Extracellular Vesicles Long RNA Sequencing Reveals Abundant mRNA, circRNA, and lncRNA in Human Blood as Potential Biomarkers for Cancer Diagnosis

Abstract

BACKGROUND Extracellular vesicles (EVs) contain a rich cargo of different RNA species with specialized functions and clinical applications. However, the landscape and characteristics of extracellular vesicle long RNA (exLR) in human blood remain largely unknown. METHODS We presented an optimized strategy for exLR sequencing (exLR-seq) of human plasma. The sample cohort included 159 healthy individuals, 150 patients with cancer (5 cancer types), and 43 patients with other diseases. Bioinformatics approaches were used to analyze the distribution and features of exLRs. Support vector machine algorithm was performed to construct the diagnosis classifier, and diagnostic efficiency was evaluated by ROC analysis. RESULTS More than 10000 exLRs, including mRNA, circRNA, and lncRNA, were reliably detected in each exLR-seq sample from 1–2 mL of plasma. We observed that blood EVs contain a substantial fraction of intact mRNAs and a large number of assembling spliced junctions; circRNA was also enriched in blood EVs. Interestingly, blood exLRs reflected their tissue origins and the relative fractions of different immune cell types. Additionally, the exLR profile could distinguish patients with cancer from healthy individuals. We further showed that 8 exLRs can serve as biomarkers for hepatocellular carcinoma (HCC) diagnosis with high diagnostic efficiency in training [area under the curve (AUC) = 0.9527; 95% CI, 0.9170–0.9883], validation cohort (AUC = 0.9825; 95% CI, 0.9606–1), and testing cohort (AUC = 0.9627; 95% CI, 0.9263–0.9991). CONCLUSIONS In summary, this study revealed abundant exLRs in human plasma and identified diverse specific markers potentially useful for cancer diagnosis.

Exosomal circular RNA sorting mechanisms and their function in promoting or inhibiting cancer (Review)

“…Recently, researchers demonstrated that human plasma is rich in mRNA, circRNA and lncRNA via EV long RNA sequencing (exLR-Seq), and these RNAs may be useful as biomarkers for tumour diagnosis and prognosis. The aforementioned study reported that 8 exLRs may be used as diagnostic biomarkers, having utility beyond the current diagnostic approaches (such as α-feto protein) for hepatocellular carcinoma (HCC), with high sensitivity and specificity (84). These findings have crucial functional and clinical implications.…”

Identification and analysis of long non-coding RNAs that are involved in inflammatory process in response to transmissible gastroenteritis virus infection

“…LncRNAs can serve as scaffold to bind to different types of proteins or transcription factors at specific domains to activate or inhibit gene transcription. LncRNA H19 decreases the transcriptional activity of p53 [30]. LncRNA SNHG10 facilitates hepatocarcinogenesis and metastasis by modulating its homolog Small Cajal body-specific RNA 13 (SCARNA13) [31].…”

Tumor‐Specific Transcripts Are Frequently Expressed in Hepatocellular Carcinoma With Clinical Implication and Potential Function

“…We showed that human blood exosomes (or extracellular vesicles [EVs]) contain an abundance of long RNA species . We speculated that TSTs may be sorted into EVs and exist in the blood of patients with HCC.…”