Whole transcriptome profiling of liquid biopsies from tumour xenografted mouse models enables specific monitoring of tumour-derived extracellular RNA

While cell-free DNA (cfDNA) is widely being investigated, free circulating RNA (extracellular RNA, exRNA) has the potential to improve cancer therapy response monitoring and detection due to its dynamic nature. However, it remains unclear in which blood subcompartment tumour-derived exRNAs primarily reside. We developed a host-xenograft deconvolution framework, exRNAxeno, with mapping strategies to either a combined human-mouse reference genome or both species genomes in parallel, applicable to exRNA sequencing data from liquid biopsies of human xenograftmousemodels. The tool enables to distinguish (human) tumoural RNA from (murine) host RNA, to specifically analyse tumour-derived exRNA. We applied the combined pipeline to total exRNA sequencing data from 95 blood-derived liquid biopsy samples from 30 mice, xenografted with 11 different tumours. Tumoural exRNA concentrations are not determined by plasma platelet levels, while host exRNA concentrations increase with platelet content. Furthermore, a large variability in exRNA abundance and transcript content across individual mice is observed. The tumoural gene detectability in plasma is largely correlated with the RNA expression levels in the tumour tissue or cell line. These findings unravel new aspects of tumour-derived exRNA biology in xenograftmodels and open new avenues to further investigate the role of exRNA in cancer.

Automated summary

This study developed a deconvolution framework to distinguish tumor-derived extracellular RNA (exRNA) from host RNA. Analysis of liquid biopsy samples from mice revealed that tumor-derived exRNA concentrations were not determined by plasma platelet levels, while host exRNA concentrations increased with platelet content. Additionally, there was a large variability in exRNA abundance and transcript content across individual mice. The detectability of tumor genes in plasma was largely correlated with RNA expression levels in the tumor tissue or cell line.