Nanopore based RNA methylation profiling of a circulating lung cancer biomarker

The characterisation of circulating nucleic acid biomarkers in liquid biopsy based diagnostics holds great potential to transform the landscape of early cancer detection and screening. In order to overcome the challenges associated with poor sensitivity, these tests are increasingly incorporating information beyond the primary sequence, to include epigenetic, fragmentomic, and other chemical properties to boost performance. RNA, in particular, can be modified with over one hundred different bases at the epitranscriptomic level, offering a rich and currently untapped source of biomarker signal. Here we have developed a method to enable the single molecule methylation profiling of a previously identified lung cancer biomarker ribosomal RNA fragment on the Oxford Nanopore platform. Importantly, we show the differential methylation profile of this blood based RNA fragment between cancer and control patients that may offer additional information for multi-modal liquid biopsies to enable enhanced diagnostic performance.基于液体活检 (liquid biopsy) 的诊断技术中，循环核酸生物标志物 (circulating nucleic acid biomarkers) 的特征分析有望彻底重塑早期癌症检测与筛查的格局。为解决灵敏度不足带来的技术难题，此类检测正愈发多地纳入原始序列之外的信息，涵盖表观遗传 (epigenetic)、片段组学 (fragmentomic) 及其他化学特性，以提升检测性能。尤为值得关注的是，RNA在表观转录组 (epitranscriptomic) 层面可被超过百种不同的碱基修饰，由此形成了丰富且尚未被充分挖掘的生物标志物信号来源。本研究开发了一种可在牛津纳米孔 (Oxford Nanopore) 平台上实现对此前已被鉴定的肺癌生物标志物——核糖体RNA (ribosomal RNA) 片段进行单分子甲基化谱分析的方法。尤为关键的是，本研究证实了该血液来源RNA片段在癌症患者与对照组患者间存在差异甲基化谱，这可为多模态液体活检提供额外信息，助力提升诊断性能。