Custom long non-coding RNA capture enhances detection sensitivity in different human sample types

Long non-coding RNAs (lncRNAs) are a heterogeneous group of transcripts that lack protein coding potential and display regulatory functions in various cellular processes. As a result of their cell- and cancer-specific expression patterns, lncRNAs have emerged as potential diagnostic and therapeutic targets. The accurate characterization of lncRNAs in bulk transcriptome data remains challenging due to their low abundance compared to protein coding genes. To tackle this issue, we describe a unique short-read custom lncRNA capture sequencing approach that relies on a comprehensive set of 565,878 capture probes for 49,372 human lncRNA genes. This custom lncRNA capture approach was evaluated on various sample types ranging from artificial high-quality RNA mixtures to more challenging formalin-fixed paraffin-embedded tissue and biofluid material. The custom enrichment approach allows the detection of a more diverse repertoire of lncRNAs, with better reproducibility and higher coverage compared to classic total RNA-sequencing.

长链非编码核糖核酸（long non-coding RNAs，简称lncRNAs）是一类异质性转录本，不具备蛋白质编码潜能，且在多种细胞进程中发挥调控功能。鉴于其细胞特异性与癌症特异性的表达模式，lncRNAs已成为潜在的诊断与治疗靶点。然而，相较于蛋白质编码基因，lncRNAs在批量转录组数据中丰度较低，因此对其进行精准表征仍面临挑战。为解决这一问题，本研究介绍了一种独特的短读长定制化lncRNA捕获测序方法，该方法依托针对49372个人类lncRNA基因设计的565878条全面覆盖的捕获探针。该定制化富集方法在多种样本类型中完成了性能评估，样本范围涵盖人工高质量RNA混合物，以及难度更高的福尔马林固定石蜡包埋组织与生物流体样本。相较于经典的全转录组RNA测序，该方法可检测到更多样化的lncRNA转录本库，且具备更优的重复性与更高的测序覆盖度。