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.

无细胞RNA（cell-free RNA, cfRNA）包含源自不同细胞类型的混合转录本片段，其在癌症检测等临床领域的应用正日益受到关注。然而，结直肠癌（Colorectal Cancer, CRC）患者血浆中cfRNA的病理生理起源尚未得到充分阐明。为明确cfRNA转录组谱的组织特异性贡献，我们招募了接受肿瘤切除手术的结直肠癌患者，获取其配对血浆样本，随后借助已发表的单细胞转录组谱对细胞类型丰度进行反卷积分析。结果显示，肠道分泌细胞来源的转录组组分在术后血浆中显著降低，这提示了结直肠癌来源cfRNA的存在。我们进一步利用49名结直肠癌患者的肿瘤组织及癌旁正常组织，对差异表达cfRNA的起源进行了验证。HPGD、PACS1与TDP2在cfRNA样本及组织样本中均表现出一致的差异表达，这支持了它们的潜在肿瘤起源特性：术前血浆样本与肿瘤组织中，PACS1呈上调表达，而HPGD与TDP2呈下调表达。我们还通过癌症基因组图谱（The Cancer Genome Atlas, TCGA）结肠腺癌（Colon Adenocarcinoma, COAD）数据集对该三基因表达特征进行了测试，成功将患者分为生存结局存在显著差异的两个组别。该三基因特征（HPGD、PACS1与TDP2）有望应用于微小残留病（minimal residual disease, MRD）检测，即用于分析治疗期间或治疗后残留的癌细胞谱型。