Whole Transcriptome Amplification for Gene Expression Profiling and Development of Molecular Archives

Formalin-fixed paraffin-embedded (FFPE) prostate specimens are rich sources of molecular pathological information. However, FFPE-based microarray analysis of tissue samples may be hampered by the degradation and chemical alteration of RNA molecules due to the preservation procedure. In this report, we employed a probe analyses of Affymetrix oligonucleotide arrays at individual probe level to compensate for the potential loss of gene identifications associated with compromised mRNA quality in FFPE preparations. Furthermore, to increase the sample quality, we utilized laser capture microdissection of prostate tumor and benign epithelial cells. Remarkably, combination of these approaches recapitulated the common prostate cancer-associated gene expression alteration. Identification of prostate cancer associated-gene expression alterations such as AMACR, Kallikrein gene family and genes associated with androgen signaling such as PDEF and STEAP were consistent with previous findings reported in prostate cancer. These data suggest that combination of laser capture dissection with computational enhancement of microarray data may be useful for the assessment of gene expression changes in FFPE prostate cancer specimens.

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“…Our study is in agreement with Tomlins et al, 17 who have recently reported promising global gene expression data from FFPE CaP specimens.…”

Section: Discussionsupporting

confidence: 93%

Transcriptome analyses of benign and malignant prostate epithelial cells in formalin-fixed paraffin-embedded whole-mounted radical prostatectomy specimens

Furusato

Shaheduzzaman

Petrovics

et al. 2007

Prostate Cancer Prostatic Dis

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“…Isolation of RNA from urine and TransPlex whole transcriptome amplification (WTA) were as described (12). Quantitative PCR (qPCR) was used to detect seven prostate cancer biomarkers (AMACR, ERG, GOLPH2, PCA3, SPINK1, TFF3, and TMPRSS2:ERG) and the control transcripts PSA and GAPDH from WTA-amplified cDNA essentially as described (12,13 fusion-positive or fusion-negative status observed in tissue samples (8,17), with positive samples defined as those with C t values of <37. As PCA3 has been reported to be a prostate tissue-specific marker (7), it was normalized against urine PSA (C tPSA À C tPCA3 ).…”

Section: Methodsmentioning

confidence: 99%

A First-Generation Multiplex Biomarker Analysis of Urine for the Early Detection of Prostate Cancer

et al. 2008

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Although prostate-specific antigen (PSA) serum level is currently the standard of care for prostate cancer screening in the United States, it lacks ideal specificity and additional biomarkers are needed to supplement or potentially replace serum PSA testing. Emerging evidence suggests that monitoring the noncoding RNA transcript PCA3 in urine may be useful in detecting prostate cancer in patients with elevated PSA levels. Here, we show that a multiplex panel of urine transcripts outperforms PCA3 transcript alone for the detection of prostate cancer. We measured the expression of seven putative prostate cancer biomarkers, including PCA3, in sedimented urine using quantitative PCR on a cohort of 234 patients presenting for biopsy or radical prostatectomy. By univariate analysis, we found that increased GOLPH2, SPINK1, and PCA3 transcript expression and TMPRSS2:ERG fusion status were significant predictors of prostate cancer. Multivariate regression analysis showed that a multiplexed model, including these biomarkers, outperformed serum PSA or PCA3 alone in detecting prostate cancer. The area under the receiver-operating characteristic curve was 0.758 for the multiplexed model versus 0.662 for PCA3 alone (P = 0.003). The sensitivity and specificity for the multiplexed model were 65.9% and 76.0%, respectively, and the positive and negative predictive values were 79.8% and 60.8%, respectively. Taken together, these results provide the framework for the development of highly optimized, multiplex urine biomarker tests for more accurate detection of prostate cancer. [Cancer Res 2008;68(3):645-9]

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“…Here state of the art techniques in RNA amplification were employed using MTOPS clinical samples in order to perform expression array analysis on 30K cDNA arrays. 48,49 These approaches were previously successful with prostate cancer samples. 49 As part of this pilot study, 30 frozen tissue samples that originated from needle biopsies of the left or right transitional zone of the prostatic gland (n=15 each) were obtained.…”

Section: Development Of a Molecular Signature For Bph Responsive To 5mentioning

confidence: 99%

“…48,49 These approaches were previously successful with prostate cancer samples. 49 As part of this pilot study, 30 frozen tissue samples that originated from needle biopsies of the left or right transitional zone of the prostatic gland (n=15 each) were obtained. Each of these MTOPS specimens represented a single case and all samples were from nonrandomized patients.…”

Section: Development Of a Molecular Signature For Bph Responsive To 5mentioning

confidence: 99%

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A Comprehensive Approach Toward Novel Serum Biomarkers for Benign Prostatic Hyperplasia: The MPSA Consortium

et al. 2008

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Purpose-Clinical benign prostatic hyperplasia (BPH) is primarily diagnosed based on a diverse array of progressive lower urinary tract symptoms (LUTS) and is likely distinct from histological BPH, which is detected by the presence of non-malignant proliferation of prostate cells but may or may not be associated with symptoms. Pharmacological management of LUTS has emerged as an effective initial treatment for clinical BPH due to the introduction of new drug therapies shown to be effective in recent large clinical trials. Despite advances in symptom management and research into BPH pathology, diagnostic strategies for prediction of BPH progression and response to drug modalities are lacking and questions remain as to the molecular differences underlying clinical (symptomatic) versus histological (non-symptomatic) BPH. Publisher's Disclaimer: This is a PDF file of an unedited manuscript that has been accepted for publication. As a service to our customers we are providing this early version of the manuscript. The manuscript will undergo copyediting, typesetting, and review of the resulting proof before it is published in its final citable form. Please note that during the production process errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain. Results-To date the MPSA has identified a number of promising biomarkers and other molecular and cellular changes associated with BPH. NIH Public AccessConclusions-These findings and ongoing consortium discovery efforts have the potential to provide a greater understanding of the defects underlying disease pathology and may lead to the development of early and more effective pharmacological treatment strategies for BPH.

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Whole Transcriptome Amplification for Gene Expression Profiling and Development of Molecular Archives

Cited by 38 publications

References 26 publications

Transcriptome analyses of benign and malignant prostate epithelial cells in formalin-fixed paraffin-embedded whole-mounted radical prostatectomy specimens

Transcriptome analyses of benign and malignant prostate epithelial cells in formalin-fixed paraffin-embedded whole-mounted radical prostatectomy specimens

A First-Generation Multiplex Biomarker Analysis of Urine for the Early Detection of Prostate Cancer

A Comprehensive Approach Toward Novel Serum Biomarkers for Benign Prostatic Hyperplasia: The MPSA Consortium

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