshirani R, Chu G: Significance analysis of microarrays applied to the ionizing radiation response. PNAS. 2001, 98: 5116-5121. 10.1073/pnas.091062498
Java TreeView. 2006, [http://genome-www5.stanford.edu]