Discovery and qualification of transcriptomic biomarkers for the early detection of aggressive prostate cancer

项目摘要 该申请建议成立密歇根大学（UM）EDRN生物标志物开发实验室 （BDL）。通过之前的EDRN BDL，我们的团队已经描述了多种重要的前列腺癌 生物标志物，最显著的是TMPRSS 2-ETS基因融合。通过与EDRN临床 验证中心（CVC; Dr. Sanda PI），我们已经开发、验证和临床实施了Mi-前列腺 评分（MiPS），一种前列腺癌早期检测测试，包括两种前列腺癌的尿液定量 特异性转录物TMPRSS 2：ERG基因融合和PCA 3与血清PSA。在我们的CLIA中引入 作为一个实验室（现在已获得纽约州的批准），MiPS有助于在PSA测试后进行共同决策 基于个体化的侵袭性前列腺癌活检风险预测。在这里，利用这项工作作为一个 模型，我们将发现和表征侵袭性前列腺癌转录组学生物标志物，重点是 长链非编码RNA（lncRNA）。虽然lncRNA生物标志物的效用在很大程度上尚未开发，但我们最近 表征了lncRNA纲要（“MiTranscriptome”），鉴定了几种前列腺癌特异性和 侵袭性前列腺癌特异性lncRNAs为了支持我们提出的方法，我们进行了初步的 lncRNA SChLAP 1作为组织中侵袭性前列腺癌特异性生物标志物的验证。同样地， 我们开发了基于RT-PCR的下一代测序（NGS）面板，能够定量 存档组织和尿液中的多重转录组学生物标志物。在这里，在三个目标，我们将提名和 开发转录组学生物标志物作为诊断时和诊断前侵袭性前列腺癌的预测因子。 在目标1中，我们将从我们的研究中鉴定新的侵袭性前列腺癌相关的转录组学改变。 MiTranscriptome分析。我们将开发单基因和多重NGS检测来研究这些 lncRNA/编码转录物作为侵袭性前列腺癌特异性生物标志物。在目标2中， 作为基于组织的侵袭性前列腺癌生物标志物。继我们之前的 方法与SChLAP 1，我们将开发个人原位杂交检测和多重NGS面板 以在充分表征的前列腺癌组织组群中表征这些转录物。在目标3中，我们 将目标1中鉴定的转录物表征为非侵入性的、基于尿的侵袭性前列腺癌早期 检测生物标志物。通过与Hologic/Gen-Probe（我们的MiPS行业合作伙伴）的合作，我们将 使用我们的平台开发和评估单个优先生物标志物的性能 生物库的尿样此外，使用多路复用NGS，我们还将表征 转录组学生物标志物组作为替代/补充方法。正如EDRN所承认的那样， 迫切需要新的侵袭性前列腺癌特异性生物标志物。重要的是，我们的方法扩展了 除了前列腺癌和我们的BDL，我们的团队积极参与了EDRN生物标志物的研究， 并期望继续与其他BDL和CVC合作，以促进整个EDRN使命。

Project Summary This application proposes the formation of a University of Michigan (UM) EDRN Biomarker Development Lab (BDL). Through previous EDRN BDLs, our team has characterized multiple important prostate cancer biomarkers, most notably TMPRSS2-ETS gene fusions. Through collaboration with an EDRN Clinical Validation Center (CVC; Dr. Sanda PI), we have developed, validated and clinically implemented Mi-Prostate Score (MiPS), a prostate cancer early detection test incorporating urine quantification of two prostate cancer specific transcripts—the TMPRSS2:ERG gene fusion and PCA3—with serum PSA. Introduced in our CLIA laboratory (and now with New York State approval), MiPS helps shared decision making after PSA testing based on individualized risk predictions of aggressive prostate cancer on biopsy. Here, using this work as a model, we will discover and characterize aggressive prostate cancer transcriptomic biomarkers, focusing on long non-coding RNAs (lncRNAs). Although lncRNA biomarker utility has been largely unexplored, we recently characterized the lncRNA compendium (“MiTranscriptome”), identifying several prostate cancer-specific and aggressive prostate cancer-specific lncRNAs. Supporting our proposed approach, we have performed initial validation of the lncRNA SChLAP1 as an aggressive prostate cancer specific biomarker in tissues. Likewise, we have developed RT-PCR based next generation sequencing (NGS) panels capable of quantifying multiplexed transcriptomic biomarkers in archived tissue and urine. Here, in three Aims, we will nominate and develop transcriptomic biomarkers as predictors of aggressive prostate cancer both at and prior to diagnosis. In Aim 1, we will identify novel aggressive prostate cancer-associated transcriptomic alterations from our MiTranscriptome analysis. We will develop single gene and multiplexed NGS assays to study these lncRNAs/coding transcripts as aggressive prostate cancers specific biomarkers. In Aim 2 we will characterize transcripts from Aim 1 as tissue based aggressive prostate cancer biomarkers. Following our previous approach with SChLAP1, we will develop individual in situ hybridization assays and a multiplexed NGS panel to characterize these transcripts in well characterized prostate cancer tissue cohorts. In Aim 3, we will characterize transcripts identified in Aim 1 as non-invasive, urine-based aggressive prostate cancer early detection biomarkers. Through collaboration with Hologic/Gen-Probe (our industry partner on MiPS), we will develop and assesses the performance of individual prioritized biomarkers using their platform on our biobanked urine samples. Additionally, using multiplexed NGS, we will also characterize the performance of a panel of transcriptomic biomarkers as an alternative/complementary approach. As recognized by the EDRN, novel aggressive prostate cancer specific biomarkers are urgently needed. Importantly, our approach extends beyond prostate cancer and our BDL, and our group has actively participated in the EDRN biomarker community and anticipates continuing work with other BDLs and CVCs to facilitate the overall EDRN mission.