Wide-spectrum profiling of plasma cell-free RNA and the potential for health-monitoring

AUTHORS

Xinxin Wang,Shaogang Li,Rijing Ou,Wending Pang,Yingying Wang,Yifan Zhang,Yu Lin,Changlin Yang,Wei Chen,Changgui Lei,Guodan Zeng,Wenwen Zhou,Yeqin Wang,Jianhua Yin,Haiqiang Zhang,Xin Jin &Yan Zhang

ABSTRACT

Circulating cell-free RNA (cfRNA) has emerged as a promising analyte for disease detection. However, the comprehensive profiling of diverse cfRNA types remains under-characterized. Here, we applied a new wide-spectrum cfRNA sequencing method and simultaneously captured rRNA, tRNA, mRNA, miRNA, lncRNA and all mitochondrial RNA. The cfRNA compositions, size distributions and highly abundant cfRNA genes were analysed for each type of cfRNA. We depicted the cfRNA cell types of origin profiles of 66 generally healthy individuals and found that BMI showed a significant impact on the kidney-derived cfRNA proportion. Three individuals with some liver problems were identified because of relatively high levels of hepatocyte-specific cfRNA. The abundance levels of different genes and RNA types, including mRNA, miRNA and lncRNA, were significantly correlated with the liver function test results. The genes of individual cfRNA variances were enriched in pathways associated with common diseases such as liver diseases, virus infections, cancers and metabolic diseases. This study provided a profiling of cfRNA and displayed the potential of cfRNA as a biomarker in health monitoring.

My contribution

The following work was completed during my undergraduate studies:

1. Developed and tested cfRNA analysis pipelines using R and shell scripts
   • Tools utilized:
     1. fastp for raw data filtering
     2. cutadapt and BBduk for adapter and polyA sequence removal
     3. hisat2 for reference genome alignment
     4. featureCounts for quantification
2. Performed contamination detection using BLAST
3. Generated test data with ART for pipeline validation

Recommended citation: Wang, X., Li, S., Ou, R., Pang, W., Wang, Y., Zhang, Y., … Zhang, Y. (2025). Wide-spectrum profiling of plasma cell-free RNA and the potential for health-monitoring. RNA Biology, 22(1), 1–15. https://doi.org/10.1080/15476286.2025.2481736
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