A comprehensive evaluation of full-spectrum cell-free RNAs highlights cell-free RNA fragments for early-stage hepatocellular carcinoma detection.
A comprehensive evaluation of full-spectrum cell-free RNAs highlights cell-free RNA fragments for early-stage hepatocellular carcinoma detection.
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DOI：
10.1016/j.ebiom.2023.104645
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发表时间：
2023-07
期刊：
影响因子：
11.1
通讯作者：
Yin, Jianhua
中科院分区：
文献类型：
--
作者：
Ning, Chun;Cai, Peng;Liu, Xiaofan;Li, Guangtao;Bao, Pengfei;Yan, Lu;Ning, Meng;Tang, Kaichen;Luo, Yi;Guo, Hua;Wang, Yunjiu;Wang, Zhuoran;Chen, Lu;Lu, Zhi John;Yin, Jianhua
各种研究已经报道了无细胞rna （cfRNAs）作为检测肝细胞癌（HCC）的无创生物标志物。然而，它们还没有得到独立的验证，有些结果是矛盾的。我们对各种类型的cfRNA生物标志物进行了综合评估，并充分挖掘了cfRNA新特征的生物标志物潜力。我们首先系统地回顾了已报道的cfRNA生物标志物，并计算了失调的转录后事件和cfRNA片段。在3个独立的多中心队列中，我们使用RT-qPCR进一步选择了6个cfRNAs，使用机器学习构建了一个名为HCCMDP的AFP面板，并在内部和外部验证了HCCMDP的性能。通过对5个cfRNA-seq数据集的系统回顾和分析，我们确定了23个候选cfRNA生物标志物。值得注意的是，我们定义了cfRNA结构域来系统地描述cfRNA片段。在验证队列（n = 183）中，cfRNA片段更有可能被验证，而circRNA和嵌合RNA候选物作为基于qpcr的生物标志物既不丰富也不稳定。在算法开发队列（= 287）中，我们构建并测试了包含6个cfRNA标记和AFP的面板HCCMDP。在独立验证队列（= 171）中，HCCMDP能够区分HCC患者与对照组（all: AUC = 0.925; CHB: AUC = 0.909; LC: AUC = 0.916），在区分早期HCC患者方面表现良好（all: AUC = 0.936; CHB: AUC = 0.917; LC: AUC = 0.928）。本研究综合评价了全谱cfRNA用于HCC检测的生物标志物类型，强调了cfRNA片段作为HCC检测中有前景的生物标志物类型，并提供了面板HCCMDP。（973计划）。
Various studies have reported cell-free RNAs (cfRNAs) as noninvasive biomarkers for detecting hepatocellular carcinoma (HCC). However, they have not been independently validated, and some results are contradictory. We provided a comprehensive evaluation of various types of cfRNA biomarkers and a full mining of the biomarker potential of new features of cfRNA. We first systematically reviewed reported cfRNA biomarkers and calculated dysregulated post-transcriptional events and cfRNA fragments. In 3 independent multicentre cohorts, we further selected 6 cfRNAs using RT-qPCR, built a panel called HCCMDP with AFP using machine learning, and internally and externally validated HCCMDP's performance. We identified 23 cfRNA biomarker candidates from a systematic review and analysis of 5 cfRNA-seq datasets. Notably, we defined the cfRNA domain to describe cfRNA fragments systematically. In the verification cohort (n = 183), cfRNA fragments were more likely to be verified, while circRNA and chimeric RNA candidates were neither abundant nor stable as qPCR-based biomarkers. In the algorithm development cohort ( = 287), we build and test the panel HCCMDP with 6 cfRNA markers and AFP. In the independent validation cohort ( = 171), HCCMDP can distinguish HCC patients from control groups (all: AUC = 0.925; CHB: AUC = 0.909; LC: AUC = 0.916), and performs well in distinguishing early-stage HCC patients (all: AUC = 0.936; CHB: AUC = 0.917; LC: AUC = 0.928). This study comprehensively evaluated full-spectrum cfRNA biomarker types for HCC detection, highlighted the cfRNA fragment as a promising biomarker type in HCC detection, and provided a panel HCCMDP. , and The (973 program).
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DOI：
10.1093/bioinformatics/btq033
发表时间：
2010-03-15
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Quinlan AR;Hall IM
通讯作者：
Hall IM
DOI：
10.1093/bioinformatics/btr064
发表时间：
2011-04-01
期刊：
Bioinformatics (Oxford, England)
影响因子：
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作者：
Grant CE;Bailey TL;Noble WS
通讯作者：
Noble WS
DOI：
10.1016/j.annonc.2020.02.011
发表时间：
2020-06
期刊：
Annals of oncology : official journal of the European Society for Medical Oncology
影响因子：
--
作者：
Liu MC;Oxnard GR;Klein EA;Swanton C;Seiden MV;CCGA Consortium
通讯作者：
CCGA Consortium
影响因子：
48
作者：
Langmead, Ben;Salzberg, Steven L.
通讯作者：
Salzberg, Steven L.
DOI：
10.1016/j.omtn.2021.01.007
发表时间：
2021-03-05
期刊：
Molecular therapy. Nucleic acids
影响因子：
--
作者：
Bu FT;Zhu Y;Chen X;Wang A;Zhang YF;You HM;Yang Y;Yang YR;Huang C;Li J
通讯作者：
Li J