ArticleeLife2022
Cancer type classification using plasma cell-free RNAs derived from human and microbes.
Article in eLife, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 49 papers.
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Who cites it
49 citing papers in PubMed.
- Systemic health impact of cancer-associated extracellular vesicles and particles.Nature reviews. Cancer · 2026Review
- Expansion of pathogens and restoration of human skin microbiome in CD4 T-cell lymphopenia.The Journal of investigative dermatology · 2026Article
- Deconformer: efficient cell-type composition profiling of cfRNA across diverse cell types.Briefings in bioinformatics · 2026Article
- Mechanism-Driven Diagnostic Development: A Specimen-Aware Framework Illustrated by Colorectal Cancer and Solid Tumours.Cancers · 2026Review
- Multifeature sequencing-based liquid biopsy for cancer diagnosis and monitoring.Genome medicine · 2026Review
- Decoding cancer circulating transcriptomic signatures with language models.Nature communications · 2026Article
- A method of comprehensive sequencing analysis of the small RNA fragmentome (RiboMarker).RNA (New York, N.Y.) · 2026Article
- Modifications of microbiome-derived cell-free RNA in plasma discriminates colorectal cancer samples.Nature biotechnology · 2026Article
- Patient-specific alterations in blood plasma cfRNA profiles enable accurate classification of cancer patients and controls.Communications medicine · 2026Article
- exoRBase 3.0: an updated resource for extracellular RNAs from human biofluids.Nucleic acids research · 2026Article
- The alternative splicing landscape of hepatocellular carcinoma and its potential for HCC detection.Hepatology communications · 2026Article
- Harnessing plasma transcriptomics for non-invasive cancer biomarker identification: a comprehensive review.Discover oncology · 2025Review
- Wide-spectrum profiling of plasma cell-free RNA and the potential for health-monitoring.RNA biology · 2025Article
- A promising frontier of circulating messenger RNA in liquid biopsy: From mechanisms to clinical applications.International journal of cancer · 2025Review
- Proceedings of cell-free noncoding RNA biomarker studies in liquid biopsy.Rheumatology and immunology research · 2025Article
- The new microbiome on the block: challenges and opportunities of using human tumor sequencing data to study microbes.Nature methods · 2025Review
- A novel sequence-based transformer model architecture for integrating multi-omics data in preterm birth risk prediction.NPJ digital medicine · 2025Article
- Cell free RNA detection of pancreatic cancer in pre diagnostic high risk and symptomatic patients.Nature communications · 2025Article
- Article
- Peak analysis of cell-free RNA finds recurrently protected narrow regions with clinical potential.Genome biology · 2025Article
Corrections and comments
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Authors and funding
21 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The utility of cell-free nucleic acids in monitoring cancer has been recognized by both scientists and clinicians. In addition to human transcripts, a fraction of cell-free nucleic acids in human plasma were proven to be derived from microbes and reported to have relevance to cancer. To obtain a better understanding of plasma cell-free RNAs (cfRNAs) in cancer patients, we profiled cfRNAs in ~300 plasma samples of 5 cancer types (colorectal cancer, stomach cancer, liver cancer, lung cancer, and esophageal cancer) and healthy donors (HDs) with RNA-seq. Microbe-derived cfRNAs were consistently detected by different computational methods when potential contaminations were carefully filtered. Clinically relevant signals were identified from human and microbial reads, and enriched Kyoto Encyclopedia of Genes and Genomes pathways of downregulated human genes and higher prevalence torque teno viruses both suggest that a fraction of cancer patients were immunosuppressed. Our data support the diagnostic value of human and microbe-derived plasma cfRNAs for cancer detection, as an area under the ROC curve of approximately 0.9 for distinguishing cancer patients from HDs was achieved. Moreover, human and microbial cfRNAs both have cancer type specificity, and combining two types of features could distinguish tumors of five different primary locations with an average recall of 60.4%. Compared to using human features alone, adding microbial features improved the average recall by approximately 8%. In summary, this work provides evidence for the clinical relevance of human and microbe-derived plasma cfRNAs and their potential utilities in cancer detection as well as the determination of tumor sites.
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