RNA-seq of exosomes identifies lncRNA profiles that distinguish early-stage esophageal squamous cell carcinoma (ESCC) from non-malignant esophagitis

We report the application of RNA sequencing technology for high-throughput profiling of transcriptomes in plasma exosomes from early-stage ESCC and esophagitis. By analyzing over 95G of clean reads (depleted rRNA), we found that expression features of exosomal lncRNAs were distinct from that of exosomal mRNAs. We identified differentially expressed exosomal lncRNAs and mRNAs for ESCC, and esophagitis. We further analyzed the biological functions of differentially expressed lncRNAs using GO, KEGG, as well as knockdown assay with siRNAs. This study provides information for identifying cancer and non-malignant disease relevant exosomal lncRNAs through integrative analyses of RNA sequencing data. Overall design: Examination and comparison of lncRNAs and mRNAs in exosomes from ESCC, esophagitis, and healthy control, respectively.