Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA.
Department of Mechanical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA.
Sci Adv. 2024 Nov 22;10(47):eadp1704. doi: 10.1126/sciadv.adp1704.
Molecular alterations in cancerous tissues exhibit intercellular genetic and epigenetic heterogeneity, complicating the performance of diagnostic assays, particularly for early cancer detection. Conventional liquid biopsy methods have limited sensitivity and/or ability to assess epigenetic heterogeneity of rare epiallelic variants cost-effectively. We report an approach, named REM-DREAMing (Ratiometric-Encoded Multiplex Discrimination of Rare EpiAlleles by Melt), which leverages a digital microfluidic platform that incorporates a ratiometric fluorescence multiplex detection scheme and precise digital high-resolution melt analysis to enable low-cost, parallelized analysis of heterogeneous methylation patterns on a molecule-by-molecule basis for the detection of cancer in liquid biopsies. We applied the platform to simultaneously assess intermolecular epigenetic heterogeneity in five methylation biomarkers for improved, blood-based screening for early-stage non-small cell lung cancer. In a cohort of 48 low-volume liquid biopsy specimens from patients with indeterminant pulmonary nodules, we show that assessment of intermolecular methylation density distributions can notably improve the performance of multigene methylation biomarker panels for the early detection of cancer.
癌症组织中的分子改变表现出细胞间遗传和表观遗传异质性，这使得诊断检测变得复杂，尤其是对于早期癌症的检测。传统的液体活检方法的灵敏度有限，并且/或者难以经济有效地评估罕见的表观等位基因变异的表观遗传异质性。我们报告了一种名为 REM-DREAMing（通过熔融比率编码的稀有 epiAlleles 多重区分）的方法，该方法利用数字微流控平台，该平台结合了比率荧光多重检测方案和精确的数字高分辨率熔解分析，能够以低成本、并行的方式对分子水平上的异质甲基化模式进行分析，从而在液体活检中检测癌症。我们应用该平台同时评估了五个甲基化生物标志物的分子间表观遗传异质性，以改善基于血液的早期非小细胞肺癌的筛选。在一个由 48 个来自有不确定肺结节的患者的低容量液体活检标本的队列中，我们表明评估分子间甲基化密度分布可以显著提高多基因甲基化生物标志物组对癌症早期检测的性能。
