Cell-Free Circulating tumor RNA in plasma as a potential prognostic biomarker in Colorectal Cancer

Cell-free RNA (cfRNA) contains a mixture of transcript fragments from different cell types, and its use is gaining traction in clinical fields such as cancer detection. However, the pathophysiological origins of cfRNAs in plasma from CRC patients are not well understood. To identify the tissue-specific contributions of cfRNAs transcriptomic profile, we obtained paired plasma samples from CRC patients who underwent tumor-ablative surgery, followed by deconvoluting the cell type abundance using published single-cell transcriptomics profile. The transcriptomic component from intestinal secretory cells was significantly decreased in the post-surgery plasmas, suggesting the existence of CRC-originating cfRNAs. We further validated the origin of the differentially expressed cfRNAs using tumor and adjacent normal tissue from 49 patients with CRC. HPGD, PACS1 and TDP2 demonstrated consistent differential expression across cfRNA and tissue samples, which supports their potential tumor origin. PACS1 was upregulated, while HPGD and TDP2 were downregulated in pre-surgery plasma samples, and tumor tissues. We further tested the three-gene expression signature using TCGA COAD dataset, and we were able to classify the patients into two groups with significant difference in survival outcome. The three-gene signature (HPGD, PACS1 and TDP2) holds promise in applying to minimal residual disease (MRD) testing, which involves profiling remnants of cancer cells after or during treatment.