PO.CL01.08 · 临床研究

用于检测血浆中游离转移性前列腺癌DNA的甲基化基因panel的开发

Development of a methylated gene panel for detection of cell-free, metastatic prostate cancer DNA in plasma

编号 2587 展板 6 时间 4/20 09:00–12:00 区域 Section 46 主讲 Gang Yu, MD;MS;PhD

分会场 Liquid Biopsies: Circulating Nucleic Acids 2

该海报暂无可下载的资料 AACR 官方页面

作者与单位 Authors & Affiliations

Gang Yu¹, Mary Jo Fackler¹, Liqun Zhang¹, Wenfei Xia¹, Roshni Saravanan¹, Ezra Baraban², Eunice Van Den Berg³, Adam Botha³, Pamela Michelow³, Reubina Wadee³, Maureen Joffe⁴, Wenlong Carl Chen⁴, Thomas Pisanic⁵, Michelle Petri⁶, Jun Luo⁷, Channing Paller¹, Samuel Denmeade¹, Leslie Cope¹, Saraswati Sukumar¹

¹Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD,²Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD,³Department of Anatomical Pathology, University of the Witwatersrand/National Health Laboratory Service, Johannesburg, South Africa,⁴Strengthening Oncology Services Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa,⁵Johns Hopkins University School of Medicine, Baltimore, MD,⁶Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD,⁷Brady Urological Institute, Johns Hopkins University School of Medicine, Baltimore, MD

摘要 Abstract

中文摘要

目的：我们旨在开发一种高灵敏度、可重复的游离甲基化DNA检测方法，以准确检测血浆中的转移性前列腺癌（mPCa）。实验设计：我们在TCGA前列腺腺癌（PRAD）450K DNA甲基化数据中鉴定了一个新的10标志物panel，用于准确检测PCa。标志物的灵敏度和特异度在两个独立的公共前列腺癌数据集（GSE112047、GSE76938）中得到验证。整合这些标志物的定量多重甲基化特异性PCR（QM-MSP）检测方法在来自美国（US，61例癌症，26例良性）和南非（SA，80例癌症，24例良性）的存档良性和前列腺癌组织中得到验证。我们对该10标志物panel使用了一种新开发的游离多重甲基化特异性PCR（cf-MMSP）检测方法。测定内和操作者内可重复性检测测试了其稳健性。cf-MMSP的性能在训练集（40例良性，40例癌症）和一个独立的测试集（19例良性，20例癌症）血浆样本中进行评估。采用Shapley值回归对cf-MMSP检测中10个基因的性能进行排序。我们基于其高性能选择了一个5基因panel。所用统计方法包括用于ROC分析的Youden指数阈值和Kruskal-Wallis检验。结果：在组织中，10基因panel检测到了前列腺癌的所有分期：在美国组织样本（n=87）中，我们实现了ROC AUC = 1.00（CI. 0.99 - 1.00），灵敏度98.36%（CI. 91.28 - 99.91），特异度100.00%（CI. 87.13 - 100.00）；在SA样本（n=104）中，ROC AUC为0.99（CI. 0.99 - 1.00），灵敏度98.28%（CI. 90.86 - 99.91），特异度100.00%（CI. 86.20 - 100.00）。cf-MMSP测定内测试显示低CV（各拷贝水平范围为1.70-5.70%）和强线性（R² = 0.93）。操作者内测试显示出色的可重复性，ICC为0.99。在血浆中，训练集里，10基因panel在区分mPCa与良性方面显示ROC AUC为0.89（CI. 0.81-0.97），灵敏度75.00%（CI. 59.81 - 85.81），特异度93.88%（CI: 83.48 - 97.90）。在测试集中，该检测的ROC AUC为0.91（CI. 0.80 -1.00），灵敏度85.00%（CI. 63.96 - 94.76），特异度93.88%（CI. 83.48 - 97.90）。使用标准化Shapley值截断值0.07，我们鉴定出五个性能最佳的基因——HAAO、DLEC1、FBN1、TMEM155和RTDR1。在血浆训练集中，精简的5基因panel子集显示ROC AUC为0.92（CI. 0.84 - 0.99），灵敏度90.00%（CI. 76.95 - 96.04），特异度90.00%（CI. 76.95 - 96.04）。在测试集中，该5基因panel实现ROC AUC为0.92（CI. 0.84 - 0.99），灵敏度90.00%（CI. 80.00 - 100.00），特异度84.20%（CI. 53.00 - 100.00）。结论：5基因cf-MMSP panel在检测血浆中mPCa方面显示出强劲的性能指标。该检测方法在广泛可及的早期检测和疾病监测方面显示出潜力，可用于mPCa的分子管理。

查看英文原文 English abstract

Purpose: We sought to develop a highly sensitive, reproducible cell-free methylated DNA assay for accurately detecting metastatic prostate cancer (mPCa) in plasma. Experimental Design: We identified a new 10-marker panel for accurate detection of PCa in the TCGA prostate adenocarcinoma (PRAD) 450K DNA methylation data. Marker sensitivity and specificity were verified in two independent public prostate cancer datasets (GSE112047, GSE76938). A quantitative multiplex methylation-specific PCR (QM-MSP) assay incorporating these markers was validated in archival benign and prostate cancer tissues from the United States (US, 61 cancer, 26 benign) and South Africa (SA, 80 cancer, 24 benign). We used a newly developed cell-free multiplex methylation-specific PCR (cf-MMSP) assay for the 10-marker panel. Intra-assay and intra-operator reproducibility assays tested its robustness. cf-MMSP performance was assessed in a Training set (40 benign, 40 cancer), and an independent Test set (19 benign, 20 cancer) of plasma. Shapley value regression was used to rank performance of the 10 genes in the cf-MMSP assay. We selected a 5-gene panel based on their high performance . Statistical methods used included the Youden index threshold for ROC analysis and Kruskal-Wallis tests. Results: In tissues, the 10-gene panel detected all stages of prostate cancer: In tissue from the US (n=87), we achieved ROC AUC = 1.00 (CI. 0.99 - 1.00), sensitivity of 98.36% (CI. 91.28 - 99.91) and specificity of 100.00% (CI. 87.13 - 100.00); in SA samples (n=104), ROC AUC was 0.99 (CI. 0.99 - 1.00), sensitivity of 98.28% (CI. 90.86 - 99.91), and specificity of 100.00% (CI. 86.20 - 100.00). cf-MMSP intra-assay test showed low CVs (1.70-5.70% across copy levels) and strong linearity (R² = 0.93). The intra-operator test showed excellent reproducibility, with an ICC of 0.99. In plasma, in the training set, the 10-gene panel showed ROC AUC of 0.89 (CI. 0.81-0.97), sensitivity of 75.00% (CI. 59.81 - 85.81) and specificity of 93.88% (CI: 83.48 - 97.90) in distinguishing mPCa from benign. In the test set, the assay performed with ROC AUC of 0.91 (CI. 0.80 -1.00), sensitivity of 85.00% (CI. 63.96 - 94.76), and specificity of 93.88% (CI. 83.48 - 97.90). Using a standardized Shapley value cutoff of 0.07, we identified the five best-performing genes- HAAO, DLEC1, FBN1, TMEM155 and RTDR1. In the training set of plasma, the refined 5-gene panel subset showed ROC AUC of 0.92 (CI. 0.84 - 0.99), sensitivity of 90.00% (CI. 76.95 - 96.04) and specificity of 90.00% (CI. 76.95 - 96.04). In the test set, this 5-gene panel achieved ROC AUC of 0.92 (CI. 0.84 - 0.99), with a sensitivity of 90.00% (CI. 80.00 - 100.00) and a specificity of 84.20% (CI. 53.00 - 100.00). Conclusions: The 5-gene cf-MMSP panel showed strong performance indices in detecting mPCa in plasma. The assay shows potential for broadly accessible early detection and disease monitoring for molecular management of mPCa.

利益披露 Disclosure

G. Yu, None.. M. Fackler, None.. L. Zhang, None.. W. Xia, None.. R. Saravanan, None.. E. Baraban, None.. E. Berg, None.. A. Botha, None.. P. Michelow, None.. R. Wadee, None.. M. Joffe, None.. W. Chen, None.. T. Pisanic, None.. M. Petri, None.. J. Luo, None.. C. Paller, None.. S. Denmeade, None.. L. Cope, None.. S. Sukumar, None.

← 返回 AACR 2026 检索