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
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DOI：
10.1038/sj.pcan.4501007
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发表时间：
2008-06-01
影响因子：
4.8
通讯作者：
Sesterhenn, I. A.
中科院分区：
文献类型：
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作者：
Furusato, B.;Shaheduzzaman, S.;Sesterhenn, I. A.
福尔马林固定石蜡包埋（FFPE）前列腺标本是分子病理学信息的丰富来源。然而，基于FFPE的组织样品微阵列分析可能会受到由于保存程序导致的RNA分子的降解和化学改变的阻碍。在这份报告中，我们采用了探针分析的Affyphase寡核苷酸阵列在个别探针水平，以弥补潜在的损失与受损的mRNA质量在FFPE制剂的基因鉴定。此外，为了提高样本质量，我们利用激光捕获显微切割前列腺肿瘤和良性上皮细胞。值得注意的是，这些方法的组合概括了常见的前列腺癌相关基因表达改变。对前列腺癌相关基因表达改变（如AMACR、激肽释放酶基因家族）和雄激素信号相关基因（如PDEF和STEAP）的鉴定与前列腺癌中先前报道的结果一致。这些数据表明，激光捕获解剖与微阵列数据的计算增强相结合，可能有助于评估FFPE前列腺癌标本中的基因表达变化。
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.