Abstract

Despite significant progress in targeted therapies, cancer recurrence remains a major cause of mortality worldwide. Identification of accurate biomarkers, through molecular profiling in healthy and cancer patient samples, will improve diagnosis and promote personalized medicine. While genetic and epigenetic alterations of DNA are currently exploited as cancer biomarkers, their robustness is limited by tumor heterogeneity. Recently, cancer-associated changes in RNA marks have emerged as a promising source of diagnostic and prognostic biomarkers. RNA epigenetics (also known as epitranscriptomics) is an emerging field in which at least 150 chemical modifications in all types of RNA (mRNA, tRNA, lncRNA, rRNA, and microRNA) have been detected. These modifications fine-tune gene expression in both physiological and pathological processes. A growing number of studies have established links between specific modified nucleoside levels in solid/liquid biopsies, and cancer onset and progression. In this review, we highlight the potential role of epitranscriptomic markers in refining cancer diagnosis and/or prognosis. RNA modification patterns may contain important information for establishing an initial diagnosis, monitoring disease evolution, and predicting response to treatment. Furthermore, recent developments in mass spectrometry allow reliable quantification of RNA marks in solid biopsies and biological fluids. We discuss the great potential of mass spectrometry for identifying epitranscriptomic biomarker signatures in cancer diagnosis. While there are various methods to quantify modified nucleosides, most are unable to detect and quantify more than one type of RNA modification at a time. Mass spectrometry analyses, especially GC-MS/MS and LC-MS/MS, overcome this limitation and simultaneously detect modified nucleosides by multiple reaction monitoring. Indeed, several groups are currently validating mass spectrometry methods that quantify several nucleosides at one time in liquid biopsies. The challenge now is to exploit these powerful analytical tools to establish epitranscriptomic signatures that should open new perspectives in personalized medicine. This review summarizes the growing clinical field of analysis of RNA modifications and discusses pre-analytical and analytical approaches, focusing in particular on the development of new mass spectrometry tools and their clinical applications.

摘要

尽管靶向治疗取得了重大进展，但癌症复发仍然是全世界死亡的主要原因。通过对健康和癌症患者样本进行分子分析，识别准确的生物标志物将改善诊断并促进个性化医疗。虽然 DNA 的遗传和表观遗传改变目前被用作癌症生物标志物，但它们的稳健性受到肿瘤异质性的限制。最近，与癌症相关的 RNA 标记变化已成为诊断和预后生物标记的有希望的来源。RNA 表观遗传学（也称为表观转录组学）是一个新兴领域，其中已检测到所有类型的 RNA（mRNA、tRNA、lncRNA、rRNA 和 microRNA）中至少有 150 种化学修饰。这些修饰在生理和病理过程中微调基因表达。越来越多的研究已经建立了固体/液体活检中特定修饰核苷水平与癌症发病和进展之间的联系。在这篇综述中，我们强调了表观转录组标记在完善癌症诊断和/或预后中的潜在作用。RNA 修饰模式可能包含用于建立初步诊断、监测疾病演变和预测治疗反应的重要信息。此外，质谱技术的最新发展允许对固体活检和生物体液中的 RNA 标记进行可靠的量化。我们讨论了质谱在癌症诊断中识别表观转录组生物标志物特征的巨大潜力。虽然有多种方法可以量化修饰的核苷，大多数人无法一次检测和量化一种以上的 RNA 修饰。质谱分析，尤其是 GC-MS/MS 和 LC-MS/MS，克服了这一限制，并通过多反应监测同时检测修饰的核苷。事实上，目前有几个小组正在验证质谱方法，这些方法可以在液体活检中一次量化几种核苷。现在的挑战是利用这些强大的分析工具来建立表观转录组学特征，从而为个性化医疗开辟新的前景。这篇综述总结了不断发展的 RNA 修饰分析临床领域，并讨论了预分析和分析方法，特别关注新质谱工具的开发及其临床应用。特别是 GC-MS/MS 和 LC-MS/MS，克服了这一限制，通过多反应监测同时检测修饰的核苷。事实上，目前有几个小组正在验证质谱方法，这些方法可以在液体活检中一次量化几种核苷。现在的挑战是利用这些强大的分析工具来建立表观转录组学特征，从而为个性化医疗开辟新的前景。这篇综述总结了不断发展的 RNA 修饰分析临床领域，并讨论了预分析和分析方法，特别关注新质谱工具的开发及其临床应用。特别是 GC-MS/MS 和 LC-MS/MS，克服了这一限制，通过多反应监测同时检测修饰的核苷。事实上，目前有几个小组正在验证质谱方法，这些方法可以在液体活检中一次量化几种核苷。现在的挑战是利用这些强大的分析工具来建立表观转录组学特征，从而为个性化医疗开辟新的前景。这篇综述总结了不断发展的 RNA 修饰分析临床领域，并讨论了预分析和分析方法，特别关注新质谱工具的开发及其临床应用。几个小组目前正在验证在液体活检中一次量化几种核苷的质谱方法。现在的挑战是利用这些强大的分析工具来建立表观转录组学特征，从而为个性化医疗开辟新的前景。这篇综述总结了不断发展的 RNA 修饰分析临床领域，并讨论了预分析和分析方法，特别关注新质谱工具的开发及其临床应用。几个小组目前正在验证在液体活检中一次量化几种核苷的质谱方法。现在的挑战是利用这些强大的分析工具来建立表观转录组学特征，从而为个性化医疗开辟新的前景。这篇综述总结了不断发展的 RNA 修饰分析临床领域，并讨论了预分析和分析方法，特别关注新质谱工具的开发及其临床应用。