Unannotated small RNA clusters associated with circulating extracellular vesicles detect early stage liver cancer
Published in Gut, 2022
Recommended citation: Johann Felden, Teresa Garcia-Lezana, Navneet Dogra, Edgar Gonzalez-Kozlova, Mehmet Ahsen, Amanda Craig, Stacey Gifford, Benjamin Wunsch, Joshua Smith, Sungcheol Kim, Jennifer Diaz, Xintong Chen, Ismail Labgaa, Philipp Haber, Reena Olsen, Dan Han, Paula Restrepo, Delia D{\textquoteright}Avola, Gabriela Hernandez-Meza, Kimaada Allette, Robert Sebra, Behnam Saberi, Parissa Tabrizian, Amon Asgharpour, Douglas Dieterich, Josep Llovet, Carlos Cordon-Cardo, Ash Tewari, Myron Schwartz, Gustavo Stolovitzky, Bojan Losic, Augusto Villanueva, "Unannotated small RNA clusters associated with circulating extracellular vesicles detect early stage liver cancer." Gut, 2022. https://gut.bmj.com/content/71/10/2069
1) Unannotated small RNAs in exRNA smRCs have the potential to serve as biomarkers for early cancer detection.
2) A 3-smRC signature showed promising results in detecting HCC, with high sensitivity and specificity.
3) The development of a blood-based, operator-independent clinical tool for HCC surveillance is a significant step forward in cancer diagnostics.
Abstract
[Objective] Surveillance tools for early cancer detection are suboptimal, including hepatocellular carcinoma (HCC), and biomarkers are urgently needed. Extracellular vesicles (EVs) have gained increasing scientific interest due to their involvement in tumor initiation and metastasis; however, most extracellular RNA (exRNA) blood-based biomarker studies are limited to annotated genomic regions. [Design] EVs were isolated with differential ultracentrifugation and integrated nanoscale deterministic lateral displacement arrays (nanoDLD) and quality assessed by electron microscopy, immunoblotting, nanoparticle tracking and deconvolution analysis. Genome-wide sequencing of the largely unexplored small exRNA landscape, including unannotated transcripts, identified and reproducibly quantified small RNA clusters (smRCs). Their key genomic features were delineated across biospecimens and EV isolation techniques in prostate cancer and HCC. Three independent exRNA cancer datasets with a total of 479 samples from 375 patients, including longitudinal samples, were used for this study.Results ExRNA smRCs were dominated by uncharacterised, unannotated small RNA with a consensus sequence of 20 nt. An unannotated 3-smRC signature was significantly overexpressed in plasma exRNA of patients with HCC (p<0.01, n=157). An independent validation in a phase 2 biomarker case's control study revealed 86% sensitivity and 91% specificity for the detection of early HCC from controls at risk (n=209) (area under the receiver operating curve (AUC): 0.87). The 3-smRC signature was independent of alpha-fetoprotein (p<0.0001) and a composite model yielded an increased AUC of 0.93. [Conclusion] These findings directly lead to the prospect of a minimally invasive, blood-only, operator-independent clinical tool for HCC surveillance, thus highlighting the potential of unannotated smRCs for biomarker research in cancer. Data are available in a public, open access repository. RNA-sequencing data have been deposited in the ArrayExpress database at EMBL-EBI (www.ebi.ac.uk/arrayexpress) under accession numbers E-MTAB-8528 and E-MTAB-8529. Code availability statement: all code will be made publicly available at Dr Losic GitHub site.