用于福尔马林固定石蜡包埋组织生物标志物发现的高多重SRM分析方法的开发

Development of a Highly Multiplexed SRM Assay for Biomarker Discovery in Formalin-Fixed Paraffin-Embedded Tissues.

作者信息

Steiner Carine, Lescuyer Pierre, Tille Jean-Christophe, Cutler Paul, Ducret Axel

机构信息

Division of Laboratory Medicine, Geneva University Hospitals, Geneva, Switzerland.

Biomarkers, Bioinformatics and Omics, Pharmaceutical Sciences, Roche Pharma Research & Early Development (pRED), Roche Innovation Center Basel, F. Hoffmann-La Roche AG, Basel, Switzerland.

出版信息

Methods Mol Biol. 2019;1959:185-203. doi: 10.1007/978-1-4939-9164-8_13.

DOI:10.1007/978-1-4939-9164-8_13

PMID:30852824

Abstract

The search for novel and clinically relevant biomarkers still represents a major clinical challenge and mass-spectrometry-based technologies are essential tools to help in this process. In this application, we demonstrate how selected reaction monitoring (SRM) can be applied in a highly multiplexed way to analyze formalin-fixed paraffin-embedded (FFPE) tissues. Such an assay can be used to analyze numerous samples for narrowing down a list of potential biomarkers to the most relevant candidates. The use of FFPE tissues is of high relevance in this context as large sample collections linked with valuable clinical information are available in hospitals around the world. Here we describe in detail how we proceeded to develop such an assay for 200 proteins in breast tumor FFPE tissues. We cover the selection of suitable peptides, which are different in FFPE compared to fresh frozen tissues and show how we deliberately biased our assay toward proteins with a high probability of being measurable in human clinical samples.

摘要

寻找新型且具有临床相关性的生物标志物仍然是一项重大的临床挑战，而基于质谱的技术是助力这一过程的重要工具。在本应用中，我们展示了如何以高度多重化的方式应用选择反应监测（SRM）来分析福尔马林固定石蜡包埋（FFPE）组织。这样的检测方法可用于分析大量样本，以便将潜在生物标志物列表缩小到最相关的候选物。在这种情况下，使用FFPE组织具有高度相关性，因为世界各地的医院都有与宝贵临床信息相关联的大量样本。在此，我们详细描述了我们如何着手为乳腺肿瘤FFPE组织中的200种蛋白质开发这样一种检测方法。我们涵盖了合适肽段的选择，这些肽段在FFPE组织中与新鲜冷冻组织不同，并展示了我们如何有意使检测偏向于在人类临床样本中具有高可测性的蛋白质。