| Experiment ID | EXP00029 |
| Reference | Title: Optimized high-throughput microRNA expression profiling provides novel biomarker assessment of clinical prostate and breast cancer biopsies. Author: Mattie MD, Benz CC, Bowers J, Sensinger K, Wong L, Scott GK, Fedele V,Ginzinger D, Getts R, Haqq C. Journal: Mol Cancer. 2006 Jun 19;5:24. Abstract: BACKGROUND: Recent studies indicate that microRNAs (miRNAs) are mechanisticallyinvolved in the development of various human malignancies, suggesting that theyrepresent a promising new class of cancer biomarkers. However, previouslyreported methods for measuring miRNA expression consume large amounts of tissue, prohibiting high-throughput miRNA profiling from typically small clinical samplessuch as excision or core needle biopsies of breast or prostate cancer. Here wedescribe a novel combination of linear amplification and labeling of miRNA forhighly sensitive expression microarray profiling requiring only picogramquantities of purified microRNA.RESULTS: Comparison of microarray and qRT-PCR measured miRNA levels from twodifferent prostate cancer cell lines showed concordance between the two platforms(Pearson correlation R2 = 0.81); and extension of the amplification, labeling andmicroarray platform was successfully demonstrated using clinical core andexcision biopsy samples from breast and prostate cancer patients. Unsupervisedclustering analysis of the prostate biopsy microarrays separated advanced andmetastatic prostate cancers from pooled normal prostatic samples and from anon-malignant precursor lesion. Unsupervised clustering of the breast cancermicroarrays significantly distinguished ErbB2-positive/ER-negative,ErbB2-positive/ER-positive, and ErbB2-negative/ER-positive breast cancerphenotypes (Fisher exact test, p = 0.03); as well, supervised analysis of thesemicroarray profiles identified distinct miRNA subsets distinguishingErbB2-positive from ErbB2-negative and ER-positive from ER-negative breastcancers, independent of other clinically important parameters (patient age; tumorsize, node status and proliferation index).CONCLUSION: In sum, these findings demonstrate that optimized high-throughputmicroRNA expression profiling offers novel biomarker identification fromtypically small clinical samples such as breast and prostate cancer biopsies. PMID: 16784538 |
| Expressiion Profile | Description: Breast tumor miRNA profiling Organism: Homo sapiens GEO ID: GSE4589 Platform: GPL3238 Number of samples: 20 |
| Design and Sample | Cancer Type: breast cancer Cancer SubType: N/D Cell Line: N/D Experimental Design: cancer vs normal Case Sample: breast tumor Control Sample: normal breast Num of Case: 20 Num of Control: 20 Quantification Software: Limma Num of miRNAs: 180 |
| Identification | Num of Up: 72 Num of Down: 71 |