SOURCE OF LIQUID BIOPSY BIOMARKER: EXOSOME VS WHOLE PLASMA, FASTING VS NON-FASTING

Purpose: We compare small noncoding RNA (ncRNA) profiles between exosomes and whole plasma to test a better source of small ncRNA biomarkers. We hypothesize that exosome is a better source of small ncRNA biomarkers compared to whole plasma. Methods: Small ncRNA sequencings were done using Illumina NextSeq500. Single-end 76 bp reads were explored using FASTQC. GeneGlobe Data Analysis Center, an online platform from Qiagen was used for the small ncRNA-seq data analysis. The mapped read counts for miRNA, piRNA and tRNA were used for differential expression analysis using DESeq2 Bioconductor in R. The small RNA species with logFC > |1| and adj.P-value <0.05 were called differentially expressed. Conclusion: Small ncRNAs extracted from exosomes were found to have the most consistent profiles among healthy individuals. Whole plasma RNA profiles contain high concentrations of blood-derived miRNAs. These miRNA levels can create batch effects among samples due to different levels of hemolysis. Our finding suggests the importance of using purified exosomes as a better source of small ncRNA biomarkers to avoid the batch effect. Overall design: RNA samples extracted from Human plasma.