Non-coding RNAs as liquid biopsy biomarkers in cancer

Abstract

Although non-coding RNAs have long been considered as non-functional "junk" RNAs, accumulating evidence in the past decade indicates that they play a critical role in pathogenesis of various cancers. In addition to their biological significance, the recognition that their expression levels are frequently dysregulated in multiple cancers have fueled the interest for exploiting their clinical potential as cancer biomarkers. In particular, microRNAs (miRNAs), a subclass of small non-coding RNAs that epigenetically modulate gene-transcription, have become one of the most well-studied substrates for the development of liquid biopsy biomarkers for cancer patients. The emergence of high-throughput sequencing technologies has enabled comprehensive molecular characterisation of various non-coding RNA expression profiles in multiple cancers. Furthermore, technological advances for quantifying lowly expressed RNAs in the circulation have facilitated robust identification of previously unrecognised and undetectable biomarkers in cancer patients. Here we summarise the latest progress on the utilisation of non-coding RNAs as non-invasive cancer biomarkers. We evaluated the suitability of multiple non-coding RNA types as blood-based cancer biomarkers and examined the impact of recent technological breakthroughs on the development of non-invasive molecular biomarkers in cancer.

Fig. 1. An overview of blood-based noncoding RNA cancer biomarker development.

(Top) Biospecimen collection and serum/plasma processing. Various types of noncoding RNAs can be found in cell free component of peripheral blood. (Middle) Sample processing and data analysis. cDNA and sequencing libraries are prepared from serum/plasma samples. Targets can be quantified by qPCR or next generation sequencing (NGS). Data are subsequently analysed and bioinformatic processes are utilised. Genes that are differentially expressed between cancer patients and healthy controls are identified (for cancer diagnostic biomarkers) and diagnostic classifiers are developed, and tissue and cancer specificities are assessed. (Bottom) Clinical applications of ncRNA biomarkers. The biomarkers can be utilised in various applications including: Cancer screening and identifying patients that are most likely to respond to a therapeutic agent.

Fig. 2. Molecular biomarker types in cancer.

A list of molecular biomarker types. (Right) Circulating DNA: DNA biomarkers can range from mutation, amplification, deletion and DNA methylation. (Centre-bottom) Circulating RNA: Circulating RNA is primarily divided into coding RNA (messenger RNA) and non-coding RNA (such as miRNAs and lncRNAs). RNAs can also exist as circular RNAs (both variants of coding and non-coding RNAs exist). In addition, RNAs are present in extracellular vesicles such as exosomes. (Centre-left) Circulating tumour cells: Circulating tumour cells can be identified using surface proteins. Furthermore, once isolated, genomic and transcriptomic profile can be examined. (Left) Protein markers have been widely utilised as cancer biomarkers. Proteins exist as free forms or within extracellular vesicles. Improvements in high-through put protein profiling may rejuvenate blood-based cancer protein biomarkers.