Extracellular RNAs as potential biomarkers for cancer

Abstract

The discovery that all cells secrete extracellular vesicles (EVs) to shuttle proteins and nucleic acids to recipient cells suggested they play an important role in intercellular communication. EVs are widely distributed in many body fluids, including blood, cerebrospinal fluid, urine and saliva. Exosomes are nano-sized EVs of endosomal origin that regulate many pathophysiological processes including immune responses, inflammation, tumour growth, and infection. Healthy individuals release exosomes with a cargo of different RNA, DNA, and protein contents into the circulation, which can be measured non-invasively as biomarkers of healthy and diseased states. Cancer-derived exosomes carry a unique set of DNA, RNA, protein and lipid reflecting the stage of tumour progression, and may serve as diagnostic and prognostic biomarkers for various cancers. However, many gaps in knowledge and technical challenges in EVs and extracellular RNA (exRNA) biology, such as mechanisms of EV biogenesis and uptake, exRNA cargo selection, and exRNA detection remain. The NIH Common Fund-supported exRNA Communication Consortium was launched in 2013 to address major scientific challenges in this field. This review focuses on scientific highlights in biomarker discovery of exosome-based exRNA in cancer and its possible clinical application as cancer biomarkers.

Keywords: Extracellular vesicles; biomarker; cancer; exosomes; extracellular RNA; liquid biopsy.

Figure 1.

A schematic diagram showing exRNA types predominantly found in a representative set of human biofluids. miRNA: microRNA; piRNA: piwi-interacting RNA; tRF: tRNA-derived RNA fragments

Figure 2.

A schematic diagram showing the biogenesis pathway of microvesicles and exosomes. Microvesicles are formed by direct budding from the plasma membrane and are capable of encapsulating multiple forms of molecular cargo including proteins and nucleic acids. The biogenesis of exosomes begins with internalization of the cell membrane leading to the formation of early endosomes. Intraluminal vesicles (ILVs) are formed by the inward invagination of endosomal membranes, resulting in the formation of multivesicular bodies (MVBs). During this process, cytosolic constituents, including nucleic acids and proteins, can be sorted into ILVs. Upon fusion of MVBs with the plasma membrane, ILVs are released as exosomes into the extracellular milieu. Exosomes can include many different types of exRNA as listed in Table 1. ER: endoplasmic reticulum; MLV: multivesicular body; ILV: intraluminal vesicle; miRNA: microRNA; piRNA: piwi-interacting RNA; tRF: tRNA-derived RNA fragments; snoRNA: small nucleolar RNA; lncRNA: long non-coding RNA

Figure 3.

Current clinical studies evaluating the use of exRNA and exosomes as cancer biomarkers. An advanced search for query terms (“extracellular RNA” OR exosome OR exRNA OR oncosome) AND biomarker focused on cancer as a disease model, was performed on ClinicalTrials.gov on 11 May 2020. The search was restricted to recruitment statuses on recruiting, not yet recruiting, active, not recruiting, completed, enrolling by invitation, and studies of unknown status. The search returned 45 studies which are summarized in Figures 3A–C. A: A world map shows the locations (in red) of all clinical studies evaluating the use of exRNA and exosomes as cancer biomarkers. The numbers indicate the clinical studies in each location; B: clinical trials were grouped by general cancer type and the number of studies focused on each cancer type are shown. Projects that did not specify cancer type were grouped together as non-specific cancer; C: the clinical trial data was parsed for the types of biofluids used in each study. Some studies examined multiple types of biofluids while other did not include biofluid sampling. The table represents biofluids examined in all 45 clinical studies

Figure 3.

Current clinical studies evaluating the use of exRNA and exosomes as cancer biomarkers. An advanced search for query terms (“extracellular RNA” OR exosome OR exRNA OR oncosome) AND biomarker focused on cancer as a disease model, was performed on ClinicalTrials.gov on 11 May 2020. The search was restricted to recruitment statuses on recruiting, not yet recruiting, active, not recruiting, completed, enrolling by invitation, and studies of unknown status. The search returned 45 studies which are summarized in Figures 3A–C. A: A world map shows the locations (in red) of all clinical studies evaluating the use of exRNA and exosomes as cancer biomarkers. The numbers indicate the clinical studies in each location; B: clinical trials were grouped by general cancer type and the number of studies focused on each cancer type are shown. Projects that did not specify cancer type were grouped together as non-specific cancer; C: the clinical trial data was parsed for the types of biofluids used in each study. Some studies examined multiple types of biofluids while other did not include biofluid sampling. The table represents biofluids examined in all 45 clinical studies

Figure 4.

NIH supported research focused on exRNA and exosomes as cancer biomarkers. An advanced text search for (“extracellular RNA” OR exosome OR exRNA OR oncosome) AND cancer AND biomarker was performed on NIH RePORTER (https://projectreporter.nih.gov/reporter.cfm) on 9 May 2020. The text search was limited to project abstracts, project title, and project terms, and was focused on new awards only (excluding subprojects), funded by any NIH Institute or Center from 2010–2020. The search returned 138 projects, which are summarized in Figures 4A and B. A: NIH funded projects were grouped by general funding types; B: NIH funded projects were grouped by general cancer type and the number of projects focused on each cancer type are shown. Projects that did not specify cancer type were grouped together as non-specific cancer